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We will learn how to +ask for changes in a pull request, how to suggest a change in a pull request, +and how to modify a pull request. + +This will enable research groups to work more collaboratively and to not only +improve the code quality but also to learn from each other. + + +## Exercise + +:::{prereq} Exercise preparation +We can continue in the same exercise repository which we have used in the +previous episode. +::: + +:::{exercise} Exercise: Practicing code review (25 min) + +**Technical requirements**: +- If you create the commits locally: [Being able to authenticate to GitHub](https://coderefinery.github.io/installation/ssh/) + +**What is familiar** from previous lessons: +- Creating a branch. +- Committing a change on the new branch. +- Opening and merging pull requests. + +**What will be new** in this exercise: +- As a reviewer, we will learn how to ask for changes in a pull request. +- As a reviewer, we will learn how to suggest a change in a pull request. +- As a submitter, we will learn how to modify a pull request without closing + the incomplete one and opening a new one. + +**Exercise tasks**: +1. Create a new branch and one or few commits: in these improve something but also + deliberately introduce a typo and also a larger mistake which we will want to fix during the code review. +1. Open a pull request towards the main branch. +1. As a reviewer to somebody else's pull request, ask for an improvement and + also directly suggest a change for the small typo. (Hint: + suggestions are possible through the GitHub web interface, view of + a pull request, "Files changed" view, after selecting some lines. + Look for the "±" button.) +1. As the submitter, learn how to accept the suggested change. (Hint: + GitHub web interface, "Files Changed" view.) +1. As the submitter, improve the pull request without having to close and open + a new one: by adding a new commit to the same branch. (Hint: push + to the branch again.) +1. Once the changes are addressed, merge the pull request. +::: + + +## Help and discussion + +From here on out, we don't give detailed steps to the solution. You +need to combine what you know, and the extra info below, in order to +solve the above. + +### How to ask for changes in a pull request + +Technically, there are at least two common ways to ask for changes in a pull +request. + +Either in the comment field of the pull request: +:::{figure} img/code-review/comment.png +:width: 60% +:class: with-border +:alt: Screenshot of a pull request comment field +:::: + +Or by using the "Review changes": +:::{figure} img/code-review/files-changed.png +:width: 100% +:class: with-border +:alt: Screenshot of a pull request navigating to the "Review changes" tab +:::: + +And always please be kind and constructive in your comments. Remember that the +goal is not gate-keeping but **collaborative learning**. + + +### How to suggest a change in a pull request as a reviewer + +If you see a very small problem that is easy to fix, you can suggest a change +as a reviewer. + +Instead of asking the submitter to tiny problem, you can suggest a change by +clicking on the plus sign next to the line number in the "Files changed" tab: +:::{figure} img/code-review/leave-comment.png +:width: 100% +:class: with-border +:alt: Screenshot of leaving a comment to a line in a pull request +:::: + +Here you can comment on specific lines or even line ranges. + +But now the interesting part is to click on the "Add a suggestion" symbol (the +one that looks like plus and minus). Now you can fix the tiny problem (in this +case a typo) and then click on the "Add single comment" button: +:::{figure} img/code-review/add-suggestion.png +:width: 60% +:class: with-border +:alt: Sequence of clicks to add a suggestion to a line in a pull request +:::: + +The result is this and the submitter can accept the change with a single click: +:::{figure} img/code-review/commit-suggestion.png +:width: 60% +:class: with-border +:alt: Screenshot of a pull request with a suggested change +:::: + +After accepting with "Commit suggestion", the improvement gets added to the +pull request. + + +### How to modify a pull request to address the review comments + +If the reviewer asks for changes, it is not necessary to close the pull request +and later open a new one. It can even be counter-productive to do so: This can +fragment the discussion and the history of the pull request and can make it +harder to understand the context of the changes. + +A much better mechanism to recognize that pull requests are not implemented +from a specific commit to a specific branch, but **always from a branch to a +branch**. + +This means that you can make amendments to the pull request by adding new +commits to the same source branch. This way the pull request will be updated +automatically and the reviewer can see the new changes and comment on them. + +The fact that pull requests are from branch to branch also strongly suggests +that it is a good practice to create a new branch for each pull request. +Otherwise you could accidentally modify an open pull request by adding new +commits to the source branch. + + +## Summary + +- Our process isn't just about code now. It's about discussion and + working together to make the whole process better. +- GitHub discussions and reviewing are quite powerful and can make + small changes easy. diff --git a/_sources/collaboration/concepts.md.txt b/_sources/collaboration/concepts.md.txt new file mode 100644 index 0000000..c0a7d27 --- /dev/null +++ b/_sources/collaboration/concepts.md.txt @@ -0,0 +1,69 @@ +(concepts)= + +# Concepts around collaboration + +```{objectives} +- Be able to decide whether to divide work at the branch level or at the repository level. +``` + + +## Commits, branches, repositories, forks, clones + +- **repository**: The project, contains all data and history (commits, branches, tags). +- **commit**: Snapshot of the project, gets a unique identifier (e.g. `c7f0e8bfc718be04525847fc7ac237f470add76e`). +- **branch**: Independent development line. The main development line is often called `main`. +- **tag**: A pointer to one commit, to be able to refer to it later. Like a [commemorative plaque](https://en.wikipedia.org/wiki/Commemorative_plaque) + that you attach to a particular commit (e.g. `phd-printed` or `paper-submitted`). +- **cloning**: Copying the whole repository to your laptop - the first time. It is not necessary to download each file one by one. +- **forking**: Taking a copy of a repository (which is typically not yours) - your + copy (fork) stays on GitHub/GitLab and you can make changes to your copy. + + +## Cloning a repository + +In order to make a complete copy a whole repository, the `git clone` command +can be used. When cloning, all the files, of all or selected branches, of a +repository are copied in one operation. Cloning of a repository is of relevance +in a few different situations: +* Working on your own, cloning is the operation that you can use to create + multiple instances of a repository on, for instance, a personal computer, a + server, and a supercomputer. +* The parent repository could be a repository that you or your colleague own. A + common use case for cloning is when working together within a smaller team + where everyone has read and write access to the same git repository. +* Alternatively, cloning can be made from a public repository of a code that + you would like to use. Perhaps you have no intention to work on the code, but + would like to stay in tune with the latest developments, also in-between + releases of new versions of the code. + + +```{figure} img/overview/forkandclone.png +:alt: Forking and cloning +:width: 100% +:class: with-border + +Forking and cloning +``` + + +## Forking a repository + +When a fork is made on GitHub/GitLab a complete copy, of all or selected +branches, of the repository is made. The copy will reside under a different +account on GitHub/GitLab. Forking of a repository is of high relevance when +working with a git repository to which you do not have write access. +* In the fork repository commits can be made to the base branch (`main` or + `master`), and to other branches. +* The commits that are made within the branches of the fork repository can be + contributed back to the parent repository by means of pull or merge requests. + + +## Synchronizing changes between repositories + +- We need a mechanism to communicate changes between the repositories. +- We will **pull** or **fetch** updates **from** remote repositories (we will soon discuss the difference between pull and fetch). +- We will **push** updates **to** remote repositories. +- We will learn how to suggest changes within repositories on GitHub and across repositories (**pull request**). +- Repositories that are forked or cloned do not automatically synchronize themselves: + We will learn how to update forks (by pulling from the "central" repository). +- A main difference between cloning a repository and forking a repository is that the former is a general operation for generating copies of a repository to different computers, whereas forking is a particular operation implemented on GitHub/GitLab. diff --git a/_sources/collaboration/demo-discussion.md.txt b/_sources/collaboration/demo-discussion.md.txt new file mode 100644 index 0000000..d6b4f28 --- /dev/null +++ b/_sources/collaboration/demo-discussion.md.txt @@ -0,0 +1,5 @@ +(collaboration-demo-discussion)= + +# Conclict resolution, rebasing, and organizational strategies + +(40 min demo and discussion) diff --git a/_sources/collaboration/forking-workflow.md.txt b/_sources/collaboration/forking-workflow.md.txt new file mode 100644 index 0000000..f8c254d --- /dev/null +++ b/_sources/collaboration/forking-workflow.md.txt @@ -0,0 +1,223 @@ +(forking-workflow)= + +# How to contribute changes to repositories that belong to others + +In this episode we prepare you to suggest and contribute changes to +repositories that belong to others. These might be open source projects that +you use in your work. + +We will see how Git and services like GitHub or GitLab can be used to suggest +modification without having to ask for write access to the repository and +accept modifications without having to grant write access to others. + + +## Exercise + +:::{prereq} Exercise preparation +- The exercise repository is now different: + (note the `-forking-exercise`). +- First **fork** the exercise repository to your GitHub account. +- Then **clone your fork** to your computer (if you wish to work locally). +- Double-check that you have forked the correct repository. +::: + +:::{exercise} Exercise: Collaborating within the same repository (25 min) + +**Technical requirements**: +- If you create the commits locally: [Being able to authenticate to GitHub](https://coderefinery.github.io/installation/ssh/) + +**What is familiar** from previous lessons: +- Forking a repository. +- Creating a branch. +- Committing a change on the new branch. +- Opening and merging pull requests. + +**What will be new** in this exercise: +- Opening a pull request towards the upstream repository. +- Pull requests can be coupled with automated testing. +- Learning that your fork can get out of date. +- After the pull requests are merged, updating your fork with the changes. +- Learn how to approach other people's repositories with ideas, changes, and requests. + +**Exercise tasks**: +1. Open an issue in the upstream exercise repository where you describe the + change you want to make. Take note of the issue number. +1. Create a new branch in your fork of the repository. +1. Make a change to the recipe book on the new branch and in the commit cross-reference the issue you opened. + See the walk-through below for how to do this. +1. Open a pull request towards the upstream repository. +1. The instructor will review and merge the pull requests. + During the review, pay attention to the automated test step (here for + demonstration purposes, we test whether the recipe contains an ingredients + and an instructions sections). +1. After few pull requests are merged, update your fork with the changes. +1. Check that in your fork you can see changes from other people's pull requests. +::: + + +## Help and discussion + + +### Help! I don't have permissions to push my local changes + +Maybe you see an error like this one: +```text +Please make sure you have the correct access rights +and the repository exists. +``` + +Or like this one: +```text +failed to push some refs to workshop-material/recipe-book-forking-exercise.git +``` + +In this case you probably try to push the changes not to your fork but to the original repository +and in this exercise you do not have write access to the original repository. + +The simpler solution is to clone again but this time your fork. + +:::{solution} Recovery + +But if you want to keep your local changes, you can change the remote URL to point to your fork. +Check where your remote points to with `git remote --verbose`. + +It should look like this (replace `USER` with your GitHub username): +```console +$ git remote --verbose + +origin git@github.com:USER/recipe-book-forking-exercise.git (fetch) +origin git@github.com:USER/recipe-book-forking-exercise.git (push) +``` + +It should **not** look like this: +```console +$ git remote --verbose + +origin git@github.com:workshop-material/recipe-book-forking-exercise.git (fetch) +origin git@github.com:workshop-material/recipe-book-forking-exercise.git (push) +``` + +In this case you can adjust "origin" to point to your fork with: +```console +$ git remote set-url origin git@github.com:USER/recipe-book-forking-exercise.git +``` +::: + + +### Opening a pull request towards the upstream repository + +We have learned in the previous episode that pull requests are always from +branch to branch. But the branch can be in a different repository. + +When you open a pull request in a fork, by default GitHub will suggest to +direct it towards the default branch of the upstream repository. + +This can be changed and it should always be verified, but in this case this is +exactly what we want to do, from fork towards upstream: +:::{figure} img/forking-workflow/pull-request-form.png +:width: 100% +:class: with-border +:alt: Screenshot of a pull request from fork towards upstream +:::: + + +### Pull requests can be coupled with automated testing + +We added an automated test here just for fun and so that you see that this is +possible to do. + +In this exercise, the test is silly. It will check whether the recipe contains +both an ingredients and an instructions section. + +In this example the test failed: +:::{figure} img/forking-workflow/all-checks-failed.png +:width: 60% +:class: with-border +:alt: Screenshot of a failed test in a pull request +:::: + +Click on the "Details" link to see the details of the failed test: +:::{figure} img/forking-workflow/check-details.png +:width: 60% +:class: with-border +:alt: Screenshot of details why the test failed +:::: + +**How can this be useful?** +- The project can define what kind of tests are expected to pass before a pull + request can be merged. +- The reviewer can see the results of the tests, without having to run them + locally. + +**How does it work?** +- We added a GitHub Actions workflow + to automatically run on each push or pull request towards the `main` branch. + +What tests or steps can you image for your project to run automatically with +each pull request? + + +### How to update your fork with changes from upstream + +This used to be difficult but now it is two mouse clicks. + +Navigate to your fork and notice how GitHub tells you that your fork is behind. +In my case, it is 9 commits behind upstream. To fix this, click on "Sync fork" +and then "Update branch": +:::{figure} img/forking-workflow/sync-fork.png +:width: 80% +:class: with-border +:alt: Screenshot on GitHub fork page showing that the fork is behind +:::: + +After the update my "branch is up to date" with the upstream repository: +:::{figure} img/forking-workflow/fork-after-update.png +:width: 80% +:class: with-border +:alt: Screenshot on GitHub after fork has been updated +:::: + + +### How to approach other people’s repositories with ideas, changes, and requests + +**Contributing very minor changes** +- Clone or fork+clone repository +- Create a branch +- Commit and push change +- Open a pull request or merge request + +**If you observe an issue and have an idea how to fix it** +- Open an issue in the repository you wish to contribute to +- Describe the problem +- If you have a suggestion on how to fix it, describe your suggestion +- Possibly **discuss and get feedback** +- If you are working on the fix, indicate it in the issue so that others know that somebody is working on it and who is working on it +- Submit your fix as pull request or merge request which references/closes the issue + +:::{admonition} Motivation +- **Inform others about an observed problem** +- Make it clear whether this issue is up for grabs or already being worked on +::: + +**If you have an idea for a new feature** +- Open an issue in the repository you wish to contribute to +- In the issue, write a short proposal for your suggested change or new feature +- Motivate why and how you wish to do this +- Also indicate where you are unsure and where you would like feedback +- **Discuss and get feedback before you code** +- Once you start coding, indicate that you are working on it +- Once you are done, submit your new feature as pull request or merge request which references/closes the issue/proposal + +:::{admonition} Motivation +- **Get agreement and feedback before writing 5000 lines of code** which might be rejected +- If we later wonder why something was done, we have the issue/proposal as + reference and can read up on the reasoning behind a code change +::: + + +## Summary + +- This forking workflow lets you propose changes to repositories for + which **you have no write access**. +- This is the way that much modern open-source software works. +- You can now contribute to any project you can view. diff --git a/_sources/collaboration/same-repository.md.txt b/_sources/collaboration/same-repository.md.txt new file mode 100644 index 0000000..1a69d1d --- /dev/null +++ b/_sources/collaboration/same-repository.md.txt @@ -0,0 +1,280 @@ +(same-repository)= + +# Collaborating within the same repository + +In this episode, we will learn how to collaborate within the same repository. +We will learn how to cross-reference issues and pull requests, how to review +pull requests, and how to use draft pull requests. + +This exercise will form a good basis for collaboration that is suitable for +most research groups. + +:::{note} +When you read or hear **pull request**, please think of a **change proposal**. +::: + + +## Exercise + +In this exercise, we will contribute to a repository via a **pull request**. +This means that you propose some change, and then it is accepted (or not). + +::::::{prereq} Exercise preparation + +- **First we need to get access** to the [exercise repository](https://github.com/workshop-material/recipe-book) to which we will + contribute. + - Instructor collects GitHub usernames from learners and adds them as collaborators to the exercise repository + (Settings -> Collaborators and teams -> Manage access -> Add people). + +- **Don't forget to accept the invitation** + - Check + - Alternatively check the inbox for the email account you registered with + GitHub. GitHub emails you an invitation link, but if you don't receive it + you can go to your GitHub notifications in the top right corner. The + maintainer can also "copy invite link" and share it within the group. + +- **Watching and unwatching repositories** + - Now that you are a collaborator, you get notified about new issues and pull + requests via email. + - If you do not wish this, you can "unwatch" a repository (top of + the project page). + - However, we recommend watching repositories you are interested + in. You can learn things from experts just by watching the + activity that come through a popular project. + :::{figure} img/unwatch.png + :alt: Unwatching a repository + + Unwatch a repository by clicking "Unwatch" in the repository view, + then "Participating and @mentions" - this way, you will get + notifications about your own interactions. + ::: +:::::: + +:::{exercise} Exercise: Collaborating within the same repository (25 min) + +**Technical requirements** (from installation instructions): +- If you create the commits locally: [Being able to authenticate to GitHub](https://coderefinery.github.io/installation/ssh/) + +**What is familiar** from the previous workshop day (not repeated here): +- Cloning a repository. +- Creating a branch. +- Committing a change on the new branch. +- Submit a pull request towards the main branch. + +**What will be new** in this exercise: +- If you create the changes locally, you will need to **push** them to the remote repository. +- Learning what a protected branch is and how to modify a protected branch: using a pull request. +- Cross-referencing issues and pull requests. +- Practice to review a pull request. +- Learn about the value of draft pull requests. + +**Exercise tasks**: +1. Start in the [exercise + repository](https://github.com/workshop-material/recipe-book) and open an + issue where you describe the change you want to make. Note down the issue + number since you will need it later. +1. Create a new branch. +1. Make a change to the recipe book on the new branch and in the commit + cross-reference the issue you opened (see the walk-through below + for how to do that). +1. Push your new branch (with the new commit) to the repository you + are working on. +1. Open a pull request towards the main branch. +1. Review somebody else's pull request and give constructive feedback. Merge their pull request. +1. Try to create a new branch with some half-finished work and open a draft + pull request. Verify that the draft pull request cannot be merged since it + is not meant to be merged yet. +::: + + +## Solution and hints + +### (1) Opening an issue + +This is done through the GitHub web interface. For example, you could +give the name of the recipe you want to add (so that others don't add +the same one). It is the "Issues" tab. + + +### (2) Create a new branch. + +If on GitHub, you can make the branch in the web interface. + + +### (3) Make a change adding the recipe + +Add a new file with the recipe in it. Commit the file. In the commit +message, include the note about the issue number, saying that this +will close that issue. + + +#### Cross-referencing issues and pull requests + +Each issue and each pull request gets a number and you can cross-reference them. + +When you open an issue, note down the issue number (in this case it is `#2`): +:::{figure} img/same-repository/issue-number.png +:width: 60% +:class: with-border +:alt: Each issue gets a number +::: + +You can reference this issue number in a commit message or in a pull request, like in this +commit message: +```text +this is the new recipe; fixes #2 +``` + +If you forget to do that in your commit message, you can also reference the issue +in the pull request description. And instead of `fixes` you can also use `closes` or `resolves` +or `fix` or `close` or `resolve` (case insensitive). + +Here are all the keywords that GitHub recognizes: + + +Then observe what happens in the issue once your commit gets merged: it will +automatically close the issue and create a link between the issue and the +commit. This is very useful for tracking what changes were made in response to +which issue and to know from when until when precisely the issue was open. + + +### (4) Push to GitHub as a new branch + +Push the branch to the repository. You should end up with a branch +visible in the GitHub web view. + +This is only necessary if you created the changes locally. If you created the +changes directly on GitHub, you can skip this step. + +:::::{tabs} +::::{group-tab} VS Code +In VS Code, you can "publish the branch" to the remote repository by clicking +the cloud icon in the bottom left corner of the window: +:::{figure} img/same-repository/vscode-publish-branch.png +:width: 60% +:class: with-border +:alt: Publishing a branch in VS Code +::: +:::: + +::::{group-tab} Command line +If you have a local branch `my-branch` and you want to push it to the remote +and make it visible there, first verify what your remote is: +```console +$ git remote --verbose + +origin git@github.com:USER/recipe-book.git (fetch) +origin git@github.com:USER/recipe-book.git (push) +``` + +In this case the remote is called `origin` and refers to the address +git@github.com:USER/recipe-book.git. Both can be used +interchangeably. Make sure it points to the right repository, ideally a +repository that you can write to. + +Now that you have a remote, you can push your branch to it: +```console +$ git push origin my-branch +``` +This will create a new branch on the remote repository with the same name as +your local branch. + +You can also do this: +```console +$ git push --set-upstream origin my-branch +``` +This will connect the local branch and the remote branch so that in the future +you can just type `git push` and `git pull` without specifying the branch name +(but this depends on your Git configuration). + + +**Troubleshooting** + +If you don't have a remote yet, you can add it with (adjust `ADDRESS` to your repository address): +```console +$ git remote add origin ADDRESS +``` + +ADDRESS is the part that you copy from here: +:::{figure} img/same-repository/clone-address.png +:width: 60% +:class: with-border +:alt: Copying the clone address from GitHub +::: + +If the remote points to the wrong place, you can change it with: +```console +$ git remote set-url origin NEWADDRESS +``` +:::: +::::: + + +### (5) Open a pull request towards the main branch + +This is done through the GitHub web interface. + + +### (6) Reviewing pull requests + +You review through the GitHub web interface. + +Checklist for reviewing a pull request: +- Be kind, on the other side is a human who has put effort into this. +- Be constructive: if you see a problem, suggest a solution. +- Towards which branch is this directed? +- Is the title descriptive? +- Is the description informative? +- Scroll down to see commits. +- Scroll down to see the changes. +- If you get incredibly many changes, also consider the license or copyright + and ask where all that code is coming from. +- Again, be kind and constructive. +- Later we will learn how to suggest changes directly in the pull request. + +If someone is new, it's often nice to say something encouraging in the +comments before merging (even if it's just "thanks"). If all is good +and there's not much else to say, you could merge directly. + + +### (7) Draft pull requests + +Try to create a draft pull request: +:::{figure} img/same-repository/draft-pr.png +:width: 60% +:class: with-border +:alt: Creating a draft pull request +:::: + +Verify that the draft pull request cannot be merged until it is marked as ready +for review: +:::{figure} img/same-repository/draft-pr-wip.png +:width: 60% +:class: with-border +:alt: Draft pull request cannot be merged +:::: + +Draft pull requests can be useful for: +- **Feedback**: You can open a pull request early to get feedback on your work without + signaling that it is ready to merge. +- **Information**: They can help communicating to others that a change is coming up and in + progress. + + +### What is a protected branch? And how to modify it? + +A protected branch on GitHub or GitLab is a branch that cannot (accidentally) +deleted or force-pushed to. It is also possible to require that a branch cannot +be directly pushed to or modified, but that changes must be submitted via a +pull request. + +To protect a branch in your own repository, go to "Settings" -> "Branches". + + + +### Summary + +- We used all the same pieces that we've learned previously. +- But we successfully contributed to a collaborative project! +- The pull request allowed us to contribute without changing directly: + this is very good when it's not mainly our project. diff --git a/_sources/credit.md.txt b/_sources/credit.md.txt new file mode 100644 index 0000000..818da97 --- /dev/null +++ b/_sources/credit.md.txt @@ -0,0 +1,8 @@ +# Credit + +The following material (all CC-BY) was reused to create this workshop material: +- +- +- + +(I will also summarize what changes have been made to the original material) diff --git a/_sources/documentation.md.txt b/_sources/documentation.md.txt new file mode 100644 index 0000000..2789a8d --- /dev/null +++ b/_sources/documentation.md.txt @@ -0,0 +1,29 @@ +(documentation)= + +# Code documentation + +- 15 min: What makes good documentation? Also https://diataxis.fr/ +- 15 min: Writing good README files +- 30 min: Exercise: Set up a Sphinx documentation and add API documentation +- 15 min: Building documentation with GitHub Actions + + +requirements.txt: +``` +sphinx +sphinx_rtd_theme >= 2.0 +sphinx_autobuild +sphinx_autoapi +myst_parser +``` + + +conf.py: +```python +extensions = [ + "myst_parser", + "autoapi.extension", +] + +autoapi_dirs = ['..'] +``` diff --git a/_sources/example.md.txt b/_sources/example.md.txt new file mode 100644 index 0000000..9805632 --- /dev/null +++ b/_sources/example.md.txt @@ -0,0 +1,95 @@ +(example-project)= + +# Example project: Simulating the motion of planets + +The [example code](https://github.com/workshop-material/planets) that we will study +is a hopefully simple N-body simulation written in Python. It is not important +or expected that we understand the code in any detail. + +:::{video} video/animation.mp4 +:width: 600 +::: + +The **big picture** is that the code simulates the motion of a number of +planets: +- We can choose the number of planets. +- Each planet starts with a random position, velocity, and mass. +- At each time step, the code calculates the gravitational force between each + pair of planets. +- The forces accelerate each planet, the acceleration modifies the velocity, + the velocity modifies the position of each planet. +- We can choose the number of time steps. +- The units were chosen to make numbers easy to read. + + +## Example run + +:::{instructor-note} +The instructor demonstrates running the code on their computer. +::: + +The code is written to accept **command-line arguments** to specify the number +of planets and the number of time steps. + +We first generate starting data: +```console +$ python generate-data.py --num-planets 10 --output-file initial.csv +``` + +The generated file (initial.csv) could look like this: +``` +px,py,pz,vx,vy,vz,mass +-46.88,-42.51,88.33,-0.86,-0.18,0.55,6.70 +-5.29,17.09,-96.13,0.66,0.45,-0.17,3.51 +83.53,-92.83,-68.77,-0.26,-0.48,0.24,6.84 +-36.31,25.48,64.16,0.85,0.75,-0.56,1.53 +-68.38,-17.21,-97.07,0.60,0.26,0.69,6.63 +-48.37,-48.74,3.92,-0.92,-0.33,-0.93,8.60 +40.53,-75.50,44.18,-0.62,-0.31,-0.53,8.04 +-27.21,10.78,-78.82,-0.09,-0.55,-0.03,5.35 +88.42,-74.95,-45.85,0.81,0.68,0.56,5.36 +39.09,53.12,-59.54,-0.54,0.56,0.07,8.98 +``` + +Then we can simulate their motion (in this case for 20 steps): +```console +$ python simulate.py --num-steps 20 \ + --input-file initial.csv \ + --output-file final.csv +``` + +The `--output-file` (final.csv) is again a CSV file (comma-separated values) +and contains the final positions of all planets. + +It is possible to run on **multiple cores** and to **animate** the result. +Here is an example with 100 planets: +```{code-block} console +--- +emphasize-lines: 7,11 +--- +$ python generate-data.py --num-planets 100 --output-file initial.csv + +$ python simulate.py --num-steps 50 \ + --input-file initial.csv \ + --output-file final.csv \ + --trajectories-file trajectories.npz \ + --num-cores 8 + +$ python animate.py --initial-file initial.csv \ + --trajectories-file trajectories.npz \ + --output-file animation.mp4 +``` + +:::{admonition} Learning goals +- What are the most important steps to make this code **reusable by others** + and **our future selves**? +- Be able to apply these techniques to your own code/script. +::: + +:::{admonition} We will not focus on ... +- ... how the code works internally in detail. +- ... whether this is the most efficient algorithm. +- ... whether the code is numerically stable. +- ... how to code scales with the number of cores. +- ... whether it is portable to other operating systems (we will discuss this later). +::: diff --git a/_sources/index.md.txt b/_sources/index.md.txt new file mode 100644 index 0000000..aab4003 --- /dev/null +++ b/_sources/index.md.txt @@ -0,0 +1,157 @@ +# Reproducible research software development using Python + + +## Big-picture goal + +This is a **hands-on course on research software engineering**. In this +workshop we assume that most workshop participants use Python in their work or +a leading a group which uses Python. Therefore, some of the examples will use +Python as the example language. + +We will work with an example project and go through all the steps of a typical +software project. Once we have seen the building blocks, we will try to apply +them to own projects. Workshop participants will receive and also learn to give +constructive code feedback. + + +## Prerequisites + +:::{prereq} Preparation +1. Get a **GitHub account** following [these instructions](https://coderefinery.github.io/installation/github/). +1. You will need a **text editor**. If you don't have a favorite one, we recommend + [VS Code](https://coderefinery.github.io/installation/vscode/). +1. **If you prefer to work in the terminal** and not in VS Code, set up these two (skip this if you use VS Code): + - [Git in the terminal](https://coderefinery.github.io/installation/git-in-terminal/) + - [SSH or HTTPS connection to GitHub from terminal](https://coderefinery.github.io/installation/ssh/) +1. **One of these two software environments** (if you are not sure which one to + choose or have no preference, choose Conda): + - {ref}`conda` + - {ref}`venv` (Snakemake is not available in this environment) +1. **Optional** and only on Linux: [Apptainer](https://apptainer.org/) following + [these instructions](https://apptainer.org/docs/admin/1.3/installation.html#install-from-pre-built-packages). +::: + + +## Schedule + +:::{note} +The schedule will very soon contain links to lesson material and exercises. +::: + + +### Day 1 + +- 13:00-13:30 - **Welcome and introduction** + - Practical information (tools, communication, breaks, etc.) + - Motivation (reproducibility, robustness, distribution, improvement, trust, etc.) + - What will learn and achieve from this course? + - {ref}`example-project` + +- 13:30-14:45 (1.25h) - **Introduction to version control with Git and GitHub (1/2)** + - Creating a repository and porting your project to Git and GitHub + - Basic commands + +- 15:00-16:30 (1.5h) - **Introduction to version control with Git and GitHub (2/2)** + - Branching and merging + - Recovering from typical mistakes + +- 16:45-18:00 - {ref}`documentation` + - In-code documentation including docstrings + - Writing good README files + - Markdown + - Sphinx + - Building documentation with GitHub Actions + - Jupyter Notebooks + + +### Day 2 + +- 09:00-10:30 - {ref}`collaboration` (1/2) + - {ref}`concepts` (10 min) + - {ref}`same-repository` (40 min) + - {ref}`code-review` (40 min) + +- 10:45-12:15 - {ref}`collaboration` (2/2) + - {ref}`forking-workflow` (50 min) + - {ref}`collaboration-demo-discussion` (40 min) + +- 16:45-18:00 - **Debriefing and Q&A** + - Participants work on their projects + - Together we study actual codes that participants wrote or work on + - Constructively we discuss possible improvements + - Give individual feedback on code projects + + +### Day 3 + +- 09:00-10:30 - {ref}`testing` + - Unit tests + - End-to-end tests + - pytest + - GitHub Actions + +- 10:45-12:15 - {ref}`reusable` + - Tracking dependencies with requirements.txt and environment.yml + - Recording environments in containers + +- 13:00-14:45 - {ref}`refactoring` + - Naming (and other) conventions, project organization, modularity + - Refactoring (explained through examples) + - Design patterns: functional design vs. object-oriented design + - How to design your code before writing it + - Structuring larger software projects in a modular way + - Command-line interfaces + - Workflows with Snakemake + +- 15:00-16:30 - {ref}`publishing` + - Licenses + - Publishing the code via Zenodo + - Packaging the code + - Sharing the code via PyPI + +- 16:45-18:00 - **Debriefing and Q&A** + - Participants work on their projects + - Together we study actual codes that participants wrote or work on + - Constructively we discuss possible improvements + - Give individual feedback on code projects + + +### If we have time left + +- {ref}`profiling` + + +```{toctree} +:maxdepth: 1 +:caption: Software environment +:hidden: + +installation/conda +installation/virtual-environment +``` + +```{toctree} +:maxdepth: 1 +:caption: Episodes +:hidden: + +example +documentation +collaboration +testing +reusable +refactoring +publishing +profiling +``` + +```{toctree} +:maxdepth: 1 +:caption: Reference +:hidden: + +credit +All lessons +CodeRefinery +Reusing +``` diff --git a/_sources/installation/conda.md.txt b/_sources/installation/conda.md.txt new file mode 100644 index 0000000..8c55ba4 --- /dev/null +++ b/_sources/installation/conda.md.txt @@ -0,0 +1,87 @@ +(conda)= + +# Conda environment + +A Conda environment is an isolated software environment that is used to manage dependencies for a project +and you decide where it is located. + +You will need a `environment.yml` file that documents the dependencies: +```yaml +name: coderefinery +channels: + - conda-forge + - bioconda +dependencies: + - python >= 3.10 + - black + - click + - flit + - ipywidgets + - isort + - jupyterlab + - jupyterlab_code_formatter + - jupyterlab-git + - matplotlib + - myst-parser + - nbdime + - numpy + - pandas + - pytest + - pytest-cov + - scalene + - seaborn + - snakemake-minimal + - sphinx + - sphinx-autoapi + - sphinx-autobuild + - sphinx_rtd_theme >= 2.0 + - vulture + - scikit-image +``` + + +## Before you create a virtual environment + +1. Create a new directory for this course. +1. In this directory, create an `environment.yml` file and copy-paste the dependencies above into it. + + +## Choose the tool to manage the environment + +If you are already using one of these tools, please continue using the tool that you like and know. +If you are new to this, **we recommend using Miniconda or Miniforge**. + +- [Anaconda](https://docs.anaconda.com/anaconda/install/) + - Advantages: easy to install, easy to use, good for beginners + - Disadvantages: large download, installs more than we will need, license restrictions +- [Miniconda](https://docs.anaconda.com/miniconda/) + - Advantages: small size, installs only what you need + - Disadvantages: no graphical interface, license restrictions +- [Miniforge](https://github.com/conda-forge/miniforge) + - Advantages: small size, no license restrictions + - Disadvantages: no graphical interface +- [Micromamba](https://mamba.readthedocs.io/en/latest/user_guide/micromamba.html) + - Advantages: fast, small size + - Disadvantages: no graphical interface +- [Pixi](https://pixi.sh/latest/) + - Advantages: fast and new + - Disadvantages: new and less tested and not documented here + + +## Creating the virtual environment + +1. Open your terminal shell (e.g. Bash or Zsh). +2. Activate `conda` using `conda activate` or `source ~/miniconda3/bin/activate`. +3. Run the following command: + ```console + $ conda env create --file environment.yml + ``` +4. Make sure that you see "coderefinery" in the output when you ask for a list of all available environments: + ```console + $ conda env list + ``` + + +## How to verify that this worked + +(this will be added) diff --git a/_sources/installation/virtual-environment.md.txt b/_sources/installation/virtual-environment.md.txt new file mode 100644 index 0000000..67e4961 --- /dev/null +++ b/_sources/installation/virtual-environment.md.txt @@ -0,0 +1,82 @@ +(venv)= + +# Virtual environment + +A virtual environment is an isolated software environment that is used to manage dependencies for a project +and you decide where it is located. + +You will need a `requirements.txt` file that documents the dependencies: +``` +black +click +flit +ipywidgets +isort +jupyterlab +jupyterlab-code-formatter +jupyterlab-git +matplotlib +myst-parser +nbdime +numpy +pandas +pytest +pytest-cov +scalene +seaborn +sphinx +sphinx-autoapi +sphinx-autobuild +sphinx_rtd_theme >= 2.0 +vulture +scikit-image +``` + + +## Before you create a virtual environment + +1. Create a new directory for this course. +1. In this directory, create a `requirements.txt` file and copy-paste the dependencies above into it. + + +## Creating the virtual environment + +Now create a virtual environment in this directory either using [pip and +venv](https://packaging.python.org/en/latest/guides/installing-using-pip-and-virtual-environments/) +(more traditional and safer) or using [uv](https://docs.astral.sh/uv/) (more modern but also less tested): + +:::::{tabs} + +::::{group-tab} pip and venv +Create a new virtual environment and activate it: +```console +$ python3 -m venv coderefinery-environment +$ source coderefinery-environment/bin/activate +``` + +Install the dependencies into the environment: +```console +$ python3 -m pip install -r requirements.txt +``` +:::: + + +::::{group-tab} uv +Create a new virtual environment and activate it: +```console +$ uv venv coderefinery-environment +$ source coderefinery-environment/bin/activate +``` + +Install the dependencies into the environment: +```console +$ uv pip install -r requirements.txt +``` +:::: + +::::: + + +## How to verify that this worked + +(this will be added) diff --git a/_sources/profiling.md.txt b/_sources/profiling.md.txt new file mode 100644 index 0000000..dbcaa1b --- /dev/null +++ b/_sources/profiling.md.txt @@ -0,0 +1,14 @@ +(profiling)= + +# Profiling memory and CPU usage + +Profilers: +- cProfile or profile +- line_profiler +- viztracer +- scalene +- Intel VTune +- PyInstrument +- py-spy +- Pyflame +- timeit diff --git a/_sources/publishing.md.txt b/_sources/publishing.md.txt new file mode 100644 index 0000000..bc3a12e --- /dev/null +++ b/_sources/publishing.md.txt @@ -0,0 +1,11 @@ +(publishing)= + +# How to release and publish your code + +Part 1: +- 30 min: Overview over software licenses and code publishing +- 15 min: We add a license, CFF file, and publish to Zenodo (sandbox) + +Part 2: +- 30 min: Creating a Python package with the help of flit +- 15 min: Deploy the package to test-PyPI using GitHub Actions diff --git a/_sources/refactoring.md.txt b/_sources/refactoring.md.txt new file mode 100644 index 0000000..0cf390d --- /dev/null +++ b/_sources/refactoring.md.txt @@ -0,0 +1,87 @@ +(refactoring)= + +# Code quality and good practices + +In this episode we will explore code quality and good practices in Python using +a hands-on approach. We will together build up a small project and improve it +step by step. + +We will start from a relatively simple image processing script which can read a +telescope image of stars and our goal is to **count the number of stars** in +the image. Later we will want to be able to process many such images. + +The (fictional) telescope images look like the one below here ([in this +repository](https://github.com/workshop-material/random-star-images) we can find more): +:::{figure} refactoring/stars.png +:alt: Generated image representing a telescope image of stars +:width: 60% + +Generated image representing a telescope image of stars. +::: + +:::{solution} Starting point (spoiler alert) + +We can imagine that we pieced together the following code +based on some examples we found online: +```python +import matplotlib.pyplot as plt +from skimage import io, filters, color +from skimage.measure import label, regionprops + + +image = io.imread("stars.png") +sigma = 0.5 + +# if there is a fourth channel (alpha channel), ignore it +rgb_image = image[:, :, :3] +gray_image = color.rgb2gray(rgb_image) + +# apply a gaussian filter to reduce noise +image_smooth = filters.gaussian(gray_image, sigma) + +# threshold the image to create a binary image (bright stars will be white, background black) +thresh = filters.threshold_otsu(image_smooth) +binary_image = image_smooth > thresh + +# label connected regions (stars) in the binary image +labeled_image = label(binary_image) + +# get properties of labeled regions +regions = regionprops(labeled_image) + +# extract star positions (centroids) +star_positions = [region.centroid for region in regions] + +# plot the original image +plt.figure(figsize=(8, 8)) +plt.imshow(image, cmap="gray") + +# overlay star positions with crosses +for star in star_positions: + plt.plot(star[1], star[0], "rx", markersize=5, markeredgewidth=0.1) + +plt.savefig("detected-stars.png", dpi=300) + +print(f"number of stars detected: {len(star_positions)}") +``` +::: + + +Part 1: +- 15 min: Discuss how we would solve the problem, run example code, and make it work + as part of a Jupyter notebook. +- 15 min: Refactor the positioning code into a function and a module +- 15 min: Now we wish to process many images - discuss how we would approach this +- 15 min: Introduce CLI and discuss the benefits + +Part 2: +- 30 min: From a script to a workflow (using Snakemake) +- 15 min: Discuss concepts + - Pure functions + - Design patterns: functional design vs. object-oriented design + - How to design your code before writing it: document-driven development + +Bonus: +- Move it under Git +- Document dependencies +- Show nbdime, black, vulture, ruff diff --git a/_sources/reusable.md.txt b/_sources/reusable.md.txt new file mode 100644 index 0000000..c86455a --- /dev/null +++ b/_sources/reusable.md.txt @@ -0,0 +1,13 @@ +(reusable)= + +# How to make the project more reusable + +Part 1: +- 15 min: Motivation +- 15 min: Best practices for managing dependencies in Python +- 20 min: Exercise + +Part 2: +- 10 min: Introduction to containers +- 20 min: Demonstration +- 10 min: Discussion diff --git a/_sources/testing.md.txt b/_sources/testing.md.txt new file mode 100644 index 0000000..7a63bd9 --- /dev/null +++ b/_sources/testing.md.txt @@ -0,0 +1,10 @@ +(testing)= + +# Automated testing + +- 15 min: Motivation +- 15 min: End-to-end tests +- 15 min: Pytest +- 15 min: Moving to GitHub Actions +- 20 min: Exercise +- 10 min: Where to go from here diff --git a/_static/_sphinx_javascript_frameworks_compat.js b/_static/_sphinx_javascript_frameworks_compat.js new file mode 100644 index 0000000..8141580 --- /dev/null +++ b/_static/_sphinx_javascript_frameworks_compat.js @@ -0,0 +1,123 @@ +/* Compatability shim for jQuery and underscores.js. + * + * Copyright Sphinx contributors + * Released under the two clause BSD licence + */ + +/** + * small helper function to urldecode strings + * + * See https://developer.mozilla.org/en-US/docs/Web/JavaScript/Reference/Global_Objects/decodeURIComponent#Decoding_query_parameters_from_a_URL + */ +jQuery.urldecode = function(x) { + if (!x) { + return x + } + return decodeURIComponent(x.replace(/\+/g, ' ')); +}; + +/** + * small helper function to urlencode strings + */ +jQuery.urlencode = encodeURIComponent; + +/** + * This function returns the parsed url parameters of the + * current request. 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+ var isInSVG = jQuery(node).closest("body, svg, foreignObject").is("svg"); + if (isInSVG) { + span = document.createElementNS("http://www.w3.org/2000/svg", "tspan"); + } else { + span = document.createElement("span"); + span.className = className; + } + span.appendChild(document.createTextNode(val.substr(pos, text.length))); + node.parentNode.insertBefore(span, node.parentNode.insertBefore( + document.createTextNode(val.substr(pos + text.length)), + node.nextSibling)); + node.nodeValue = val.substr(0, pos); + if (isInSVG) { + var rect = document.createElementNS("http://www.w3.org/2000/svg", "rect"); + var bbox = node.parentElement.getBBox(); + rect.x.baseVal.value = bbox.x; + rect.y.baseVal.value = bbox.y; + rect.width.baseVal.value = bbox.width; + rect.height.baseVal.value = bbox.height; + rect.setAttribute('class', className); + addItems.push({ + "parent": node.parentNode, + "target": rect}); + } + } + } + else if (!jQuery(node).is("button, select, textarea")) { + jQuery.each(node.childNodes, function() { + highlight(this, addItems); + }); + } + } + var addItems = []; + var result = this.each(function() { + highlight(this, addItems); + }); + for (var i = 0; i < addItems.length; ++i) { + jQuery(addItems[i].parent).before(addItems[i].target); + } + return result; +}; + +/* + * backward compatibility for jQuery.browser + * This will be supported until firefox bug is fixed. + */ +if (!jQuery.browser) { + jQuery.uaMatch = function(ua) { + ua = ua.toLowerCase(); + + var match = /(chrome)[ \/]([\w.]+)/.exec(ua) || + /(webkit)[ \/]([\w.]+)/.exec(ua) || + /(opera)(?:.*version|)[ \/]([\w.]+)/.exec(ua) || + /(msie) ([\w.]+)/.exec(ua) || + ua.indexOf("compatible") < 0 && /(mozilla)(?:.*? rv:([\w.]+)|)/.exec(ua) || + []; + + return { + browser: match[ 1 ] || "", + version: match[ 2 ] || "0" + }; + }; + jQuery.browser = {}; + jQuery.browser[jQuery.uaMatch(navigator.userAgent).browser] = true; +} diff --git a/_static/basic.css b/_static/basic.css new file mode 100644 index 0000000..f316efc --- /dev/null +++ b/_static/basic.css @@ -0,0 +1,925 @@ +/* + * basic.css + * ~~~~~~~~~ + * + * Sphinx stylesheet -- basic theme. + * + * :copyright: Copyright 2007-2024 by the Sphinx team, see AUTHORS. + * :license: BSD, see LICENSE for details. + * + */ + +/* -- main layout ----------------------------------------------------------- */ + +div.clearer { + clear: both; +} + +div.section::after { + display: block; + content: ''; + clear: left; +} + +/* -- relbar ---------------------------------------------------------------- */ + +div.related { + width: 100%; + font-size: 90%; +} + +div.related h3 { + display: none; +} + +div.related ul { + margin: 0; + padding: 0 0 0 10px; + list-style: none; +} + +div.related li { + display: inline; +} + +div.related li.right { + float: right; + margin-right: 5px; +} + +/* -- sidebar --------------------------------------------------------------- */ + +div.sphinxsidebarwrapper { + padding: 10px 5px 0 10px; +} + +div.sphinxsidebar { + float: left; + width: 230px; + margin-left: -100%; + font-size: 90%; + word-wrap: break-word; + overflow-wrap : break-word; +} + +div.sphinxsidebar ul { + list-style: none; +} + +div.sphinxsidebar ul ul, +div.sphinxsidebar ul.want-points { + margin-left: 20px; + list-style: square; +} + +div.sphinxsidebar ul ul { + margin-top: 0; + margin-bottom: 0; +} + +div.sphinxsidebar form { + margin-top: 10px; +} + +div.sphinxsidebar input { + border: 1px solid #98dbcc; + font-family: sans-serif; + font-size: 1em; +} + +div.sphinxsidebar #searchbox form.search { + overflow: hidden; +} + +div.sphinxsidebar #searchbox input[type="text"] { + float: left; + width: 80%; + padding: 0.25em; + box-sizing: border-box; +} + +div.sphinxsidebar #searchbox input[type="submit"] { + float: left; + width: 20%; + border-left: none; + padding: 0.25em; + box-sizing: border-box; +} + + +img { + border: 0; + max-width: 100%; +} + +/* -- search page ----------------------------------------------------------- */ + +ul.search { + margin: 10px 0 0 20px; + padding: 0; +} + +ul.search li { + padding: 5px 0 5px 20px; + background-image: url(file.png); + background-repeat: no-repeat; + background-position: 0 7px; +} + +ul.search li a { + font-weight: bold; +} + +ul.search li p.context { + color: #888; + margin: 2px 0 0 30px; + text-align: left; +} + +ul.keywordmatches li.goodmatch a { + font-weight: bold; +} + +/* -- index page ------------------------------------------------------------ */ + +table.contentstable { + width: 90%; + margin-left: auto; + margin-right: auto; +} + +table.contentstable p.biglink { + line-height: 150%; +} + +a.biglink { + font-size: 1.3em; +} + +span.linkdescr { + font-style: italic; + padding-top: 5px; + font-size: 90%; +} + +/* -- general index --------------------------------------------------------- */ + +table.indextable { + width: 100%; +} + +table.indextable td { + text-align: left; + vertical-align: top; +} + +table.indextable ul { + margin-top: 0; + margin-bottom: 0; + list-style-type: none; +} + +table.indextable > tbody > tr > td > ul { + padding-left: 0em; +} + +table.indextable tr.pcap { + height: 10px; +} + +table.indextable tr.cap { + margin-top: 10px; + background-color: #f2f2f2; +} + +img.toggler { + margin-right: 3px; + margin-top: 3px; + cursor: pointer; +} + +div.modindex-jumpbox { + border-top: 1px solid #ddd; + border-bottom: 1px solid #ddd; + margin: 1em 0 1em 0; + padding: 0.4em; +} + +div.genindex-jumpbox { + border-top: 1px solid #ddd; + border-bottom: 1px solid #ddd; + margin: 1em 0 1em 0; + padding: 0.4em; +} + +/* -- domain module index --------------------------------------------------- */ + +table.modindextable td { + padding: 2px; + border-collapse: collapse; +} + +/* -- general body styles --------------------------------------------------- */ + +div.body { + min-width: 360px; + max-width: 800px; +} + +div.body p, div.body dd, div.body li, div.body blockquote { + -moz-hyphens: auto; + -ms-hyphens: auto; + -webkit-hyphens: auto; + hyphens: auto; +} + +a.headerlink { + visibility: hidden; +} + +a:visited { + color: #551A8B; +} + +h1:hover > a.headerlink, +h2:hover > a.headerlink, +h3:hover > a.headerlink, +h4:hover > a.headerlink, +h5:hover > a.headerlink, +h6:hover > a.headerlink, +dt:hover > a.headerlink, +caption:hover > a.headerlink, +p.caption:hover > a.headerlink, +div.code-block-caption:hover > a.headerlink { + visibility: visible; +} + +div.body p.caption { + text-align: inherit; +} + +div.body td { + text-align: left; +} + +.first { + margin-top: 0 !important; +} + +p.rubric { + margin-top: 30px; + font-weight: bold; +} + +img.align-left, figure.align-left, .figure.align-left, object.align-left { + clear: left; + float: left; + margin-right: 1em; +} + +img.align-right, figure.align-right, .figure.align-right, object.align-right { + clear: right; + float: right; + margin-left: 1em; +} + +img.align-center, figure.align-center, .figure.align-center, object.align-center { + display: block; + margin-left: auto; + margin-right: auto; +} + +img.align-default, figure.align-default, .figure.align-default { + display: block; + margin-left: auto; + margin-right: auto; +} + +.align-left { + text-align: left; +} + +.align-center { + text-align: center; +} + +.align-default { + text-align: center; +} + +.align-right { + text-align: right; +} + +/* -- sidebars -------------------------------------------------------------- */ + +div.sidebar, +aside.sidebar { + margin: 0 0 0.5em 1em; + border: 1px solid #ddb; + padding: 7px; + background-color: #ffe; + width: 40%; + float: right; + clear: right; + overflow-x: auto; +} + +p.sidebar-title { + font-weight: bold; +} + +nav.contents, +aside.topic, +div.admonition, div.topic, blockquote { + clear: left; +} + +/* -- topics ---------------------------------------------------------------- */ + +nav.contents, +aside.topic, +div.topic { + border: 1px solid #ccc; + padding: 7px; + margin: 10px 0 10px 0; +} + +p.topic-title { + font-size: 1.1em; + font-weight: bold; + margin-top: 10px; +} + +/* -- admonitions ----------------------------------------------------------- */ + +div.admonition { + margin-top: 10px; + margin-bottom: 10px; + padding: 7px; +} + +div.admonition dt { + font-weight: bold; +} + +p.admonition-title { + margin: 0px 10px 5px 0px; + font-weight: bold; +} + +div.body p.centered { + text-align: center; + margin-top: 25px; +} + +/* -- content of sidebars/topics/admonitions -------------------------------- */ + +div.sidebar > :last-child, +aside.sidebar > :last-child, +nav.contents > :last-child, +aside.topic > :last-child, +div.topic > :last-child, +div.admonition > :last-child { + margin-bottom: 0; +} + +div.sidebar::after, +aside.sidebar::after, +nav.contents::after, +aside.topic::after, +div.topic::after, +div.admonition::after, +blockquote::after { + display: block; + content: ''; + clear: both; +} + +/* -- tables ---------------------------------------------------------------- */ + +table.docutils { + margin-top: 10px; + margin-bottom: 10px; + border: 0; + border-collapse: collapse; +} + +table.align-center { + margin-left: auto; + margin-right: auto; +} + +table.align-default { + margin-left: auto; + margin-right: auto; +} + +table caption span.caption-number { + font-style: italic; +} + +table caption span.caption-text { +} + +table.docutils td, table.docutils th { + padding: 1px 8px 1px 5px; + border-top: 0; + border-left: 0; + border-right: 0; + border-bottom: 1px solid #aaa; +} + +th { + text-align: left; + padding-right: 5px; +} + +table.citation { + border-left: solid 1px gray; + margin-left: 1px; +} + +table.citation td { + border-bottom: none; +} + +th > :first-child, +td > :first-child { + margin-top: 0px; +} + +th > :last-child, +td > :last-child { + margin-bottom: 0px; +} + +/* -- figures --------------------------------------------------------------- */ + +div.figure, figure { + margin: 0.5em; + padding: 0.5em; +} + +div.figure p.caption, figcaption { + padding: 0.3em; +} + +div.figure p.caption span.caption-number, +figcaption span.caption-number { + font-style: italic; +} + +div.figure p.caption span.caption-text, +figcaption span.caption-text { +} + +/* -- field list styles ----------------------------------------------------- */ + +table.field-list td, table.field-list th { + border: 0 !important; +} + +.field-list ul { + margin: 0; + padding-left: 1em; +} + +.field-list p { + margin: 0; +} + +.field-name { + -moz-hyphens: manual; + -ms-hyphens: manual; + -webkit-hyphens: manual; + hyphens: manual; +} + +/* -- hlist styles ---------------------------------------------------------- */ + +table.hlist { + margin: 1em 0; +} + +table.hlist td { + vertical-align: top; +} + +/* -- object description styles --------------------------------------------- */ + +.sig { + font-family: 'Consolas', 'Menlo', 'DejaVu Sans Mono', 'Bitstream Vera Sans Mono', monospace; +} + +.sig-name, code.descname { + background-color: transparent; + font-weight: bold; +} + +.sig-name { + font-size: 1.1em; +} + +code.descname { + font-size: 1.2em; +} + +.sig-prename, code.descclassname { + background-color: transparent; +} + +.optional { + font-size: 1.3em; +} + +.sig-paren { + font-size: larger; +} + +.sig-param.n { + font-style: italic; +} + +/* C++ specific styling */ + +.sig-inline.c-texpr, +.sig-inline.cpp-texpr { + font-family: unset; +} + +.sig.c .k, .sig.c .kt, +.sig.cpp .k, .sig.cpp .kt { + color: #0033B3; +} + +.sig.c .m, +.sig.cpp .m { + color: #1750EB; +} + +.sig.c .s, .sig.c .sc, +.sig.cpp .s, .sig.cpp .sc { + color: #067D17; +} + + +/* -- other body styles ----------------------------------------------------- */ + +ol.arabic { + list-style: decimal; +} + +ol.loweralpha { + list-style: lower-alpha; +} + +ol.upperalpha { + list-style: upper-alpha; +} + +ol.lowerroman { + list-style: lower-roman; +} + +ol.upperroman { + list-style: upper-roman; +} + +:not(li) > ol > li:first-child > :first-child, +:not(li) > ul > li:first-child > :first-child { + margin-top: 0px; +} + +:not(li) > ol > li:last-child > :last-child, +:not(li) > ul > li:last-child > :last-child { + margin-bottom: 0px; +} + +ol.simple ol p, +ol.simple ul p, +ul.simple ol p, +ul.simple ul p { + margin-top: 0; +} + +ol.simple > li:not(:first-child) > p, +ul.simple > li:not(:first-child) > p { + margin-top: 0; +} + +ol.simple p, +ul.simple p { + margin-bottom: 0; +} + +aside.footnote > span, +div.citation > span { + float: left; +} +aside.footnote > span:last-of-type, +div.citation > span:last-of-type { + padding-right: 0.5em; +} +aside.footnote > p { + margin-left: 2em; +} +div.citation > p { + margin-left: 4em; +} +aside.footnote > p:last-of-type, +div.citation > p:last-of-type { + margin-bottom: 0em; +} +aside.footnote > p:last-of-type:after, +div.citation > p:last-of-type:after { + content: ""; + clear: both; +} + +dl.field-list { + display: grid; + grid-template-columns: fit-content(30%) auto; +} + +dl.field-list > dt { + font-weight: bold; + word-break: break-word; + padding-left: 0.5em; + padding-right: 5px; +} + +dl.field-list > dd { + padding-left: 0.5em; + margin-top: 0em; + margin-left: 0em; + margin-bottom: 0em; +} + +dl { + margin-bottom: 15px; +} + +dd > :first-child { + margin-top: 0px; +} + +dd ul, dd table { + margin-bottom: 10px; +} + +dd { + margin-top: 3px; + margin-bottom: 10px; + margin-left: 30px; +} + +.sig dd { + margin-top: 0px; + margin-bottom: 0px; +} + +.sig dl { + margin-top: 0px; + margin-bottom: 0px; +} + +dl > dd:last-child, +dl > dd:last-child > :last-child { + margin-bottom: 0; +} + +dt:target, span.highlighted { + background-color: #fbe54e; +} + +rect.highlighted { + fill: #fbe54e; +} + +dl.glossary dt { + font-weight: bold; + font-size: 1.1em; +} + +.versionmodified { + font-style: italic; +} + +.system-message { + background-color: #fda; + padding: 5px; + border: 3px solid red; +} + +.footnote:target { + background-color: #ffa; +} + +.line-block { + display: block; + margin-top: 1em; + margin-bottom: 1em; +} + +.line-block .line-block { + margin-top: 0; + margin-bottom: 0; + margin-left: 1.5em; +} + +.guilabel, .menuselection { + font-family: sans-serif; +} + +.accelerator { + text-decoration: underline; +} + +.classifier { + font-style: oblique; +} + +.classifier:before { + font-style: normal; + margin: 0 0.5em; + content: ":"; + display: inline-block; +} + +abbr, acronym { + border-bottom: dotted 1px; + cursor: help; +} + +.translated { + background-color: rgba(207, 255, 207, 0.2) +} + +.untranslated { + background-color: rgba(255, 207, 207, 0.2) +} + +/* -- code displays --------------------------------------------------------- */ + +pre { + overflow: auto; + overflow-y: hidden; /* fixes display issues on Chrome browsers */ +} + +pre, div[class*="highlight-"] { + clear: both; +} + +span.pre { + -moz-hyphens: none; + -ms-hyphens: none; + -webkit-hyphens: none; + hyphens: none; + white-space: nowrap; +} + +div[class*="highlight-"] { + margin: 1em 0; +} + +td.linenos pre { + border: 0; + background-color: transparent; + color: #aaa; +} + +table.highlighttable { + display: block; +} + +table.highlighttable tbody { + display: block; +} + +table.highlighttable tr { + display: flex; +} + +table.highlighttable td { + margin: 0; + padding: 0; +} + +table.highlighttable td.linenos { + padding-right: 0.5em; +} + +table.highlighttable td.code { + flex: 1; + overflow: hidden; +} + +.highlight .hll { + display: block; +} + +div.highlight pre, +table.highlighttable pre { + margin: 0; +} + +div.code-block-caption + div { + margin-top: 0; +} + +div.code-block-caption { + margin-top: 1em; + padding: 2px 5px; + font-size: small; +} + +div.code-block-caption code { + background-color: transparent; +} + +table.highlighttable td.linenos, +span.linenos, +div.highlight span.gp { /* gp: Generic.Prompt */ + user-select: none; + -webkit-user-select: text; /* Safari fallback only */ + -webkit-user-select: none; /* Chrome/Safari */ + -moz-user-select: none; /* Firefox */ + -ms-user-select: none; /* IE10+ */ +} + +div.code-block-caption span.caption-number { + padding: 0.1em 0.3em; + font-style: italic; +} + +div.code-block-caption span.caption-text { +} + +div.literal-block-wrapper { + margin: 1em 0; +} + +code.xref, a code { + background-color: transparent; + font-weight: bold; +} + +h1 code, h2 code, h3 code, h4 code, h5 code, h6 code { + background-color: transparent; +} + +.viewcode-link { + float: right; +} + +.viewcode-back { + float: right; + font-family: sans-serif; +} + +div.viewcode-block:target { + margin: -1px -10px; + padding: 0 10px; +} + +/* -- math display ---------------------------------------------------------- */ + +img.math { + vertical-align: middle; +} + +div.body div.math p { + text-align: center; +} + +span.eqno { + float: right; +} + +span.eqno a.headerlink { + position: absolute; + z-index: 1; +} + +div.math:hover a.headerlink { + visibility: visible; +} + +/* -- printout stylesheet --------------------------------------------------- */ + +@media print { + div.document, + div.documentwrapper, + div.bodywrapper { + margin: 0 !important; + width: 100%; + } + + div.sphinxsidebar, + div.related, + div.footer, + #top-link { + display: none; + } +} \ No newline at end of file diff --git a/_static/check-solid.svg b/_static/check-solid.svg new file mode 100644 index 0000000..92fad4b --- /dev/null +++ b/_static/check-solid.svg @@ -0,0 +1,4 @@ + + + + diff --git a/_static/clipboard.min.js b/_static/clipboard.min.js new file mode 100644 index 0000000..54b3c46 --- /dev/null +++ b/_static/clipboard.min.js @@ -0,0 +1,7 @@ +/*! + * clipboard.js v2.0.8 + * https://clipboardjs.com/ + * + * Licensed MIT © Zeno Rocha + */ +!function(t,e){"object"==typeof exports&&"object"==typeof module?module.exports=e():"function"==typeof define&&define.amd?define([],e):"object"==typeof exports?exports.ClipboardJS=e():t.ClipboardJS=e()}(this,function(){return n={686:function(t,e,n){"use strict";n.d(e,{default:function(){return o}});var e=n(279),i=n.n(e),e=n(370),u=n.n(e),e=n(817),c=n.n(e);function a(t){try{return document.execCommand(t)}catch(t){return}}var f=function(t){t=c()(t);return a("cut"),t};var l=function(t){var e,n,o,r=1 + + + + diff --git a/_static/copybutton.css b/_static/copybutton.css new file mode 100644 index 0000000..40eafe5 --- /dev/null +++ b/_static/copybutton.css @@ -0,0 +1,93 @@ +/* Copy buttons */ +button.copybtn { + position: absolute; + display: flex; + top: .3em; + right: .3em; + width: 1.7em; + height: 1.7em; + opacity: 0; + transition: opacity 0.3s, border .3s, background-color .3s; + user-select: none; + padding: 0; + border: none; + outline: none; + border-radius: 0.4em; + /* The colors that GitHub uses */ + border: #1b1f2426 1px solid; + background-color: #f6f8fa; + color: #57606a; +} + +button.copybtn.success { + border-color: #22863a; + color: #22863a; +} + +button.copybtn svg { + stroke: currentColor; + width: 1.5em; + height: 1.5em; + padding: 0.1em; +} + +div.highlight { + position: relative; +} + +.highlight:hover button.copybtn { + opacity: 1; +} + +.highlight button.copybtn:hover { + background-color: rgb(235, 235, 235); +} + +.highlight button.copybtn:active { + background-color: rgb(187, 187, 187); +} + +/** + * A minimal CSS-only tooltip copied from: + * https://codepen.io/mildrenben/pen/rVBrpK + * + * To use, write HTML like the following: + * + *

Short

+ */ + .o-tooltip--left { + position: relative; + } + + .o-tooltip--left:after { + opacity: 0; + visibility: hidden; + position: absolute; + content: attr(data-tooltip); + padding: .2em; + font-size: .8em; + left: -.2em; + background: grey; + color: white; + white-space: nowrap; + z-index: 2; + border-radius: 2px; + transform: translateX(-102%) translateY(0); + transition: opacity 0.2s cubic-bezier(0.64, 0.09, 0.08, 1), transform 0.2s cubic-bezier(0.64, 0.09, 0.08, 1); +} + +.o-tooltip--left:hover:after { + display: block; + opacity: 1; + visibility: visible; + transform: translateX(-100%) translateY(0); + transition: opacity 0.2s cubic-bezier(0.64, 0.09, 0.08, 1), transform 0.2s cubic-bezier(0.64, 0.09, 0.08, 1); + transition-delay: .5s; +} + +/* By default the copy button shouldn't show up when printing a page */ +@media print { + button.copybtn { + display: none; + } +} diff --git a/_static/copybutton.js b/_static/copybutton.js new file mode 100644 index 0000000..f3ecd03 --- /dev/null +++ b/_static/copybutton.js @@ -0,0 +1,241 @@ +// Localization support +const messages = { + 'en': { + 'copy': 'Copy', + 'copy_to_clipboard': 'Copy to clipboard', + 'copy_success': 'Copied!', + 'copy_failure': 'Failed to copy', + }, + 'es' : { + 'copy': 'Copiar', + 'copy_to_clipboard': 'Copiar al portapapeles', + 'copy_success': '¡Copiado!', + 'copy_failure': 'Error al copiar', + }, + 'de' : { + 'copy': 'Kopieren', + 'copy_to_clipboard': 'In die Zwischenablage kopieren', + 'copy_success': 'Kopiert!', + 'copy_failure': 'Fehler beim Kopieren', + }, + 'fr' : { + 'copy': 'Copier', + 'copy_to_clipboard': 'Copié dans le presse-papier', + 'copy_success': 'Copié !', + 'copy_failure': 'Échec de la copie', + }, + 'ru': { + 'copy': 'Скопировать', + 'copy_to_clipboard': 'Скопировать в буфер', + 'copy_success': 'Скопировано!', + 'copy_failure': 'Не удалось скопировать', + }, + 'zh-CN': { + 'copy': '复制', + 'copy_to_clipboard': '复制到剪贴板', + 'copy_success': '复制成功!', + 'copy_failure': '复制失败', + }, + 'it' : { + 'copy': 'Copiare', + 'copy_to_clipboard': 'Copiato negli appunti', + 'copy_success': 'Copiato!', + 'copy_failure': 'Errore durante la copia', + } +} + +let locale = 'en' +if( document.documentElement.lang !== undefined + && messages[document.documentElement.lang] !== undefined ) { + locale = document.documentElement.lang +} + +let doc_url_root = DOCUMENTATION_OPTIONS.URL_ROOT; +if (doc_url_root == '#') { + doc_url_root = ''; +} + +/** + * SVG files for our copy buttons + */ +let iconCheck = ` + ${messages[locale]['copy_success']} + + +` + +// If the user specified their own SVG use that, otherwise use the default +let iconCopy = ``; +if (!iconCopy) { + iconCopy = ` + ${messages[locale]['copy_to_clipboard']} + + + +` +} + +/** + * Set up copy/paste for code blocks + */ + +const runWhenDOMLoaded = cb => { + if (document.readyState != 'loading') { + cb() + } else if (document.addEventListener) { + document.addEventListener('DOMContentLoaded', cb) + } else { + document.attachEvent('onreadystatechange', function() { + if (document.readyState == 'complete') cb() + }) + } +} + +const codeCellId = index => `codecell${index}` + +// Clears selected text since ClipboardJS will select the text when copying +const clearSelection = () => { + if (window.getSelection) { + window.getSelection().removeAllRanges() + } else if (document.selection) { + document.selection.empty() + } +} + +// Changes tooltip text for two seconds, then changes it back +const temporarilyChangeTooltip = (el, oldText, newText) => { + el.setAttribute('data-tooltip', newText) + el.classList.add('success') + setTimeout(() => el.setAttribute('data-tooltip', oldText), 2000) + setTimeout(() => el.classList.remove('success'), 2000) +} + +// Changes the copy button icon for two seconds, then changes it back +const temporarilyChangeIcon = (el) => { + el.innerHTML = iconCheck; + setTimeout(() => {el.innerHTML = iconCopy}, 2000) +} + +const addCopyButtonToCodeCells = () => { + // If ClipboardJS hasn't loaded, wait a bit and try again. This + // happens because we load ClipboardJS asynchronously. + if (window.ClipboardJS === undefined) { + setTimeout(addCopyButtonToCodeCells, 250) + return + } + + // Add copybuttons to all of our code cells + const COPYBUTTON_SELECTOR = 'div.highlight pre'; + const codeCells = document.querySelectorAll(COPYBUTTON_SELECTOR) + codeCells.forEach((codeCell, index) => { + const id = codeCellId(index) + codeCell.setAttribute('id', id) + + const clipboardButton = id => + `` + codeCell.insertAdjacentHTML('afterend', clipboardButton(id)) + }) + +function escapeRegExp(string) { + return string.replace(/[.*+?^${}()|[\]\\]/g, '\\$&'); // $& means the whole matched string +} + +/** + * Removes excluded text from a Node. + * + * @param {Node} target Node to filter. + * @param {string} exclude CSS selector of nodes to exclude. + * @returns {DOMString} Text from `target` with text removed. + */ +function filterText(target, exclude) { + const clone = target.cloneNode(true); // clone as to not modify the live DOM + if (exclude) { + // remove excluded nodes + clone.querySelectorAll(exclude).forEach(node => node.remove()); + } + return clone.innerText; +} + +// Callback when a copy button is clicked. Will be passed the node that was clicked +// should then grab the text and replace pieces of text that shouldn't be used in output +function formatCopyText(textContent, copybuttonPromptText, isRegexp = false, onlyCopyPromptLines = true, removePrompts = true, copyEmptyLines = true, lineContinuationChar = "", hereDocDelim = "") { + var regexp; + var match; + + // Do we check for line continuation characters and "HERE-documents"? + var useLineCont = !!lineContinuationChar + var useHereDoc = !!hereDocDelim + + // create regexp to capture prompt and remaining line + if (isRegexp) { + regexp = new RegExp('^(' + copybuttonPromptText + ')(.*)') + } else { + regexp = new RegExp('^(' + escapeRegExp(copybuttonPromptText) + ')(.*)') + } + + const outputLines = []; + var promptFound = false; + var gotLineCont = false; + var gotHereDoc = false; + const lineGotPrompt = []; + for (const line of textContent.split('\n')) { + match = line.match(regexp) + if (match || gotLineCont || gotHereDoc) { + promptFound = regexp.test(line) + lineGotPrompt.push(promptFound) + if (removePrompts && promptFound) { + outputLines.push(match[2]) + } else { + outputLines.push(line) + } + gotLineCont = line.endsWith(lineContinuationChar) & useLineCont + if (line.includes(hereDocDelim) & useHereDoc) + gotHereDoc = !gotHereDoc + } else if (!onlyCopyPromptLines) { + outputLines.push(line) + } else if (copyEmptyLines && line.trim() === '') { + outputLines.push(line) + } + } + + // If no lines with the prompt were found then just use original lines + if (lineGotPrompt.some(v => v === true)) { + textContent = outputLines.join('\n'); + } + + // Remove a trailing newline to avoid auto-running when pasting + if (textContent.endsWith("\n")) { + textContent = textContent.slice(0, -1) + } + return textContent +} + + +var copyTargetText = (trigger) => { + var target = document.querySelector(trigger.attributes['data-clipboard-target'].value); + + // get filtered text + let exclude = '.linenos, .gp'; + + let text = filterText(target, exclude); + return formatCopyText(text, '', false, true, true, true, '', '') +} + + // Initialize with a callback so we can modify the text before copy + const clipboard = new ClipboardJS('.copybtn', {text: copyTargetText}) + + // Update UI with error/success messages + clipboard.on('success', event => { + clearSelection() + temporarilyChangeTooltip(event.trigger, messages[locale]['copy'], messages[locale]['copy_success']) + temporarilyChangeIcon(event.trigger) + }) + + clipboard.on('error', event => { + temporarilyChangeTooltip(event.trigger, messages[locale]['copy'], messages[locale]['copy_failure']) + }) +} + +runWhenDOMLoaded(addCopyButtonToCodeCells) \ No newline at end of file diff --git a/_static/copybutton_funcs.js b/_static/copybutton_funcs.js new file mode 100644 index 0000000..dbe1aaa --- /dev/null +++ b/_static/copybutton_funcs.js @@ -0,0 +1,73 @@ +function escapeRegExp(string) { + return string.replace(/[.*+?^${}()|[\]\\]/g, '\\$&'); // $& means the whole matched string +} + +/** + * Removes excluded text from a Node. + * + * @param {Node} target Node to filter. + * @param {string} exclude CSS selector of nodes to exclude. + * @returns {DOMString} Text from `target` with text removed. + */ +export function filterText(target, exclude) { + const clone = target.cloneNode(true); // clone as to not modify the live DOM + if (exclude) { + // remove excluded nodes + clone.querySelectorAll(exclude).forEach(node => node.remove()); + } + return clone.innerText; +} + +// Callback when a copy button is clicked. Will be passed the node that was clicked +// should then grab the text and replace pieces of text that shouldn't be used in output +export function formatCopyText(textContent, copybuttonPromptText, isRegexp = false, onlyCopyPromptLines = true, removePrompts = true, copyEmptyLines = true, lineContinuationChar = "", hereDocDelim = "") { + var regexp; + var match; + + // Do we check for line continuation characters and "HERE-documents"? + var useLineCont = !!lineContinuationChar + var useHereDoc = !!hereDocDelim + + // create regexp to capture prompt and remaining line + if (isRegexp) { + regexp = new RegExp('^(' + copybuttonPromptText + ')(.*)') + } else { + regexp = new RegExp('^(' + escapeRegExp(copybuttonPromptText) + ')(.*)') + } + + const outputLines = []; + var promptFound = false; + var gotLineCont = false; + var gotHereDoc = false; + const lineGotPrompt = []; + for (const line of textContent.split('\n')) { + match = line.match(regexp) + if (match || gotLineCont || gotHereDoc) { + promptFound = regexp.test(line) + lineGotPrompt.push(promptFound) + if (removePrompts && promptFound) { + outputLines.push(match[2]) + } else { + outputLines.push(line) + } + gotLineCont = line.endsWith(lineContinuationChar) & useLineCont + if (line.includes(hereDocDelim) & useHereDoc) + gotHereDoc = !gotHereDoc + } else if (!onlyCopyPromptLines) { + outputLines.push(line) + } else if (copyEmptyLines && line.trim() === '') { + outputLines.push(line) + } + } + + // If no lines with the prompt were found then just use original lines + if (lineGotPrompt.some(v => v === true)) { + textContent = outputLines.join('\n'); + } + + // Remove a trailing newline to avoid auto-running when pasting + if (textContent.endsWith("\n")) { + textContent = textContent.slice(0, -1) + } + return textContent +} diff --git a/_static/css/badge_only.css b/_static/css/badge_only.css new file mode 100644 index 0000000..c718cee --- /dev/null +++ b/_static/css/badge_only.css @@ -0,0 +1 @@ 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+ border-left-width: medium; + border-radius: var(--mystnb-source-border-radius); +} + +div.cell_input>div, +div.cell_output div.output>div.highlight { + margin: 0em !important; + border: none !important; +} + +/* All cell outputs */ +.cell_output { + padding-left: 1em; + padding-right: 0em; + margin-top: 1em; +} + +/* Text outputs from cells */ +.cell_output .output.text_plain, +.cell_output .output.traceback, +.cell_output .output.stream, +.cell_output .output.stderr { + margin-top: 1em; + margin-bottom: 0em; + box-shadow: none; +} + +.cell_output .output.text_plain, +.cell_output .output.stream { + background: var(--mystnb-stdout-bg-color); + border: 1px solid var(--mystnb-stdout-border-color); +} + +.cell_output .output.stderr { + background: var(--mystnb-stderr-bg-color); + border: 1px solid var(--mystnb-stderr-border-color); +} + +.cell_output .output.traceback { + background: var(--mystnb-traceback-bg-color); + border: 1px solid var(--mystnb-traceback-border-color); +} + +/* Collapsible cell content */ +div.cell details.above-input div.cell_input { + border-top-left-radius: 0; 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Pulled from the Jupyter / nbsphinx CSS */ +div.cell_output table { + border: none; + border-collapse: collapse; + border-spacing: 0; + color: black; + font-size: 1em; + table-layout: fixed; +} + +div.cell_output thead { + border-bottom: 1px solid black; + vertical-align: bottom; +} + +div.cell_output tr, +div.cell_output th, +div.cell_output td { + text-align: right; + vertical-align: middle; + padding: 0.5em 0.5em; + line-height: normal; + white-space: normal; + max-width: none; + border: none; +} + +div.cell_output th { + font-weight: bold; +} + +div.cell_output tbody tr:nth-child(odd) { + background: #f5f5f5; +} + +div.cell_output tbody tr:hover { + background: rgba(66, 165, 245, 0.2); +} + +/** source code line numbers **/ +span.linenos { + opacity: 0.5; +} + +/* Inline text from `paste` operation */ + +span.pasted-text { + font-weight: bold; +} + +span.pasted-inline img { + max-height: 2em; +} + +tbody span.pasted-inline img { + max-height: none; +} + +/* Font colors for 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+} + +div.highlight .-Color[class*=-C41] { + color: #00D75F +} + +div.highlight .-Color[class*=-BGC41] { + background-color: #00D75F +} + +div.highlight .-Color[class*=-C42] { + color: #00D787 +} + +div.highlight .-Color[class*=-BGC42] { + background-color: #00D787 +} + +div.highlight .-Color[class*=-C43] { + color: #00D7AF +} + +div.highlight .-Color[class*=-BGC43] { + background-color: #00D7AF +} + +div.highlight .-Color[class*=-C44] { + color: #00D7D7 +} + +div.highlight .-Color[class*=-BGC44] { + background-color: #00D7D7 +} + +div.highlight .-Color[class*=-C45] { + color: #00D7FF +} + +div.highlight .-Color[class*=-BGC45] { + background-color: #00D7FF +} + +div.highlight .-Color[class*=-C46] { + color: #00FF00 +} + +div.highlight .-Color[class*=-BGC46] { + background-color: #00FF00 +} + +div.highlight .-Color[class*=-C47] { + color: #00FF5F +} + +div.highlight .-Color[class*=-BGC47] { + background-color: #00FF5F +} + +div.highlight .-Color[class*=-C48] { + color: #00FF87 +} + 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+} + +div.highlight .-Color[class*=-C56] { + color: #5F00D7 +} + +div.highlight .-Color[class*=-BGC56] { + background-color: #5F00D7 +} + +div.highlight .-Color[class*=-C57] { + color: #5F00FF +} + +div.highlight .-Color[class*=-BGC57] { + background-color: #5F00FF +} + +div.highlight .-Color[class*=-C58] { + color: #5F5F00 +} + +div.highlight .-Color[class*=-BGC58] { + background-color: #5F5F00 +} + +div.highlight .-Color[class*=-C59] { + color: #5F5F5F +} + +div.highlight .-Color[class*=-BGC59] { + background-color: #5F5F5F +} + +div.highlight .-Color[class*=-C60] { + color: #5F5F87 +} + +div.highlight .-Color[class*=-BGC60] { + background-color: #5F5F87 +} + +div.highlight .-Color[class*=-C61] { + color: #5F5FAF +} + +div.highlight .-Color[class*=-BGC61] { + background-color: #5F5FAF +} + +div.highlight .-Color[class*=-C62] { + color: #5F5FD7 +} + +div.highlight .-Color[class*=-BGC62] { + background-color: #5F5FD7 +} + +div.highlight .-Color[class*=-C63] { + color: #5F5FFF +} + 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+} + +div.highlight .-Color[class*=-C71] { + color: #5FAF5F +} + +div.highlight .-Color[class*=-BGC71] { + background-color: #5FAF5F +} + +div.highlight .-Color[class*=-C72] { + color: #5FAF87 +} + +div.highlight .-Color[class*=-BGC72] { + background-color: #5FAF87 +} + +div.highlight .-Color[class*=-C73] { + color: #5FAFAF +} + +div.highlight .-Color[class*=-BGC73] { + background-color: #5FAFAF +} + +div.highlight .-Color[class*=-C74] { + color: #5FAFD7 +} + +div.highlight .-Color[class*=-BGC74] { + background-color: #5FAFD7 +} + +div.highlight .-Color[class*=-C75] { + color: #5FAFFF +} + +div.highlight .-Color[class*=-BGC75] { + background-color: #5FAFFF +} + +div.highlight .-Color[class*=-C76] { + color: #5FD700 +} + +div.highlight .-Color[class*=-BGC76] { + background-color: #5FD700 +} + +div.highlight .-Color[class*=-C77] { + color: #5FD75F +} + +div.highlight .-Color[class*=-BGC77] { + background-color: #5FD75F +} + +div.highlight .-Color[class*=-C78] { + color: #5FD787 +} + +div.highlight .-Color[class*=-BGC78] { + background-color: #5FD787 +} + +div.highlight .-Color[class*=-C79] { + color: #5FD7AF +} + +div.highlight .-Color[class*=-BGC79] { + background-color: #5FD7AF +} + +div.highlight .-Color[class*=-C80] { + color: #5FD7D7 +} + +div.highlight .-Color[class*=-BGC80] { + background-color: #5FD7D7 +} + +div.highlight .-Color[class*=-C81] { + color: #5FD7FF +} + +div.highlight .-Color[class*=-BGC81] { + background-color: #5FD7FF +} + +div.highlight .-Color[class*=-C82] { + color: #5FFF00 +} + +div.highlight .-Color[class*=-BGC82] { + background-color: #5FFF00 +} + +div.highlight .-Color[class*=-C83] { + color: #5FFF5F +} + +div.highlight .-Color[class*=-BGC83] { + background-color: #5FFF5F +} + +div.highlight .-Color[class*=-C84] { + color: #5FFF87 +} + +div.highlight .-Color[class*=-BGC84] { + background-color: #5FFF87 +} + +div.highlight .-Color[class*=-C85] { + color: #5FFFAF +} + +div.highlight .-Color[class*=-BGC85] { + background-color: #5FFFAF +} + +div.highlight .-Color[class*=-C86] { + color: #5FFFD7 +} + +div.highlight .-Color[class*=-BGC86] { + background-color: #5FFFD7 +} + +div.highlight .-Color[class*=-C87] { + color: #5FFFFF +} + +div.highlight .-Color[class*=-BGC87] { + background-color: #5FFFFF +} + +div.highlight .-Color[class*=-C88] { + color: #870000 +} + +div.highlight .-Color[class*=-BGC88] { + background-color: #870000 +} + +div.highlight .-Color[class*=-C89] { + color: #87005F +} + +div.highlight .-Color[class*=-BGC89] { + background-color: #87005F +} + +div.highlight .-Color[class*=-C90] { + color: #870087 +} + +div.highlight .-Color[class*=-BGC90] { + background-color: #870087 +} + +div.highlight .-Color[class*=-C91] { + color: #8700AF +} + +div.highlight .-Color[class*=-BGC91] { + background-color: #8700AF +} + +div.highlight .-Color[class*=-C92] { + color: #8700D7 +} + +div.highlight .-Color[class*=-BGC92] { + background-color: #8700D7 +} + +div.highlight .-Color[class*=-C93] { + color: #8700FF +} + +div.highlight .-Color[class*=-BGC93] { + background-color: #8700FF +} + +div.highlight .-Color[class*=-C94] { + color: #875F00 +} + +div.highlight .-Color[class*=-BGC94] { + background-color: #875F00 +} + +div.highlight .-Color[class*=-C95] { + color: #875F5F +} + +div.highlight .-Color[class*=-BGC95] { + background-color: #875F5F +} + +div.highlight .-Color[class*=-C96] { + color: #875F87 +} + +div.highlight .-Color[class*=-BGC96] { + background-color: #875F87 +} + +div.highlight .-Color[class*=-C97] { + color: #875FAF +} + +div.highlight .-Color[class*=-BGC97] { + background-color: #875FAF +} + +div.highlight .-Color[class*=-C98] { + color: #875FD7 +} + +div.highlight .-Color[class*=-BGC98] { + background-color: #875FD7 +} + +div.highlight .-Color[class*=-C99] { + color: #875FFF +} + +div.highlight .-Color[class*=-BGC99] { + background-color: #875FFF +} + +div.highlight .-Color[class*=-C100] { + color: #878700 +} + +div.highlight .-Color[class*=-BGC100] { + background-color: #878700 +} + +div.highlight .-Color[class*=-C101] { + color: #87875F +} + +div.highlight .-Color[class*=-BGC101] { + background-color: #87875F +} + +div.highlight .-Color[class*=-C102] { + color: #878787 +} + +div.highlight .-Color[class*=-BGC102] { + background-color: #878787 +} + +div.highlight .-Color[class*=-C103] { + color: #8787AF +} + +div.highlight .-Color[class*=-BGC103] { + background-color: #8787AF +} + +div.highlight .-Color[class*=-C104] { + color: #8787D7 +} + +div.highlight .-Color[class*=-BGC104] { + background-color: #8787D7 +} + +div.highlight .-Color[class*=-C105] { + color: #8787FF +} + +div.highlight .-Color[class*=-BGC105] { + background-color: #8787FF +} + +div.highlight .-Color[class*=-C106] { + color: #87AF00 +} + +div.highlight .-Color[class*=-BGC106] { + background-color: #87AF00 +} + +div.highlight .-Color[class*=-C107] { + color: #87AF5F +} + +div.highlight .-Color[class*=-BGC107] { + background-color: #87AF5F +} + +div.highlight .-Color[class*=-C108] { + color: #87AF87 +} + +div.highlight .-Color[class*=-BGC108] { + background-color: #87AF87 +} + +div.highlight .-Color[class*=-C109] { + color: #87AFAF +} + +div.highlight .-Color[class*=-BGC109] { + background-color: #87AFAF +} + +div.highlight .-Color[class*=-C110] { + color: #87AFD7 +} + +div.highlight .-Color[class*=-BGC110] { + background-color: #87AFD7 +} + +div.highlight .-Color[class*=-C111] { + color: #87AFFF +} + +div.highlight .-Color[class*=-BGC111] { + background-color: #87AFFF +} + +div.highlight .-Color[class*=-C112] { + color: #87D700 +} + +div.highlight .-Color[class*=-BGC112] { + background-color: #87D700 +} + +div.highlight .-Color[class*=-C113] { + color: #87D75F +} + +div.highlight .-Color[class*=-BGC113] { + background-color: #87D75F +} + +div.highlight .-Color[class*=-C114] { + color: #87D787 +} + +div.highlight .-Color[class*=-BGC114] { + background-color: #87D787 +} + +div.highlight .-Color[class*=-C115] { + color: #87D7AF +} + +div.highlight .-Color[class*=-BGC115] { + background-color: #87D7AF +} + +div.highlight .-Color[class*=-C116] { + color: #87D7D7 +} + +div.highlight .-Color[class*=-BGC116] { + background-color: #87D7D7 +} + +div.highlight .-Color[class*=-C117] { + color: #87D7FF +} + +div.highlight .-Color[class*=-BGC117] { + background-color: #87D7FF +} + +div.highlight .-Color[class*=-C118] { + color: #87FF00 +} + +div.highlight .-Color[class*=-BGC118] { + background-color: #87FF00 +} + +div.highlight .-Color[class*=-C119] { + color: #87FF5F +} + +div.highlight .-Color[class*=-BGC119] { + background-color: #87FF5F +} + +div.highlight .-Color[class*=-C120] { + color: #87FF87 +} + +div.highlight .-Color[class*=-BGC120] { + background-color: #87FF87 +} + +div.highlight .-Color[class*=-C121] { + color: #87FFAF +} + +div.highlight .-Color[class*=-BGC121] { + background-color: #87FFAF +} + +div.highlight .-Color[class*=-C122] { + color: #87FFD7 +} + +div.highlight .-Color[class*=-BGC122] { + background-color: #87FFD7 +} + +div.highlight .-Color[class*=-C123] { + color: #87FFFF +} + +div.highlight .-Color[class*=-BGC123] { + background-color: #87FFFF +} + +div.highlight .-Color[class*=-C124] { + color: #AF0000 +} + +div.highlight .-Color[class*=-BGC124] { + background-color: #AF0000 +} + +div.highlight .-Color[class*=-C125] { + color: #AF005F +} + +div.highlight .-Color[class*=-BGC125] { + background-color: #AF005F +} + +div.highlight .-Color[class*=-C126] { + color: #AF0087 +} + +div.highlight .-Color[class*=-BGC126] { + background-color: #AF0087 +} + +div.highlight .-Color[class*=-C127] { + color: #AF00AF +} + +div.highlight .-Color[class*=-BGC127] { + background-color: #AF00AF +} + +div.highlight .-Color[class*=-C128] { + color: #AF00D7 +} + +div.highlight .-Color[class*=-BGC128] { + background-color: #AF00D7 +} + +div.highlight .-Color[class*=-C129] { + color: #AF00FF +} + +div.highlight .-Color[class*=-BGC129] { + background-color: #AF00FF +} + +div.highlight .-Color[class*=-C130] { + color: #AF5F00 +} + +div.highlight .-Color[class*=-BGC130] { + background-color: #AF5F00 +} + +div.highlight .-Color[class*=-C131] { + color: #AF5F5F +} + +div.highlight .-Color[class*=-BGC131] { + background-color: #AF5F5F +} + +div.highlight .-Color[class*=-C132] { + color: #AF5F87 +} + +div.highlight .-Color[class*=-BGC132] { + background-color: #AF5F87 +} + +div.highlight .-Color[class*=-C133] { + color: #AF5FAF +} + +div.highlight .-Color[class*=-BGC133] { + background-color: #AF5FAF +} + +div.highlight .-Color[class*=-C134] { + color: #AF5FD7 +} + +div.highlight .-Color[class*=-BGC134] { + background-color: #AF5FD7 +} + +div.highlight .-Color[class*=-C135] { + color: #AF5FFF +} + +div.highlight .-Color[class*=-BGC135] { + background-color: #AF5FFF +} + +div.highlight .-Color[class*=-C136] { + color: #AF8700 +} + +div.highlight .-Color[class*=-BGC136] { + background-color: #AF8700 +} + +div.highlight .-Color[class*=-C137] { + color: #AF875F +} + +div.highlight .-Color[class*=-BGC137] { + background-color: #AF875F +} + +div.highlight .-Color[class*=-C138] { + color: #AF8787 +} + +div.highlight .-Color[class*=-BGC138] { + background-color: #AF8787 +} + +div.highlight .-Color[class*=-C139] { + color: #AF87AF +} + +div.highlight .-Color[class*=-BGC139] { + background-color: #AF87AF +} + +div.highlight .-Color[class*=-C140] { + color: #AF87D7 +} + +div.highlight .-Color[class*=-BGC140] { + background-color: #AF87D7 +} + +div.highlight .-Color[class*=-C141] { + color: #AF87FF +} + +div.highlight .-Color[class*=-BGC141] { + background-color: #AF87FF +} + +div.highlight .-Color[class*=-C142] { + color: #AFAF00 +} + +div.highlight .-Color[class*=-BGC142] { + background-color: #AFAF00 +} + +div.highlight .-Color[class*=-C143] { + color: #AFAF5F +} + +div.highlight .-Color[class*=-BGC143] { + background-color: #AFAF5F +} + +div.highlight .-Color[class*=-C144] { + color: #AFAF87 +} + +div.highlight .-Color[class*=-BGC144] { + background-color: #AFAF87 +} + +div.highlight .-Color[class*=-C145] { + color: #AFAFAF +} + +div.highlight .-Color[class*=-BGC145] { + background-color: #AFAFAF +} + +div.highlight .-Color[class*=-C146] { + color: #AFAFD7 +} + +div.highlight .-Color[class*=-BGC146] { + background-color: #AFAFD7 +} + +div.highlight .-Color[class*=-C147] { + color: #AFAFFF +} + +div.highlight .-Color[class*=-BGC147] { + background-color: #AFAFFF +} + +div.highlight .-Color[class*=-C148] { + color: #AFD700 +} + +div.highlight .-Color[class*=-BGC148] { + background-color: #AFD700 +} + +div.highlight .-Color[class*=-C149] { + color: #AFD75F +} + +div.highlight .-Color[class*=-BGC149] { + background-color: #AFD75F +} + +div.highlight .-Color[class*=-C150] { + color: #AFD787 +} + +div.highlight .-Color[class*=-BGC150] { + background-color: #AFD787 +} + +div.highlight .-Color[class*=-C151] { + color: #AFD7AF +} + +div.highlight .-Color[class*=-BGC151] { + background-color: #AFD7AF +} + +div.highlight .-Color[class*=-C152] { + color: #AFD7D7 +} + +div.highlight .-Color[class*=-BGC152] { + background-color: #AFD7D7 +} + +div.highlight .-Color[class*=-C153] { + color: #AFD7FF +} + +div.highlight .-Color[class*=-BGC153] { + background-color: #AFD7FF +} + +div.highlight .-Color[class*=-C154] { + color: #AFFF00 +} + +div.highlight .-Color[class*=-BGC154] { + background-color: #AFFF00 +} + +div.highlight .-Color[class*=-C155] { + color: #AFFF5F +} + +div.highlight .-Color[class*=-BGC155] { + background-color: #AFFF5F +} + +div.highlight .-Color[class*=-C156] { + color: #AFFF87 +} + +div.highlight .-Color[class*=-BGC156] { + background-color: #AFFF87 +} + +div.highlight .-Color[class*=-C157] { + color: #AFFFAF +} + +div.highlight .-Color[class*=-BGC157] { + background-color: #AFFFAF +} + +div.highlight .-Color[class*=-C158] { + color: #AFFFD7 +} + +div.highlight .-Color[class*=-BGC158] { + background-color: #AFFFD7 +} + +div.highlight .-Color[class*=-C159] { + color: #AFFFFF +} + +div.highlight .-Color[class*=-BGC159] { + background-color: #AFFFFF +} + +div.highlight .-Color[class*=-C160] { + color: #D70000 +} + +div.highlight .-Color[class*=-BGC160] { + background-color: #D70000 +} + +div.highlight .-Color[class*=-C161] { + color: #D7005F +} + +div.highlight .-Color[class*=-BGC161] { + background-color: #D7005F +} + +div.highlight .-Color[class*=-C162] { + color: #D70087 +} + +div.highlight .-Color[class*=-BGC162] { + background-color: #D70087 +} + +div.highlight .-Color[class*=-C163] { + color: #D700AF +} + +div.highlight .-Color[class*=-BGC163] { + background-color: #D700AF +} + +div.highlight .-Color[class*=-C164] { + color: #D700D7 +} + +div.highlight .-Color[class*=-BGC164] { + background-color: #D700D7 +} + +div.highlight .-Color[class*=-C165] { + color: #D700FF +} + +div.highlight .-Color[class*=-BGC165] { + background-color: #D700FF +} + +div.highlight .-Color[class*=-C166] { + color: #D75F00 +} + +div.highlight .-Color[class*=-BGC166] { + background-color: #D75F00 +} + +div.highlight .-Color[class*=-C167] { + color: #D75F5F +} + +div.highlight .-Color[class*=-BGC167] { + background-color: #D75F5F +} + +div.highlight .-Color[class*=-C168] { + color: #D75F87 +} + +div.highlight .-Color[class*=-BGC168] { + background-color: #D75F87 +} + +div.highlight .-Color[class*=-C169] { + color: #D75FAF +} + +div.highlight .-Color[class*=-BGC169] { + background-color: #D75FAF +} + +div.highlight .-Color[class*=-C170] { + color: #D75FD7 +} + +div.highlight .-Color[class*=-BGC170] { + background-color: #D75FD7 +} + +div.highlight .-Color[class*=-C171] { + color: #D75FFF +} + +div.highlight .-Color[class*=-BGC171] { + background-color: #D75FFF +} + +div.highlight .-Color[class*=-C172] { + color: #D78700 +} + +div.highlight .-Color[class*=-BGC172] { + background-color: #D78700 +} + +div.highlight .-Color[class*=-C173] { + color: #D7875F +} + +div.highlight .-Color[class*=-BGC173] { + background-color: #D7875F +} + +div.highlight .-Color[class*=-C174] { + color: #D78787 +} + +div.highlight .-Color[class*=-BGC174] { + background-color: #D78787 +} + +div.highlight .-Color[class*=-C175] { + color: #D787AF +} + +div.highlight .-Color[class*=-BGC175] { + background-color: #D787AF +} + +div.highlight .-Color[class*=-C176] { + color: #D787D7 +} + +div.highlight .-Color[class*=-BGC176] { + background-color: #D787D7 +} + +div.highlight .-Color[class*=-C177] { + color: #D787FF +} + +div.highlight .-Color[class*=-BGC177] { + background-color: #D787FF +} + +div.highlight .-Color[class*=-C178] { + color: #D7AF00 +} + +div.highlight .-Color[class*=-BGC178] { + background-color: #D7AF00 +} + +div.highlight .-Color[class*=-C179] { + color: #D7AF5F +} + +div.highlight .-Color[class*=-BGC179] { + background-color: #D7AF5F +} + +div.highlight .-Color[class*=-C180] { + color: #D7AF87 +} + +div.highlight .-Color[class*=-BGC180] { + background-color: #D7AF87 +} + +div.highlight .-Color[class*=-C181] { + color: #D7AFAF +} + +div.highlight .-Color[class*=-BGC181] { + background-color: #D7AFAF +} + +div.highlight .-Color[class*=-C182] { + color: #D7AFD7 +} + +div.highlight .-Color[class*=-BGC182] { + background-color: #D7AFD7 +} + +div.highlight .-Color[class*=-C183] { + color: #D7AFFF +} + +div.highlight .-Color[class*=-BGC183] { + background-color: #D7AFFF +} + +div.highlight .-Color[class*=-C184] { + color: #D7D700 +} + +div.highlight .-Color[class*=-BGC184] { + background-color: #D7D700 +} + +div.highlight .-Color[class*=-C185] { + color: #D7D75F +} + +div.highlight .-Color[class*=-BGC185] { + background-color: #D7D75F +} + +div.highlight .-Color[class*=-C186] { + color: #D7D787 +} + +div.highlight .-Color[class*=-BGC186] { + background-color: #D7D787 +} + +div.highlight .-Color[class*=-C187] { + color: #D7D7AF +} + +div.highlight .-Color[class*=-BGC187] { + background-color: #D7D7AF +} + +div.highlight .-Color[class*=-C188] { + color: #D7D7D7 +} + +div.highlight .-Color[class*=-BGC188] { + background-color: #D7D7D7 +} + +div.highlight .-Color[class*=-C189] { + color: #D7D7FF +} + +div.highlight .-Color[class*=-BGC189] { + background-color: #D7D7FF +} + +div.highlight .-Color[class*=-C190] { + color: #D7FF00 +} + +div.highlight .-Color[class*=-BGC190] { + background-color: #D7FF00 +} + +div.highlight .-Color[class*=-C191] { + color: #D7FF5F +} + +div.highlight .-Color[class*=-BGC191] { + background-color: #D7FF5F +} + +div.highlight .-Color[class*=-C192] { + color: #D7FF87 +} + +div.highlight .-Color[class*=-BGC192] { + background-color: #D7FF87 +} + +div.highlight .-Color[class*=-C193] { + color: #D7FFAF +} + +div.highlight .-Color[class*=-BGC193] { + background-color: #D7FFAF +} + +div.highlight .-Color[class*=-C194] { + color: #D7FFD7 +} + +div.highlight .-Color[class*=-BGC194] { + background-color: #D7FFD7 +} + +div.highlight .-Color[class*=-C195] { + color: #D7FFFF +} + +div.highlight .-Color[class*=-BGC195] { + background-color: #D7FFFF +} + +div.highlight .-Color[class*=-C196] { + color: #FF0000 +} + +div.highlight .-Color[class*=-BGC196] { + background-color: #FF0000 +} + +div.highlight .-Color[class*=-C197] { + color: #FF005F +} + +div.highlight .-Color[class*=-BGC197] { + background-color: #FF005F +} + +div.highlight .-Color[class*=-C198] { + color: #FF0087 +} + +div.highlight .-Color[class*=-BGC198] { + background-color: #FF0087 +} + +div.highlight .-Color[class*=-C199] { + color: #FF00AF +} + +div.highlight .-Color[class*=-BGC199] { + background-color: #FF00AF +} + +div.highlight .-Color[class*=-C200] { + color: #FF00D7 +} + +div.highlight .-Color[class*=-BGC200] { + background-color: #FF00D7 +} + +div.highlight .-Color[class*=-C201] { + color: #FF00FF +} + +div.highlight .-Color[class*=-BGC201] { + background-color: #FF00FF +} + +div.highlight .-Color[class*=-C202] { + color: #FF5F00 +} + +div.highlight .-Color[class*=-BGC202] { + background-color: #FF5F00 +} + +div.highlight .-Color[class*=-C203] { + color: #FF5F5F +} + +div.highlight .-Color[class*=-BGC203] { + background-color: #FF5F5F +} + +div.highlight .-Color[class*=-C204] { + color: #FF5F87 +} + +div.highlight .-Color[class*=-BGC204] { + background-color: #FF5F87 +} + +div.highlight .-Color[class*=-C205] { + color: #FF5FAF +} + +div.highlight .-Color[class*=-BGC205] { + background-color: #FF5FAF +} + +div.highlight .-Color[class*=-C206] { + color: #FF5FD7 +} + +div.highlight .-Color[class*=-BGC206] { + background-color: #FF5FD7 +} + +div.highlight .-Color[class*=-C207] { + color: #FF5FFF +} + +div.highlight .-Color[class*=-BGC207] { + background-color: #FF5FFF +} + +div.highlight .-Color[class*=-C208] { + color: #FF8700 +} + +div.highlight .-Color[class*=-BGC208] { + background-color: #FF8700 +} + +div.highlight .-Color[class*=-C209] { + color: #FF875F +} + +div.highlight .-Color[class*=-BGC209] { + background-color: #FF875F +} + +div.highlight .-Color[class*=-C210] { + color: #FF8787 +} + +div.highlight .-Color[class*=-BGC210] { + background-color: #FF8787 +} + +div.highlight 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score for each result + // The function takes a result array [docname, title, anchor, descr, score, filename] + // and returns the new score. + /* + score: result => { + const [docname, title, anchor, descr, score, filename] = result + return score + }, + */ + + // query matches the full name of an object + objNameMatch: 11, + // or matches in the last dotted part of the object name + objPartialMatch: 6, + // Additive scores depending on the priority of the object + objPrio: { + 0: 15, // used to be importantResults + 1: 5, // used to be objectResults + 2: -5, // used to be unimportantResults + }, + // Used when the priority is not in the mapping. + objPrioDefault: 0, + + // query found in title + title: 15, + partialTitle: 7, + // query found in terms + term: 5, + partialTerm: 2, + }; +} + +const _removeChildren = (element) => { + while (element && element.lastChild) element.removeChild(element.lastChild); +}; + +/** + * See https://developer.mozilla.org/en-US/docs/Web/JavaScript/Guide/Regular_Expressions#escaping + */ +const _escapeRegExp = (string) => + string.replace(/[.*+\-?^${}()|[\]\\]/g, "\\$&"); // $& means the whole matched string + +const _displayItem = (item, searchTerms, highlightTerms) => { + const docBuilder = DOCUMENTATION_OPTIONS.BUILDER; + const docFileSuffix = DOCUMENTATION_OPTIONS.FILE_SUFFIX; + const docLinkSuffix = DOCUMENTATION_OPTIONS.LINK_SUFFIX; + const showSearchSummary = DOCUMENTATION_OPTIONS.SHOW_SEARCH_SUMMARY; + const contentRoot = document.documentElement.dataset.content_root; + + const [docName, title, anchor, descr, score, _filename] = item; + + let listItem = document.createElement("li"); + let requestUrl; + let linkUrl; + if (docBuilder === "dirhtml") { + // dirhtml builder + let dirname = docName + "/"; + if (dirname.match(/\/index\/$/)) + dirname = dirname.substring(0, dirname.length - 6); + else if (dirname === "index/") dirname = ""; + requestUrl = contentRoot + dirname; + linkUrl = requestUrl; + } else { + // normal html builders + requestUrl = contentRoot + docName + docFileSuffix; + linkUrl = docName + docLinkSuffix; + } + let linkEl = listItem.appendChild(document.createElement("a")); + linkEl.href = linkUrl + anchor; + linkEl.dataset.score = score; + linkEl.innerHTML = title; + if (descr) { + listItem.appendChild(document.createElement("span")).innerHTML = + " (" + descr + ")"; + // highlight search terms in the description + if (SPHINX_HIGHLIGHT_ENABLED) // set in sphinx_highlight.js + highlightTerms.forEach((term) => _highlightText(listItem, term, "highlighted")); + } + else if (showSearchSummary) + fetch(requestUrl) + .then((responseData) => responseData.text()) + .then((data) => { + if (data) + listItem.appendChild( + Search.makeSearchSummary(data, searchTerms, anchor) + ); + // highlight search terms in the summary + if (SPHINX_HIGHLIGHT_ENABLED) // set in sphinx_highlight.js + highlightTerms.forEach((term) => _highlightText(listItem, term, "highlighted")); + }); + Search.output.appendChild(listItem); +}; +const _finishSearch = (resultCount) => { + Search.stopPulse(); + Search.title.innerText = _("Search Results"); + if (!resultCount) + Search.status.innerText = Documentation.gettext( + "Your search did not match any documents. Please make sure that all words are spelled correctly and that you've selected enough categories." + ); + else + Search.status.innerText = _( + "Search finished, found ${resultCount} page(s) matching the search query." + ).replace('${resultCount}', resultCount); +}; +const _displayNextItem = ( + results, + resultCount, + searchTerms, + highlightTerms, +) => { + // results left, load the summary and display it + // this is intended to be dynamic (don't sub resultsCount) + if (results.length) { + _displayItem(results.pop(), searchTerms, highlightTerms); + setTimeout( + () => _displayNextItem(results, resultCount, searchTerms, highlightTerms), + 5 + ); + } + // search finished, update title and status message + else _finishSearch(resultCount); +}; +// Helper function used by query() to order search results. +// Each input is an array of [docname, title, anchor, descr, score, filename]. +// Order the results by score (in opposite order of appearance, since the +// `_displayNextItem` function uses pop() to retrieve items) and then alphabetically. +const _orderResultsByScoreThenName = (a, b) => { + const leftScore = a[4]; + const rightScore = b[4]; + if (leftScore === rightScore) { + // same score: sort alphabetically + const leftTitle = a[1].toLowerCase(); + const rightTitle = b[1].toLowerCase(); + if (leftTitle === rightTitle) return 0; + return leftTitle > rightTitle ? -1 : 1; // inverted is intentional + } + return leftScore > rightScore ? 1 : -1; +}; + +/** + * Default splitQuery function. Can be overridden in ``sphinx.search`` with a + * custom function per language. + * + * The regular expression works by splitting the string on consecutive characters + * that are not Unicode letters, numbers, underscores, or emoji characters. + * This is the same as ``\W+`` in Python, preserving the surrogate pair area. + */ +if (typeof splitQuery === "undefined") { + var splitQuery = (query) => query + .split(/[^\p{Letter}\p{Number}_\p{Emoji_Presentation}]+/gu) + .filter(term => term) // remove remaining empty strings +} + +/** + * Search Module + */ +const Search = { + _index: null, + _queued_query: null, + _pulse_status: -1, + + htmlToText: (htmlString, anchor) => { + const htmlElement = new DOMParser().parseFromString(htmlString, 'text/html'); + for (const removalQuery of [".headerlink", "script", "style"]) { + htmlElement.querySelectorAll(removalQuery).forEach((el) => { el.remove() }); + } + if (anchor) { + const anchorContent = htmlElement.querySelector(`[role="main"] ${anchor}`); + if (anchorContent) return anchorContent.textContent; + + console.warn( + `Anchored content block not found. Sphinx search tries to obtain it via DOM query '[role=main] ${anchor}'. Check your theme or template.` + ); + } + + // if anchor not specified or not found, fall back to main content + const docContent = htmlElement.querySelector('[role="main"]'); + if (docContent) return docContent.textContent; + + console.warn( + "Content block not found. Sphinx search tries to obtain it via DOM query '[role=main]'. Check your theme or template." + ); + return ""; + }, + + init: () => { + const query = new URLSearchParams(window.location.search).get("q"); + document + .querySelectorAll('input[name="q"]') + .forEach((el) => (el.value = query)); + if (query) Search.performSearch(query); + }, + + loadIndex: (url) => + (document.body.appendChild(document.createElement("script")).src = url), + + setIndex: (index) => { + Search._index = index; + if (Search._queued_query !== null) { + const query = Search._queued_query; + Search._queued_query = null; + Search.query(query); + } + }, + + hasIndex: () => Search._index !== null, + + deferQuery: (query) => (Search._queued_query = query), + + stopPulse: () => (Search._pulse_status = -1), + + startPulse: () => { + if (Search._pulse_status >= 0) return; + + const pulse = () => { + Search._pulse_status = (Search._pulse_status + 1) % 4; + Search.dots.innerText = ".".repeat(Search._pulse_status); + if (Search._pulse_status >= 0) window.setTimeout(pulse, 500); + }; + pulse(); + }, + + /** + * perform a search for something (or wait until index is loaded) + */ + performSearch: (query) => { + // create the required interface elements + const searchText = document.createElement("h2"); + searchText.textContent = _("Searching"); + const searchSummary = document.createElement("p"); + searchSummary.classList.add("search-summary"); + searchSummary.innerText = ""; + const searchList = document.createElement("ul"); + searchList.classList.add("search"); + + const out = document.getElementById("search-results"); + Search.title = out.appendChild(searchText); + Search.dots = Search.title.appendChild(document.createElement("span")); + Search.status = out.appendChild(searchSummary); + Search.output = out.appendChild(searchList); + + const searchProgress = document.getElementById("search-progress"); + // Some themes don't use the search progress node + if (searchProgress) { + searchProgress.innerText = _("Preparing search..."); + } + Search.startPulse(); + + // index already loaded, the browser was quick! + if (Search.hasIndex()) Search.query(query); + else Search.deferQuery(query); + }, + + _parseQuery: (query) => { + // stem the search terms and add them to the correct list + const stemmer = new Stemmer(); + const searchTerms = new Set(); + const excludedTerms = new Set(); + const highlightTerms = new Set(); + const objectTerms = new Set(splitQuery(query.toLowerCase().trim())); + splitQuery(query.trim()).forEach((queryTerm) => { + const queryTermLower = queryTerm.toLowerCase(); + + // maybe skip this "word" + // stopwords array is from language_data.js + if ( + stopwords.indexOf(queryTermLower) !== -1 || + queryTerm.match(/^\d+$/) + ) + return; + + // stem the word + let word = stemmer.stemWord(queryTermLower); + // select the correct list + if (word[0] === "-") excludedTerms.add(word.substr(1)); + else { + searchTerms.add(word); + highlightTerms.add(queryTermLower); + } + }); + + if (SPHINX_HIGHLIGHT_ENABLED) { // set in sphinx_highlight.js + localStorage.setItem("sphinx_highlight_terms", [...highlightTerms].join(" ")) + } + + // console.debug("SEARCH: searching for:"); + // console.info("required: ", [...searchTerms]); + // console.info("excluded: ", [...excludedTerms]); + + return [query, searchTerms, excludedTerms, highlightTerms, objectTerms]; + }, + + /** + * execute search (requires search index to be loaded) + */ + _performSearch: (query, searchTerms, excludedTerms, highlightTerms, objectTerms) => { + const filenames = Search._index.filenames; + const docNames = Search._index.docnames; + const titles = Search._index.titles; + const allTitles = Search._index.alltitles; + const indexEntries = Search._index.indexentries; + + // Collect multiple result groups to be sorted separately and then ordered. + // Each is an array of [docname, title, anchor, descr, score, filename]. + const normalResults = []; + const nonMainIndexResults = []; + + _removeChildren(document.getElementById("search-progress")); + + const queryLower = query.toLowerCase().trim(); + for (const [title, foundTitles] of Object.entries(allTitles)) { + if (title.toLowerCase().trim().includes(queryLower) && (queryLower.length >= title.length/2)) { + for (const [file, id] of foundTitles) { + const score = Math.round(Scorer.title * queryLower.length / title.length); + const boost = titles[file] === title ? 1 : 0; // add a boost for document titles + normalResults.push([ + docNames[file], + titles[file] !== title ? `${titles[file]} > ${title}` : title, + id !== null ? "#" + id : "", + null, + score + boost, + filenames[file], + ]); + } + } + } + + // search for explicit entries in index directives + for (const [entry, foundEntries] of Object.entries(indexEntries)) { + if (entry.includes(queryLower) && (queryLower.length >= entry.length/2)) { + for (const [file, id, isMain] of foundEntries) { + const score = Math.round(100 * queryLower.length / entry.length); + const result = [ + docNames[file], + titles[file], + id ? "#" + id : "", + null, + score, + filenames[file], + ]; + if (isMain) { + normalResults.push(result); + } else { + nonMainIndexResults.push(result); + } + } + } + } + + // lookup as object + objectTerms.forEach((term) => + normalResults.push(...Search.performObjectSearch(term, objectTerms)) + ); + + // lookup as search terms in fulltext + normalResults.push(...Search.performTermsSearch(searchTerms, excludedTerms)); + + // let the scorer override scores with a custom scoring function + if (Scorer.score) { + normalResults.forEach((item) => (item[4] = Scorer.score(item))); + nonMainIndexResults.forEach((item) => (item[4] = Scorer.score(item))); + } + + // Sort each group of results by score and then alphabetically by name. + normalResults.sort(_orderResultsByScoreThenName); + nonMainIndexResults.sort(_orderResultsByScoreThenName); + + // Combine the result groups in (reverse) order. + // Non-main index entries are typically arbitrary cross-references, + // so display them after other results. + let results = [...nonMainIndexResults, ...normalResults]; + + // remove duplicate search results + // note the reversing of results, so that in the case of duplicates, the highest-scoring entry is kept + let seen = new Set(); + results = results.reverse().reduce((acc, result) => { + let resultStr = result.slice(0, 4).concat([result[5]]).map(v => String(v)).join(','); + if (!seen.has(resultStr)) { + acc.push(result); + seen.add(resultStr); + } + return acc; + }, []); + + return results.reverse(); + }, + + query: (query) => { + const [searchQuery, searchTerms, excludedTerms, highlightTerms, objectTerms] = Search._parseQuery(query); + const results = Search._performSearch(searchQuery, searchTerms, excludedTerms, highlightTerms, objectTerms); + + // for debugging + //Search.lastresults = results.slice(); // a copy + // console.info("search results:", Search.lastresults); + + // print the results + _displayNextItem(results, results.length, searchTerms, highlightTerms); + }, + + /** + * search for object names + */ + performObjectSearch: (object, objectTerms) => { + const filenames = Search._index.filenames; + const docNames = Search._index.docnames; + const objects = Search._index.objects; + const objNames = Search._index.objnames; + const titles = Search._index.titles; + + const results = []; + + const objectSearchCallback = (prefix, match) => { + const name = match[4] + const fullname = (prefix ? prefix + "." : "") + name; + const fullnameLower = fullname.toLowerCase(); + if (fullnameLower.indexOf(object) < 0) return; + + let score = 0; + const parts = fullnameLower.split("."); + + // check for different match types: exact matches of full name or + // "last name" (i.e. last dotted part) + if (fullnameLower === object || parts.slice(-1)[0] === object) + score += Scorer.objNameMatch; + else if (parts.slice(-1)[0].indexOf(object) > -1) + score += Scorer.objPartialMatch; // matches in last name + + const objName = objNames[match[1]][2]; + const title = titles[match[0]]; + + // If more than one term searched for, we require other words to be + // found in the name/title/description + const otherTerms = new Set(objectTerms); + otherTerms.delete(object); + if (otherTerms.size > 0) { + const haystack = `${prefix} ${name} ${objName} ${title}`.toLowerCase(); + if ( + [...otherTerms].some((otherTerm) => haystack.indexOf(otherTerm) < 0) + ) + return; + } + + let anchor = match[3]; + if (anchor === "") anchor = fullname; + else if (anchor === "-") anchor = objNames[match[1]][1] + "-" + fullname; + + const descr = objName + _(", in ") + title; + + // add custom score for some objects according to scorer + if (Scorer.objPrio.hasOwnProperty(match[2])) + score += Scorer.objPrio[match[2]]; + else score += Scorer.objPrioDefault; + + results.push([ + docNames[match[0]], + fullname, + "#" + anchor, + descr, + score, + filenames[match[0]], + ]); + }; + Object.keys(objects).forEach((prefix) => + objects[prefix].forEach((array) => + objectSearchCallback(prefix, array) + ) + ); + return results; + }, + + /** + * search for full-text terms in the index + */ + performTermsSearch: (searchTerms, excludedTerms) => { + // prepare search + const terms = Search._index.terms; + const titleTerms = Search._index.titleterms; + const filenames = Search._index.filenames; + const docNames = Search._index.docnames; + const titles = Search._index.titles; + + const scoreMap = new Map(); + const fileMap = new Map(); + + // perform the search on the required terms + searchTerms.forEach((word) => { + const files = []; + const arr = [ + { files: terms[word], score: Scorer.term }, + { files: titleTerms[word], score: Scorer.title }, + ]; + // add support for partial matches + if (word.length > 2) { + const escapedWord = _escapeRegExp(word); + if (!terms.hasOwnProperty(word)) { + Object.keys(terms).forEach((term) => { + if (term.match(escapedWord)) + arr.push({ files: terms[term], score: Scorer.partialTerm }); + }); + } + if (!titleTerms.hasOwnProperty(word)) { + Object.keys(titleTerms).forEach((term) => { + if (term.match(escapedWord)) + arr.push({ files: titleTerms[term], score: Scorer.partialTitle }); + }); + } + } + + // no match but word was a required one + if (arr.every((record) => record.files === undefined)) return; + + // found search word in contents + arr.forEach((record) => { + if (record.files === undefined) return; + + let recordFiles = record.files; + if (recordFiles.length === undefined) recordFiles = [recordFiles]; + files.push(...recordFiles); + + // set score for the word in each file + recordFiles.forEach((file) => { + if (!scoreMap.has(file)) scoreMap.set(file, {}); + scoreMap.get(file)[word] = record.score; + }); + }); + + // create the mapping + files.forEach((file) => { + if (!fileMap.has(file)) fileMap.set(file, [word]); + else if (fileMap.get(file).indexOf(word) === -1) fileMap.get(file).push(word); + }); + }); + + // now check if the files don't contain excluded terms + const results = []; + for (const [file, wordList] of fileMap) { + // check if all requirements are matched + + // as search terms with length < 3 are discarded + const filteredTermCount = [...searchTerms].filter( + (term) => term.length > 2 + ).length; + if ( + wordList.length !== searchTerms.size && + wordList.length !== filteredTermCount + ) + continue; + + // ensure that none of the excluded terms is in the search result + if ( + [...excludedTerms].some( + (term) => + terms[term] === file || + titleTerms[term] === file || + (terms[term] || []).includes(file) || + (titleTerms[term] || []).includes(file) + ) + ) + break; + + // select one (max) score for the file. + const score = Math.max(...wordList.map((w) => scoreMap.get(file)[w])); + // add result to the result list + results.push([ + docNames[file], + titles[file], + "", + null, + score, + filenames[file], + ]); + } + return results; + }, + + /** + * helper function to return a node containing the + * search summary for a given text. keywords is a list + * of stemmed words. + */ + makeSearchSummary: (htmlText, keywords, anchor) => { + const text = Search.htmlToText(htmlText, anchor); + if (text === "") return null; + + const textLower = text.toLowerCase(); + const actualStartPosition = [...keywords] + .map((k) => textLower.indexOf(k.toLowerCase())) + .filter((i) => i > -1) + .slice(-1)[0]; + const startWithContext = Math.max(actualStartPosition - 120, 0); + + const top = startWithContext === 0 ? "" : "..."; + const tail = startWithContext + 240 < text.length ? "..." : ""; + + let summary = document.createElement("p"); + summary.classList.add("context"); + summary.textContent = top + text.substr(startWithContext, 240).trim() + tail; + + return summary; + }, +}; + +_ready(Search.init); diff --git a/_static/sphinx_highlight.js b/_static/sphinx_highlight.js new file mode 100644 index 0000000..8a96c69 --- /dev/null +++ b/_static/sphinx_highlight.js @@ -0,0 +1,154 @@ +/* Highlighting utilities for Sphinx HTML documentation. */ +"use strict"; + +const SPHINX_HIGHLIGHT_ENABLED = true + +/** + * highlight a given string on a node by wrapping it in + * span elements with the given class name. + */ +const _highlight = (node, addItems, text, className) => { + if (node.nodeType === Node.TEXT_NODE) { + const val = node.nodeValue; + const parent = node.parentNode; + const pos = val.toLowerCase().indexOf(text); + if ( + pos >= 0 && + !parent.classList.contains(className) && + !parent.classList.contains("nohighlight") + ) { + let span; + + const closestNode = parent.closest("body, svg, foreignObject"); + const isInSVG = closestNode && closestNode.matches("svg"); + if (isInSVG) { + span = document.createElementNS("http://www.w3.org/2000/svg", "tspan"); + } else { + span = document.createElement("span"); + span.classList.add(className); + } + + span.appendChild(document.createTextNode(val.substr(pos, text.length))); + const rest = document.createTextNode(val.substr(pos + text.length)); + parent.insertBefore( + span, + parent.insertBefore( + rest, + node.nextSibling + ) + ); + node.nodeValue = val.substr(0, pos); + /* There may be more occurrences of search term in this node. So call this + * function recursively on the remaining fragment. + */ + _highlight(rest, addItems, text, className); + + if (isInSVG) { + const rect = document.createElementNS( + "http://www.w3.org/2000/svg", + "rect" + ); + const bbox = parent.getBBox(); + rect.x.baseVal.value = bbox.x; + rect.y.baseVal.value = bbox.y; + rect.width.baseVal.value = bbox.width; + rect.height.baseVal.value = bbox.height; + rect.setAttribute("class", className); + addItems.push({ parent: parent, target: rect }); + } + } + } else if (node.matches && !node.matches("button, select, textarea")) { + node.childNodes.forEach((el) => _highlight(el, addItems, text, className)); + } +}; +const _highlightText = (thisNode, text, className) => { + let addItems = []; + _highlight(thisNode, addItems, text, className); + addItems.forEach((obj) => + obj.parent.insertAdjacentElement("beforebegin", obj.target) + ); +}; + +/** + * Small JavaScript module for the documentation. + */ +const SphinxHighlight = { + + /** + * highlight the search words provided in localstorage in the text + */ + highlightSearchWords: () => { + if (!SPHINX_HIGHLIGHT_ENABLED) return; // bail if no highlight + + // get and clear terms from localstorage + const url = new URL(window.location); + const highlight = + localStorage.getItem("sphinx_highlight_terms") + || url.searchParams.get("highlight") + || ""; + localStorage.removeItem("sphinx_highlight_terms") + url.searchParams.delete("highlight"); + window.history.replaceState({}, "", url); + + // get individual terms from highlight string + const terms = highlight.toLowerCase().split(/\s+/).filter(x => x); + if (terms.length === 0) return; // nothing to do + + // There should never be more than one element matching "div.body" + const divBody = document.querySelectorAll("div.body"); + const body = divBody.length ? divBody[0] : document.querySelector("body"); + window.setTimeout(() => { + terms.forEach((term) => _highlightText(body, term, "highlighted")); + }, 10); + + const searchBox = document.getElementById("searchbox"); + if (searchBox === null) return; + searchBox.appendChild( + document + .createRange() + .createContextualFragment( + '" + ) + ); + }, + + /** + * helper function to hide the search marks again + */ + hideSearchWords: () => { + document + .querySelectorAll("#searchbox .highlight-link") + .forEach((el) => el.remove()); + document + .querySelectorAll("span.highlighted") + .forEach((el) => el.classList.remove("highlighted")); + localStorage.removeItem("sphinx_highlight_terms") + }, + + initEscapeListener: () => { + // only install a listener if it is really needed + if (!DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS) return; + + document.addEventListener("keydown", (event) => { + // bail for input elements + if (BLACKLISTED_KEY_CONTROL_ELEMENTS.has(document.activeElement.tagName)) return; + // bail with special keys + if (event.shiftKey || event.altKey || event.ctrlKey || event.metaKey) return; + if (DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS && (event.key === "Escape")) { + SphinxHighlight.hideSearchWords(); + event.preventDefault(); + } + }); + }, +}; + +_ready(() => { + /* Do not call highlightSearchWords() when we are on the search page. + * It will highlight words from the *previous* search query. + */ + if (typeof Search === "undefined") SphinxHighlight.highlightSearchWords(); + SphinxHighlight.initEscapeListener(); +}); diff --git a/_static/sphinx_lesson.css b/_static/sphinx_lesson.css new file mode 100644 index 0000000..14b20c6 --- /dev/null +++ b/_static/sphinx_lesson.css @@ -0,0 +1,51 @@ +/* sphinx_lesson.css */ + +body.wy-body-for-nav img.with-border { + border: 2px solid; +} + +.rst-content .admonition-no-content { + padding-bottom: 0px; +} + +.rst-content .demo > .admonition-title::before { + content: "\01F440"; /* Eyes */ } +.rst-content .type-along > .admonition-title::before { + content: "\02328\0FE0F"; /* Keyboard */ } +.rst-content .exercise > .admonition-title::before { + content: "\0270D\0FE0F"; /* Hand */ } +.rst-content .solution > .admonition-title::before { + content: "\02714\0FE0E"; /* Check mark */ } +.rst-content .homework > .admonition-title::before { + content: "\01F4DD"; /* Memo */ } +.rst-content .discussion > .admonition-title::before { + content: "\01F4AC"; /* Speech balloon */ } +.rst-content .questions > .admonition-title::before { + content: "\02753\0FE0E"; /* Question mark */ } +.rst-content .prerequisites > .admonition-title::before { + content: "\02699"; /* Gear */ } +.rst-content .seealso > .admonition-title::before { + content: "\027A1\0FE0E"; /* Question mark */ } + + +/* instructor-note */ +.rst-content .instructor-note { + background: #e7e7e7; +} +.rst-content .instructor-note > .admonition-title { + background: #6a6a6a; +} +.rst-content .instructor-note > .admonition-title::before { + content: ""; +} + + +/* sphinx_toggle_button, make the font white */ +.rst-content .toggle.admonition button.toggle-button { + color: white; +} + +/* sphinx-togglebutton, remove underflow when toggled to hidden mode */ +.rst-content .admonition.toggle-hidden { + padding-bottom: 0px; +} diff --git a/_static/sphinx_rtd_theme_ext_color_contrast.css b/_static/sphinx_rtd_theme_ext_color_contrast.css new file mode 100644 index 0000000..e68feb8 --- /dev/null +++ b/_static/sphinx_rtd_theme_ext_color_contrast.css @@ -0,0 +1,47 @@ +/* The following are for web accessibility of sphinx_rtd_theme: they + * solve some of the most frequent contrast issues. Remove when this + * solved: + * https://github.com/readthedocs/sphinx_rtd_theme/issues/971 + */ +/* background: #fcfcfc, note boxes #E7F2FA */ +a { color: #2573A7; } /* original #2980B9, #1F5C84; */ +body { color: #242424; } /* original #404040, #383838 */ +.wy-side-nav-search>a, .wy-side-nav-search .wy-dropdown>a { + color: #ffffff; +} /* original #fcfcfc */ +footer { color: #737373; } /* original gray=#808080*/ +footer span.commit code, footer span.commit .rst-content tt, .rst-content footer span.commit tt { + color: #737373; +} /* original gray=#808080*/ +.rst-content tt.literal, .rst-content tt.literal, .rst-content code.literal { + color: #AB2314; +} +/* Sidebar background */ +.wy-side-nav-search { background-color: #277CB4;} + +/* Same, but for pygments */ +.highlight .ch { color: #3E7A89; } /* #! line */ +.highlight .c1 { color: #3E7A89; } /* also comments */ +.highlight .nv { color: #AD3ECC; } /* variable */ +.highlight .gp { color: #B45608; } /* prompt character, $*/ +.highlight .si { color: #3975B1; } /* ${} variable text */ +.highlight .nc { color: #0C78A7; } + +/* Sphinx admonitions */ +/* warning */ +.wy-alert.wy-alert-warning .wy-alert-title, .rst-content .wy-alert-warning.note .wy-alert-title, .rst-content .attention .wy-alert-title, .rst-content .caution .wy-alert-title, .rst-content .wy-alert-warning.danger .wy-alert-title, .rst-content .wy-alert-warning.error .wy-alert-title, .rst-content .wy-alert-warning.hint .wy-alert-title, .rst-content .wy-alert-warning.important .wy-alert-title, .rst-content .wy-alert-warning.tip .wy-alert-title, .rst-content .warning .wy-alert-title, .rst-content .wy-alert-warning.seealso .wy-alert-title, .rst-content .admonition-todo .wy-alert-title, .rst-content .wy-alert-warning.admonition .wy-alert-title, .wy-alert.wy-alert-warning .rst-content .admonition-title, .rst-content .wy-alert.wy-alert-warning .admonition-title, .rst-content .wy-alert-warning.note .admonition-title, .rst-content .attention .admonition-title, .rst-content .caution .admonition-title, .rst-content .wy-alert-warning.danger .admonition-title, .rst-content .wy-alert-warning.error .admonition-title, .rst-content .wy-alert-warning.hint .admonition-title, .rst-content .wy-alert-warning.important .admonition-title, .rst-content .wy-alert-warning.tip .admonition-title, .rst-content .warning .admonition-title, .rst-content .wy-alert-warning.seealso .admonition-title, .rst-content .admonition-todo .admonition-title, .rst-content .wy-alert-warning.admonition .admonition-title { + background: #B15E16; } +/* important */ +.wy-alert.wy-alert-success .wy-alert-title, .rst-content .wy-alert-success.note .wy-alert-title, .rst-content .wy-alert-success.attention .wy-alert-title, .rst-content .wy-alert-success.caution .wy-alert-title, .rst-content .wy-alert-success.danger .wy-alert-title, .rst-content .wy-alert-success.error .wy-alert-title, .rst-content .hint .wy-alert-title, .rst-content .important .wy-alert-title, .rst-content .tip .wy-alert-title, .rst-content .wy-alert-success.warning .wy-alert-title, .rst-content .wy-alert-success.seealso .wy-alert-title, .rst-content .wy-alert-success.admonition-todo .wy-alert-title, .rst-content .wy-alert-success.admonition .wy-alert-title, .wy-alert.wy-alert-success .rst-content .admonition-title, .rst-content .wy-alert.wy-alert-success .admonition-title, .rst-content .wy-alert-success.note .admonition-title, .rst-content .wy-alert-success.attention .admonition-title, .rst-content .wy-alert-success.caution .admonition-title, .rst-content .wy-alert-success.danger .admonition-title, .rst-content .wy-alert-success.error .admonition-title, .rst-content .hint .admonition-title, .rst-content .important .admonition-title, .rst-content .tip .admonition-title, .rst-content .wy-alert-success.warning .admonition-title, .rst-content .wy-alert-success.seealso .admonition-title, .rst-content .wy-alert-success.admonition-todo .admonition-title, .rst-content .wy-alert-success.admonition .admonition-title { + background: #12826C; } +/* seealso, note, etc */ +.wy-alert.wy-alert-info .wy-alert-title, .rst-content .note .wy-alert-title, .rst-content .wy-alert-info.attention .wy-alert-title, .rst-content .wy-alert-info.caution .wy-alert-title, .rst-content .wy-alert-info.danger .wy-alert-title, .rst-content .wy-alert-info.error .wy-alert-title, .rst-content .wy-alert-info.hint .wy-alert-title, .rst-content .wy-alert-info.important .wy-alert-title, .rst-content .wy-alert-info.tip .wy-alert-title, .rst-content .wy-alert-info.warning .wy-alert-title, .rst-content .seealso .wy-alert-title, .rst-content .wy-alert-info.admonition-todo .wy-alert-title, .rst-content .wy-alert-info.admonition .wy-alert-title, .wy-alert.wy-alert-info .rst-content .admonition-title, .rst-content .wy-alert.wy-alert-info .admonition-title, .rst-content .note .admonition-title, .rst-content .wy-alert-info.attention .admonition-title, .rst-content .wy-alert-info.caution .admonition-title, .rst-content .wy-alert-info.danger .admonition-title, .rst-content .wy-alert-info.error .admonition-title, .rst-content .wy-alert-info.hint .admonition-title, .rst-content .wy-alert-info.important .admonition-title, .rst-content .wy-alert-info.tip .admonition-title, .rst-content .wy-alert-info.warning .admonition-title, .rst-content .seealso .admonition-title, .rst-content .wy-alert-info.admonition-todo .admonition-title, .rst-content .wy-alert-info.admonition .admonition-title { + background: #277CB4; } +/* error, danger */ +.rst-content .danger .admonition-title, .rst-content .danger .wy-alert-title, .rst-content .error .admonition-title, .rst-content .error .wy-alert-title, .rst-content .wy-alert-danger.admonition-todo .admonition-title, .rst-content .wy-alert-danger.admonition-todo .wy-alert-title, .rst-content .wy-alert-danger.admonition .admonition-title, .rst-content .wy-alert-danger.admonition .wy-alert-title, .rst-content .wy-alert-danger.attention .admonition-title, .rst-content .wy-alert-danger.attention .wy-alert-title, .rst-content .wy-alert-danger.caution .admonition-title, .rst-content .wy-alert-danger.caution .wy-alert-title, .rst-content .wy-alert-danger.hint .admonition-title, .rst-content .wy-alert-danger.hint .wy-alert-title, .rst-content .wy-alert-danger.important .admonition-title, .rst-content .wy-alert-danger.important .wy-alert-title, .rst-content .wy-alert-danger.note .admonition-title, .rst-content .wy-alert-danger.note .wy-alert-title, .rst-content .wy-alert-danger.seealso .admonition-title, .rst-content .wy-alert-danger.seealso .wy-alert-title, .rst-content .wy-alert-danger.tip .admonition-title, .rst-content .wy-alert-danger.tip .wy-alert-title, .rst-content .wy-alert-danger.warning .admonition-title, .rst-content .wy-alert-danger.warning .wy-alert-title, .rst-content .wy-alert.wy-alert-danger .admonition-title, .wy-alert.wy-alert-danger .rst-content .admonition-title, .wy-alert.wy-alert-danger .wy-alert-title { + background: #e31704; +} + +/* Generic admonition titles */ +.wy-alert-title, .rst-content .admonition-title { + background: #277CB4; } diff --git a/_static/style.css b/_static/style.css new file mode 100644 index 0000000..59e60ee --- /dev/null +++ b/_static/style.css @@ -0,0 +1,6 @@ +.rst-content .objectives { + background: #fee0d2; +} +.rst-content .objectives > .admonition-title { + background: #fc9272; +} diff --git a/_static/tabs.css b/_static/tabs.css new file mode 100644 index 0000000..957ba60 --- /dev/null +++ b/_static/tabs.css @@ -0,0 +1,89 @@ +.sphinx-tabs { + margin-bottom: 1rem; +} + +[role="tablist"] { + border-bottom: 1px solid #a0b3bf; +} + +.sphinx-tabs-tab { + position: relative; + font-family: Lato,'Helvetica Neue',Arial,Helvetica,sans-serif; + color: #1D5C87; + line-height: 24px; + margin: 0; + font-size: 16px; + font-weight: 400; + background-color: rgba(255, 255, 255, 0); + border-radius: 5px 5px 0 0; + border: 0; + padding: 1rem 1.5rem; + margin-bottom: 0; +} + +.sphinx-tabs-tab[aria-selected="true"] { + font-weight: 700; + border: 1px solid #a0b3bf; + border-bottom: 1px solid white; + margin: -1px; + background-color: white; +} + +.sphinx-tabs-tab:focus { + z-index: 1; + outline-offset: 1px; +} + +.sphinx-tabs-panel { + position: relative; + padding: 1rem; + border: 1px solid #a0b3bf; + margin: 0px -1px -1px -1px; + border-radius: 0 0 5px 5px; + border-top: 0; + background: white; +} + +.sphinx-tabs-panel.code-tab { + padding: 0.4rem; +} + +.sphinx-tab img { + margin-bottom: 24 px; +} + +/* Dark theme preference styling */ + +@media (prefers-color-scheme: dark) { + body[data-theme="auto"] .sphinx-tabs-panel { + color: white; + background-color: rgb(50, 50, 50); + } + + body[data-theme="auto"] .sphinx-tabs-tab { + color: white; + background-color: rgba(255, 255, 255, 0.05); + } + + body[data-theme="auto"] .sphinx-tabs-tab[aria-selected="true"] { + border-bottom: 1px solid rgb(50, 50, 50); + background-color: rgb(50, 50, 50); + } +} + +/* Explicit dark theme styling */ + +body[data-theme="dark"] .sphinx-tabs-panel { + color: white; + background-color: rgb(50, 50, 50); +} + +body[data-theme="dark"] .sphinx-tabs-tab { + color: white; + background-color: rgba(255, 255, 255, 0.05); +} + +body[data-theme="dark"] .sphinx-tabs-tab[aria-selected="true"] { + border-bottom: 2px solid rgb(50, 50, 50); + background-color: rgb(50, 50, 50); +} diff --git a/_static/tabs.js b/_static/tabs.js new file mode 100644 index 0000000..48dc303 --- /dev/null +++ b/_static/tabs.js @@ -0,0 +1,145 @@ +try { + var session = window.sessionStorage || {}; +} catch (e) { + var session = {}; +} + +window.addEventListener("DOMContentLoaded", () => { + const allTabs = document.querySelectorAll('.sphinx-tabs-tab'); + const tabLists = document.querySelectorAll('[role="tablist"]'); + + allTabs.forEach(tab => { + tab.addEventListener("click", changeTabs); + }); + + tabLists.forEach(tabList => { + tabList.addEventListener("keydown", keyTabs); + }); + + // Restore group tab selection from session + const lastSelected = session.getItem('sphinx-tabs-last-selected'); + if (lastSelected != null) selectNamedTabs(lastSelected); +}); + +/** + * Key focus left and right between sibling elements using arrows + * @param {Node} e the element in focus when key was pressed + */ +function keyTabs(e) { + const tab = e.target; + let nextTab = null; + if (e.keyCode === 39 || e.keyCode === 37) { + tab.setAttribute("tabindex", -1); + // Move right + if (e.keyCode === 39) { + nextTab = tab.nextElementSibling; + if (nextTab === null) { + nextTab = tab.parentNode.firstElementChild; + } + // Move left + } else if (e.keyCode === 37) { + nextTab = tab.previousElementSibling; + if (nextTab === null) { + nextTab = tab.parentNode.lastElementChild; + } + } + } + + if (nextTab !== null) { + nextTab.setAttribute("tabindex", 0); + nextTab.focus(); + } +} + +/** + * Select or deselect clicked tab. If a group tab + * is selected, also select tab in other tabLists. + * @param {Node} e the element that was clicked + */ +function changeTabs(e) { + // Use this instead of the element that was clicked, in case it's a child + const notSelected = this.getAttribute("aria-selected") === "false"; + const positionBefore = this.parentNode.getBoundingClientRect().top; + const notClosable = !this.parentNode.classList.contains("closeable"); + + deselectTabList(this); + + if (notSelected || notClosable) { + selectTab(this); + const name = this.getAttribute("name"); + selectNamedTabs(name, this.id); + + if (this.classList.contains("group-tab")) { + // Persist during session + session.setItem('sphinx-tabs-last-selected', name); + } + } + + const positionAfter = this.parentNode.getBoundingClientRect().top; + const positionDelta = positionAfter - positionBefore; + // Scroll to offset content resizing + window.scrollTo(0, window.scrollY + positionDelta); +} + +/** + * Select tab and show associated panel. + * @param {Node} tab tab to select + */ +function selectTab(tab) { + tab.setAttribute("aria-selected", true); + + // Show the associated panel + document + .getElementById(tab.getAttribute("aria-controls")) + .removeAttribute("hidden"); +} + +/** + * Hide the panels associated with all tabs within the + * tablist containing this tab. + * @param {Node} tab a tab within the tablist to deselect + */ +function deselectTabList(tab) { + const parent = tab.parentNode; + const grandparent = parent.parentNode; + + Array.from(parent.children) + .forEach(t => t.setAttribute("aria-selected", false)); + + Array.from(grandparent.children) + .slice(1) // Skip tablist + .forEach(panel => panel.setAttribute("hidden", true)); +} + +/** + * Select grouped tabs with the same name, but no the tab + * with the given id. + * @param {Node} name name of grouped tab to be selected + * @param {Node} clickedId id of clicked tab + */ +function selectNamedTabs(name, clickedId=null) { + const groupedTabs = document.querySelectorAll(`.sphinx-tabs-tab[name="${name}"]`); + const tabLists = Array.from(groupedTabs).map(tab => tab.parentNode); + + tabLists + .forEach(tabList => { + // Don't want to change the tabList containing the clicked tab + const clickedTab = tabList.querySelector(`[id="${clickedId}"]`); + if (clickedTab === null ) { + // Select first tab with matching name + const tab = tabList.querySelector(`.sphinx-tabs-tab[name="${name}"]`); + deselectTabList(tab); + selectTab(tab); + } + }) +} + +if (typeof exports === 'undefined') { + exports = {}; +} + +exports.keyTabs = keyTabs; +exports.changeTabs = changeTabs; +exports.selectTab = selectTab; +exports.deselectTabList = deselectTabList; +exports.selectNamedTabs = selectNamedTabs; diff --git a/_static/term_role_formatting.css b/_static/term_role_formatting.css new file mode 100644 index 0000000..0b66095 --- /dev/null +++ b/_static/term_role_formatting.css @@ -0,0 +1,4 @@ +/* Make terms bold */ +a.reference span.std-term { + font-weight: bold; +} diff --git a/_static/togglebutton.css b/_static/togglebutton.css new file mode 100644 index 0000000..54a6787 --- /dev/null +++ b/_static/togglebutton.css @@ -0,0 +1,160 @@ +/** + * Admonition-based toggles + */ + +/* Visibility of the target */ +.admonition.toggle .admonition-title ~ * { + transition: opacity .3s, height .3s; +} + +/* Toggle buttons inside admonitions so we see the title */ +.admonition.toggle { + position: relative; +} + +/* Titles should cut off earlier to avoid overlapping w/ button */ +.admonition.toggle .admonition-title { + padding-right: 25%; + cursor: pointer; +} + +/* Hovering will cause a slight shift in color to make it feel interactive */ +.admonition.toggle .admonition-title:hover { + box-shadow: inset 0 0 0px 20px rgb(0 0 0 / 1%); +} + +/* Hovering will cause a slight shift in color to make it feel interactive */ +.admonition.toggle .admonition-title:active { + box-shadow: inset 0 0 0px 20px rgb(0 0 0 / 3%); +} + +/* Remove extra whitespace below the admonition title when hidden */ +.admonition.toggle-hidden { + padding-bottom: 0; +} + +.admonition.toggle-hidden .admonition-title { + margin-bottom: 0; +} + +/* hides all the content of a page until de-toggled */ +.admonition.toggle-hidden .admonition-title ~ * { + height: 0; + margin: 0; + opacity: 0; + visibility: hidden; +} + +/* General button style and position*/ +button.toggle-button { + /** + * Background and shape. By default there's no background + * but users can style as they wish + */ + background: none; + border: none; + outline: none; + + /* Positioning just inside the admonition title */ + position: absolute; + right: 0.5em; + padding: 0px; + border: none; + outline: none; +} + +/* Display the toggle hint on wide screens */ +@media (min-width: 768px) { + button.toggle-button.toggle-button-hidden:before { + content: attr(data-toggle-hint); /* This will be filled in by JS */ + font-size: .8em; + align-self: center; + } +} + +/* Icon behavior */ +.tb-icon { + transition: transform .2s ease-out; + height: 1.5em; + width: 1.5em; + stroke: currentColor; /* So that we inherit the color of other text */ +} + +/* The icon should point right when closed, down when open. */ +/* Open */ +.admonition.toggle button .tb-icon { + transform: rotate(90deg); +} + +/* Closed */ +.admonition.toggle button.toggle-button-hidden .tb-icon { + transform: rotate(0deg); +} + +/* With details toggles, we don't rotate the icon so it points right */ +details.toggle-details .tb-icon { + height: 1.4em; + width: 1.4em; + margin-top: 0.1em; /* To center the button vertically */ +} + + +/** + * Details-based toggles. + * In this case, we wrap elements with `.toggle` in a details block. + */ + +/* Details blocks */ +details.toggle-details { + margin: 1em 0; +} + + +details.toggle-details summary { + display: flex; + align-items: center; + cursor: pointer; + list-style: none; + border-radius: .2em; + border-left: 3px solid #1976d2; + background-color: rgb(204 204 204 / 10%); + padding: 0.2em 0.7em 0.3em 0.5em; /* Less padding on left because the SVG has left margin */ + font-size: 0.9em; +} + +details.toggle-details summary:hover { + background-color: rgb(204 204 204 / 20%); +} + +details.toggle-details summary:active { + background: rgb(204 204 204 / 28%); +} + +.toggle-details__summary-text { + margin-left: 0.2em; +} + +details.toggle-details[open] summary { + margin-bottom: .5em; +} + +details.toggle-details[open] summary .tb-icon { + transform: rotate(90deg); +} + +details.toggle-details[open] summary ~ * { + animation: toggle-fade-in .3s ease-out; +} + +@keyframes toggle-fade-in { + from {opacity: 0%;} + to {opacity: 100%;} +} + +/* Print rules - we hide all toggle button elements at print */ +@media print { + /* Always hide the summary so the button doesn't show up */ + details.toggle-details summary { + display: none; + } +} \ No newline at end of file diff --git a/_static/togglebutton.js b/_static/togglebutton.js new file mode 100644 index 0000000..215a7ee --- /dev/null +++ b/_static/togglebutton.js @@ -0,0 +1,187 @@ +/** + * Add Toggle Buttons to elements + */ + +let toggleChevron = ` + + + +`; + +var initToggleItems = () => { + var itemsToToggle = document.querySelectorAll(togglebuttonSelector); + console.log(`[togglebutton]: Adding toggle buttons to ${itemsToToggle.length} items`) + // Add the button to each admonition and hook up a callback to toggle visibility + itemsToToggle.forEach((item, index) => { + if (item.classList.contains("admonition")) { + // If it's an admonition block, then we'll add a button inside + // Generate unique IDs for this item + var toggleID = `toggle-${index}`; + var buttonID = `button-${toggleID}`; + + item.setAttribute('id', toggleID); + if (!item.classList.contains("toggle")){ + item.classList.add("toggle"); + } + // This is the button that will be added to each item to trigger the toggle + var collapseButton = ` + `; + + title = item.querySelector(".admonition-title") + title.insertAdjacentHTML("beforeend", collapseButton); + thisButton = document.getElementById(buttonID); + + // Add click handlers for the button + admonition title (if admonition) + admonitionTitle = document.querySelector(`#${toggleID} > .admonition-title`) + if (admonitionTitle) { + // If an admonition, then make the whole title block clickable + admonitionTitle.addEventListener('click', toggleClickHandler); + admonitionTitle.dataset.target = toggleID + admonitionTitle.dataset.button = buttonID + } else { + // If not an admonition then we'll listen for the button click + thisButton.addEventListener('click', toggleClickHandler); + } + + // Now hide the item for this toggle button unless explicitly noted to show + if (!item.classList.contains("toggle-shown")) { + toggleHidden(thisButton); + } + } else { + // If not an admonition, wrap the block in a
block + // Define the structure of the details block and insert it as a sibling + var detailsBlock = ` +
+ + ${toggleChevron} + ${toggleHintShow} + +
`; + item.insertAdjacentHTML("beforebegin", detailsBlock); + + // Now move the toggle-able content inside of the details block + details = item.previousElementSibling + details.appendChild(item) + item.classList.add("toggle-details__container") + + // Set up a click trigger to change the text as needed + details.addEventListener('click', (click) => { + let parent = click.target.parentElement; + if (parent.tagName.toLowerCase() == "details") { + summary = parent.querySelector("summary"); + details = parent; + } else { + summary = parent; + details = parent.parentElement; + } + // Update the inner text for the proper hint + if (details.open) { + summary.querySelector("span.toggle-details__summary-text").innerText = toggleHintShow; + } else { + summary.querySelector("span.toggle-details__summary-text").innerText = toggleHintHide; + } + + }); + + // If we have a toggle-shown class, open details block should be open + if (item.classList.contains("toggle-shown")) { + details.click(); + } + } + }) +}; + +// This should simply add / remove the collapsed class and change the button text +var toggleHidden = (button) => { + target = button.dataset['target'] + var itemToToggle = document.getElementById(target); + if (itemToToggle.classList.contains("toggle-hidden")) { + itemToToggle.classList.remove("toggle-hidden"); + button.classList.remove("toggle-button-hidden"); + } else { + itemToToggle.classList.add("toggle-hidden"); + button.classList.add("toggle-button-hidden"); + } +} + +var toggleClickHandler = (click) => { + // Be cause the admonition title is clickable and extends to the whole admonition + // We only look for a click event on this title to trigger the toggle. + + if (click.target.classList.contains("admonition-title")) { + button = click.target.querySelector(".toggle-button"); + } else if (click.target.classList.contains("tb-icon")) { + // We've clicked the icon and need to search up one parent for the button + button = click.target.parentElement; + } else if (click.target.tagName == "polyline") { + // We've clicked the SVG elements inside the button, need to up 2 layers + button = click.target.parentElement.parentElement; + } else if (click.target.classList.contains("toggle-button")) { + // We've clicked the button itself and so don't need to do anything + button = click.target; + } else { + console.log(`[togglebutton]: Couldn't find button for ${click.target}`) + } + target = document.getElementById(button.dataset['button']); + toggleHidden(target); +} + +// If we want to blanket-add toggle classes to certain cells +var addToggleToSelector = () => { + const selector = ""; + if (selector.length > 0) { + document.querySelectorAll(selector).forEach((item) => { + item.classList.add("toggle"); + }) + } +} + +// Helper function to run when the DOM is finished +const sphinxToggleRunWhenDOMLoaded = cb => { + if (document.readyState != 'loading') { + cb() + } else if (document.addEventListener) { + document.addEventListener('DOMContentLoaded', cb) + } else { + document.attachEvent('onreadystatechange', function() { + if (document.readyState == 'complete') cb() + }) + } +} +sphinxToggleRunWhenDOMLoaded(addToggleToSelector) +sphinxToggleRunWhenDOMLoaded(initToggleItems) + +/** Toggle details blocks to be open when printing */ +if (toggleOpenOnPrint == "true") { + window.addEventListener("beforeprint", () => { + // Open the details + document.querySelectorAll("details.toggle-details").forEach((el) => { + el.dataset["togglestatus"] = el.open; + el.open = true; + }); + + // Open the admonitions + document.querySelectorAll(".admonition.toggle.toggle-hidden").forEach((el) => { + console.log(el); + el.querySelector("button.toggle-button").click(); + el.dataset["toggle_after_print"] = "true"; + }); + }); + window.addEventListener("afterprint", () => { + // Re-close the details that were closed + document.querySelectorAll("details.toggle-details").forEach((el) => { + el.open = el.dataset["togglestatus"] == "true"; + delete el.dataset["togglestatus"]; + }); + + // Re-close the admonition toggle buttons + document.querySelectorAll(".admonition.toggle").forEach((el) => { + if (el.dataset["toggle_after_print"] == "true") { + el.querySelector("button.toggle-button").click(); + delete el.dataset["toggle_after_print"]; + } + }); + }); +} diff --git a/branch/main/_images/add-suggestion.png b/branch/main/_images/add-suggestion.png new file mode 100644 index 0000000..0a28544 Binary files /dev/null and b/branch/main/_images/add-suggestion.png differ diff --git a/branch/main/_images/all-checks-failed.png b/branch/main/_images/all-checks-failed.png new file mode 100644 index 0000000..5175684 Binary files /dev/null and b/branch/main/_images/all-checks-failed.png differ diff --git a/branch/main/_images/animation.mp4 b/branch/main/_images/animation.mp4 new file mode 100644 index 0000000..f037fd4 Binary files /dev/null and b/branch/main/_images/animation.mp4 differ diff --git a/branch/main/_images/check-details.png 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/dev/null and b/branch/main/_images/unwatch.png differ diff --git a/branch/main/_images/vscode-publish-branch.png b/branch/main/_images/vscode-publish-branch.png new file mode 100644 index 0000000..323ffb2 Binary files /dev/null and b/branch/main/_images/vscode-publish-branch.png differ diff --git a/branch/main/_sources/collaboration.md.txt b/branch/main/_sources/collaboration.md.txt new file mode 100644 index 0000000..12efbc1 --- /dev/null +++ b/branch/main/_sources/collaboration.md.txt @@ -0,0 +1,13 @@ +(collaboration)= + +# Collaborative version control and code review + +```{toctree} +:maxdepth: 1 + +collaboration/concepts.md +collaboration/same-repository.md +collaboration/code-review.md +collaboration/forking-workflow.md +collaboration/demo-discussion.md +``` diff --git a/branch/main/_sources/collaboration/code-review.md.txt b/branch/main/_sources/collaboration/code-review.md.txt new file mode 100644 index 0000000..4a55b03 --- /dev/null +++ b/branch/main/_sources/collaboration/code-review.md.txt @@ -0,0 +1,144 @@ +(code-review)= + +# Practicing code review + +In this episode we will practice the code review process. We will learn how to +ask for changes in a pull request, how to suggest a change in a pull request, +and how to modify a pull request. + +This will enable research groups to work more collaboratively and to not only +improve the code quality but also to learn from each other. + + +## Exercise + +:::{prereq} Exercise preparation +We can continue in the same exercise repository which we have used in the +previous episode. +::: + +:::{exercise} Exercise: Practicing code review (25 min) + +**Technical requirements**: +- If you create the commits locally: [Being able to authenticate to GitHub](https://coderefinery.github.io/installation/ssh/) + +**What is familiar** from previous lessons: +- Creating a branch. +- Committing a change on the new branch. +- Opening and merging pull requests. + +**What will be new** in this exercise: +- As a reviewer, we will learn how to ask for changes in a pull request. +- As a reviewer, we will learn how to suggest a change in a pull request. +- As a submitter, we will learn how to modify a pull request without closing + the incomplete one and opening a new one. + +**Exercise tasks**: +1. Create a new branch and one or few commits: in these improve something but also + deliberately introduce a typo and also a larger mistake which we will want to fix during the code review. +1. Open a pull request towards the main branch. +1. As a reviewer to somebody else's pull request, ask for an improvement and + also directly suggest a change for the small typo. (Hint: + suggestions are possible through the GitHub web interface, view of + a pull request, "Files changed" view, after selecting some lines. + Look for the "±" button.) +1. As the submitter, learn how to accept the suggested change. (Hint: + GitHub web interface, "Files Changed" view.) +1. As the submitter, improve the pull request without having to close and open + a new one: by adding a new commit to the same branch. (Hint: push + to the branch again.) +1. Once the changes are addressed, merge the pull request. +::: + + +## Help and discussion + +From here on out, we don't give detailed steps to the solution. You +need to combine what you know, and the extra info below, in order to +solve the above. + +### How to ask for changes in a pull request + +Technically, there are at least two common ways to ask for changes in a pull +request. + +Either in the comment field of the pull request: +:::{figure} img/code-review/comment.png +:width: 60% +:class: with-border +:alt: Screenshot of a pull request comment field +:::: + +Or by using the "Review changes": +:::{figure} img/code-review/files-changed.png +:width: 100% +:class: with-border +:alt: Screenshot of a pull request navigating to the "Review changes" tab +:::: + +And always please be kind and constructive in your comments. Remember that the +goal is not gate-keeping but **collaborative learning**. + + +### How to suggest a change in a pull request as a reviewer + +If you see a very small problem that is easy to fix, you can suggest a change +as a reviewer. + +Instead of asking the submitter to tiny problem, you can suggest a change by +clicking on the plus sign next to the line number in the "Files changed" tab: +:::{figure} img/code-review/leave-comment.png +:width: 100% +:class: with-border +:alt: Screenshot of leaving a comment to a line in a pull request +:::: + +Here you can comment on specific lines or even line ranges. + +But now the interesting part is to click on the "Add a suggestion" symbol (the +one that looks like plus and minus). Now you can fix the tiny problem (in this +case a typo) and then click on the "Add single comment" button: +:::{figure} img/code-review/add-suggestion.png +:width: 60% +:class: with-border +:alt: Sequence of clicks to add a suggestion to a line in a pull request +:::: + +The result is this and the submitter can accept the change with a single click: +:::{figure} img/code-review/commit-suggestion.png +:width: 60% +:class: with-border +:alt: Screenshot of a pull request with a suggested change +:::: + +After accepting with "Commit suggestion", the improvement gets added to the +pull request. + + +### How to modify a pull request to address the review comments + +If the reviewer asks for changes, it is not necessary to close the pull request +and later open a new one. It can even be counter-productive to do so: This can +fragment the discussion and the history of the pull request and can make it +harder to understand the context of the changes. + +A much better mechanism to recognize that pull requests are not implemented +from a specific commit to a specific branch, but **always from a branch to a +branch**. + +This means that you can make amendments to the pull request by adding new +commits to the same source branch. This way the pull request will be updated +automatically and the reviewer can see the new changes and comment on them. + +The fact that pull requests are from branch to branch also strongly suggests +that it is a good practice to create a new branch for each pull request. +Otherwise you could accidentally modify an open pull request by adding new +commits to the source branch. + + +## Summary + +- Our process isn't just about code now. It's about discussion and + working together to make the whole process better. +- GitHub discussions and reviewing are quite powerful and can make + small changes easy. diff --git a/branch/main/_sources/collaboration/concepts.md.txt b/branch/main/_sources/collaboration/concepts.md.txt new file mode 100644 index 0000000..c0a7d27 --- /dev/null +++ b/branch/main/_sources/collaboration/concepts.md.txt @@ -0,0 +1,69 @@ +(concepts)= + +# Concepts around collaboration + +```{objectives} +- Be able to decide whether to divide work at the branch level or at the repository level. +``` + + +## Commits, branches, repositories, forks, clones + +- **repository**: The project, contains all data and history (commits, branches, tags). +- **commit**: Snapshot of the project, gets a unique identifier (e.g. `c7f0e8bfc718be04525847fc7ac237f470add76e`). +- **branch**: Independent development line. The main development line is often called `main`. +- **tag**: A pointer to one commit, to be able to refer to it later. Like a [commemorative plaque](https://en.wikipedia.org/wiki/Commemorative_plaque) + that you attach to a particular commit (e.g. `phd-printed` or `paper-submitted`). +- **cloning**: Copying the whole repository to your laptop - the first time. It is not necessary to download each file one by one. +- **forking**: Taking a copy of a repository (which is typically not yours) - your + copy (fork) stays on GitHub/GitLab and you can make changes to your copy. + + +## Cloning a repository + +In order to make a complete copy a whole repository, the `git clone` command +can be used. When cloning, all the files, of all or selected branches, of a +repository are copied in one operation. Cloning of a repository is of relevance +in a few different situations: +* Working on your own, cloning is the operation that you can use to create + multiple instances of a repository on, for instance, a personal computer, a + server, and a supercomputer. +* The parent repository could be a repository that you or your colleague own. A + common use case for cloning is when working together within a smaller team + where everyone has read and write access to the same git repository. +* Alternatively, cloning can be made from a public repository of a code that + you would like to use. Perhaps you have no intention to work on the code, but + would like to stay in tune with the latest developments, also in-between + releases of new versions of the code. + + +```{figure} img/overview/forkandclone.png +:alt: Forking and cloning +:width: 100% +:class: with-border + +Forking and cloning +``` + + +## Forking a repository + +When a fork is made on GitHub/GitLab a complete copy, of all or selected +branches, of the repository is made. The copy will reside under a different +account on GitHub/GitLab. Forking of a repository is of high relevance when +working with a git repository to which you do not have write access. +* In the fork repository commits can be made to the base branch (`main` or + `master`), and to other branches. +* The commits that are made within the branches of the fork repository can be + contributed back to the parent repository by means of pull or merge requests. + + +## Synchronizing changes between repositories + +- We need a mechanism to communicate changes between the repositories. +- We will **pull** or **fetch** updates **from** remote repositories (we will soon discuss the difference between pull and fetch). +- We will **push** updates **to** remote repositories. +- We will learn how to suggest changes within repositories on GitHub and across repositories (**pull request**). +- Repositories that are forked or cloned do not automatically synchronize themselves: + We will learn how to update forks (by pulling from the "central" repository). +- A main difference between cloning a repository and forking a repository is that the former is a general operation for generating copies of a repository to different computers, whereas forking is a particular operation implemented on GitHub/GitLab. diff --git a/branch/main/_sources/collaboration/demo-discussion.md.txt b/branch/main/_sources/collaboration/demo-discussion.md.txt new file mode 100644 index 0000000..d6b4f28 --- /dev/null +++ b/branch/main/_sources/collaboration/demo-discussion.md.txt @@ -0,0 +1,5 @@ +(collaboration-demo-discussion)= + +# Conclict resolution, rebasing, and organizational strategies + +(40 min demo and discussion) diff --git a/branch/main/_sources/collaboration/forking-workflow.md.txt b/branch/main/_sources/collaboration/forking-workflow.md.txt new file mode 100644 index 0000000..f8c254d --- /dev/null +++ b/branch/main/_sources/collaboration/forking-workflow.md.txt @@ -0,0 +1,223 @@ +(forking-workflow)= + +# How to contribute changes to repositories that belong to others + +In this episode we prepare you to suggest and contribute changes to +repositories that belong to others. These might be open source projects that +you use in your work. + +We will see how Git and services like GitHub or GitLab can be used to suggest +modification without having to ask for write access to the repository and +accept modifications without having to grant write access to others. + + +## Exercise + +:::{prereq} Exercise preparation +- The exercise repository is now different: + (note the `-forking-exercise`). +- First **fork** the exercise repository to your GitHub account. +- Then **clone your fork** to your computer (if you wish to work locally). +- Double-check that you have forked the correct repository. +::: + +:::{exercise} Exercise: Collaborating within the same repository (25 min) + +**Technical requirements**: +- If you create the commits locally: [Being able to authenticate to GitHub](https://coderefinery.github.io/installation/ssh/) + +**What is familiar** from previous lessons: +- Forking a repository. +- Creating a branch. +- Committing a change on the new branch. +- Opening and merging pull requests. + +**What will be new** in this exercise: +- Opening a pull request towards the upstream repository. +- Pull requests can be coupled with automated testing. +- Learning that your fork can get out of date. +- After the pull requests are merged, updating your fork with the changes. +- Learn how to approach other people's repositories with ideas, changes, and requests. + +**Exercise tasks**: +1. Open an issue in the upstream exercise repository where you describe the + change you want to make. Take note of the issue number. +1. Create a new branch in your fork of the repository. +1. Make a change to the recipe book on the new branch and in the commit cross-reference the issue you opened. + See the walk-through below for how to do this. +1. Open a pull request towards the upstream repository. +1. The instructor will review and merge the pull requests. + During the review, pay attention to the automated test step (here for + demonstration purposes, we test whether the recipe contains an ingredients + and an instructions sections). +1. After few pull requests are merged, update your fork with the changes. +1. Check that in your fork you can see changes from other people's pull requests. +::: + + +## Help and discussion + + +### Help! I don't have permissions to push my local changes + +Maybe you see an error like this one: +```text +Please make sure you have the correct access rights +and the repository exists. +``` + +Or like this one: +```text +failed to push some refs to workshop-material/recipe-book-forking-exercise.git +``` + +In this case you probably try to push the changes not to your fork but to the original repository +and in this exercise you do not have write access to the original repository. + +The simpler solution is to clone again but this time your fork. + +:::{solution} Recovery + +But if you want to keep your local changes, you can change the remote URL to point to your fork. +Check where your remote points to with `git remote --verbose`. + +It should look like this (replace `USER` with your GitHub username): +```console +$ git remote --verbose + +origin git@github.com:USER/recipe-book-forking-exercise.git (fetch) +origin git@github.com:USER/recipe-book-forking-exercise.git (push) +``` + +It should **not** look like this: +```console +$ git remote --verbose + +origin git@github.com:workshop-material/recipe-book-forking-exercise.git (fetch) +origin git@github.com:workshop-material/recipe-book-forking-exercise.git (push) +``` + +In this case you can adjust "origin" to point to your fork with: +```console +$ git remote set-url origin git@github.com:USER/recipe-book-forking-exercise.git +``` +::: + + +### Opening a pull request towards the upstream repository + +We have learned in the previous episode that pull requests are always from +branch to branch. But the branch can be in a different repository. + +When you open a pull request in a fork, by default GitHub will suggest to +direct it towards the default branch of the upstream repository. + +This can be changed and it should always be verified, but in this case this is +exactly what we want to do, from fork towards upstream: +:::{figure} img/forking-workflow/pull-request-form.png +:width: 100% +:class: with-border +:alt: Screenshot of a pull request from fork towards upstream +:::: + + +### Pull requests can be coupled with automated testing + +We added an automated test here just for fun and so that you see that this is +possible to do. + +In this exercise, the test is silly. It will check whether the recipe contains +both an ingredients and an instructions section. + +In this example the test failed: +:::{figure} img/forking-workflow/all-checks-failed.png +:width: 60% +:class: with-border +:alt: Screenshot of a failed test in a pull request +:::: + +Click on the "Details" link to see the details of the failed test: +:::{figure} img/forking-workflow/check-details.png +:width: 60% +:class: with-border +:alt: Screenshot of details why the test failed +:::: + +**How can this be useful?** +- The project can define what kind of tests are expected to pass before a pull + request can be merged. +- The reviewer can see the results of the tests, without having to run them + locally. + +**How does it work?** +- We added a GitHub Actions workflow + to automatically run on each push or pull request towards the `main` branch. + +What tests or steps can you image for your project to run automatically with +each pull request? + + +### How to update your fork with changes from upstream + +This used to be difficult but now it is two mouse clicks. + +Navigate to your fork and notice how GitHub tells you that your fork is behind. +In my case, it is 9 commits behind upstream. To fix this, click on "Sync fork" +and then "Update branch": +:::{figure} img/forking-workflow/sync-fork.png +:width: 80% +:class: with-border +:alt: Screenshot on GitHub fork page showing that the fork is behind +:::: + +After the update my "branch is up to date" with the upstream repository: +:::{figure} img/forking-workflow/fork-after-update.png +:width: 80% +:class: with-border +:alt: Screenshot on GitHub after fork has been updated +:::: + + +### How to approach other people’s repositories with ideas, changes, and requests + +**Contributing very minor changes** +- Clone or fork+clone repository +- Create a branch +- Commit and push change +- Open a pull request or merge request + +**If you observe an issue and have an idea how to fix it** +- Open an issue in the repository you wish to contribute to +- Describe the problem +- If you have a suggestion on how to fix it, describe your suggestion +- Possibly **discuss and get feedback** +- If you are working on the fix, indicate it in the issue so that others know that somebody is working on it and who is working on it +- Submit your fix as pull request or merge request which references/closes the issue + +:::{admonition} Motivation +- **Inform others about an observed problem** +- Make it clear whether this issue is up for grabs or already being worked on +::: + +**If you have an idea for a new feature** +- Open an issue in the repository you wish to contribute to +- In the issue, write a short proposal for your suggested change or new feature +- Motivate why and how you wish to do this +- Also indicate where you are unsure and where you would like feedback +- **Discuss and get feedback before you code** +- Once you start coding, indicate that you are working on it +- Once you are done, submit your new feature as pull request or merge request which references/closes the issue/proposal + +:::{admonition} Motivation +- **Get agreement and feedback before writing 5000 lines of code** which might be rejected +- If we later wonder why something was done, we have the issue/proposal as + reference and can read up on the reasoning behind a code change +::: + + +## Summary + +- This forking workflow lets you propose changes to repositories for + which **you have no write access**. +- This is the way that much modern open-source software works. +- You can now contribute to any project you can view. diff --git a/branch/main/_sources/collaboration/same-repository.md.txt b/branch/main/_sources/collaboration/same-repository.md.txt new file mode 100644 index 0000000..1a69d1d --- /dev/null +++ b/branch/main/_sources/collaboration/same-repository.md.txt @@ -0,0 +1,280 @@ +(same-repository)= + +# Collaborating within the same repository + +In this episode, we will learn how to collaborate within the same repository. +We will learn how to cross-reference issues and pull requests, how to review +pull requests, and how to use draft pull requests. + +This exercise will form a good basis for collaboration that is suitable for +most research groups. + +:::{note} +When you read or hear **pull request**, please think of a **change proposal**. +::: + + +## Exercise + +In this exercise, we will contribute to a repository via a **pull request**. +This means that you propose some change, and then it is accepted (or not). + +::::::{prereq} Exercise preparation + +- **First we need to get access** to the [exercise repository](https://github.com/workshop-material/recipe-book) to which we will + contribute. + - Instructor collects GitHub usernames from learners and adds them as collaborators to the exercise repository + (Settings -> Collaborators and teams -> Manage access -> Add people). + +- **Don't forget to accept the invitation** + - Check + - Alternatively check the inbox for the email account you registered with + GitHub. GitHub emails you an invitation link, but if you don't receive it + you can go to your GitHub notifications in the top right corner. The + maintainer can also "copy invite link" and share it within the group. + +- **Watching and unwatching repositories** + - Now that you are a collaborator, you get notified about new issues and pull + requests via email. + - If you do not wish this, you can "unwatch" a repository (top of + the project page). + - However, we recommend watching repositories you are interested + in. You can learn things from experts just by watching the + activity that come through a popular project. + :::{figure} img/unwatch.png + :alt: Unwatching a repository + + Unwatch a repository by clicking "Unwatch" in the repository view, + then "Participating and @mentions" - this way, you will get + notifications about your own interactions. + ::: +:::::: + +:::{exercise} Exercise: Collaborating within the same repository (25 min) + +**Technical requirements** (from installation instructions): +- If you create the commits locally: [Being able to authenticate to GitHub](https://coderefinery.github.io/installation/ssh/) + +**What is familiar** from the previous workshop day (not repeated here): +- Cloning a repository. +- Creating a branch. +- Committing a change on the new branch. +- Submit a pull request towards the main branch. + +**What will be new** in this exercise: +- If you create the changes locally, you will need to **push** them to the remote repository. +- Learning what a protected branch is and how to modify a protected branch: using a pull request. +- Cross-referencing issues and pull requests. +- Practice to review a pull request. +- Learn about the value of draft pull requests. + +**Exercise tasks**: +1. Start in the [exercise + repository](https://github.com/workshop-material/recipe-book) and open an + issue where you describe the change you want to make. Note down the issue + number since you will need it later. +1. Create a new branch. +1. Make a change to the recipe book on the new branch and in the commit + cross-reference the issue you opened (see the walk-through below + for how to do that). +1. Push your new branch (with the new commit) to the repository you + are working on. +1. Open a pull request towards the main branch. +1. Review somebody else's pull request and give constructive feedback. Merge their pull request. +1. Try to create a new branch with some half-finished work and open a draft + pull request. Verify that the draft pull request cannot be merged since it + is not meant to be merged yet. +::: + + +## Solution and hints + +### (1) Opening an issue + +This is done through the GitHub web interface. For example, you could +give the name of the recipe you want to add (so that others don't add +the same one). It is the "Issues" tab. + + +### (2) Create a new branch. + +If on GitHub, you can make the branch in the web interface. + + +### (3) Make a change adding the recipe + +Add a new file with the recipe in it. Commit the file. In the commit +message, include the note about the issue number, saying that this +will close that issue. + + +#### Cross-referencing issues and pull requests + +Each issue and each pull request gets a number and you can cross-reference them. + +When you open an issue, note down the issue number (in this case it is `#2`): +:::{figure} img/same-repository/issue-number.png +:width: 60% +:class: with-border +:alt: Each issue gets a number +::: + +You can reference this issue number in a commit message or in a pull request, like in this +commit message: +```text +this is the new recipe; fixes #2 +``` + +If you forget to do that in your commit message, you can also reference the issue +in the pull request description. And instead of `fixes` you can also use `closes` or `resolves` +or `fix` or `close` or `resolve` (case insensitive). + +Here are all the keywords that GitHub recognizes: + + +Then observe what happens in the issue once your commit gets merged: it will +automatically close the issue and create a link between the issue and the +commit. This is very useful for tracking what changes were made in response to +which issue and to know from when until when precisely the issue was open. + + +### (4) Push to GitHub as a new branch + +Push the branch to the repository. You should end up with a branch +visible in the GitHub web view. + +This is only necessary if you created the changes locally. If you created the +changes directly on GitHub, you can skip this step. + +:::::{tabs} +::::{group-tab} VS Code +In VS Code, you can "publish the branch" to the remote repository by clicking +the cloud icon in the bottom left corner of the window: +:::{figure} img/same-repository/vscode-publish-branch.png +:width: 60% +:class: with-border +:alt: Publishing a branch in VS Code +::: +:::: + +::::{group-tab} Command line +If you have a local branch `my-branch` and you want to push it to the remote +and make it visible there, first verify what your remote is: +```console +$ git remote --verbose + +origin git@github.com:USER/recipe-book.git (fetch) +origin git@github.com:USER/recipe-book.git (push) +``` + +In this case the remote is called `origin` and refers to the address +git@github.com:USER/recipe-book.git. Both can be used +interchangeably. Make sure it points to the right repository, ideally a +repository that you can write to. + +Now that you have a remote, you can push your branch to it: +```console +$ git push origin my-branch +``` +This will create a new branch on the remote repository with the same name as +your local branch. + +You can also do this: +```console +$ git push --set-upstream origin my-branch +``` +This will connect the local branch and the remote branch so that in the future +you can just type `git push` and `git pull` without specifying the branch name +(but this depends on your Git configuration). + + +**Troubleshooting** + +If you don't have a remote yet, you can add it with (adjust `ADDRESS` to your repository address): +```console +$ git remote add origin ADDRESS +``` + +ADDRESS is the part that you copy from here: +:::{figure} img/same-repository/clone-address.png +:width: 60% +:class: with-border +:alt: Copying the clone address from GitHub +::: + +If the remote points to the wrong place, you can change it with: +```console +$ git remote set-url origin NEWADDRESS +``` +:::: +::::: + + +### (5) Open a pull request towards the main branch + +This is done through the GitHub web interface. + + +### (6) Reviewing pull requests + +You review through the GitHub web interface. + +Checklist for reviewing a pull request: +- Be kind, on the other side is a human who has put effort into this. +- Be constructive: if you see a problem, suggest a solution. +- Towards which branch is this directed? +- Is the title descriptive? +- Is the description informative? +- Scroll down to see commits. +- Scroll down to see the changes. +- If you get incredibly many changes, also consider the license or copyright + and ask where all that code is coming from. +- Again, be kind and constructive. +- Later we will learn how to suggest changes directly in the pull request. + +If someone is new, it's often nice to say something encouraging in the +comments before merging (even if it's just "thanks"). If all is good +and there's not much else to say, you could merge directly. + + +### (7) Draft pull requests + +Try to create a draft pull request: +:::{figure} img/same-repository/draft-pr.png +:width: 60% +:class: with-border +:alt: Creating a draft pull request +:::: + +Verify that the draft pull request cannot be merged until it is marked as ready +for review: +:::{figure} img/same-repository/draft-pr-wip.png +:width: 60% +:class: with-border +:alt: Draft pull request cannot be merged +:::: + +Draft pull requests can be useful for: +- **Feedback**: You can open a pull request early to get feedback on your work without + signaling that it is ready to merge. +- **Information**: They can help communicating to others that a change is coming up and in + progress. + + +### What is a protected branch? And how to modify it? + +A protected branch on GitHub or GitLab is a branch that cannot (accidentally) +deleted or force-pushed to. It is also possible to require that a branch cannot +be directly pushed to or modified, but that changes must be submitted via a +pull request. + +To protect a branch in your own repository, go to "Settings" -> "Branches". + + + +### Summary + +- We used all the same pieces that we've learned previously. +- But we successfully contributed to a collaborative project! +- The pull request allowed us to contribute without changing directly: + this is very good when it's not mainly our project. diff --git a/branch/main/_sources/credit.md.txt b/branch/main/_sources/credit.md.txt new file mode 100644 index 0000000..818da97 --- /dev/null +++ b/branch/main/_sources/credit.md.txt @@ -0,0 +1,8 @@ +# Credit + +The following material (all CC-BY) was reused to create this workshop material: +- +- +- + +(I will also summarize what changes have been made to the original material) diff --git a/branch/main/_sources/documentation.md.txt b/branch/main/_sources/documentation.md.txt new file mode 100644 index 0000000..2789a8d --- /dev/null +++ b/branch/main/_sources/documentation.md.txt @@ -0,0 +1,29 @@ +(documentation)= + +# Code documentation + +- 15 min: What makes good documentation? Also https://diataxis.fr/ +- 15 min: Writing good README files +- 30 min: Exercise: Set up a Sphinx documentation and add API documentation +- 15 min: Building documentation with GitHub Actions + + +requirements.txt: +``` +sphinx +sphinx_rtd_theme >= 2.0 +sphinx_autobuild +sphinx_autoapi +myst_parser +``` + + +conf.py: +```python +extensions = [ + "myst_parser", + "autoapi.extension", +] + +autoapi_dirs = ['..'] +``` diff --git a/branch/main/_sources/example.md.txt b/branch/main/_sources/example.md.txt new file mode 100644 index 0000000..9805632 --- /dev/null +++ b/branch/main/_sources/example.md.txt @@ -0,0 +1,95 @@ +(example-project)= + +# Example project: Simulating the motion of planets + +The [example code](https://github.com/workshop-material/planets) that we will study +is a hopefully simple N-body simulation written in Python. It is not important +or expected that we understand the code in any detail. + +:::{video} video/animation.mp4 +:width: 600 +::: + +The **big picture** is that the code simulates the motion of a number of +planets: +- We can choose the number of planets. +- Each planet starts with a random position, velocity, and mass. +- At each time step, the code calculates the gravitational force between each + pair of planets. +- The forces accelerate each planet, the acceleration modifies the velocity, + the velocity modifies the position of each planet. +- We can choose the number of time steps. +- The units were chosen to make numbers easy to read. + + +## Example run + +:::{instructor-note} +The instructor demonstrates running the code on their computer. +::: + +The code is written to accept **command-line arguments** to specify the number +of planets and the number of time steps. + +We first generate starting data: +```console +$ python generate-data.py --num-planets 10 --output-file initial.csv +``` + +The generated file (initial.csv) could look like this: +``` +px,py,pz,vx,vy,vz,mass +-46.88,-42.51,88.33,-0.86,-0.18,0.55,6.70 +-5.29,17.09,-96.13,0.66,0.45,-0.17,3.51 +83.53,-92.83,-68.77,-0.26,-0.48,0.24,6.84 +-36.31,25.48,64.16,0.85,0.75,-0.56,1.53 +-68.38,-17.21,-97.07,0.60,0.26,0.69,6.63 +-48.37,-48.74,3.92,-0.92,-0.33,-0.93,8.60 +40.53,-75.50,44.18,-0.62,-0.31,-0.53,8.04 +-27.21,10.78,-78.82,-0.09,-0.55,-0.03,5.35 +88.42,-74.95,-45.85,0.81,0.68,0.56,5.36 +39.09,53.12,-59.54,-0.54,0.56,0.07,8.98 +``` + +Then we can simulate their motion (in this case for 20 steps): +```console +$ python simulate.py --num-steps 20 \ + --input-file initial.csv \ + --output-file final.csv +``` + +The `--output-file` (final.csv) is again a CSV file (comma-separated values) +and contains the final positions of all planets. + +It is possible to run on **multiple cores** and to **animate** the result. +Here is an example with 100 planets: +```{code-block} console +--- +emphasize-lines: 7,11 +--- +$ python generate-data.py --num-planets 100 --output-file initial.csv + +$ python simulate.py --num-steps 50 \ + --input-file initial.csv \ + --output-file final.csv \ + --trajectories-file trajectories.npz \ + --num-cores 8 + +$ python animate.py --initial-file initial.csv \ + --trajectories-file trajectories.npz \ + --output-file animation.mp4 +``` + +:::{admonition} Learning goals +- What are the most important steps to make this code **reusable by others** + and **our future selves**? +- Be able to apply these techniques to your own code/script. +::: + +:::{admonition} We will not focus on ... +- ... how the code works internally in detail. +- ... whether this is the most efficient algorithm. +- ... whether the code is numerically stable. +- ... how to code scales with the number of cores. +- ... whether it is portable to other operating systems (we will discuss this later). +::: diff --git a/branch/main/_sources/index.md.txt b/branch/main/_sources/index.md.txt new file mode 100644 index 0000000..aab4003 --- /dev/null +++ b/branch/main/_sources/index.md.txt @@ -0,0 +1,157 @@ +# Reproducible research software development using Python + + +## Big-picture goal + +This is a **hands-on course on research software engineering**. In this +workshop we assume that most workshop participants use Python in their work or +a leading a group which uses Python. Therefore, some of the examples will use +Python as the example language. + +We will work with an example project and go through all the steps of a typical +software project. Once we have seen the building blocks, we will try to apply +them to own projects. Workshop participants will receive and also learn to give +constructive code feedback. + + +## Prerequisites + +:::{prereq} Preparation +1. Get a **GitHub account** following [these instructions](https://coderefinery.github.io/installation/github/). +1. You will need a **text editor**. If you don't have a favorite one, we recommend + [VS Code](https://coderefinery.github.io/installation/vscode/). +1. **If you prefer to work in the terminal** and not in VS Code, set up these two (skip this if you use VS Code): + - [Git in the terminal](https://coderefinery.github.io/installation/git-in-terminal/) + - [SSH or HTTPS connection to GitHub from terminal](https://coderefinery.github.io/installation/ssh/) +1. **One of these two software environments** (if you are not sure which one to + choose or have no preference, choose Conda): + - {ref}`conda` + - {ref}`venv` (Snakemake is not available in this environment) +1. **Optional** and only on Linux: [Apptainer](https://apptainer.org/) following + [these instructions](https://apptainer.org/docs/admin/1.3/installation.html#install-from-pre-built-packages). +::: + + +## Schedule + +:::{note} +The schedule will very soon contain links to lesson material and exercises. +::: + + +### Day 1 + +- 13:00-13:30 - **Welcome and introduction** + - Practical information (tools, communication, breaks, etc.) + - Motivation (reproducibility, robustness, distribution, improvement, trust, etc.) + - What will learn and achieve from this course? + - {ref}`example-project` + +- 13:30-14:45 (1.25h) - **Introduction to version control with Git and GitHub (1/2)** + - Creating a repository and porting your project to Git and GitHub + - Basic commands + +- 15:00-16:30 (1.5h) - **Introduction to version control with Git and GitHub (2/2)** + - Branching and merging + - Recovering from typical mistakes + +- 16:45-18:00 - {ref}`documentation` + - In-code documentation including docstrings + - Writing good README files + - Markdown + - Sphinx + - Building documentation with GitHub Actions + - Jupyter Notebooks + + +### Day 2 + +- 09:00-10:30 - {ref}`collaboration` (1/2) + - {ref}`concepts` (10 min) + - {ref}`same-repository` (40 min) + - {ref}`code-review` (40 min) + +- 10:45-12:15 - {ref}`collaboration` (2/2) + - {ref}`forking-workflow` (50 min) + - {ref}`collaboration-demo-discussion` (40 min) + +- 16:45-18:00 - **Debriefing and Q&A** + - Participants work on their projects + - Together we study actual codes that participants wrote or work on + - Constructively we discuss possible improvements + - Give individual feedback on code projects + + +### Day 3 + +- 09:00-10:30 - {ref}`testing` + - Unit tests + - End-to-end tests + - pytest + - GitHub Actions + +- 10:45-12:15 - {ref}`reusable` + - Tracking dependencies with requirements.txt and environment.yml + - Recording environments in containers + +- 13:00-14:45 - {ref}`refactoring` + - Naming (and other) conventions, project organization, modularity + - Refactoring (explained through examples) + - Design patterns: functional design vs. object-oriented design + - How to design your code before writing it + - Structuring larger software projects in a modular way + - Command-line interfaces + - Workflows with Snakemake + +- 15:00-16:30 - {ref}`publishing` + - Licenses + - Publishing the code via Zenodo + - Packaging the code + - Sharing the code via PyPI + +- 16:45-18:00 - **Debriefing and Q&A** + - Participants work on their projects + - Together we study actual codes that participants wrote or work on + - Constructively we discuss possible improvements + - Give individual feedback on code projects + + +### If we have time left + +- {ref}`profiling` + + +```{toctree} +:maxdepth: 1 +:caption: Software environment +:hidden: + +installation/conda +installation/virtual-environment +``` + +```{toctree} +:maxdepth: 1 +:caption: Episodes +:hidden: + +example +documentation +collaboration +testing +reusable +refactoring +publishing +profiling +``` + +```{toctree} +:maxdepth: 1 +:caption: Reference +:hidden: + +credit +All lessons +CodeRefinery +Reusing +``` diff --git a/branch/main/_sources/installation/conda.md.txt b/branch/main/_sources/installation/conda.md.txt new file mode 100644 index 0000000..8c55ba4 --- /dev/null +++ b/branch/main/_sources/installation/conda.md.txt @@ -0,0 +1,87 @@ +(conda)= + +# Conda environment + +A Conda environment is an isolated software environment that is used to manage dependencies for a project +and you decide where it is located. + +You will need a `environment.yml` file that documents the dependencies: +```yaml +name: coderefinery +channels: + - conda-forge + - bioconda +dependencies: + - python >= 3.10 + - black + - click + - flit + - ipywidgets + - isort + - jupyterlab + - jupyterlab_code_formatter + - jupyterlab-git + - matplotlib + - myst-parser + - nbdime + - numpy + - pandas + - pytest + - pytest-cov + - scalene + - seaborn + - snakemake-minimal + - sphinx + - sphinx-autoapi + - sphinx-autobuild + - sphinx_rtd_theme >= 2.0 + - vulture + - scikit-image +``` + + +## Before you create a virtual environment + +1. Create a new directory for this course. +1. In this directory, create an `environment.yml` file and copy-paste the dependencies above into it. + + +## Choose the tool to manage the environment + +If you are already using one of these tools, please continue using the tool that you like and know. +If you are new to this, **we recommend using Miniconda or Miniforge**. + +- [Anaconda](https://docs.anaconda.com/anaconda/install/) + - Advantages: easy to install, easy to use, good for beginners + - Disadvantages: large download, installs more than we will need, license restrictions +- [Miniconda](https://docs.anaconda.com/miniconda/) + - Advantages: small size, installs only what you need + - Disadvantages: no graphical interface, license restrictions +- [Miniforge](https://github.com/conda-forge/miniforge) + - Advantages: small size, no license restrictions + - Disadvantages: no graphical interface +- [Micromamba](https://mamba.readthedocs.io/en/latest/user_guide/micromamba.html) + - Advantages: fast, small size + - Disadvantages: no graphical interface +- [Pixi](https://pixi.sh/latest/) + - Advantages: fast and new + - Disadvantages: new and less tested and not documented here + + +## Creating the virtual environment + +1. Open your terminal shell (e.g. Bash or Zsh). +2. Activate `conda` using `conda activate` or `source ~/miniconda3/bin/activate`. +3. Run the following command: + ```console + $ conda env create --file environment.yml + ``` +4. Make sure that you see "coderefinery" in the output when you ask for a list of all available environments: + ```console + $ conda env list + ``` + + +## How to verify that this worked + +(this will be added) diff --git a/branch/main/_sources/installation/virtual-environment.md.txt b/branch/main/_sources/installation/virtual-environment.md.txt new file mode 100644 index 0000000..67e4961 --- /dev/null +++ b/branch/main/_sources/installation/virtual-environment.md.txt @@ -0,0 +1,82 @@ +(venv)= + +# Virtual environment + +A virtual environment is an isolated software environment that is used to manage dependencies for a project +and you decide where it is located. + +You will need a `requirements.txt` file that documents the dependencies: +``` +black +click +flit +ipywidgets +isort +jupyterlab +jupyterlab-code-formatter +jupyterlab-git +matplotlib +myst-parser +nbdime +numpy +pandas +pytest +pytest-cov +scalene +seaborn +sphinx +sphinx-autoapi +sphinx-autobuild +sphinx_rtd_theme >= 2.0 +vulture +scikit-image +``` + + +## Before you create a virtual environment + +1. Create a new directory for this course. +1. In this directory, create a `requirements.txt` file and copy-paste the dependencies above into it. + + +## Creating the virtual environment + +Now create a virtual environment in this directory either using [pip and +venv](https://packaging.python.org/en/latest/guides/installing-using-pip-and-virtual-environments/) +(more traditional and safer) or using [uv](https://docs.astral.sh/uv/) (more modern but also less tested): + +:::::{tabs} + +::::{group-tab} pip and venv +Create a new virtual environment and activate it: +```console +$ python3 -m venv coderefinery-environment +$ source coderefinery-environment/bin/activate +``` + +Install the dependencies into the environment: +```console +$ python3 -m pip install -r requirements.txt +``` +:::: + + +::::{group-tab} uv +Create a new virtual environment and activate it: +```console +$ uv venv coderefinery-environment +$ source coderefinery-environment/bin/activate +``` + +Install the dependencies into the environment: +```console +$ uv pip install -r requirements.txt +``` +:::: + +::::: + + +## How to verify that this worked + +(this will be added) diff --git a/branch/main/_sources/profiling.md.txt b/branch/main/_sources/profiling.md.txt new file mode 100644 index 0000000..dbcaa1b --- /dev/null +++ b/branch/main/_sources/profiling.md.txt @@ -0,0 +1,14 @@ +(profiling)= + +# Profiling memory and CPU usage + +Profilers: +- cProfile or profile +- line_profiler +- viztracer +- scalene +- Intel VTune +- PyInstrument +- py-spy +- Pyflame +- timeit diff --git a/branch/main/_sources/publishing.md.txt b/branch/main/_sources/publishing.md.txt new file mode 100644 index 0000000..bc3a12e --- /dev/null +++ b/branch/main/_sources/publishing.md.txt @@ -0,0 +1,11 @@ +(publishing)= + +# How to release and publish your code + +Part 1: +- 30 min: Overview over software licenses and code publishing +- 15 min: We add a license, CFF file, and publish to Zenodo (sandbox) + +Part 2: +- 30 min: Creating a Python package with the help of flit +- 15 min: Deploy the package to test-PyPI using GitHub Actions diff --git a/branch/main/_sources/refactoring.md.txt b/branch/main/_sources/refactoring.md.txt new file mode 100644 index 0000000..0cf390d --- /dev/null +++ b/branch/main/_sources/refactoring.md.txt @@ -0,0 +1,87 @@ +(refactoring)= + +# Code quality and good practices + +In this episode we will explore code quality and good practices in Python using +a hands-on approach. We will together build up a small project and improve it +step by step. + +We will start from a relatively simple image processing script which can read a +telescope image of stars and our goal is to **count the number of stars** in +the image. Later we will want to be able to process many such images. + +The (fictional) telescope images look like the one below here ([in this +repository](https://github.com/workshop-material/random-star-images) we can find more): +:::{figure} refactoring/stars.png +:alt: Generated image representing a telescope image of stars +:width: 60% + +Generated image representing a telescope image of stars. +::: + +:::{solution} Starting point (spoiler alert) + +We can imagine that we pieced together the following code +based on some examples we found online: +```python +import matplotlib.pyplot as plt +from skimage import io, filters, color +from skimage.measure import label, regionprops + + +image = io.imread("stars.png") +sigma = 0.5 + +# if there is a fourth channel (alpha channel), ignore it +rgb_image = image[:, :, :3] +gray_image = color.rgb2gray(rgb_image) + +# apply a gaussian filter to reduce noise +image_smooth = filters.gaussian(gray_image, sigma) + +# threshold the image to create a binary image (bright stars will be white, background black) +thresh = filters.threshold_otsu(image_smooth) +binary_image = image_smooth > thresh + +# label connected regions (stars) in the binary image +labeled_image = label(binary_image) + +# get properties of labeled regions +regions = regionprops(labeled_image) + +# extract star positions (centroids) +star_positions = [region.centroid for region in regions] + +# plot the original image +plt.figure(figsize=(8, 8)) +plt.imshow(image, cmap="gray") + +# overlay star positions with crosses +for star in star_positions: + plt.plot(star[1], star[0], "rx", markersize=5, markeredgewidth=0.1) + +plt.savefig("detected-stars.png", dpi=300) + +print(f"number of stars detected: {len(star_positions)}") +``` +::: + + +Part 1: +- 15 min: Discuss how we would solve the problem, run example code, and make it work + as part of a Jupyter notebook. +- 15 min: Refactor the positioning code into a function and a module +- 15 min: Now we wish to process many images - discuss how we would approach this +- 15 min: Introduce CLI and discuss the benefits + +Part 2: +- 30 min: From a script to a workflow (using Snakemake) +- 15 min: Discuss concepts + - Pure functions + - Design patterns: functional design vs. object-oriented design + - How to design your code before writing it: document-driven development + +Bonus: +- Move it under Git +- Document dependencies +- Show nbdime, black, vulture, ruff diff --git a/branch/main/_sources/reusable.md.txt b/branch/main/_sources/reusable.md.txt new file mode 100644 index 0000000..c86455a --- /dev/null +++ b/branch/main/_sources/reusable.md.txt @@ -0,0 +1,13 @@ +(reusable)= + +# How to make the project more reusable + +Part 1: +- 15 min: Motivation +- 15 min: Best practices for managing dependencies in Python +- 20 min: Exercise + +Part 2: +- 10 min: Introduction to containers +- 20 min: Demonstration +- 10 min: Discussion diff --git a/branch/main/_sources/testing.md.txt b/branch/main/_sources/testing.md.txt new file mode 100644 index 0000000..7a63bd9 --- /dev/null +++ b/branch/main/_sources/testing.md.txt @@ -0,0 +1,10 @@ +(testing)= + +# Automated testing + +- 15 min: Motivation +- 15 min: End-to-end tests +- 15 min: Pytest +- 15 min: Moving to GitHub Actions +- 20 min: Exercise +- 10 min: Where to go from here diff --git a/branch/main/_static/_sphinx_javascript_frameworks_compat.js b/branch/main/_static/_sphinx_javascript_frameworks_compat.js new file mode 100644 index 0000000..8141580 --- /dev/null +++ b/branch/main/_static/_sphinx_javascript_frameworks_compat.js @@ -0,0 +1,123 @@ +/* Compatability shim for jQuery and underscores.js. + * + * Copyright Sphinx contributors + * Released under the two clause BSD licence + */ + +/** + * small helper function to urldecode strings + * + * See https://developer.mozilla.org/en-US/docs/Web/JavaScript/Reference/Global_Objects/decodeURIComponent#Decoding_query_parameters_from_a_URL + */ +jQuery.urldecode = function(x) { + if (!x) { + return x + } + return decodeURIComponent(x.replace(/\+/g, ' ')); +}; + +/** + * small helper function to urlencode strings + */ +jQuery.urlencode = encodeURIComponent; + +/** + * This function returns the parsed url parameters of the + * current request. 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+ var isInSVG = jQuery(node).closest("body, svg, foreignObject").is("svg"); + if (isInSVG) { + span = document.createElementNS("http://www.w3.org/2000/svg", "tspan"); + } else { + span = document.createElement("span"); + span.className = className; + } + span.appendChild(document.createTextNode(val.substr(pos, text.length))); + node.parentNode.insertBefore(span, node.parentNode.insertBefore( + document.createTextNode(val.substr(pos + text.length)), + node.nextSibling)); + node.nodeValue = val.substr(0, pos); + if (isInSVG) { + var rect = document.createElementNS("http://www.w3.org/2000/svg", "rect"); + var bbox = node.parentElement.getBBox(); + rect.x.baseVal.value = bbox.x; + rect.y.baseVal.value = bbox.y; + rect.width.baseVal.value = bbox.width; + rect.height.baseVal.value = bbox.height; + rect.setAttribute('class', className); + addItems.push({ + "parent": node.parentNode, + "target": rect}); + } + } + } + else if (!jQuery(node).is("button, select, textarea")) { + jQuery.each(node.childNodes, function() { + highlight(this, addItems); + }); + } + } + var addItems = []; + var result = this.each(function() { + highlight(this, addItems); + }); + for (var i = 0; i < addItems.length; ++i) { + jQuery(addItems[i].parent).before(addItems[i].target); + } + return result; +}; + +/* + * backward compatibility for jQuery.browser + * This will be supported until firefox bug is fixed. + */ +if (!jQuery.browser) { + jQuery.uaMatch = function(ua) { + ua = ua.toLowerCase(); + + var match = /(chrome)[ \/]([\w.]+)/.exec(ua) || + /(webkit)[ \/]([\w.]+)/.exec(ua) || + /(opera)(?:.*version|)[ \/]([\w.]+)/.exec(ua) || + /(msie) ([\w.]+)/.exec(ua) || + ua.indexOf("compatible") < 0 && /(mozilla)(?:.*? rv:([\w.]+)|)/.exec(ua) || + []; + + return { + browser: match[ 1 ] || "", + version: match[ 2 ] || "0" + }; + }; + jQuery.browser = {}; + jQuery.browser[jQuery.uaMatch(navigator.userAgent).browser] = true; +} diff --git a/branch/main/_static/basic.css b/branch/main/_static/basic.css new file mode 100644 index 0000000..f316efc --- /dev/null +++ b/branch/main/_static/basic.css @@ -0,0 +1,925 @@ +/* + * basic.css + * ~~~~~~~~~ + * + * Sphinx stylesheet -- basic theme. + * + * :copyright: Copyright 2007-2024 by the Sphinx team, see AUTHORS. + * :license: BSD, see LICENSE for details. + * + */ + +/* -- main layout ----------------------------------------------------------- */ + +div.clearer { + clear: both; +} + +div.section::after { + display: block; + content: ''; + clear: left; +} + +/* -- relbar ---------------------------------------------------------------- */ + +div.related { + width: 100%; + font-size: 90%; +} + +div.related h3 { + display: none; +} + +div.related ul { + margin: 0; + padding: 0 0 0 10px; + list-style: none; +} + +div.related li { + display: inline; +} + +div.related li.right { + float: right; + margin-right: 5px; +} + +/* -- sidebar --------------------------------------------------------------- */ + +div.sphinxsidebarwrapper { + padding: 10px 5px 0 10px; +} + +div.sphinxsidebar { + float: left; + width: 230px; + margin-left: -100%; + font-size: 90%; + word-wrap: break-word; + overflow-wrap : break-word; +} + +div.sphinxsidebar ul { + list-style: none; +} + +div.sphinxsidebar ul ul, +div.sphinxsidebar ul.want-points { + margin-left: 20px; + list-style: square; +} + +div.sphinxsidebar ul ul { + margin-top: 0; + margin-bottom: 0; +} + +div.sphinxsidebar form { + margin-top: 10px; +} + +div.sphinxsidebar input { + border: 1px solid #98dbcc; + font-family: sans-serif; + font-size: 1em; +} + +div.sphinxsidebar #searchbox form.search { + overflow: hidden; +} + +div.sphinxsidebar #searchbox input[type="text"] { + float: left; + width: 80%; + padding: 0.25em; + box-sizing: border-box; +} + +div.sphinxsidebar #searchbox input[type="submit"] { + float: left; + width: 20%; + border-left: none; + padding: 0.25em; + box-sizing: border-box; +} + + +img { + border: 0; + max-width: 100%; +} + +/* -- search page ----------------------------------------------------------- */ + +ul.search { + margin: 10px 0 0 20px; + padding: 0; +} + +ul.search li { + padding: 5px 0 5px 20px; + background-image: url(file.png); + background-repeat: no-repeat; + background-position: 0 7px; +} + +ul.search li a { + font-weight: bold; +} + +ul.search li p.context { + color: #888; + margin: 2px 0 0 30px; + text-align: left; +} + +ul.keywordmatches li.goodmatch a { + font-weight: bold; +} + +/* -- index page ------------------------------------------------------------ */ + +table.contentstable { + width: 90%; + margin-left: auto; + margin-right: auto; +} + +table.contentstable p.biglink { + line-height: 150%; +} + +a.biglink { + font-size: 1.3em; +} + +span.linkdescr { + font-style: italic; + padding-top: 5px; + font-size: 90%; +} + +/* -- general index --------------------------------------------------------- */ + +table.indextable { + width: 100%; +} + +table.indextable td { + text-align: left; + vertical-align: top; +} + +table.indextable ul { + margin-top: 0; + margin-bottom: 0; + list-style-type: none; +} + +table.indextable > tbody > tr > td > ul { + padding-left: 0em; +} + +table.indextable tr.pcap { + height: 10px; +} + +table.indextable tr.cap { + margin-top: 10px; + background-color: #f2f2f2; +} + +img.toggler { + margin-right: 3px; + margin-top: 3px; + cursor: pointer; +} + +div.modindex-jumpbox { + border-top: 1px solid #ddd; + border-bottom: 1px solid #ddd; + margin: 1em 0 1em 0; + padding: 0.4em; +} + +div.genindex-jumpbox { + border-top: 1px solid #ddd; + border-bottom: 1px solid #ddd; + margin: 1em 0 1em 0; + padding: 0.4em; +} + +/* -- domain module index --------------------------------------------------- */ + +table.modindextable td { + padding: 2px; + border-collapse: collapse; +} + +/* -- general body styles --------------------------------------------------- */ + +div.body { + min-width: 360px; + max-width: 800px; +} + +div.body p, div.body dd, div.body li, div.body blockquote { + -moz-hyphens: auto; + -ms-hyphens: auto; + -webkit-hyphens: auto; + hyphens: auto; +} + +a.headerlink { + visibility: hidden; +} + +a:visited { + color: #551A8B; +} + +h1:hover > a.headerlink, +h2:hover > a.headerlink, +h3:hover > a.headerlink, +h4:hover > a.headerlink, +h5:hover > a.headerlink, +h6:hover > a.headerlink, +dt:hover > a.headerlink, +caption:hover > a.headerlink, +p.caption:hover > a.headerlink, +div.code-block-caption:hover > a.headerlink { + visibility: visible; +} + +div.body p.caption { + text-align: inherit; +} + +div.body td { + text-align: left; +} + +.first { + margin-top: 0 !important; +} + +p.rubric { + margin-top: 30px; + font-weight: bold; +} + +img.align-left, figure.align-left, .figure.align-left, object.align-left { + clear: left; + float: left; + margin-right: 1em; +} + +img.align-right, figure.align-right, .figure.align-right, object.align-right { + clear: right; + float: right; + margin-left: 1em; +} + +img.align-center, figure.align-center, .figure.align-center, object.align-center { + display: block; + margin-left: auto; + margin-right: auto; +} + +img.align-default, figure.align-default, .figure.align-default { + display: block; + margin-left: auto; + margin-right: auto; +} + +.align-left { + text-align: left; +} + +.align-center { + text-align: center; +} + +.align-default { + text-align: center; +} + +.align-right { + text-align: right; +} + +/* -- sidebars -------------------------------------------------------------- */ + +div.sidebar, +aside.sidebar { + margin: 0 0 0.5em 1em; + border: 1px solid #ddb; + padding: 7px; + background-color: #ffe; + width: 40%; + float: right; + clear: right; + overflow-x: auto; +} + +p.sidebar-title { + font-weight: bold; +} + +nav.contents, +aside.topic, +div.admonition, div.topic, blockquote { + clear: left; +} + +/* -- topics ---------------------------------------------------------------- */ + +nav.contents, +aside.topic, +div.topic { + border: 1px solid #ccc; + padding: 7px; + margin: 10px 0 10px 0; +} + +p.topic-title { + font-size: 1.1em; + font-weight: bold; + margin-top: 10px; +} + +/* -- admonitions ----------------------------------------------------------- */ + +div.admonition { + margin-top: 10px; + margin-bottom: 10px; + padding: 7px; +} + +div.admonition dt { + font-weight: bold; +} + +p.admonition-title { + margin: 0px 10px 5px 0px; + font-weight: bold; +} + +div.body p.centered { + text-align: center; + margin-top: 25px; +} + +/* -- content of sidebars/topics/admonitions -------------------------------- */ + +div.sidebar > :last-child, +aside.sidebar > :last-child, +nav.contents > :last-child, +aside.topic > :last-child, +div.topic > :last-child, +div.admonition > :last-child { + margin-bottom: 0; +} + +div.sidebar::after, +aside.sidebar::after, +nav.contents::after, +aside.topic::after, +div.topic::after, +div.admonition::after, +blockquote::after { + display: block; + content: ''; + clear: both; +} + +/* -- tables ---------------------------------------------------------------- */ + +table.docutils { + margin-top: 10px; + margin-bottom: 10px; + border: 0; + border-collapse: collapse; +} + +table.align-center { + margin-left: auto; + margin-right: auto; +} + +table.align-default { + margin-left: auto; + margin-right: auto; +} + +table caption span.caption-number { + font-style: italic; +} + +table caption span.caption-text { +} + +table.docutils td, table.docutils th { + padding: 1px 8px 1px 5px; + border-top: 0; + border-left: 0; + border-right: 0; + border-bottom: 1px solid #aaa; +} + +th { + text-align: left; + padding-right: 5px; +} + +table.citation { + border-left: solid 1px gray; + margin-left: 1px; +} + +table.citation td { + border-bottom: none; +} + +th > :first-child, +td > :first-child { + margin-top: 0px; +} + +th > :last-child, +td > :last-child { + margin-bottom: 0px; +} + +/* -- figures --------------------------------------------------------------- */ + +div.figure, figure { + margin: 0.5em; + padding: 0.5em; +} + +div.figure p.caption, figcaption { + padding: 0.3em; +} + +div.figure p.caption span.caption-number, +figcaption span.caption-number { + font-style: italic; +} + +div.figure p.caption span.caption-text, +figcaption span.caption-text { +} + +/* -- field list styles ----------------------------------------------------- */ + +table.field-list td, table.field-list th { + border: 0 !important; +} + +.field-list ul { + margin: 0; + padding-left: 1em; +} + +.field-list p { + margin: 0; +} + +.field-name { + -moz-hyphens: manual; + -ms-hyphens: manual; + -webkit-hyphens: manual; + hyphens: manual; +} + +/* -- hlist styles ---------------------------------------------------------- */ + +table.hlist { + margin: 1em 0; +} + +table.hlist td { + vertical-align: top; +} + +/* -- object description styles --------------------------------------------- */ + +.sig { + font-family: 'Consolas', 'Menlo', 'DejaVu Sans Mono', 'Bitstream Vera Sans Mono', monospace; +} + +.sig-name, code.descname { + background-color: transparent; + font-weight: bold; +} + +.sig-name { + font-size: 1.1em; +} + +code.descname { + font-size: 1.2em; +} + +.sig-prename, code.descclassname { + background-color: transparent; +} + +.optional { + font-size: 1.3em; +} + +.sig-paren { + font-size: larger; +} + +.sig-param.n { + font-style: italic; +} + +/* C++ specific styling */ + +.sig-inline.c-texpr, +.sig-inline.cpp-texpr { + font-family: unset; +} + +.sig.c .k, .sig.c .kt, +.sig.cpp .k, .sig.cpp .kt { + color: #0033B3; +} + +.sig.c .m, +.sig.cpp .m { + color: #1750EB; +} + +.sig.c .s, .sig.c .sc, +.sig.cpp .s, .sig.cpp .sc { + color: #067D17; +} + + +/* -- other body styles ----------------------------------------------------- */ + +ol.arabic { + list-style: decimal; +} + +ol.loweralpha { + list-style: lower-alpha; +} + +ol.upperalpha { + list-style: upper-alpha; +} + +ol.lowerroman { + list-style: lower-roman; +} + +ol.upperroman { + list-style: upper-roman; +} + +:not(li) > ol > li:first-child > :first-child, +:not(li) > ul > li:first-child > :first-child { + margin-top: 0px; +} + +:not(li) > ol > li:last-child > :last-child, +:not(li) > ul > li:last-child > :last-child { + margin-bottom: 0px; +} + +ol.simple ol p, +ol.simple ul p, +ul.simple ol p, +ul.simple ul p { + margin-top: 0; +} + +ol.simple > li:not(:first-child) > p, +ul.simple > li:not(:first-child) > p { + margin-top: 0; +} + +ol.simple p, +ul.simple p { + margin-bottom: 0; +} + +aside.footnote > span, +div.citation > span { + float: left; +} +aside.footnote > span:last-of-type, +div.citation > span:last-of-type { + padding-right: 0.5em; +} +aside.footnote > p { + margin-left: 2em; +} +div.citation > p { + margin-left: 4em; +} +aside.footnote > p:last-of-type, +div.citation > p:last-of-type { + margin-bottom: 0em; +} +aside.footnote > p:last-of-type:after, +div.citation > p:last-of-type:after { + content: ""; + clear: both; +} + +dl.field-list { + display: grid; + grid-template-columns: fit-content(30%) auto; +} + +dl.field-list > dt { + font-weight: bold; + word-break: break-word; + padding-left: 0.5em; + padding-right: 5px; +} + +dl.field-list > dd { + padding-left: 0.5em; + margin-top: 0em; + margin-left: 0em; + margin-bottom: 0em; +} + +dl { + margin-bottom: 15px; +} + +dd > :first-child { + margin-top: 0px; +} + +dd ul, dd table { + margin-bottom: 10px; +} + +dd { + margin-top: 3px; + margin-bottom: 10px; + margin-left: 30px; +} + +.sig dd { + margin-top: 0px; + margin-bottom: 0px; +} + +.sig dl { + margin-top: 0px; + margin-bottom: 0px; +} + +dl > dd:last-child, +dl > dd:last-child > :last-child { + margin-bottom: 0; +} + +dt:target, span.highlighted { + background-color: #fbe54e; +} + +rect.highlighted { + fill: #fbe54e; +} + +dl.glossary dt { + font-weight: bold; + font-size: 1.1em; +} + +.versionmodified { + font-style: italic; +} + +.system-message { + background-color: #fda; + padding: 5px; + border: 3px solid red; +} + +.footnote:target { + background-color: #ffa; +} + +.line-block { + display: block; + margin-top: 1em; + margin-bottom: 1em; +} + +.line-block .line-block { + margin-top: 0; + margin-bottom: 0; + margin-left: 1.5em; +} + +.guilabel, .menuselection { + font-family: sans-serif; +} + +.accelerator { + text-decoration: underline; +} + +.classifier { + font-style: oblique; +} + +.classifier:before { + font-style: normal; + margin: 0 0.5em; + content: ":"; + display: inline-block; +} + +abbr, acronym { + border-bottom: dotted 1px; + cursor: help; +} + +.translated { + background-color: rgba(207, 255, 207, 0.2) +} + +.untranslated { + background-color: rgba(255, 207, 207, 0.2) +} + +/* -- code displays --------------------------------------------------------- */ + +pre { + overflow: auto; + overflow-y: hidden; /* fixes display issues on Chrome browsers */ +} + +pre, div[class*="highlight-"] { + clear: both; +} + +span.pre { + -moz-hyphens: none; + -ms-hyphens: none; + -webkit-hyphens: none; + hyphens: none; + white-space: nowrap; +} + +div[class*="highlight-"] { + margin: 1em 0; +} + +td.linenos pre { + border: 0; + background-color: transparent; + color: #aaa; +} + +table.highlighttable { + display: block; +} + +table.highlighttable tbody { + display: block; +} + +table.highlighttable tr { + display: flex; +} + +table.highlighttable td { + margin: 0; + padding: 0; +} + +table.highlighttable td.linenos { + padding-right: 0.5em; +} + +table.highlighttable td.code { + flex: 1; + overflow: hidden; +} + +.highlight .hll { + display: block; +} + +div.highlight pre, +table.highlighttable pre { + margin: 0; +} + +div.code-block-caption + div { + margin-top: 0; +} + +div.code-block-caption { + margin-top: 1em; + padding: 2px 5px; + font-size: small; +} + +div.code-block-caption code { + background-color: transparent; +} + +table.highlighttable td.linenos, +span.linenos, +div.highlight span.gp { /* gp: Generic.Prompt */ + user-select: none; + -webkit-user-select: text; /* Safari fallback only */ + -webkit-user-select: none; /* Chrome/Safari */ + -moz-user-select: none; /* Firefox */ + -ms-user-select: none; /* IE10+ */ +} + +div.code-block-caption span.caption-number { + padding: 0.1em 0.3em; + font-style: italic; +} + +div.code-block-caption span.caption-text { +} + +div.literal-block-wrapper { + margin: 1em 0; +} + +code.xref, a code { + background-color: transparent; + font-weight: bold; +} + +h1 code, h2 code, h3 code, h4 code, h5 code, h6 code { + background-color: transparent; +} + +.viewcode-link { + float: right; +} + +.viewcode-back { + float: right; + font-family: sans-serif; +} + +div.viewcode-block:target { + margin: -1px -10px; + padding: 0 10px; +} + +/* -- math display ---------------------------------------------------------- */ + +img.math { + vertical-align: middle; +} + +div.body div.math p { + text-align: center; +} + +span.eqno { + float: right; +} + +span.eqno a.headerlink { + position: absolute; + z-index: 1; +} + +div.math:hover a.headerlink { + visibility: visible; +} + +/* -- printout stylesheet --------------------------------------------------- */ + +@media print { + div.document, + div.documentwrapper, + div.bodywrapper { + margin: 0 !important; + width: 100%; + } + + div.sphinxsidebar, + div.related, + div.footer, + #top-link { + display: none; + } +} \ No newline at end of file diff --git a/branch/main/_static/check-solid.svg b/branch/main/_static/check-solid.svg new file mode 100644 index 0000000..92fad4b --- /dev/null +++ b/branch/main/_static/check-solid.svg @@ -0,0 +1,4 @@ + + + + diff --git a/branch/main/_static/clipboard.min.js b/branch/main/_static/clipboard.min.js new file mode 100644 index 0000000..54b3c46 --- /dev/null +++ b/branch/main/_static/clipboard.min.js @@ -0,0 +1,7 @@ +/*! + * clipboard.js v2.0.8 + * https://clipboardjs.com/ + * + * Licensed MIT © Zeno Rocha + */ +!function(t,e){"object"==typeof exports&&"object"==typeof module?module.exports=e():"function"==typeof define&&define.amd?define([],e):"object"==typeof exports?exports.ClipboardJS=e():t.ClipboardJS=e()}(this,function(){return n={686:function(t,e,n){"use strict";n.d(e,{default:function(){return o}});var e=n(279),i=n.n(e),e=n(370),u=n.n(e),e=n(817),c=n.n(e);function a(t){try{return document.execCommand(t)}catch(t){return}}var f=function(t){t=c()(t);return a("cut"),t};var l=function(t){var e,n,o,r=1 + + + + diff --git a/branch/main/_static/copybutton.css b/branch/main/_static/copybutton.css new file mode 100644 index 0000000..40eafe5 --- /dev/null +++ b/branch/main/_static/copybutton.css @@ -0,0 +1,93 @@ +/* Copy buttons */ +button.copybtn { + position: absolute; + display: flex; + top: .3em; + right: .3em; + width: 1.7em; + height: 1.7em; + opacity: 0; + transition: opacity 0.3s, border .3s, background-color .3s; + user-select: none; + padding: 0; + border: none; + outline: none; + border-radius: 0.4em; + /* The colors that GitHub uses */ + border: #1b1f2426 1px solid; + background-color: #f6f8fa; + color: #57606a; +} + +button.copybtn.success { + border-color: #22863a; + color: #22863a; +} + +button.copybtn svg { + stroke: currentColor; + width: 1.5em; + height: 1.5em; + padding: 0.1em; +} + +div.highlight { + position: relative; +} + +.highlight:hover button.copybtn { + opacity: 1; +} + +.highlight button.copybtn:hover { + background-color: rgb(235, 235, 235); +} + +.highlight button.copybtn:active { + background-color: rgb(187, 187, 187); +} + +/** + * A minimal CSS-only tooltip copied from: + * https://codepen.io/mildrenben/pen/rVBrpK + * + * To use, write HTML like the following: + * + *

Short

+ */ + .o-tooltip--left { + position: relative; + } + + .o-tooltip--left:after { + opacity: 0; + visibility: hidden; + position: absolute; + content: attr(data-tooltip); + padding: .2em; + font-size: .8em; + left: -.2em; + background: grey; + color: white; + white-space: nowrap; + z-index: 2; + border-radius: 2px; + transform: translateX(-102%) translateY(0); + transition: opacity 0.2s cubic-bezier(0.64, 0.09, 0.08, 1), transform 0.2s cubic-bezier(0.64, 0.09, 0.08, 1); +} + +.o-tooltip--left:hover:after { + display: block; + opacity: 1; + visibility: visible; + transform: translateX(-100%) translateY(0); + transition: opacity 0.2s cubic-bezier(0.64, 0.09, 0.08, 1), transform 0.2s cubic-bezier(0.64, 0.09, 0.08, 1); + transition-delay: .5s; +} + +/* By default the copy button shouldn't show up when printing a page */ +@media print { + button.copybtn { + display: none; + } +} diff --git a/branch/main/_static/copybutton.js b/branch/main/_static/copybutton.js new file mode 100644 index 0000000..f3ecd03 --- /dev/null +++ b/branch/main/_static/copybutton.js @@ -0,0 +1,241 @@ +// Localization support +const messages = { + 'en': { + 'copy': 'Copy', + 'copy_to_clipboard': 'Copy to clipboard', + 'copy_success': 'Copied!', + 'copy_failure': 'Failed to copy', + }, + 'es' : { + 'copy': 'Copiar', + 'copy_to_clipboard': 'Copiar al portapapeles', + 'copy_success': '¡Copiado!', + 'copy_failure': 'Error al copiar', + }, + 'de' : { + 'copy': 'Kopieren', + 'copy_to_clipboard': 'In die Zwischenablage kopieren', + 'copy_success': 'Kopiert!', + 'copy_failure': 'Fehler beim Kopieren', + }, + 'fr' : { + 'copy': 'Copier', + 'copy_to_clipboard': 'Copié dans le presse-papier', + 'copy_success': 'Copié !', + 'copy_failure': 'Échec de la copie', + }, + 'ru': { + 'copy': 'Скопировать', + 'copy_to_clipboard': 'Скопировать в буфер', + 'copy_success': 'Скопировано!', + 'copy_failure': 'Не удалось скопировать', + }, + 'zh-CN': { + 'copy': '复制', + 'copy_to_clipboard': '复制到剪贴板', + 'copy_success': '复制成功!', + 'copy_failure': '复制失败', + }, + 'it' : { + 'copy': 'Copiare', + 'copy_to_clipboard': 'Copiato negli appunti', + 'copy_success': 'Copiato!', + 'copy_failure': 'Errore durante la copia', + } +} + +let locale = 'en' +if( document.documentElement.lang !== undefined + && messages[document.documentElement.lang] !== undefined ) { + locale = document.documentElement.lang +} + +let doc_url_root = DOCUMENTATION_OPTIONS.URL_ROOT; +if (doc_url_root == '#') { + doc_url_root = ''; +} + +/** + * SVG files for our copy buttons + */ +let iconCheck = ` + ${messages[locale]['copy_success']} + + +` + +// If the user specified their own SVG use that, otherwise use the default +let iconCopy = ``; +if (!iconCopy) { + iconCopy = ` + ${messages[locale]['copy_to_clipboard']} + + + +` +} + +/** + * Set up copy/paste for code blocks + */ + +const runWhenDOMLoaded = cb => { + if (document.readyState != 'loading') { + cb() + } else if (document.addEventListener) { + document.addEventListener('DOMContentLoaded', cb) + } else { + document.attachEvent('onreadystatechange', function() { + if (document.readyState == 'complete') cb() + }) + } +} + +const codeCellId = index => `codecell${index}` + +// Clears selected text since ClipboardJS will select the text when copying +const clearSelection = () => { + if (window.getSelection) { + window.getSelection().removeAllRanges() + } else if (document.selection) { + document.selection.empty() + } +} + +// Changes tooltip text for two seconds, then changes it back +const temporarilyChangeTooltip = (el, oldText, newText) => { + el.setAttribute('data-tooltip', newText) + el.classList.add('success') + setTimeout(() => el.setAttribute('data-tooltip', oldText), 2000) + setTimeout(() => el.classList.remove('success'), 2000) +} + +// Changes the copy button icon for two seconds, then changes it back +const temporarilyChangeIcon = (el) => { + el.innerHTML = iconCheck; + setTimeout(() => {el.innerHTML = iconCopy}, 2000) +} + +const addCopyButtonToCodeCells = () => { + // If ClipboardJS hasn't loaded, wait a bit and try again. This + // happens because we load ClipboardJS asynchronously. + if (window.ClipboardJS === undefined) { + setTimeout(addCopyButtonToCodeCells, 250) + return + } + + // Add copybuttons to all of our code cells + const COPYBUTTON_SELECTOR = 'div.highlight pre'; + const codeCells = document.querySelectorAll(COPYBUTTON_SELECTOR) + codeCells.forEach((codeCell, index) => { + const id = codeCellId(index) + codeCell.setAttribute('id', id) + + const clipboardButton = id => + `` + codeCell.insertAdjacentHTML('afterend', clipboardButton(id)) + }) + +function escapeRegExp(string) { + return string.replace(/[.*+?^${}()|[\]\\]/g, '\\$&'); // $& means the whole matched string +} + +/** + * Removes excluded text from a Node. + * + * @param {Node} target Node to filter. + * @param {string} exclude CSS selector of nodes to exclude. + * @returns {DOMString} Text from `target` with text removed. + */ +function filterText(target, exclude) { + const clone = target.cloneNode(true); // clone as to not modify the live DOM + if (exclude) { + // remove excluded nodes + clone.querySelectorAll(exclude).forEach(node => node.remove()); + } + return clone.innerText; +} + +// Callback when a copy button is clicked. Will be passed the node that was clicked +// should then grab the text and replace pieces of text that shouldn't be used in output +function formatCopyText(textContent, copybuttonPromptText, isRegexp = false, onlyCopyPromptLines = true, removePrompts = true, copyEmptyLines = true, lineContinuationChar = "", hereDocDelim = "") { + var regexp; + var match; + + // Do we check for line continuation characters and "HERE-documents"? + var useLineCont = !!lineContinuationChar + var useHereDoc = !!hereDocDelim + + // create regexp to capture prompt and remaining line + if (isRegexp) { + regexp = new RegExp('^(' + copybuttonPromptText + ')(.*)') + } else { + regexp = new RegExp('^(' + escapeRegExp(copybuttonPromptText) + ')(.*)') + } + + const outputLines = []; + var promptFound = false; + var gotLineCont = false; + var gotHereDoc = false; + const lineGotPrompt = []; + for (const line of textContent.split('\n')) { + match = line.match(regexp) + if (match || gotLineCont || gotHereDoc) { + promptFound = regexp.test(line) + lineGotPrompt.push(promptFound) + if (removePrompts && promptFound) { + outputLines.push(match[2]) + } else { + outputLines.push(line) + } + gotLineCont = line.endsWith(lineContinuationChar) & useLineCont + if (line.includes(hereDocDelim) & useHereDoc) + gotHereDoc = !gotHereDoc + } else if (!onlyCopyPromptLines) { + outputLines.push(line) + } else if (copyEmptyLines && line.trim() === '') { + outputLines.push(line) + } + } + + // If no lines with the prompt were found then just use original lines + if (lineGotPrompt.some(v => v === true)) { + textContent = outputLines.join('\n'); + } + + // Remove a trailing newline to avoid auto-running when pasting + if (textContent.endsWith("\n")) { + textContent = textContent.slice(0, -1) + } + return textContent +} + + +var copyTargetText = (trigger) => { + var target = document.querySelector(trigger.attributes['data-clipboard-target'].value); + + // get filtered text + let exclude = '.linenos, .gp'; + + let text = filterText(target, exclude); + return formatCopyText(text, '', false, true, true, true, '', '') +} + + // Initialize with a callback so we can modify the text before copy + const clipboard = new ClipboardJS('.copybtn', {text: copyTargetText}) + + // Update UI with error/success messages + clipboard.on('success', event => { + clearSelection() + temporarilyChangeTooltip(event.trigger, messages[locale]['copy'], messages[locale]['copy_success']) + temporarilyChangeIcon(event.trigger) + }) + + clipboard.on('error', event => { + temporarilyChangeTooltip(event.trigger, messages[locale]['copy'], messages[locale]['copy_failure']) + }) +} + +runWhenDOMLoaded(addCopyButtonToCodeCells) \ No newline at end of file diff --git a/branch/main/_static/copybutton_funcs.js b/branch/main/_static/copybutton_funcs.js new file mode 100644 index 0000000..dbe1aaa --- /dev/null +++ b/branch/main/_static/copybutton_funcs.js @@ -0,0 +1,73 @@ +function escapeRegExp(string) { + return string.replace(/[.*+?^${}()|[\]\\]/g, '\\$&'); // $& means the whole matched string +} + +/** + * Removes excluded text from a Node. + * + * @param {Node} target Node to filter. + * @param {string} exclude CSS selector of nodes to exclude. + * @returns {DOMString} Text from `target` with text removed. + */ +export function filterText(target, exclude) { + const clone = target.cloneNode(true); // clone as to not modify the live DOM + if (exclude) { + // remove excluded nodes + clone.querySelectorAll(exclude).forEach(node => node.remove()); + } + return clone.innerText; +} + +// Callback when a copy button is clicked. Will be passed the node that was clicked +// should then grab the text and replace pieces of text that shouldn't be used in output +export function formatCopyText(textContent, copybuttonPromptText, isRegexp = false, onlyCopyPromptLines = true, removePrompts = true, copyEmptyLines = true, lineContinuationChar = "", hereDocDelim = "") { + var regexp; + var match; + + // Do we check for line continuation characters and "HERE-documents"? + var useLineCont = !!lineContinuationChar + var useHereDoc = !!hereDocDelim + + // create regexp to capture prompt and remaining line + if (isRegexp) { + regexp = new RegExp('^(' + copybuttonPromptText + ')(.*)') + } else { + regexp = new RegExp('^(' + escapeRegExp(copybuttonPromptText) + ')(.*)') + } + + const outputLines = []; + var promptFound = false; + var gotLineCont = false; + var gotHereDoc = false; + const lineGotPrompt = []; + for (const line of textContent.split('\n')) { + match = line.match(regexp) + if (match || gotLineCont || gotHereDoc) { + promptFound = regexp.test(line) + lineGotPrompt.push(promptFound) + if (removePrompts && promptFound) { + outputLines.push(match[2]) + } else { + outputLines.push(line) + } + gotLineCont = line.endsWith(lineContinuationChar) & useLineCont + if (line.includes(hereDocDelim) & useHereDoc) + gotHereDoc = !gotHereDoc + } else if (!onlyCopyPromptLines) { + outputLines.push(line) + } else if (copyEmptyLines && line.trim() === '') { + outputLines.push(line) + } + } + + // If no lines with the prompt were found then just use original lines + if (lineGotPrompt.some(v => v === true)) { + textContent = outputLines.join('\n'); + } + + // Remove a trailing newline to avoid auto-running when pasting + if (textContent.endsWith("\n")) { + textContent = textContent.slice(0, -1) + } + return textContent +} diff --git a/branch/main/_static/css/badge_only.css b/branch/main/_static/css/badge_only.css new file mode 100644 index 0000000..c718cee --- /dev/null +++ b/branch/main/_static/css/badge_only.css @@ 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+ return this; // for chaining... + } +})(jQuery); + +// NO good way to do this!. Copy a hack from here +// https://stackoverflow.com/questions/901115/how-can-i-get-query-string-values-in-javascript +// https://stackoverflow.com/a/2880929 +var urlParams; +(window.onpopstate = function () { + var match, + pl = /\+/g, // Regex for replacing addition symbol with a space + search = /([^&=]+)=?([^&]*)/g, + decode = function (s) { return decodeURIComponent(s.replace(pl, " ")); }, + query = window.location.search.substring(1); + urlParams = {}; + while (match = search.exec(query)) + urlParams[decode(match[1])] = decode(match[2]); +})(); + +// Select heading levels +var maxHeading = urlParams['h'] +if (maxHeading === undefined) maxHeading = 2 +var headingLevels = []; +for (h=2 ; h (sections.length-1) ) { + // if we would scroll past bottom, or above top, do nothing + return; + } + + console.log('xxxxxx'); + var targetSection = sections[targetPos]; + console.log(targetSection, typeof(targetSection)); + + // Return targetSection top and height + var secProperties = section_top_and_height(targetSection); + var top = secProperties['top']; + var height = secProperties['height'] + var win_height = window.innerHeight; + //console.info(top, height, win_height) + + var scroll_to = 0; + if (height >= win_height || height == 0) { + scroll_to = top; + } else { + scroll_to = top - (win_height-height)/3.; + } + //console.info(top, height, win_height, scroll_to) + + $('html, body').animate({ + scrollTop: scroll_to //+ 'px' + }, 'fast'); + +} + + +function minipres() { + /* Enable the minipres mode: + - call the hide() function + - set up the scrolling listener + */ + document.addEventListener('keydown', function (event) { + switch(event.which) { + case 37: // left + switch_slide(-1); + event.preventDefault(); + return false; + break; + //case 38: // up + case 39: // right + switch_slide(+1); + event.preventDefault(); + return false; + break; + //case 40: // down + default: + return; // exit this handler for other keys + } + }, true) + + hide() + + // Increase space between sections + //$("div .section").css('margin-bottom', '50%'); 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+} + +/* Pandas tables. Pulled from the Jupyter / nbsphinx CSS */ +div.cell_output table { + border: none; + border-collapse: collapse; + border-spacing: 0; + color: black; + font-size: 1em; + table-layout: fixed; +} + +div.cell_output thead { + border-bottom: 1px solid black; + vertical-align: bottom; +} + +div.cell_output tr, +div.cell_output th, +div.cell_output td { + text-align: right; + vertical-align: middle; + padding: 0.5em 0.5em; + line-height: normal; + white-space: normal; + max-width: none; + border: none; +} + +div.cell_output th { + font-weight: bold; +} + +div.cell_output tbody tr:nth-child(odd) { + background: #f5f5f5; +} + +div.cell_output tbody tr:hover { + background: rgba(66, 165, 245, 0.2); +} + +/** source code line numbers **/ +span.linenos { + opacity: 0.5; +} + +/* Inline text from `paste` operation */ + +span.pasted-text { + font-weight: bold; +} + +span.pasted-inline img { + max-height: 2em; +} + +tbody span.pasted-inline img { + max-height: none; +} + +/* Font colors for 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background-color: #E75C58 +} + +div.highlight .-Color[class*=-BGGreen] { + background-color: #00A250 +} + +div.highlight .-Color[class*=-BGYellow] { + background-color: #DDB62B +} + +div.highlight .-Color[class*=-BGBlue] { + background-color: #208FFB +} + +div.highlight .-Color[class*=-BGMagenta] { + background-color: #D160C4 +} + +div.highlight .-Color[class*=-BGCyan] { + background-color: #60C6C8 +} + +div.highlight .-Color[class*=-BGWhite] { + background-color: #C5C1B4 +} + +/* Font colors for 8-bit ANSI */ + +div.highlight .-Color[class*=-C0] { + color: #000000 +} + +div.highlight .-Color[class*=-BGC0] { + background-color: #000000 +} + +div.highlight .-Color[class*=-C1] { + color: #800000 +} + +div.highlight .-Color[class*=-BGC1] { + background-color: #800000 +} + +div.highlight .-Color[class*=-C2] { + color: #008000 +} + +div.highlight .-Color[class*=-BGC2] { + background-color: #008000 +} + +div.highlight .-Color[class*=-C3] { + color: #808000 +} + +div.highlight .-Color[class*=-BGC3] { + background-color: #808000 +} + +div.highlight .-Color[class*=-C4] { + color: #000080 +} + +div.highlight .-Color[class*=-BGC4] { + background-color: #000080 +} + +div.highlight .-Color[class*=-C5] { + color: #800080 +} + +div.highlight .-Color[class*=-BGC5] { + background-color: #800080 +} + +div.highlight .-Color[class*=-C6] { + color: #008080 +} + +div.highlight .-Color[class*=-BGC6] { + background-color: #008080 +} + +div.highlight .-Color[class*=-C7] { + color: #C0C0C0 +} + +div.highlight .-Color[class*=-BGC7] { + background-color: #C0C0C0 +} + +div.highlight .-Color[class*=-C8] { + color: #808080 +} + +div.highlight .-Color[class*=-BGC8] { + background-color: #808080 +} + +div.highlight .-Color[class*=-C9] { + color: #FF0000 +} + +div.highlight .-Color[class*=-BGC9] { + background-color: #FF0000 +} + +div.highlight .-Color[class*=-C10] { + color: #00FF00 +} + +div.highlight .-Color[class*=-BGC10] { + background-color: #00FF00 +} + +div.highlight .-Color[class*=-C11] { + color: #FFFF00 +} + +div.highlight .-Color[class*=-BGC11] { + background-color: #FFFF00 +} + +div.highlight .-Color[class*=-C12] { + color: #0000FF +} + +div.highlight .-Color[class*=-BGC12] { + background-color: #0000FF +} + +div.highlight .-Color[class*=-C13] { + color: #FF00FF +} + +div.highlight .-Color[class*=-BGC13] { + background-color: #FF00FF +} + +div.highlight .-Color[class*=-C14] { + color: #00FFFF +} + +div.highlight .-Color[class*=-BGC14] { + background-color: #00FFFF +} + +div.highlight .-Color[class*=-C15] { + color: #FFFFFF +} + +div.highlight .-Color[class*=-BGC15] { + background-color: #FFFFFF +} + +div.highlight .-Color[class*=-C16] { + color: #000000 +} + +div.highlight .-Color[class*=-BGC16] { + background-color: #000000 +} + +div.highlight .-Color[class*=-C17] { + color: #00005F +} + +div.highlight .-Color[class*=-BGC17] { + background-color: #00005F +} + +div.highlight .-Color[class*=-C18] { + color: #000087 +} + +div.highlight .-Color[class*=-BGC18] { + background-color: #000087 +} + +div.highlight .-Color[class*=-C19] { + color: #0000AF +} + +div.highlight .-Color[class*=-BGC19] { + background-color: #0000AF +} + +div.highlight .-Color[class*=-C20] { + color: #0000D7 +} + +div.highlight .-Color[class*=-BGC20] { + background-color: #0000D7 +} + +div.highlight .-Color[class*=-C21] { + color: #0000FF +} + +div.highlight .-Color[class*=-BGC21] { + background-color: #0000FF +} + +div.highlight .-Color[class*=-C22] { + color: #005F00 +} + +div.highlight .-Color[class*=-BGC22] { + background-color: #005F00 +} + +div.highlight .-Color[class*=-C23] { + color: #005F5F +} + +div.highlight .-Color[class*=-BGC23] { + background-color: #005F5F +} + +div.highlight .-Color[class*=-C24] { + color: #005F87 +} + +div.highlight .-Color[class*=-BGC24] { + background-color: #005F87 +} + +div.highlight .-Color[class*=-C25] { + color: #005FAF +} + +div.highlight .-Color[class*=-BGC25] { + background-color: #005FAF +} + +div.highlight .-Color[class*=-C26] { + color: #005FD7 +} + +div.highlight .-Color[class*=-BGC26] { + background-color: #005FD7 +} + +div.highlight .-Color[class*=-C27] { + color: #005FFF +} + +div.highlight .-Color[class*=-BGC27] { + background-color: #005FFF +} + +div.highlight .-Color[class*=-C28] { + color: #008700 +} + +div.highlight .-Color[class*=-BGC28] { + background-color: #008700 +} + +div.highlight .-Color[class*=-C29] { + color: #00875F +} + +div.highlight .-Color[class*=-BGC29] { + background-color: #00875F +} + +div.highlight .-Color[class*=-C30] { + color: #008787 +} + +div.highlight .-Color[class*=-BGC30] { + background-color: #008787 +} + +div.highlight .-Color[class*=-C31] { + color: #0087AF +} + +div.highlight .-Color[class*=-BGC31] { + background-color: #0087AF +} + +div.highlight .-Color[class*=-C32] { + color: #0087D7 +} + +div.highlight .-Color[class*=-BGC32] { + background-color: #0087D7 +} + +div.highlight .-Color[class*=-C33] { + color: #0087FF +} + +div.highlight .-Color[class*=-BGC33] { + background-color: #0087FF +} + +div.highlight .-Color[class*=-C34] { + color: #00AF00 +} + +div.highlight .-Color[class*=-BGC34] { + background-color: #00AF00 +} + +div.highlight .-Color[class*=-C35] { + color: #00AF5F +} + +div.highlight .-Color[class*=-BGC35] { + background-color: #00AF5F +} + +div.highlight .-Color[class*=-C36] { + color: #00AF87 +} + +div.highlight .-Color[class*=-BGC36] { + background-color: #00AF87 +} + +div.highlight .-Color[class*=-C37] { + color: #00AFAF +} + +div.highlight .-Color[class*=-BGC37] { + background-color: #00AFAF +} + +div.highlight .-Color[class*=-C38] { + color: #00AFD7 +} + +div.highlight .-Color[class*=-BGC38] { + background-color: #00AFD7 +} + +div.highlight .-Color[class*=-C39] { + color: #00AFFF +} + +div.highlight .-Color[class*=-BGC39] { + background-color: #00AFFF +} + +div.highlight .-Color[class*=-C40] { + color: #00D700 +} + +div.highlight .-Color[class*=-BGC40] { + background-color: #00D700 +} + +div.highlight .-Color[class*=-C41] { + color: #00D75F +} + +div.highlight .-Color[class*=-BGC41] { + background-color: #00D75F +} + +div.highlight .-Color[class*=-C42] { + color: #00D787 +} + +div.highlight .-Color[class*=-BGC42] { + background-color: #00D787 +} + +div.highlight .-Color[class*=-C43] { + color: #00D7AF +} + +div.highlight .-Color[class*=-BGC43] { + background-color: #00D7AF +} + +div.highlight .-Color[class*=-C44] { + color: #00D7D7 +} + +div.highlight .-Color[class*=-BGC44] { + background-color: #00D7D7 +} + +div.highlight .-Color[class*=-C45] { + color: #00D7FF +} + +div.highlight .-Color[class*=-BGC45] { + background-color: #00D7FF +} + +div.highlight .-Color[class*=-C46] { + color: #00FF00 +} + +div.highlight .-Color[class*=-BGC46] { + background-color: #00FF00 +} + +div.highlight .-Color[class*=-C47] { + color: #00FF5F +} + +div.highlight .-Color[class*=-BGC47] { + background-color: #00FF5F +} + +div.highlight .-Color[class*=-C48] { + color: #00FF87 +} + +div.highlight .-Color[class*=-BGC48] { + background-color: #00FF87 +} + +div.highlight .-Color[class*=-C49] { + color: #00FFAF +} + +div.highlight .-Color[class*=-BGC49] { + background-color: #00FFAF +} + +div.highlight .-Color[class*=-C50] { + color: #00FFD7 +} + +div.highlight .-Color[class*=-BGC50] { + background-color: #00FFD7 +} + +div.highlight .-Color[class*=-C51] { + color: #00FFFF +} + +div.highlight .-Color[class*=-BGC51] { + background-color: #00FFFF +} + +div.highlight .-Color[class*=-C52] { + color: #5F0000 +} + +div.highlight .-Color[class*=-BGC52] { + background-color: #5F0000 +} + +div.highlight .-Color[class*=-C53] { + color: #5F005F +} + +div.highlight .-Color[class*=-BGC53] { + background-color: #5F005F +} + +div.highlight .-Color[class*=-C54] { + color: #5F0087 +} + +div.highlight .-Color[class*=-BGC54] { + background-color: #5F0087 +} + +div.highlight .-Color[class*=-C55] { + color: #5F00AF +} + +div.highlight .-Color[class*=-BGC55] { + background-color: #5F00AF +} + +div.highlight .-Color[class*=-C56] { + color: #5F00D7 +} + +div.highlight .-Color[class*=-BGC56] { + background-color: #5F00D7 +} + +div.highlight .-Color[class*=-C57] { + color: #5F00FF +} + +div.highlight .-Color[class*=-BGC57] { + background-color: #5F00FF +} + +div.highlight .-Color[class*=-C58] { + color: #5F5F00 +} + +div.highlight .-Color[class*=-BGC58] { + background-color: #5F5F00 +} + +div.highlight .-Color[class*=-C59] { + color: #5F5F5F +} + +div.highlight .-Color[class*=-BGC59] { + background-color: #5F5F5F +} + +div.highlight .-Color[class*=-C60] { + color: #5F5F87 +} + +div.highlight .-Color[class*=-BGC60] { + background-color: #5F5F87 +} + +div.highlight .-Color[class*=-C61] { + color: #5F5FAF +} + +div.highlight .-Color[class*=-BGC61] { + background-color: #5F5FAF +} + +div.highlight .-Color[class*=-C62] { + color: #5F5FD7 +} + +div.highlight .-Color[class*=-BGC62] { + background-color: #5F5FD7 +} + +div.highlight .-Color[class*=-C63] { + color: #5F5FFF +} + +div.highlight .-Color[class*=-BGC63] { + background-color: #5F5FFF +} + +div.highlight .-Color[class*=-C64] { + color: #5F8700 +} + +div.highlight .-Color[class*=-BGC64] { + background-color: #5F8700 +} + +div.highlight .-Color[class*=-C65] { + color: #5F875F +} + +div.highlight .-Color[class*=-BGC65] { + background-color: #5F875F +} + +div.highlight .-Color[class*=-C66] { + color: #5F8787 +} + +div.highlight .-Color[class*=-BGC66] { + background-color: #5F8787 +} + +div.highlight .-Color[class*=-C67] { + color: #5F87AF +} + +div.highlight .-Color[class*=-BGC67] { + background-color: #5F87AF +} + +div.highlight .-Color[class*=-C68] { + color: #5F87D7 +} + +div.highlight .-Color[class*=-BGC68] { + background-color: #5F87D7 +} + +div.highlight .-Color[class*=-C69] { + color: #5F87FF +} + +div.highlight .-Color[class*=-BGC69] { + background-color: #5F87FF +} + +div.highlight .-Color[class*=-C70] { + color: #5FAF00 +} + +div.highlight .-Color[class*=-BGC70] { + background-color: #5FAF00 +} + +div.highlight .-Color[class*=-C71] { + color: #5FAF5F +} + +div.highlight .-Color[class*=-BGC71] { + background-color: #5FAF5F +} + +div.highlight .-Color[class*=-C72] { + color: #5FAF87 +} + +div.highlight .-Color[class*=-BGC72] { + background-color: #5FAF87 +} + +div.highlight .-Color[class*=-C73] { + color: #5FAFAF +} + +div.highlight .-Color[class*=-BGC73] { + background-color: #5FAFAF +} + +div.highlight .-Color[class*=-C74] { + color: #5FAFD7 +} + +div.highlight .-Color[class*=-BGC74] { + background-color: #5FAFD7 +} + +div.highlight .-Color[class*=-C75] { + color: #5FAFFF +} + +div.highlight .-Color[class*=-BGC75] { + background-color: #5FAFFF +} + +div.highlight .-Color[class*=-C76] { + color: #5FD700 +} + +div.highlight .-Color[class*=-BGC76] { + background-color: #5FD700 +} + +div.highlight .-Color[class*=-C77] { + color: #5FD75F +} + +div.highlight .-Color[class*=-BGC77] { + background-color: #5FD75F +} + +div.highlight .-Color[class*=-C78] { + color: #5FD787 +} + +div.highlight .-Color[class*=-BGC78] { + background-color: #5FD787 +} + +div.highlight .-Color[class*=-C79] { + color: #5FD7AF +} + +div.highlight .-Color[class*=-BGC79] { + background-color: #5FD7AF +} + +div.highlight .-Color[class*=-C80] { + color: #5FD7D7 +} + +div.highlight .-Color[class*=-BGC80] { + background-color: #5FD7D7 +} + +div.highlight .-Color[class*=-C81] { + color: #5FD7FF +} + +div.highlight .-Color[class*=-BGC81] { + background-color: #5FD7FF +} + +div.highlight .-Color[class*=-C82] { + color: #5FFF00 +} + +div.highlight .-Color[class*=-BGC82] { + background-color: #5FFF00 +} + +div.highlight .-Color[class*=-C83] { + color: #5FFF5F +} + +div.highlight .-Color[class*=-BGC83] { + background-color: #5FFF5F +} + +div.highlight .-Color[class*=-C84] { + color: #5FFF87 +} + +div.highlight .-Color[class*=-BGC84] { + background-color: #5FFF87 +} + +div.highlight .-Color[class*=-C85] { + color: #5FFFAF +} + +div.highlight .-Color[class*=-BGC85] { + background-color: #5FFFAF +} + +div.highlight .-Color[class*=-C86] { + color: #5FFFD7 +} + +div.highlight .-Color[class*=-BGC86] { + background-color: #5FFFD7 +} + +div.highlight .-Color[class*=-C87] { + color: #5FFFFF +} + +div.highlight .-Color[class*=-BGC87] { + background-color: #5FFFFF +} + +div.highlight .-Color[class*=-C88] { + color: #870000 +} + +div.highlight .-Color[class*=-BGC88] { + background-color: #870000 +} + +div.highlight .-Color[class*=-C89] { + color: #87005F +} + +div.highlight .-Color[class*=-BGC89] { + background-color: #87005F +} + +div.highlight .-Color[class*=-C90] { + color: #870087 +} + +div.highlight .-Color[class*=-BGC90] { + background-color: #870087 +} + +div.highlight .-Color[class*=-C91] { + color: #8700AF +} + +div.highlight .-Color[class*=-BGC91] { + background-color: #8700AF +} + +div.highlight .-Color[class*=-C92] { + color: #8700D7 +} + +div.highlight .-Color[class*=-BGC92] { + background-color: #8700D7 +} + +div.highlight .-Color[class*=-C93] { + color: #8700FF +} + +div.highlight .-Color[class*=-BGC93] { + background-color: #8700FF +} + +div.highlight .-Color[class*=-C94] { + color: #875F00 +} + +div.highlight .-Color[class*=-BGC94] { + background-color: #875F00 +} + +div.highlight .-Color[class*=-C95] { + color: #875F5F +} + +div.highlight .-Color[class*=-BGC95] { + background-color: #875F5F +} + +div.highlight .-Color[class*=-C96] { + color: #875F87 +} + +div.highlight .-Color[class*=-BGC96] { + background-color: #875F87 +} + +div.highlight .-Color[class*=-C97] { + color: #875FAF +} + +div.highlight .-Color[class*=-BGC97] { + background-color: #875FAF +} + +div.highlight .-Color[class*=-C98] { + color: #875FD7 +} + +div.highlight .-Color[class*=-BGC98] { + background-color: #875FD7 +} + +div.highlight .-Color[class*=-C99] { + color: #875FFF +} + +div.highlight .-Color[class*=-BGC99] { + background-color: #875FFF +} + +div.highlight .-Color[class*=-C100] { + color: #878700 +} + +div.highlight .-Color[class*=-BGC100] { + background-color: #878700 +} + +div.highlight .-Color[class*=-C101] { + color: #87875F +} + +div.highlight .-Color[class*=-BGC101] { + background-color: #87875F +} + +div.highlight .-Color[class*=-C102] { + color: #878787 +} + +div.highlight .-Color[class*=-BGC102] { + background-color: #878787 +} + +div.highlight .-Color[class*=-C103] { + color: #8787AF +} + +div.highlight .-Color[class*=-BGC103] { + background-color: #8787AF +} + +div.highlight .-Color[class*=-C104] { + color: #8787D7 +} + +div.highlight .-Color[class*=-BGC104] { + background-color: #8787D7 +} + +div.highlight .-Color[class*=-C105] { + color: #8787FF +} + +div.highlight .-Color[class*=-BGC105] { + background-color: #8787FF +} + +div.highlight .-Color[class*=-C106] { + color: #87AF00 +} + +div.highlight .-Color[class*=-BGC106] { + background-color: #87AF00 +} + +div.highlight .-Color[class*=-C107] { + color: #87AF5F +} + +div.highlight .-Color[class*=-BGC107] { + background-color: #87AF5F +} + +div.highlight .-Color[class*=-C108] { + color: #87AF87 +} + +div.highlight .-Color[class*=-BGC108] { + background-color: #87AF87 +} + +div.highlight .-Color[class*=-C109] { + color: #87AFAF +} + +div.highlight .-Color[class*=-BGC109] { + background-color: #87AFAF +} + +div.highlight .-Color[class*=-C110] { + color: #87AFD7 +} + +div.highlight .-Color[class*=-BGC110] { + background-color: #87AFD7 +} + +div.highlight .-Color[class*=-C111] { + color: #87AFFF +} + +div.highlight .-Color[class*=-BGC111] { + background-color: #87AFFF +} + +div.highlight .-Color[class*=-C112] { + color: #87D700 +} + +div.highlight .-Color[class*=-BGC112] { + background-color: #87D700 +} + +div.highlight .-Color[class*=-C113] { + color: #87D75F +} + +div.highlight .-Color[class*=-BGC113] { + background-color: #87D75F +} + +div.highlight .-Color[class*=-C114] { + color: #87D787 +} + +div.highlight .-Color[class*=-BGC114] { + background-color: #87D787 +} + +div.highlight .-Color[class*=-C115] { + color: #87D7AF +} + +div.highlight .-Color[class*=-BGC115] { + background-color: #87D7AF +} + +div.highlight .-Color[class*=-C116] { + color: #87D7D7 +} + +div.highlight .-Color[class*=-BGC116] { + background-color: #87D7D7 +} + +div.highlight .-Color[class*=-C117] { + color: #87D7FF +} + +div.highlight .-Color[class*=-BGC117] { + background-color: #87D7FF +} + +div.highlight .-Color[class*=-C118] { + color: #87FF00 +} + +div.highlight .-Color[class*=-BGC118] { + background-color: #87FF00 +} + +div.highlight .-Color[class*=-C119] { + color: #87FF5F +} + +div.highlight .-Color[class*=-BGC119] { + background-color: #87FF5F +} + +div.highlight .-Color[class*=-C120] { + color: #87FF87 +} + +div.highlight .-Color[class*=-BGC120] { + background-color: #87FF87 +} + +div.highlight .-Color[class*=-C121] { + color: #87FFAF +} + +div.highlight .-Color[class*=-BGC121] { + background-color: #87FFAF +} + +div.highlight .-Color[class*=-C122] { + color: #87FFD7 +} + +div.highlight .-Color[class*=-BGC122] { + background-color: #87FFD7 +} + +div.highlight .-Color[class*=-C123] { + color: #87FFFF +} + +div.highlight .-Color[class*=-BGC123] { + background-color: #87FFFF +} + +div.highlight .-Color[class*=-C124] { + color: #AF0000 +} + +div.highlight .-Color[class*=-BGC124] { + background-color: #AF0000 +} + +div.highlight .-Color[class*=-C125] { + color: #AF005F +} + +div.highlight .-Color[class*=-BGC125] { + background-color: #AF005F +} + +div.highlight .-Color[class*=-C126] { + color: #AF0087 +} + +div.highlight .-Color[class*=-BGC126] { + background-color: #AF0087 +} + +div.highlight .-Color[class*=-C127] { + color: #AF00AF +} + +div.highlight .-Color[class*=-BGC127] { + background-color: #AF00AF +} + +div.highlight .-Color[class*=-C128] { + color: #AF00D7 +} + +div.highlight .-Color[class*=-BGC128] { + background-color: #AF00D7 +} + +div.highlight .-Color[class*=-C129] { + color: #AF00FF +} + +div.highlight .-Color[class*=-BGC129] { + background-color: #AF00FF +} + +div.highlight .-Color[class*=-C130] { + color: #AF5F00 +} + +div.highlight .-Color[class*=-BGC130] { + background-color: #AF5F00 +} + +div.highlight .-Color[class*=-C131] { + color: #AF5F5F +} + +div.highlight .-Color[class*=-BGC131] { + background-color: #AF5F5F +} + +div.highlight .-Color[class*=-C132] { + color: #AF5F87 +} + +div.highlight .-Color[class*=-BGC132] { + background-color: #AF5F87 +} + +div.highlight .-Color[class*=-C133] { + color: #AF5FAF +} + +div.highlight .-Color[class*=-BGC133] { + background-color: #AF5FAF +} + +div.highlight .-Color[class*=-C134] { + color: #AF5FD7 +} + +div.highlight .-Color[class*=-BGC134] { + background-color: #AF5FD7 +} + +div.highlight .-Color[class*=-C135] { + color: #AF5FFF +} + +div.highlight .-Color[class*=-BGC135] { + background-color: #AF5FFF +} + +div.highlight .-Color[class*=-C136] { + color: #AF8700 +} + +div.highlight .-Color[class*=-BGC136] { + background-color: #AF8700 +} + +div.highlight .-Color[class*=-C137] { + color: #AF875F +} + +div.highlight .-Color[class*=-BGC137] { + background-color: #AF875F +} + +div.highlight .-Color[class*=-C138] { + color: #AF8787 +} + +div.highlight .-Color[class*=-BGC138] { + background-color: #AF8787 +} + +div.highlight .-Color[class*=-C139] { + color: #AF87AF +} + +div.highlight .-Color[class*=-BGC139] { + background-color: #AF87AF +} + +div.highlight .-Color[class*=-C140] { + color: #AF87D7 +} + +div.highlight .-Color[class*=-BGC140] { + background-color: #AF87D7 +} + +div.highlight .-Color[class*=-C141] { + color: #AF87FF +} + +div.highlight .-Color[class*=-BGC141] { + background-color: #AF87FF +} + +div.highlight .-Color[class*=-C142] { + color: #AFAF00 +} + +div.highlight .-Color[class*=-BGC142] { + background-color: #AFAF00 +} + +div.highlight .-Color[class*=-C143] { + color: #AFAF5F +} + +div.highlight .-Color[class*=-BGC143] { + background-color: #AFAF5F +} + +div.highlight .-Color[class*=-C144] { + color: #AFAF87 +} + +div.highlight .-Color[class*=-BGC144] { + background-color: #AFAF87 +} + +div.highlight .-Color[class*=-C145] { + color: #AFAFAF +} + +div.highlight .-Color[class*=-BGC145] { + background-color: #AFAFAF +} + +div.highlight .-Color[class*=-C146] { + color: #AFAFD7 +} + +div.highlight .-Color[class*=-BGC146] { + background-color: #AFAFD7 +} + +div.highlight .-Color[class*=-C147] { + color: #AFAFFF +} + +div.highlight .-Color[class*=-BGC147] { + background-color: #AFAFFF +} + +div.highlight .-Color[class*=-C148] { + color: #AFD700 +} + +div.highlight .-Color[class*=-BGC148] { + background-color: #AFD700 +} + +div.highlight .-Color[class*=-C149] { + color: #AFD75F +} + +div.highlight .-Color[class*=-BGC149] { + background-color: #AFD75F +} + +div.highlight .-Color[class*=-C150] { + color: #AFD787 +} + +div.highlight .-Color[class*=-BGC150] { + background-color: #AFD787 +} + +div.highlight .-Color[class*=-C151] { + color: #AFD7AF +} + +div.highlight .-Color[class*=-BGC151] { + background-color: #AFD7AF +} + +div.highlight .-Color[class*=-C152] { + color: #AFD7D7 +} + +div.highlight .-Color[class*=-BGC152] { + background-color: #AFD7D7 +} + +div.highlight .-Color[class*=-C153] { + color: #AFD7FF +} + +div.highlight .-Color[class*=-BGC153] { + background-color: #AFD7FF +} + +div.highlight .-Color[class*=-C154] { + color: #AFFF00 +} + +div.highlight .-Color[class*=-BGC154] { + background-color: #AFFF00 +} + +div.highlight .-Color[class*=-C155] { + color: #AFFF5F +} + +div.highlight .-Color[class*=-BGC155] { + background-color: #AFFF5F +} + +div.highlight .-Color[class*=-C156] { + color: #AFFF87 +} + +div.highlight .-Color[class*=-BGC156] { + background-color: #AFFF87 +} + +div.highlight .-Color[class*=-C157] { + color: #AFFFAF +} + +div.highlight .-Color[class*=-BGC157] { + background-color: #AFFFAF +} + +div.highlight .-Color[class*=-C158] { + color: #AFFFD7 +} + +div.highlight .-Color[class*=-BGC158] { + background-color: #AFFFD7 +} + +div.highlight .-Color[class*=-C159] { + color: #AFFFFF +} + +div.highlight .-Color[class*=-BGC159] { + background-color: #AFFFFF +} + +div.highlight .-Color[class*=-C160] { + color: #D70000 +} + +div.highlight .-Color[class*=-BGC160] { + background-color: #D70000 +} + +div.highlight .-Color[class*=-C161] { + color: #D7005F +} + +div.highlight .-Color[class*=-BGC161] { + background-color: #D7005F +} + +div.highlight .-Color[class*=-C162] { + color: #D70087 +} + +div.highlight .-Color[class*=-BGC162] { + background-color: #D70087 +} + +div.highlight .-Color[class*=-C163] { + color: #D700AF +} + +div.highlight .-Color[class*=-BGC163] { + background-color: #D700AF +} + +div.highlight .-Color[class*=-C164] { + color: #D700D7 +} + +div.highlight .-Color[class*=-BGC164] { + background-color: #D700D7 +} + +div.highlight .-Color[class*=-C165] { + color: #D700FF +} + +div.highlight .-Color[class*=-BGC165] { + background-color: #D700FF +} + +div.highlight .-Color[class*=-C166] { + color: #D75F00 +} + +div.highlight .-Color[class*=-BGC166] { + background-color: #D75F00 +} + +div.highlight .-Color[class*=-C167] { + color: #D75F5F +} + +div.highlight .-Color[class*=-BGC167] { + background-color: #D75F5F +} + +div.highlight .-Color[class*=-C168] { + color: #D75F87 +} + +div.highlight .-Color[class*=-BGC168] { + background-color: #D75F87 +} + +div.highlight .-Color[class*=-C169] { + color: #D75FAF +} + +div.highlight .-Color[class*=-BGC169] { + background-color: #D75FAF +} + +div.highlight .-Color[class*=-C170] { + color: #D75FD7 +} + +div.highlight .-Color[class*=-BGC170] { + background-color: #D75FD7 +} + +div.highlight .-Color[class*=-C171] { + color: #D75FFF +} + +div.highlight .-Color[class*=-BGC171] { + background-color: #D75FFF +} + +div.highlight .-Color[class*=-C172] { + color: #D78700 +} + +div.highlight .-Color[class*=-BGC172] { + background-color: #D78700 +} + +div.highlight .-Color[class*=-C173] { + color: #D7875F +} + +div.highlight .-Color[class*=-BGC173] { + background-color: #D7875F +} + +div.highlight .-Color[class*=-C174] { + color: #D78787 +} + +div.highlight .-Color[class*=-BGC174] { + background-color: #D78787 +} + +div.highlight .-Color[class*=-C175] { + color: #D787AF +} + +div.highlight .-Color[class*=-BGC175] { + background-color: #D787AF +} + +div.highlight .-Color[class*=-C176] { + color: #D787D7 +} + +div.highlight .-Color[class*=-BGC176] { + background-color: #D787D7 +} + +div.highlight .-Color[class*=-C177] { + color: #D787FF +} + +div.highlight .-Color[class*=-BGC177] { + background-color: #D787FF +} + +div.highlight .-Color[class*=-C178] { + color: #D7AF00 +} + +div.highlight .-Color[class*=-BGC178] { + background-color: #D7AF00 +} + +div.highlight .-Color[class*=-C179] { + color: #D7AF5F +} + +div.highlight .-Color[class*=-BGC179] { + background-color: #D7AF5F +} + +div.highlight .-Color[class*=-C180] { + color: #D7AF87 +} + +div.highlight .-Color[class*=-BGC180] { + background-color: #D7AF87 +} + +div.highlight .-Color[class*=-C181] { + color: #D7AFAF +} + +div.highlight .-Color[class*=-BGC181] { + background-color: #D7AFAF +} + +div.highlight .-Color[class*=-C182] { + color: #D7AFD7 +} + +div.highlight .-Color[class*=-BGC182] { + background-color: #D7AFD7 +} + +div.highlight .-Color[class*=-C183] { + color: #D7AFFF +} + +div.highlight .-Color[class*=-BGC183] { + background-color: #D7AFFF +} + +div.highlight .-Color[class*=-C184] { + color: #D7D700 +} + +div.highlight .-Color[class*=-BGC184] { + background-color: #D7D700 +} + +div.highlight .-Color[class*=-C185] { + color: #D7D75F +} + +div.highlight .-Color[class*=-BGC185] { + background-color: #D7D75F +} + +div.highlight .-Color[class*=-C186] { + color: #D7D787 +} + +div.highlight .-Color[class*=-BGC186] { + background-color: #D7D787 +} + +div.highlight .-Color[class*=-C187] { + color: #D7D7AF +} + +div.highlight .-Color[class*=-BGC187] { + background-color: #D7D7AF +} + +div.highlight .-Color[class*=-C188] { + color: #D7D7D7 +} + +div.highlight .-Color[class*=-BGC188] { + background-color: #D7D7D7 +} + +div.highlight .-Color[class*=-C189] { + color: #D7D7FF +} + +div.highlight .-Color[class*=-BGC189] { + background-color: #D7D7FF +} + +div.highlight .-Color[class*=-C190] { + color: #D7FF00 +} + +div.highlight .-Color[class*=-BGC190] { + background-color: #D7FF00 +} + +div.highlight .-Color[class*=-C191] { + color: #D7FF5F +} + +div.highlight .-Color[class*=-BGC191] { + background-color: #D7FF5F +} + +div.highlight .-Color[class*=-C192] { + color: #D7FF87 +} + +div.highlight .-Color[class*=-BGC192] { + background-color: #D7FF87 +} + +div.highlight .-Color[class*=-C193] { + color: #D7FFAF +} + +div.highlight .-Color[class*=-BGC193] { + background-color: #D7FFAF +} + +div.highlight .-Color[class*=-C194] { + color: #D7FFD7 +} + +div.highlight .-Color[class*=-BGC194] { + background-color: #D7FFD7 +} + +div.highlight .-Color[class*=-C195] { + color: #D7FFFF +} + +div.highlight .-Color[class*=-BGC195] { + background-color: #D7FFFF +} + +div.highlight .-Color[class*=-C196] { + color: #FF0000 +} + +div.highlight .-Color[class*=-BGC196] { + background-color: #FF0000 +} + +div.highlight .-Color[class*=-C197] { + color: #FF005F +} + +div.highlight .-Color[class*=-BGC197] { + background-color: #FF005F +} + +div.highlight .-Color[class*=-C198] { + color: #FF0087 +} + +div.highlight .-Color[class*=-BGC198] { + background-color: #FF0087 +} + +div.highlight .-Color[class*=-C199] { + color: #FF00AF +} + +div.highlight .-Color[class*=-BGC199] { + background-color: #FF00AF +} + +div.highlight .-Color[class*=-C200] { + color: #FF00D7 +} + +div.highlight .-Color[class*=-BGC200] { + background-color: #FF00D7 +} + +div.highlight .-Color[class*=-C201] { + color: #FF00FF +} + +div.highlight .-Color[class*=-BGC201] { + background-color: #FF00FF +} + +div.highlight .-Color[class*=-C202] { + color: #FF5F00 +} + +div.highlight .-Color[class*=-BGC202] { + background-color: #FF5F00 +} + +div.highlight .-Color[class*=-C203] { + color: #FF5F5F +} + +div.highlight .-Color[class*=-BGC203] { + background-color: #FF5F5F +} + +div.highlight .-Color[class*=-C204] { + color: #FF5F87 +} + +div.highlight .-Color[class*=-BGC204] { + background-color: #FF5F87 +} + +div.highlight .-Color[class*=-C205] { + color: #FF5FAF +} + +div.highlight .-Color[class*=-BGC205] { + background-color: #FF5FAF +} + +div.highlight .-Color[class*=-C206] { + color: #FF5FD7 +} + +div.highlight .-Color[class*=-BGC206] { + background-color: #FF5FD7 +} + +div.highlight .-Color[class*=-C207] { + color: #FF5FFF +} + +div.highlight .-Color[class*=-BGC207] { + background-color: #FF5FFF +} + +div.highlight .-Color[class*=-C208] { + color: #FF8700 +} + +div.highlight .-Color[class*=-BGC208] { + background-color: #FF8700 +} + +div.highlight .-Color[class*=-C209] { + color: #FF875F +} + +div.highlight .-Color[class*=-BGC209] { + background-color: #FF875F +} + +div.highlight .-Color[class*=-C210] { + color: #FF8787 +} + +div.highlight .-Color[class*=-BGC210] { + background-color: #FF8787 +} + +div.highlight .-Color[class*=-C211] { + color: #FF87AF +} + +div.highlight .-Color[class*=-BGC211] { + background-color: #FF87AF +} + +div.highlight .-Color[class*=-C212] { + color: #FF87D7 +} + +div.highlight .-Color[class*=-BGC212] { + background-color: #FF87D7 +} + +div.highlight .-Color[class*=-C213] { + color: #FF87FF +} + +div.highlight .-Color[class*=-BGC213] { + background-color: #FF87FF +} + +div.highlight .-Color[class*=-C214] { + color: #FFAF00 +} + +div.highlight .-Color[class*=-BGC214] { + background-color: #FFAF00 +} + +div.highlight .-Color[class*=-C215] { + color: #FFAF5F +} + +div.highlight .-Color[class*=-BGC215] { + background-color: #FFAF5F +} + +div.highlight .-Color[class*=-C216] { + color: #FFAF87 +} + +div.highlight .-Color[class*=-BGC216] { + background-color: #FFAF87 +} + +div.highlight .-Color[class*=-C217] { + color: #FFAFAF +} + +div.highlight .-Color[class*=-BGC217] { + background-color: #FFAFAF +} + +div.highlight .-Color[class*=-C218] { + color: #FFAFD7 +} + +div.highlight .-Color[class*=-BGC218] { + background-color: #FFAFD7 +} + +div.highlight .-Color[class*=-C219] { + color: #FFAFFF +} + +div.highlight .-Color[class*=-BGC219] { + background-color: #FFAFFF +} + +div.highlight .-Color[class*=-C220] { + color: #FFD700 +} + +div.highlight .-Color[class*=-BGC220] { + background-color: #FFD700 +} + +div.highlight .-Color[class*=-C221] { + color: #FFD75F +} + +div.highlight .-Color[class*=-BGC221] { + background-color: #FFD75F +} + +div.highlight .-Color[class*=-C222] { + color: #FFD787 +} + +div.highlight .-Color[class*=-BGC222] { + background-color: #FFD787 +} + +div.highlight .-Color[class*=-C223] { + color: #FFD7AF +} + +div.highlight .-Color[class*=-BGC223] { + background-color: #FFD7AF +} + +div.highlight .-Color[class*=-C224] { + color: #FFD7D7 +} + +div.highlight .-Color[class*=-BGC224] { + background-color: #FFD7D7 +} + +div.highlight .-Color[class*=-C225] { + color: #FFD7FF +} + +div.highlight .-Color[class*=-BGC225] { + background-color: #FFD7FF +} + +div.highlight .-Color[class*=-C226] { + color: #FFFF00 +} + +div.highlight .-Color[class*=-BGC226] { + background-color: #FFFF00 +} + +div.highlight .-Color[class*=-C227] { + color: #FFFF5F +} + +div.highlight .-Color[class*=-BGC227] { + background-color: #FFFF5F +} + +div.highlight .-Color[class*=-C228] { + color: #FFFF87 +} + +div.highlight .-Color[class*=-BGC228] { + background-color: #FFFF87 +} + +div.highlight .-Color[class*=-C229] { + color: #FFFFAF +} + +div.highlight .-Color[class*=-BGC229] { + background-color: #FFFFAF +} + +div.highlight .-Color[class*=-C230] { + color: #FFFFD7 +} + +div.highlight .-Color[class*=-BGC230] { + background-color: #FFFFD7 +} + +div.highlight .-Color[class*=-C231] { + color: #FFFFFF +} + +div.highlight .-Color[class*=-BGC231] { + background-color: #FFFFFF +} + +div.highlight .-Color[class*=-C232] { + color: #080808 +} + +div.highlight .-Color[class*=-BGC232] { + background-color: #080808 +} + +div.highlight .-Color[class*=-C233] { + color: #121212 +} + +div.highlight .-Color[class*=-BGC233] { + background-color: #121212 +} + +div.highlight .-Color[class*=-C234] { + color: #1C1C1C +} + +div.highlight .-Color[class*=-BGC234] { + background-color: #1C1C1C +} + +div.highlight .-Color[class*=-C235] { + color: #262626 +} + +div.highlight .-Color[class*=-BGC235] { + background-color: #262626 +} + +div.highlight .-Color[class*=-C236] { + color: #303030 +} + +div.highlight .-Color[class*=-BGC236] { + background-color: #303030 +} + +div.highlight .-Color[class*=-C237] { + color: #3A3A3A +} + +div.highlight .-Color[class*=-BGC237] { + background-color: #3A3A3A +} + +div.highlight .-Color[class*=-C238] { + color: #444444 +} + +div.highlight .-Color[class*=-BGC238] { + background-color: #444444 +} + +div.highlight .-Color[class*=-C239] { + color: #4E4E4E +} + +div.highlight .-Color[class*=-BGC239] { + background-color: #4E4E4E +} + +div.highlight .-Color[class*=-C240] { + color: #585858 +} + +div.highlight .-Color[class*=-BGC240] { + background-color: #585858 +} + +div.highlight .-Color[class*=-C241] { + color: #626262 +} + +div.highlight .-Color[class*=-BGC241] { + background-color: #626262 +} + +div.highlight .-Color[class*=-C242] { + color: #6C6C6C +} + +div.highlight .-Color[class*=-BGC242] { + background-color: #6C6C6C +} + +div.highlight .-Color[class*=-C243] { + color: #767676 +} + +div.highlight .-Color[class*=-BGC243] { + background-color: #767676 +} + +div.highlight .-Color[class*=-C244] { + color: #808080 +} + +div.highlight .-Color[class*=-BGC244] { + background-color: #808080 +} + +div.highlight .-Color[class*=-C245] { + color: #8A8A8A +} + +div.highlight .-Color[class*=-BGC245] { + background-color: #8A8A8A +} + +div.highlight .-Color[class*=-C246] { + color: #949494 +} + +div.highlight .-Color[class*=-BGC246] { + background-color: #949494 +} + +div.highlight .-Color[class*=-C247] { + color: #9E9E9E +} + +div.highlight .-Color[class*=-BGC247] { + background-color: #9E9E9E +} + +div.highlight .-Color[class*=-C248] { + color: #A8A8A8 +} + +div.highlight .-Color[class*=-BGC248] { + background-color: #A8A8A8 +} + +div.highlight .-Color[class*=-C249] { + color: #B2B2B2 +} + +div.highlight .-Color[class*=-BGC249] { + background-color: #B2B2B2 +} + +div.highlight .-Color[class*=-C250] { + color: #BCBCBC +} + +div.highlight .-Color[class*=-BGC250] { + background-color: #BCBCBC +} + +div.highlight .-Color[class*=-C251] { + color: #C6C6C6 +} + +div.highlight .-Color[class*=-BGC251] { + background-color: #C6C6C6 +} + +div.highlight .-Color[class*=-C252] { + color: #D0D0D0 +} + +div.highlight .-Color[class*=-BGC252] { + background-color: #D0D0D0 +} + +div.highlight .-Color[class*=-C253] { + color: #DADADA +} + +div.highlight .-Color[class*=-BGC253] { + background-color: #DADADA +} + +div.highlight .-Color[class*=-C254] { + color: #E4E4E4 +} + +div.highlight .-Color[class*=-BGC254] { + background-color: #E4E4E4 +} + +div.highlight .-Color[class*=-C255] { + color: #EEEEEE +} + +div.highlight .-Color[class*=-BGC255] { + background-color: #EEEEEE +} diff --git a/branch/main/_static/plus.png b/branch/main/_static/plus.png new file mode 100644 index 0000000..7107cec Binary files /dev/null and b/branch/main/_static/plus.png differ diff --git a/branch/main/_static/pygments.css b/branch/main/_static/pygments.css new file mode 100644 index 0000000..84ab303 --- /dev/null +++ b/branch/main/_static/pygments.css @@ -0,0 +1,75 @@ +pre { line-height: 125%; } +td.linenos .normal { color: inherit; background-color: transparent; padding-left: 5px; padding-right: 5px; } +span.linenos { color: inherit; background-color: transparent; padding-left: 5px; padding-right: 5px; } +td.linenos .special { color: #000000; background-color: #ffffc0; padding-left: 5px; padding-right: 5px; } +span.linenos.special { color: #000000; background-color: #ffffc0; padding-left: 5px; padding-right: 5px; } +.highlight .hll { background-color: #ffffcc } 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#19177C } /* Literal.String.Symbol */ +.highlight .bp { color: #008000 } /* Name.Builtin.Pseudo */ +.highlight .fm { color: #0000FF } /* Name.Function.Magic */ +.highlight .vc { color: #19177C } /* Name.Variable.Class */ +.highlight .vg { color: #19177C } /* Name.Variable.Global */ +.highlight .vi { color: #19177C } /* Name.Variable.Instance */ +.highlight .vm { color: #19177C } /* Name.Variable.Magic */ +.highlight .il { color: #666666 } /* Literal.Number.Integer.Long */ \ No newline at end of file diff --git a/branch/main/_static/searchtools.js b/branch/main/_static/searchtools.js new file mode 100644 index 0000000..b08d58c --- /dev/null +++ b/branch/main/_static/searchtools.js @@ -0,0 +1,620 @@ +/* + * searchtools.js + * ~~~~~~~~~~~~~~~~ + * + * Sphinx JavaScript utilities for the full-text search. + * + * :copyright: Copyright 2007-2024 by the Sphinx team, see AUTHORS. + * :license: BSD, see LICENSE for details. + * + */ +"use strict"; + +/** + * Simple result scoring code. + */ +if (typeof Scorer === "undefined") { + var Scorer = { + // Implement the following function to further tweak the score for each result + // The function takes a result array [docname, title, anchor, descr, score, filename] + // and returns the new score. + /* + score: result => { + const [docname, title, anchor, descr, score, filename] = result + return score + }, + */ + + // query matches the full name of an object + objNameMatch: 11, + // or matches in the last dotted part of the object name + objPartialMatch: 6, + // Additive scores depending on the priority of the object + objPrio: { + 0: 15, // used to be importantResults + 1: 5, // used to be objectResults + 2: -5, // used to be unimportantResults + }, + // Used when the priority is not in the mapping. + objPrioDefault: 0, + + // query found in title + title: 15, + partialTitle: 7, + // query found in terms + term: 5, + partialTerm: 2, + }; +} + +const _removeChildren = (element) => { + while (element && element.lastChild) element.removeChild(element.lastChild); +}; + +/** + * See https://developer.mozilla.org/en-US/docs/Web/JavaScript/Guide/Regular_Expressions#escaping + */ +const _escapeRegExp = (string) => + string.replace(/[.*+\-?^${}()|[\]\\]/g, "\\$&"); // $& means the whole matched string + +const _displayItem = (item, searchTerms, highlightTerms) => { + const docBuilder = DOCUMENTATION_OPTIONS.BUILDER; + const docFileSuffix = DOCUMENTATION_OPTIONS.FILE_SUFFIX; + const docLinkSuffix = DOCUMENTATION_OPTIONS.LINK_SUFFIX; + const showSearchSummary = DOCUMENTATION_OPTIONS.SHOW_SEARCH_SUMMARY; + const contentRoot = document.documentElement.dataset.content_root; + + const [docName, title, anchor, descr, score, _filename] = item; + + let listItem = document.createElement("li"); + let requestUrl; + let linkUrl; + if (docBuilder === "dirhtml") { + // dirhtml builder + let dirname = docName + "/"; + if (dirname.match(/\/index\/$/)) + dirname = dirname.substring(0, dirname.length - 6); + else if (dirname === "index/") dirname = ""; + requestUrl = contentRoot + dirname; + linkUrl = requestUrl; + } else { + // normal html builders + requestUrl = contentRoot + docName + docFileSuffix; + linkUrl = docName + docLinkSuffix; + } + let linkEl = listItem.appendChild(document.createElement("a")); + linkEl.href = linkUrl + anchor; + linkEl.dataset.score = score; + linkEl.innerHTML = title; + if (descr) { + listItem.appendChild(document.createElement("span")).innerHTML = + " (" + descr + ")"; + // highlight search terms in the description + if (SPHINX_HIGHLIGHT_ENABLED) // set in sphinx_highlight.js + highlightTerms.forEach((term) => _highlightText(listItem, term, "highlighted")); + } + else if (showSearchSummary) + fetch(requestUrl) + .then((responseData) => responseData.text()) + .then((data) => { + if (data) + listItem.appendChild( + Search.makeSearchSummary(data, searchTerms, anchor) + ); + // highlight search terms in the summary + if (SPHINX_HIGHLIGHT_ENABLED) // set in sphinx_highlight.js + highlightTerms.forEach((term) => _highlightText(listItem, term, "highlighted")); + }); + Search.output.appendChild(listItem); +}; +const _finishSearch = (resultCount) => { + Search.stopPulse(); + Search.title.innerText = _("Search Results"); + if (!resultCount) + Search.status.innerText = Documentation.gettext( + "Your search did not match any documents. Please make sure that all words are spelled correctly and that you've selected enough categories." + ); + else + Search.status.innerText = _( + "Search finished, found ${resultCount} page(s) matching the search query." + ).replace('${resultCount}', resultCount); +}; +const _displayNextItem = ( + results, + resultCount, + searchTerms, + highlightTerms, +) => { + // results left, load the summary and display it + // this is intended to be dynamic (don't sub resultsCount) + if (results.length) { + _displayItem(results.pop(), searchTerms, highlightTerms); + setTimeout( + () => _displayNextItem(results, resultCount, searchTerms, highlightTerms), + 5 + ); + } + // search finished, update title and status message + else _finishSearch(resultCount); +}; +// Helper function used by query() to order search results. +// Each input is an array of [docname, title, anchor, descr, score, filename]. +// Order the results by score (in opposite order of appearance, since the +// `_displayNextItem` function uses pop() to retrieve items) and then alphabetically. +const _orderResultsByScoreThenName = (a, b) => { + const leftScore = a[4]; + const rightScore = b[4]; + if (leftScore === rightScore) { + // same score: sort alphabetically + const leftTitle = a[1].toLowerCase(); + const rightTitle = b[1].toLowerCase(); + if (leftTitle === rightTitle) return 0; + return leftTitle > rightTitle ? -1 : 1; // inverted is intentional + } + return leftScore > rightScore ? 1 : -1; +}; + +/** + * Default splitQuery function. Can be overridden in ``sphinx.search`` with a + * custom function per language. + * + * The regular expression works by splitting the string on consecutive characters + * that are not Unicode letters, numbers, underscores, or emoji characters. + * This is the same as ``\W+`` in Python, preserving the surrogate pair area. + */ +if (typeof splitQuery === "undefined") { + var splitQuery = (query) => query + .split(/[^\p{Letter}\p{Number}_\p{Emoji_Presentation}]+/gu) + .filter(term => term) // remove remaining empty strings +} + +/** + * Search Module + */ +const Search = { + _index: null, + _queued_query: null, + _pulse_status: -1, + + htmlToText: (htmlString, anchor) => { + const htmlElement = new DOMParser().parseFromString(htmlString, 'text/html'); + for (const removalQuery of [".headerlink", "script", "style"]) { + htmlElement.querySelectorAll(removalQuery).forEach((el) => { el.remove() }); + } + if (anchor) { + const anchorContent = htmlElement.querySelector(`[role="main"] ${anchor}`); + if (anchorContent) return anchorContent.textContent; + + console.warn( + `Anchored content block not found. Sphinx search tries to obtain it via DOM query '[role=main] ${anchor}'. Check your theme or template.` + ); + } + + // if anchor not specified or not found, fall back to main content + const docContent = htmlElement.querySelector('[role="main"]'); + if (docContent) return docContent.textContent; + + console.warn( + "Content block not found. Sphinx search tries to obtain it via DOM query '[role=main]'. Check your theme or template." + ); + return ""; + }, + + init: () => { + const query = new URLSearchParams(window.location.search).get("q"); + document + .querySelectorAll('input[name="q"]') + .forEach((el) => (el.value = query)); + if (query) Search.performSearch(query); + }, + + loadIndex: (url) => + (document.body.appendChild(document.createElement("script")).src = url), + + setIndex: (index) => { + Search._index = index; + if (Search._queued_query !== null) { + const query = Search._queued_query; + Search._queued_query = null; + Search.query(query); + } + }, + + hasIndex: () => Search._index !== null, + + deferQuery: (query) => (Search._queued_query = query), + + stopPulse: () => (Search._pulse_status = -1), + + startPulse: () => { + if (Search._pulse_status >= 0) return; + + const pulse = () => { + Search._pulse_status = (Search._pulse_status + 1) % 4; + Search.dots.innerText = ".".repeat(Search._pulse_status); + if (Search._pulse_status >= 0) window.setTimeout(pulse, 500); + }; + pulse(); + }, + + /** + * perform a search for something (or wait until index is loaded) + */ + performSearch: (query) => { + // create the required interface elements + const searchText = document.createElement("h2"); + searchText.textContent = _("Searching"); + const searchSummary = document.createElement("p"); + searchSummary.classList.add("search-summary"); + searchSummary.innerText = ""; + const searchList = document.createElement("ul"); + searchList.classList.add("search"); + + const out = document.getElementById("search-results"); + Search.title = out.appendChild(searchText); + Search.dots = Search.title.appendChild(document.createElement("span")); + Search.status = out.appendChild(searchSummary); + Search.output = out.appendChild(searchList); + + const searchProgress = document.getElementById("search-progress"); + // Some themes don't use the search progress node + if (searchProgress) { + searchProgress.innerText = _("Preparing search..."); + } + Search.startPulse(); + + // index already loaded, the browser was quick! + if (Search.hasIndex()) Search.query(query); + else Search.deferQuery(query); + }, + + _parseQuery: (query) => { + // stem the search terms and add them to the correct list + const stemmer = new Stemmer(); + const searchTerms = new Set(); + const excludedTerms = new Set(); + const highlightTerms = new Set(); + const objectTerms = new Set(splitQuery(query.toLowerCase().trim())); + splitQuery(query.trim()).forEach((queryTerm) => { + const queryTermLower = queryTerm.toLowerCase(); + + // maybe skip this "word" + // stopwords array is from language_data.js + if ( + stopwords.indexOf(queryTermLower) !== -1 || + queryTerm.match(/^\d+$/) + ) + return; + + // stem the word + let word = stemmer.stemWord(queryTermLower); + // select the correct list + if (word[0] === "-") excludedTerms.add(word.substr(1)); + else { + searchTerms.add(word); + highlightTerms.add(queryTermLower); + } + }); + + if (SPHINX_HIGHLIGHT_ENABLED) { // set in sphinx_highlight.js + localStorage.setItem("sphinx_highlight_terms", [...highlightTerms].join(" ")) + } + + // console.debug("SEARCH: searching for:"); + // console.info("required: ", [...searchTerms]); + // console.info("excluded: ", [...excludedTerms]); + + return [query, searchTerms, excludedTerms, highlightTerms, objectTerms]; + }, + + /** + * execute search (requires search index to be loaded) + */ + _performSearch: (query, searchTerms, excludedTerms, highlightTerms, objectTerms) => { + const filenames = Search._index.filenames; + const docNames = Search._index.docnames; + const titles = Search._index.titles; + const allTitles = Search._index.alltitles; + const indexEntries = Search._index.indexentries; + + // Collect multiple result groups to be sorted separately and then ordered. + // Each is an array of [docname, title, anchor, descr, score, filename]. + const normalResults = []; + const nonMainIndexResults = []; + + _removeChildren(document.getElementById("search-progress")); + + const queryLower = query.toLowerCase().trim(); + for (const [title, foundTitles] of Object.entries(allTitles)) { + if (title.toLowerCase().trim().includes(queryLower) && (queryLower.length >= title.length/2)) { + for (const [file, id] of foundTitles) { + const score = Math.round(Scorer.title * queryLower.length / title.length); + const boost = titles[file] === title ? 1 : 0; // add a boost for document titles + normalResults.push([ + docNames[file], + titles[file] !== title ? `${titles[file]} > ${title}` : title, + id !== null ? "#" + id : "", + null, + score + boost, + filenames[file], + ]); + } + } + } + + // search for explicit entries in index directives + for (const [entry, foundEntries] of Object.entries(indexEntries)) { + if (entry.includes(queryLower) && (queryLower.length >= entry.length/2)) { + for (const [file, id, isMain] of foundEntries) { + const score = Math.round(100 * queryLower.length / entry.length); + const result = [ + docNames[file], + titles[file], + id ? "#" + id : "", + null, + score, + filenames[file], + ]; + if (isMain) { + normalResults.push(result); + } else { + nonMainIndexResults.push(result); + } + } + } + } + + // lookup as object + objectTerms.forEach((term) => + normalResults.push(...Search.performObjectSearch(term, objectTerms)) + ); + + // lookup as search terms in fulltext + normalResults.push(...Search.performTermsSearch(searchTerms, excludedTerms)); + + // let the scorer override scores with a custom scoring function + if (Scorer.score) { + normalResults.forEach((item) => (item[4] = Scorer.score(item))); + nonMainIndexResults.forEach((item) => (item[4] = Scorer.score(item))); + } + + // Sort each group of results by score and then alphabetically by name. + normalResults.sort(_orderResultsByScoreThenName); + nonMainIndexResults.sort(_orderResultsByScoreThenName); + + // Combine the result groups in (reverse) order. + // Non-main index entries are typically arbitrary cross-references, + // so display them after other results. + let results = [...nonMainIndexResults, ...normalResults]; + + // remove duplicate search results + // note the reversing of results, so that in the case of duplicates, the highest-scoring entry is kept + let seen = new Set(); + results = results.reverse().reduce((acc, result) => { + let resultStr = result.slice(0, 4).concat([result[5]]).map(v => String(v)).join(','); + if (!seen.has(resultStr)) { + acc.push(result); + seen.add(resultStr); + } + return acc; + }, []); + + return results.reverse(); + }, + + query: (query) => { + const [searchQuery, searchTerms, excludedTerms, highlightTerms, objectTerms] = Search._parseQuery(query); + const results = Search._performSearch(searchQuery, searchTerms, excludedTerms, highlightTerms, objectTerms); + + // for debugging + //Search.lastresults = results.slice(); // a copy + // console.info("search results:", Search.lastresults); + + // print the results + _displayNextItem(results, results.length, searchTerms, highlightTerms); + }, + + /** + * search for object names + */ + performObjectSearch: (object, objectTerms) => { + const filenames = Search._index.filenames; + const docNames = Search._index.docnames; + const objects = Search._index.objects; + const objNames = Search._index.objnames; + const titles = Search._index.titles; + + const results = []; + + const objectSearchCallback = (prefix, match) => { + const name = match[4] + const fullname = (prefix ? prefix + "." : "") + name; + const fullnameLower = fullname.toLowerCase(); + if (fullnameLower.indexOf(object) < 0) return; + + let score = 0; + const parts = fullnameLower.split("."); + + // check for different match types: exact matches of full name or + // "last name" (i.e. last dotted part) + if (fullnameLower === object || parts.slice(-1)[0] === object) + score += Scorer.objNameMatch; + else if (parts.slice(-1)[0].indexOf(object) > -1) + score += Scorer.objPartialMatch; // matches in last name + + const objName = objNames[match[1]][2]; + const title = titles[match[0]]; + + // If more than one term searched for, we require other words to be + // found in the name/title/description + const otherTerms = new Set(objectTerms); + otherTerms.delete(object); + if (otherTerms.size > 0) { + const haystack = `${prefix} ${name} ${objName} ${title}`.toLowerCase(); + if ( + [...otherTerms].some((otherTerm) => haystack.indexOf(otherTerm) < 0) + ) + return; + } + + let anchor = match[3]; + if (anchor === "") anchor = fullname; + else if (anchor === "-") anchor = objNames[match[1]][1] + "-" + fullname; + + const descr = objName + _(", in ") + title; + + // add custom score for some objects according to scorer + if (Scorer.objPrio.hasOwnProperty(match[2])) + score += Scorer.objPrio[match[2]]; + else score += Scorer.objPrioDefault; + + results.push([ + docNames[match[0]], + fullname, + "#" + anchor, + descr, + score, + filenames[match[0]], + ]); + }; + Object.keys(objects).forEach((prefix) => + objects[prefix].forEach((array) => + objectSearchCallback(prefix, array) + ) + ); + return results; + }, + + /** + * search for full-text terms in the index + */ + performTermsSearch: (searchTerms, excludedTerms) => { + // prepare search + const terms = Search._index.terms; + const titleTerms = Search._index.titleterms; + const filenames = Search._index.filenames; + const docNames = Search._index.docnames; + const titles = Search._index.titles; + + const scoreMap = new Map(); + const fileMap = new Map(); + + // perform the search on the required terms + searchTerms.forEach((word) => { + const files = []; + const arr = [ + { files: terms[word], score: Scorer.term }, + { files: titleTerms[word], score: Scorer.title }, + ]; + // add support for partial matches + if (word.length > 2) { + const escapedWord = _escapeRegExp(word); + if (!terms.hasOwnProperty(word)) { + Object.keys(terms).forEach((term) => { + if (term.match(escapedWord)) + arr.push({ files: terms[term], score: Scorer.partialTerm }); + }); + } + if (!titleTerms.hasOwnProperty(word)) { + Object.keys(titleTerms).forEach((term) => { + if (term.match(escapedWord)) + arr.push({ files: titleTerms[term], score: Scorer.partialTitle }); + }); + } + } + + // no match but word was a required one + if (arr.every((record) => record.files === undefined)) return; + + // found search word in contents + arr.forEach((record) => { + if (record.files === undefined) return; + + let recordFiles = record.files; + if (recordFiles.length === undefined) recordFiles = [recordFiles]; + files.push(...recordFiles); + + // set score for the word in each file + recordFiles.forEach((file) => { + if (!scoreMap.has(file)) scoreMap.set(file, {}); + scoreMap.get(file)[word] = record.score; + }); + }); + + // create the mapping + files.forEach((file) => { + if (!fileMap.has(file)) fileMap.set(file, [word]); + else if (fileMap.get(file).indexOf(word) === -1) fileMap.get(file).push(word); + }); + }); + + // now check if the files don't contain excluded terms + const results = []; + for (const [file, wordList] of fileMap) { + // check if all requirements are matched + + // as search terms with length < 3 are discarded + const filteredTermCount = [...searchTerms].filter( + (term) => term.length > 2 + ).length; + if ( + wordList.length !== searchTerms.size && + wordList.length !== filteredTermCount + ) + continue; + + // ensure that none of the excluded terms is in the search result + if ( + [...excludedTerms].some( + (term) => + terms[term] === file || + titleTerms[term] === file || + (terms[term] || []).includes(file) || + (titleTerms[term] || []).includes(file) + ) + ) + break; + + // select one (max) score for the file. + const score = Math.max(...wordList.map((w) => scoreMap.get(file)[w])); + // add result to the result list + results.push([ + docNames[file], + titles[file], + "", + null, + score, + filenames[file], + ]); + } + return results; + }, + + /** + * helper function to return a node containing the + * search summary for a given text. keywords is a list + * of stemmed words. + */ + makeSearchSummary: (htmlText, keywords, anchor) => { + const text = Search.htmlToText(htmlText, anchor); + if (text === "") return null; + + const textLower = text.toLowerCase(); + const actualStartPosition = [...keywords] + .map((k) => textLower.indexOf(k.toLowerCase())) + .filter((i) => i > -1) + .slice(-1)[0]; + const startWithContext = Math.max(actualStartPosition - 120, 0); + + const top = startWithContext === 0 ? "" : "..."; + const tail = startWithContext + 240 < text.length ? "..." : ""; + + let summary = document.createElement("p"); + summary.classList.add("context"); + summary.textContent = top + text.substr(startWithContext, 240).trim() + tail; + + return summary; + }, +}; + +_ready(Search.init); diff --git a/branch/main/_static/sphinx_highlight.js b/branch/main/_static/sphinx_highlight.js new file mode 100644 index 0000000..8a96c69 --- /dev/null +++ b/branch/main/_static/sphinx_highlight.js @@ -0,0 +1,154 @@ +/* Highlighting utilities for Sphinx HTML documentation. */ +"use strict"; + +const SPHINX_HIGHLIGHT_ENABLED = true + +/** + * highlight a given string on a node by wrapping it in + * span elements with the given class name. + */ +const _highlight = (node, addItems, text, className) => { + if (node.nodeType === Node.TEXT_NODE) { + const val = node.nodeValue; + const parent = node.parentNode; + const pos = val.toLowerCase().indexOf(text); + if ( + pos >= 0 && + !parent.classList.contains(className) && + !parent.classList.contains("nohighlight") + ) { + let span; + + const closestNode = parent.closest("body, svg, foreignObject"); + const isInSVG = closestNode && closestNode.matches("svg"); + if (isInSVG) { + span = document.createElementNS("http://www.w3.org/2000/svg", "tspan"); + } else { + span = document.createElement("span"); + span.classList.add(className); + } + + span.appendChild(document.createTextNode(val.substr(pos, text.length))); + const rest = document.createTextNode(val.substr(pos + text.length)); + parent.insertBefore( + span, + parent.insertBefore( + rest, + node.nextSibling + ) + ); + node.nodeValue = val.substr(0, pos); + /* There may be more occurrences of search term in this node. So call this + * function recursively on the remaining fragment. + */ + _highlight(rest, addItems, text, className); + + if (isInSVG) { + const rect = document.createElementNS( + "http://www.w3.org/2000/svg", + "rect" + ); + const bbox = parent.getBBox(); + rect.x.baseVal.value = bbox.x; + rect.y.baseVal.value = bbox.y; + rect.width.baseVal.value = bbox.width; + rect.height.baseVal.value = bbox.height; + rect.setAttribute("class", className); + addItems.push({ parent: parent, target: rect }); + } + } + } else if (node.matches && !node.matches("button, select, textarea")) { + node.childNodes.forEach((el) => _highlight(el, addItems, text, className)); + } +}; +const _highlightText = (thisNode, text, className) => { + let addItems = []; + _highlight(thisNode, addItems, text, className); + addItems.forEach((obj) => + obj.parent.insertAdjacentElement("beforebegin", obj.target) + ); +}; + +/** + * Small JavaScript module for the documentation. + */ +const SphinxHighlight = { + + /** + * highlight the search words provided in localstorage in the text + */ + highlightSearchWords: () => { + if (!SPHINX_HIGHLIGHT_ENABLED) return; // bail if no highlight + + // get and clear terms from localstorage + const url = new URL(window.location); + const highlight = + localStorage.getItem("sphinx_highlight_terms") + || url.searchParams.get("highlight") + || ""; + localStorage.removeItem("sphinx_highlight_terms") + url.searchParams.delete("highlight"); + window.history.replaceState({}, "", url); + + // get individual terms from highlight string + const terms = highlight.toLowerCase().split(/\s+/).filter(x => x); + if (terms.length === 0) return; // nothing to do + + // There should never be more than one element matching "div.body" + const divBody = document.querySelectorAll("div.body"); + const body = divBody.length ? divBody[0] : document.querySelector("body"); + window.setTimeout(() => { + terms.forEach((term) => _highlightText(body, term, "highlighted")); + }, 10); + + const searchBox = document.getElementById("searchbox"); + if (searchBox === null) return; + searchBox.appendChild( + document + .createRange() + .createContextualFragment( + '" + ) + ); + }, + + /** + * helper function to hide the search marks again + */ + hideSearchWords: () => { + document + .querySelectorAll("#searchbox .highlight-link") + .forEach((el) => el.remove()); + document + .querySelectorAll("span.highlighted") + .forEach((el) => el.classList.remove("highlighted")); + localStorage.removeItem("sphinx_highlight_terms") + }, + + initEscapeListener: () => { + // only install a listener if it is really needed + if (!DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS) return; + + document.addEventListener("keydown", (event) => { + // bail for input elements + if (BLACKLISTED_KEY_CONTROL_ELEMENTS.has(document.activeElement.tagName)) return; + // bail with special keys + if (event.shiftKey || event.altKey || event.ctrlKey || event.metaKey) return; + if (DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS && (event.key === "Escape")) { + SphinxHighlight.hideSearchWords(); + event.preventDefault(); + } + }); + }, +}; + +_ready(() => { + /* Do not call highlightSearchWords() when we are on the search page. + * It will highlight words from the *previous* search query. + */ + if (typeof Search === "undefined") SphinxHighlight.highlightSearchWords(); + SphinxHighlight.initEscapeListener(); +}); diff --git a/branch/main/_static/sphinx_lesson.css b/branch/main/_static/sphinx_lesson.css new file mode 100644 index 0000000..14b20c6 --- /dev/null +++ b/branch/main/_static/sphinx_lesson.css @@ -0,0 +1,51 @@ +/* sphinx_lesson.css */ + +body.wy-body-for-nav img.with-border { + border: 2px solid; +} + +.rst-content .admonition-no-content { + padding-bottom: 0px; +} + +.rst-content .demo > .admonition-title::before { + content: "\01F440"; /* Eyes */ } +.rst-content .type-along > .admonition-title::before { + content: "\02328\0FE0F"; /* Keyboard */ } +.rst-content .exercise > .admonition-title::before { + content: "\0270D\0FE0F"; /* Hand */ } +.rst-content .solution > .admonition-title::before { + content: "\02714\0FE0E"; /* Check mark */ } +.rst-content .homework > .admonition-title::before { + content: "\01F4DD"; /* Memo */ } +.rst-content .discussion > .admonition-title::before { + content: "\01F4AC"; /* Speech balloon */ } +.rst-content .questions > .admonition-title::before { + content: "\02753\0FE0E"; /* Question mark */ } +.rst-content .prerequisites > .admonition-title::before { + content: "\02699"; /* Gear */ } +.rst-content .seealso > .admonition-title::before { + content: "\027A1\0FE0E"; /* Question mark */ } + + +/* instructor-note */ +.rst-content .instructor-note { + background: #e7e7e7; +} +.rst-content .instructor-note > .admonition-title { + background: #6a6a6a; +} +.rst-content .instructor-note > .admonition-title::before { + content: ""; +} + + +/* sphinx_toggle_button, make the font white */ +.rst-content .toggle.admonition button.toggle-button { + color: white; +} + +/* sphinx-togglebutton, remove underflow when toggled to hidden mode */ +.rst-content .admonition.toggle-hidden { + padding-bottom: 0px; +} diff --git a/branch/main/_static/sphinx_rtd_theme_ext_color_contrast.css b/branch/main/_static/sphinx_rtd_theme_ext_color_contrast.css new file mode 100644 index 0000000..e68feb8 --- /dev/null +++ b/branch/main/_static/sphinx_rtd_theme_ext_color_contrast.css @@ -0,0 +1,47 @@ +/* The following are for web accessibility of sphinx_rtd_theme: they + * solve some of the most frequent contrast issues. Remove when this + * solved: + * https://github.com/readthedocs/sphinx_rtd_theme/issues/971 + */ +/* background: #fcfcfc, note boxes #E7F2FA */ +a { color: #2573A7; } /* original #2980B9, #1F5C84; */ +body { color: #242424; } /* original #404040, #383838 */ +.wy-side-nav-search>a, .wy-side-nav-search .wy-dropdown>a { + color: #ffffff; +} /* original #fcfcfc */ +footer { color: #737373; } /* original gray=#808080*/ +footer span.commit code, footer span.commit .rst-content tt, .rst-content footer span.commit tt { + color: #737373; +} /* original gray=#808080*/ +.rst-content tt.literal, .rst-content tt.literal, .rst-content code.literal { + color: #AB2314; +} +/* Sidebar background */ +.wy-side-nav-search { background-color: #277CB4;} + +/* Same, but for pygments */ +.highlight .ch { color: #3E7A89; } /* #! line */ +.highlight .c1 { color: #3E7A89; } /* also comments */ +.highlight .nv { color: #AD3ECC; } /* variable */ +.highlight .gp { color: #B45608; } /* prompt character, $*/ +.highlight .si { color: #3975B1; } /* ${} variable text */ +.highlight .nc { color: #0C78A7; } + +/* Sphinx admonitions */ +/* warning */ +.wy-alert.wy-alert-warning .wy-alert-title, .rst-content .wy-alert-warning.note .wy-alert-title, .rst-content .attention .wy-alert-title, .rst-content .caution .wy-alert-title, .rst-content .wy-alert-warning.danger .wy-alert-title, .rst-content .wy-alert-warning.error .wy-alert-title, .rst-content .wy-alert-warning.hint .wy-alert-title, .rst-content .wy-alert-warning.important .wy-alert-title, .rst-content .wy-alert-warning.tip .wy-alert-title, .rst-content .warning .wy-alert-title, .rst-content .wy-alert-warning.seealso .wy-alert-title, .rst-content .admonition-todo .wy-alert-title, .rst-content .wy-alert-warning.admonition .wy-alert-title, .wy-alert.wy-alert-warning .rst-content .admonition-title, .rst-content .wy-alert.wy-alert-warning .admonition-title, .rst-content .wy-alert-warning.note .admonition-title, .rst-content .attention .admonition-title, .rst-content .caution .admonition-title, .rst-content .wy-alert-warning.danger .admonition-title, .rst-content .wy-alert-warning.error .admonition-title, .rst-content .wy-alert-warning.hint .admonition-title, .rst-content .wy-alert-warning.important .admonition-title, .rst-content .wy-alert-warning.tip .admonition-title, .rst-content .warning .admonition-title, .rst-content .wy-alert-warning.seealso .admonition-title, .rst-content .admonition-todo .admonition-title, .rst-content .wy-alert-warning.admonition .admonition-title { + background: #B15E16; } +/* important */ +.wy-alert.wy-alert-success .wy-alert-title, .rst-content .wy-alert-success.note .wy-alert-title, .rst-content .wy-alert-success.attention .wy-alert-title, .rst-content .wy-alert-success.caution .wy-alert-title, .rst-content .wy-alert-success.danger .wy-alert-title, .rst-content .wy-alert-success.error .wy-alert-title, .rst-content .hint .wy-alert-title, .rst-content .important .wy-alert-title, .rst-content .tip .wy-alert-title, .rst-content .wy-alert-success.warning .wy-alert-title, .rst-content .wy-alert-success.seealso .wy-alert-title, .rst-content .wy-alert-success.admonition-todo .wy-alert-title, .rst-content .wy-alert-success.admonition .wy-alert-title, .wy-alert.wy-alert-success .rst-content .admonition-title, .rst-content .wy-alert.wy-alert-success .admonition-title, .rst-content .wy-alert-success.note .admonition-title, .rst-content .wy-alert-success.attention .admonition-title, .rst-content .wy-alert-success.caution .admonition-title, .rst-content .wy-alert-success.danger .admonition-title, .rst-content .wy-alert-success.error .admonition-title, .rst-content .hint .admonition-title, .rst-content .important .admonition-title, .rst-content .tip .admonition-title, .rst-content .wy-alert-success.warning .admonition-title, .rst-content .wy-alert-success.seealso .admonition-title, .rst-content .wy-alert-success.admonition-todo .admonition-title, .rst-content .wy-alert-success.admonition .admonition-title { + background: #12826C; } +/* seealso, note, etc */ +.wy-alert.wy-alert-info .wy-alert-title, .rst-content .note .wy-alert-title, .rst-content .wy-alert-info.attention .wy-alert-title, .rst-content .wy-alert-info.caution .wy-alert-title, .rst-content .wy-alert-info.danger .wy-alert-title, .rst-content .wy-alert-info.error .wy-alert-title, .rst-content .wy-alert-info.hint .wy-alert-title, .rst-content .wy-alert-info.important .wy-alert-title, .rst-content .wy-alert-info.tip .wy-alert-title, .rst-content .wy-alert-info.warning .wy-alert-title, .rst-content .seealso .wy-alert-title, .rst-content .wy-alert-info.admonition-todo .wy-alert-title, .rst-content .wy-alert-info.admonition .wy-alert-title, .wy-alert.wy-alert-info .rst-content .admonition-title, .rst-content .wy-alert.wy-alert-info .admonition-title, .rst-content .note .admonition-title, .rst-content .wy-alert-info.attention .admonition-title, .rst-content .wy-alert-info.caution .admonition-title, .rst-content .wy-alert-info.danger .admonition-title, .rst-content .wy-alert-info.error .admonition-title, .rst-content .wy-alert-info.hint .admonition-title, .rst-content .wy-alert-info.important .admonition-title, .rst-content .wy-alert-info.tip .admonition-title, .rst-content .wy-alert-info.warning .admonition-title, .rst-content .seealso .admonition-title, .rst-content .wy-alert-info.admonition-todo .admonition-title, .rst-content .wy-alert-info.admonition .admonition-title { + background: #277CB4; } +/* error, danger */ +.rst-content .danger .admonition-title, .rst-content .danger .wy-alert-title, .rst-content .error .admonition-title, .rst-content .error .wy-alert-title, .rst-content .wy-alert-danger.admonition-todo .admonition-title, .rst-content .wy-alert-danger.admonition-todo .wy-alert-title, .rst-content .wy-alert-danger.admonition .admonition-title, .rst-content .wy-alert-danger.admonition .wy-alert-title, .rst-content .wy-alert-danger.attention .admonition-title, .rst-content .wy-alert-danger.attention .wy-alert-title, .rst-content .wy-alert-danger.caution .admonition-title, .rst-content .wy-alert-danger.caution .wy-alert-title, .rst-content .wy-alert-danger.hint .admonition-title, .rst-content .wy-alert-danger.hint .wy-alert-title, .rst-content .wy-alert-danger.important .admonition-title, .rst-content .wy-alert-danger.important .wy-alert-title, .rst-content .wy-alert-danger.note .admonition-title, .rst-content .wy-alert-danger.note .wy-alert-title, .rst-content .wy-alert-danger.seealso .admonition-title, .rst-content .wy-alert-danger.seealso .wy-alert-title, .rst-content .wy-alert-danger.tip .admonition-title, .rst-content .wy-alert-danger.tip .wy-alert-title, .rst-content .wy-alert-danger.warning .admonition-title, .rst-content .wy-alert-danger.warning .wy-alert-title, .rst-content .wy-alert.wy-alert-danger .admonition-title, .wy-alert.wy-alert-danger .rst-content .admonition-title, .wy-alert.wy-alert-danger .wy-alert-title { + background: #e31704; +} + +/* Generic admonition titles */ +.wy-alert-title, .rst-content .admonition-title { + background: #277CB4; } diff --git a/branch/main/_static/style.css b/branch/main/_static/style.css new file mode 100644 index 0000000..59e60ee --- /dev/null +++ b/branch/main/_static/style.css @@ -0,0 +1,6 @@ +.rst-content .objectives { + background: #fee0d2; +} +.rst-content .objectives > .admonition-title { + background: #fc9272; +} diff --git a/branch/main/_static/tabs.css b/branch/main/_static/tabs.css new file mode 100644 index 0000000..957ba60 --- /dev/null +++ b/branch/main/_static/tabs.css @@ -0,0 +1,89 @@ +.sphinx-tabs { + margin-bottom: 1rem; +} + +[role="tablist"] { + border-bottom: 1px solid #a0b3bf; +} + +.sphinx-tabs-tab { + position: relative; + font-family: Lato,'Helvetica Neue',Arial,Helvetica,sans-serif; + color: #1D5C87; + line-height: 24px; + margin: 0; + font-size: 16px; + font-weight: 400; + background-color: rgba(255, 255, 255, 0); + border-radius: 5px 5px 0 0; + border: 0; + padding: 1rem 1.5rem; + margin-bottom: 0; +} + +.sphinx-tabs-tab[aria-selected="true"] { + font-weight: 700; + border: 1px solid #a0b3bf; + border-bottom: 1px solid white; + margin: -1px; + background-color: white; +} + +.sphinx-tabs-tab:focus { + z-index: 1; + outline-offset: 1px; +} + +.sphinx-tabs-panel { + position: relative; + padding: 1rem; + border: 1px solid #a0b3bf; + margin: 0px -1px -1px -1px; + border-radius: 0 0 5px 5px; + border-top: 0; + background: white; +} + +.sphinx-tabs-panel.code-tab { + padding: 0.4rem; +} + +.sphinx-tab img { + margin-bottom: 24 px; +} + +/* Dark theme preference styling */ + +@media (prefers-color-scheme: dark) { + body[data-theme="auto"] .sphinx-tabs-panel { + color: white; + background-color: rgb(50, 50, 50); + } + + body[data-theme="auto"] .sphinx-tabs-tab { + color: white; + background-color: rgba(255, 255, 255, 0.05); + } + + body[data-theme="auto"] .sphinx-tabs-tab[aria-selected="true"] { + border-bottom: 1px solid rgb(50, 50, 50); + background-color: rgb(50, 50, 50); + } +} + +/* Explicit dark theme styling */ + +body[data-theme="dark"] .sphinx-tabs-panel { + color: white; + background-color: rgb(50, 50, 50); +} + +body[data-theme="dark"] .sphinx-tabs-tab { + color: white; + background-color: rgba(255, 255, 255, 0.05); +} + +body[data-theme="dark"] .sphinx-tabs-tab[aria-selected="true"] { + border-bottom: 2px solid rgb(50, 50, 50); + background-color: rgb(50, 50, 50); +} diff --git a/branch/main/_static/tabs.js b/branch/main/_static/tabs.js new file mode 100644 index 0000000..48dc303 --- /dev/null +++ b/branch/main/_static/tabs.js @@ -0,0 +1,145 @@ +try { + var session = window.sessionStorage || {}; +} catch (e) { + var session = {}; +} + +window.addEventListener("DOMContentLoaded", () => { + const allTabs = document.querySelectorAll('.sphinx-tabs-tab'); + const tabLists = document.querySelectorAll('[role="tablist"]'); + + allTabs.forEach(tab => { + tab.addEventListener("click", changeTabs); + }); + + tabLists.forEach(tabList => { + tabList.addEventListener("keydown", keyTabs); + }); + + // Restore group tab selection from session + const lastSelected = session.getItem('sphinx-tabs-last-selected'); + if (lastSelected != null) selectNamedTabs(lastSelected); +}); + +/** + * Key focus left and right between sibling elements using arrows + * @param {Node} e the element in focus when key was pressed + */ +function keyTabs(e) { + const tab = e.target; + let nextTab = null; + if (e.keyCode === 39 || e.keyCode === 37) { + tab.setAttribute("tabindex", -1); + // Move right + if (e.keyCode === 39) { + nextTab = tab.nextElementSibling; + if (nextTab === null) { + nextTab = tab.parentNode.firstElementChild; + } + // Move left + } else if (e.keyCode === 37) { + nextTab = tab.previousElementSibling; + if (nextTab === null) { + nextTab = tab.parentNode.lastElementChild; + } + } + } + + if (nextTab !== null) { + nextTab.setAttribute("tabindex", 0); + nextTab.focus(); + } +} + +/** + * Select or deselect clicked tab. If a group tab + * is selected, also select tab in other tabLists. + * @param {Node} e the element that was clicked + */ +function changeTabs(e) { + // Use this instead of the element that was clicked, in case it's a child + const notSelected = this.getAttribute("aria-selected") === "false"; + const positionBefore = this.parentNode.getBoundingClientRect().top; + const notClosable = !this.parentNode.classList.contains("closeable"); + + deselectTabList(this); + + if (notSelected || notClosable) { + selectTab(this); + const name = this.getAttribute("name"); + selectNamedTabs(name, this.id); + + if (this.classList.contains("group-tab")) { + // Persist during session + session.setItem('sphinx-tabs-last-selected', name); + } + } + + const positionAfter = this.parentNode.getBoundingClientRect().top; + const positionDelta = positionAfter - positionBefore; + // Scroll to offset content resizing + window.scrollTo(0, window.scrollY + positionDelta); +} + +/** + * Select tab and show associated panel. + * @param {Node} tab tab to select + */ +function selectTab(tab) { + tab.setAttribute("aria-selected", true); + + // Show the associated panel + document + .getElementById(tab.getAttribute("aria-controls")) + .removeAttribute("hidden"); +} + +/** + * Hide the panels associated with all tabs within the + * tablist containing this tab. + * @param {Node} tab a tab within the tablist to deselect + */ +function deselectTabList(tab) { + const parent = tab.parentNode; + const grandparent = parent.parentNode; + + Array.from(parent.children) + .forEach(t => t.setAttribute("aria-selected", false)); + + Array.from(grandparent.children) + .slice(1) // Skip tablist + .forEach(panel => panel.setAttribute("hidden", true)); +} + +/** + * Select grouped tabs with the same name, but no the tab + * with the given id. + * @param {Node} name name of grouped tab to be selected + * @param {Node} clickedId id of clicked tab + */ +function selectNamedTabs(name, clickedId=null) { + const groupedTabs = document.querySelectorAll(`.sphinx-tabs-tab[name="${name}"]`); + const tabLists = Array.from(groupedTabs).map(tab => tab.parentNode); + + tabLists + .forEach(tabList => { + // Don't want to change the tabList containing the clicked tab + const clickedTab = tabList.querySelector(`[id="${clickedId}"]`); + if (clickedTab === null ) { + // Select first tab with matching name + const tab = tabList.querySelector(`.sphinx-tabs-tab[name="${name}"]`); + deselectTabList(tab); + selectTab(tab); + } + }) +} + +if (typeof exports === 'undefined') { + exports = {}; +} + +exports.keyTabs = keyTabs; +exports.changeTabs = changeTabs; +exports.selectTab = selectTab; +exports.deselectTabList = deselectTabList; +exports.selectNamedTabs = selectNamedTabs; diff --git a/branch/main/_static/term_role_formatting.css b/branch/main/_static/term_role_formatting.css new file mode 100644 index 0000000..0b66095 --- /dev/null +++ b/branch/main/_static/term_role_formatting.css @@ -0,0 +1,4 @@ +/* Make terms bold */ +a.reference span.std-term { + font-weight: bold; +} diff --git a/branch/main/_static/togglebutton.css b/branch/main/_static/togglebutton.css new file mode 100644 index 0000000..54a6787 --- /dev/null +++ b/branch/main/_static/togglebutton.css @@ -0,0 +1,160 @@ +/** + * Admonition-based toggles + */ + +/* Visibility of the target */ +.admonition.toggle .admonition-title ~ * { + transition: opacity .3s, height .3s; +} + +/* Toggle buttons inside admonitions so we see the title */ +.admonition.toggle { + position: relative; +} + +/* Titles should cut off earlier to avoid overlapping w/ button */ +.admonition.toggle .admonition-title { + padding-right: 25%; + cursor: pointer; +} + +/* Hovering will cause a slight shift in color to make it feel interactive */ +.admonition.toggle .admonition-title:hover { + box-shadow: inset 0 0 0px 20px rgb(0 0 0 / 1%); +} + +/* Hovering will cause a slight shift in color to make it feel interactive */ +.admonition.toggle .admonition-title:active { + box-shadow: inset 0 0 0px 20px rgb(0 0 0 / 3%); +} + +/* Remove extra whitespace below the admonition title when hidden */ +.admonition.toggle-hidden { + padding-bottom: 0; +} + +.admonition.toggle-hidden .admonition-title { + margin-bottom: 0; +} + +/* hides all the content of a page until de-toggled */ +.admonition.toggle-hidden .admonition-title ~ * { + height: 0; + margin: 0; + opacity: 0; + visibility: hidden; +} + +/* General button style and position*/ +button.toggle-button { + /** + * Background and shape. By default there's no background + * but users can style as they wish + */ + background: none; + border: none; + outline: none; + + /* Positioning just inside the admonition title */ + position: absolute; + right: 0.5em; + padding: 0px; + border: none; + outline: none; +} + +/* Display the toggle hint on wide screens */ +@media (min-width: 768px) { + button.toggle-button.toggle-button-hidden:before { + content: attr(data-toggle-hint); /* This will be filled in by JS */ + font-size: .8em; + align-self: center; + } +} + +/* Icon behavior */ +.tb-icon { + transition: transform .2s ease-out; + height: 1.5em; + width: 1.5em; + stroke: currentColor; /* So that we inherit the color of other text */ +} + +/* The icon should point right when closed, down when open. */ +/* Open */ +.admonition.toggle button .tb-icon { + transform: rotate(90deg); +} + +/* Closed */ +.admonition.toggle button.toggle-button-hidden .tb-icon { + transform: rotate(0deg); +} + +/* With details toggles, we don't rotate the icon so it points right */ +details.toggle-details .tb-icon { + height: 1.4em; + width: 1.4em; + margin-top: 0.1em; /* To center the button vertically */ +} + + +/** + * Details-based toggles. + * In this case, we wrap elements with `.toggle` in a details block. + */ + +/* Details blocks */ +details.toggle-details { + margin: 1em 0; +} + + +details.toggle-details summary { + display: flex; + align-items: center; + cursor: pointer; + list-style: none; + border-radius: .2em; + border-left: 3px solid #1976d2; + background-color: rgb(204 204 204 / 10%); + padding: 0.2em 0.7em 0.3em 0.5em; /* Less padding on left because the SVG has left margin */ + font-size: 0.9em; +} + +details.toggle-details summary:hover { + background-color: rgb(204 204 204 / 20%); +} + +details.toggle-details summary:active { + background: rgb(204 204 204 / 28%); +} + +.toggle-details__summary-text { + margin-left: 0.2em; +} + +details.toggle-details[open] summary { + margin-bottom: .5em; +} + +details.toggle-details[open] summary .tb-icon { + transform: rotate(90deg); +} + +details.toggle-details[open] summary ~ * { + animation: toggle-fade-in .3s ease-out; +} + +@keyframes toggle-fade-in { + from {opacity: 0%;} + to {opacity: 100%;} +} + +/* Print rules - we hide all toggle button elements at print */ +@media print { + /* Always hide the summary so the button doesn't show up */ + details.toggle-details summary { + display: none; + } +} \ No newline at end of file diff --git a/branch/main/_static/togglebutton.js b/branch/main/_static/togglebutton.js new file mode 100644 index 0000000..215a7ee --- /dev/null +++ b/branch/main/_static/togglebutton.js @@ -0,0 +1,187 @@ +/** + * Add Toggle Buttons to elements + */ + +let toggleChevron = ` + + + +`; + +var initToggleItems = () => { + var itemsToToggle = document.querySelectorAll(togglebuttonSelector); + console.log(`[togglebutton]: Adding toggle buttons to ${itemsToToggle.length} items`) + // Add the button to each admonition and hook up a callback to toggle visibility + itemsToToggle.forEach((item, index) => { + if (item.classList.contains("admonition")) { + // If it's an admonition block, then we'll add a button inside + // Generate unique IDs for this item + var toggleID = `toggle-${index}`; + var buttonID = `button-${toggleID}`; + + item.setAttribute('id', toggleID); + if (!item.classList.contains("toggle")){ + item.classList.add("toggle"); + } + // This is the button that will be added to each item to trigger the toggle + var collapseButton = ` + `; + + title = item.querySelector(".admonition-title") + title.insertAdjacentHTML("beforeend", collapseButton); + thisButton = document.getElementById(buttonID); + + // Add click handlers for the button + admonition title (if admonition) + admonitionTitle = document.querySelector(`#${toggleID} > .admonition-title`) + if (admonitionTitle) { + // If an admonition, then make the whole title block clickable + admonitionTitle.addEventListener('click', toggleClickHandler); + admonitionTitle.dataset.target = toggleID + admonitionTitle.dataset.button = buttonID + } else { + // If not an admonition then we'll listen for the button click + thisButton.addEventListener('click', toggleClickHandler); + } + + // Now hide the item for this toggle button unless explicitly noted to show + if (!item.classList.contains("toggle-shown")) { + toggleHidden(thisButton); + } + } else { + // If not an admonition, wrap the block in a
block + // Define the structure of the details block and insert it as a sibling + var detailsBlock = ` +
+ + ${toggleChevron} + ${toggleHintShow} + +
`; + item.insertAdjacentHTML("beforebegin", detailsBlock); + + // Now move the toggle-able content inside of the details block + details = item.previousElementSibling + details.appendChild(item) + item.classList.add("toggle-details__container") + + // Set up a click trigger to change the text as needed + details.addEventListener('click', (click) => { + let parent = click.target.parentElement; + if (parent.tagName.toLowerCase() == "details") { + summary = parent.querySelector("summary"); + details = parent; + } else { + summary = parent; + details = parent.parentElement; + } + // Update the inner text for the proper hint + if (details.open) { + summary.querySelector("span.toggle-details__summary-text").innerText = toggleHintShow; + } else { + summary.querySelector("span.toggle-details__summary-text").innerText = toggleHintHide; + } + + }); + + // If we have a toggle-shown class, open details block should be open + if (item.classList.contains("toggle-shown")) { + details.click(); + } + } + }) +}; + +// This should simply add / remove the collapsed class and change the button text +var toggleHidden = (button) => { + target = button.dataset['target'] + var itemToToggle = document.getElementById(target); + if (itemToToggle.classList.contains("toggle-hidden")) { + itemToToggle.classList.remove("toggle-hidden"); + button.classList.remove("toggle-button-hidden"); + } else { + itemToToggle.classList.add("toggle-hidden"); + button.classList.add("toggle-button-hidden"); + } +} + +var toggleClickHandler = (click) => { + // Be cause the admonition title is clickable and extends to the whole admonition + // We only look for a click event on this title to trigger the toggle. + + if (click.target.classList.contains("admonition-title")) { + button = click.target.querySelector(".toggle-button"); + } else if (click.target.classList.contains("tb-icon")) { + // We've clicked the icon and need to search up one parent for the button + button = click.target.parentElement; + } else if (click.target.tagName == "polyline") { + // We've clicked the SVG elements inside the button, need to up 2 layers + button = click.target.parentElement.parentElement; + } else if (click.target.classList.contains("toggle-button")) { + // We've clicked the button itself and so don't need to do anything + button = click.target; + } else { + console.log(`[togglebutton]: Couldn't find button for ${click.target}`) + } + target = document.getElementById(button.dataset['button']); + toggleHidden(target); +} + +// If we want to blanket-add toggle classes to certain cells +var addToggleToSelector = () => { + const selector = ""; + if (selector.length > 0) { + document.querySelectorAll(selector).forEach((item) => { + item.classList.add("toggle"); + }) + } +} + +// Helper function to run when the DOM is finished +const sphinxToggleRunWhenDOMLoaded = cb => { + if (document.readyState != 'loading') { + cb() + } else if (document.addEventListener) { + document.addEventListener('DOMContentLoaded', cb) + } else { + document.attachEvent('onreadystatechange', function() { + if (document.readyState == 'complete') cb() + }) + } +} +sphinxToggleRunWhenDOMLoaded(addToggleToSelector) +sphinxToggleRunWhenDOMLoaded(initToggleItems) + +/** Toggle details blocks to be open when printing */ +if (toggleOpenOnPrint == "true") { + window.addEventListener("beforeprint", () => { + // Open the details + document.querySelectorAll("details.toggle-details").forEach((el) => { + el.dataset["togglestatus"] = el.open; + el.open = true; + }); + + // Open the admonitions + document.querySelectorAll(".admonition.toggle.toggle-hidden").forEach((el) => { + console.log(el); + el.querySelector("button.toggle-button").click(); + el.dataset["toggle_after_print"] = "true"; + }); + }); + window.addEventListener("afterprint", () => { + // Re-close the details that were closed + document.querySelectorAll("details.toggle-details").forEach((el) => { + el.open = el.dataset["togglestatus"] == "true"; + delete el.dataset["togglestatus"]; + }); + + // Re-close the admonition toggle buttons + document.querySelectorAll(".admonition.toggle").forEach((el) => { + if (el.dataset["toggle_after_print"] == "true") { + el.querySelector("button.toggle-button").click(); + delete el.dataset["toggle_after_print"]; + } + }); + }); +} diff --git a/branch/main/collaboration/code-review/index.html b/branch/main/collaboration/code-review/index.html new file mode 100644 index 0000000..2186f04 --- /dev/null +++ b/branch/main/collaboration/code-review/index.html @@ -0,0 +1,287 @@ + + + + + + + Practicing code review — Reproducible research software development using Python documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

Practicing code review

+

In this episode we will practice the code review process. We will learn how to +ask for changes in a pull request, how to suggest a change in a pull request, +and how to modify a pull request.

+

This will enable research groups to work more collaboratively and to not only +improve the code quality but also to learn from each other.

+
+

Exercise

+
+

Exercise preparation

+

We can continue in the same exercise repository which we have used in the +previous episode.

+
+
+

Exercise: Practicing code review (25 min)

+

Technical requirements:

+ +

What is familiar from previous lessons:

+
    +
  • Creating a branch.

  • +
  • Committing a change on the new branch.

  • +
  • Opening and merging pull requests.

  • +
+

What will be new in this exercise:

+
    +
  • As a reviewer, we will learn how to ask for changes in a pull request.

  • +
  • As a reviewer, we will learn how to suggest a change in a pull request.

  • +
  • As a submitter, we will learn how to modify a pull request without closing +the incomplete one and opening a new one.

  • +
+

Exercise tasks:

+
    +
  1. Create a new branch and one or few commits: in these improve something but also +deliberately introduce a typo and also a larger mistake which we will want to fix during the code review.

  2. +
  3. Open a pull request towards the main branch.

  4. +
  5. As a reviewer to somebody else’s pull request, ask for an improvement and +also directly suggest a change for the small typo. (Hint: +suggestions are possible through the GitHub web interface, view of +a pull request, “Files changed” view, after selecting some lines. +Look for the “±” button.)

  6. +
  7. As the submitter, learn how to accept the suggested change. (Hint: +GitHub web interface, “Files Changed” view.)

  8. +
  9. As the submitter, improve the pull request without having to close and open +a new one: by adding a new commit to the same branch. (Hint: push +to the branch again.)

  10. +
  11. Once the changes are addressed, merge the pull request.

  12. +
+
+
+
+

Help and discussion

+

From here on out, we don’t give detailed steps to the solution. You +need to combine what you know, and the extra info below, in order to +solve the above.

+
+

How to ask for changes in a pull request

+

Technically, there are at least two common ways to ask for changes in a pull +request.

+

Either in the comment field of the pull request:

+
+Screenshot of a pull request comment field +
+

Or by using the “Review changes”:

+
+Screenshot of a pull request navigating to the "Review changes" tab +
+

And always please be kind and constructive in your comments. Remember that the +goal is not gate-keeping but collaborative learning.

+
+
+

How to suggest a change in a pull request as a reviewer

+

If you see a very small problem that is easy to fix, you can suggest a change +as a reviewer.

+

Instead of asking the submitter to tiny problem, you can suggest a change by +clicking on the plus sign next to the line number in the “Files changed” tab:

+
+Screenshot of leaving a comment to a line in a pull request +
+

Here you can comment on specific lines or even line ranges.

+

But now the interesting part is to click on the “Add a suggestion” symbol (the +one that looks like plus and minus). Now you can fix the tiny problem (in this +case a typo) and then click on the “Add single comment” button:

+
+Sequence of clicks to add a suggestion to a line in a pull request +
+

The result is this and the submitter can accept the change with a single click:

+
+Screenshot of a pull request with a suggested change +
+

After accepting with “Commit suggestion”, the improvement gets added to the +pull request.

+
+
+

How to modify a pull request to address the review comments

+

If the reviewer asks for changes, it is not necessary to close the pull request +and later open a new one. It can even be counter-productive to do so: This can +fragment the discussion and the history of the pull request and can make it +harder to understand the context of the changes.

+

A much better mechanism to recognize that pull requests are not implemented +from a specific commit to a specific branch, but always from a branch to a +branch.

+

This means that you can make amendments to the pull request by adding new +commits to the same source branch. This way the pull request will be updated +automatically and the reviewer can see the new changes and comment on them.

+

The fact that pull requests are from branch to branch also strongly suggests +that it is a good practice to create a new branch for each pull request. +Otherwise you could accidentally modify an open pull request by adding new +commits to the source branch.

+
+
+
+

Summary

+
    +
  • Our process isn’t just about code now. It’s about discussion and +working together to make the whole process better.

  • +
  • GitHub discussions and reviewing are quite powerful and can make +small changes easy.

  • +
+
+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/branch/main/collaboration/concepts/index.html b/branch/main/collaboration/concepts/index.html new file mode 100644 index 0000000..850bb42 --- /dev/null +++ b/branch/main/collaboration/concepts/index.html @@ -0,0 +1,232 @@ + + + + + + + Concepts around collaboration — Reproducible research software development using Python documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

Concepts around collaboration

+
+

Objectives

+
    +
  • Be able to decide whether to divide work at the branch level or at the repository level.

  • +
+
+
+

Commits, branches, repositories, forks, clones

+
    +
  • repository: The project, contains all data and history (commits, branches, tags).

  • +
  • commit: Snapshot of the project, gets a unique identifier (e.g. c7f0e8bfc718be04525847fc7ac237f470add76e).

  • +
  • branch: Independent development line. The main development line is often called main.

  • +
  • tag: A pointer to one commit, to be able to refer to it later. Like a commemorative plaque +that you attach to a particular commit (e.g. phd-printed or paper-submitted).

  • +
  • cloning: Copying the whole repository to your laptop - the first time. It is not necessary to download each file one by one.

  • +
  • forking: Taking a copy of a repository (which is typically not yours) - your +copy (fork) stays on GitHub/GitLab and you can make changes to your copy.

  • +
+
+
+

Cloning a repository

+

In order to make a complete copy a whole repository, the git clone command +can be used. When cloning, all the files, of all or selected branches, of a +repository are copied in one operation. Cloning of a repository is of relevance +in a few different situations:

+
    +
  • Working on your own, cloning is the operation that you can use to create +multiple instances of a repository on, for instance, a personal computer, a +server, and a supercomputer.

  • +
  • The parent repository could be a repository that you or your colleague own. A +common use case for cloning is when working together within a smaller team +where everyone has read and write access to the same git repository.

  • +
  • Alternatively, cloning can be made from a public repository of a code that +you would like to use. Perhaps you have no intention to work on the code, but +would like to stay in tune with the latest developments, also in-between +releases of new versions of the code.

  • +
+
+Forking and cloning +
+

Forking and cloning

+
+
+
+
+

Forking a repository

+

When a fork is made on GitHub/GitLab a complete copy, of all or selected +branches, of the repository is made. The copy will reside under a different +account on GitHub/GitLab. Forking of a repository is of high relevance when +working with a git repository to which you do not have write access.

+
    +
  • In the fork repository commits can be made to the base branch (main or +master), and to other branches.

  • +
  • The commits that are made within the branches of the fork repository can be +contributed back to the parent repository by means of pull or merge requests.

  • +
+
+
+

Synchronizing changes between repositories

+
    +
  • We need a mechanism to communicate changes between the repositories.

  • +
  • We will pull or fetch updates from remote repositories (we will soon discuss the difference between pull and fetch).

  • +
  • We will push updates to remote repositories.

  • +
  • We will learn how to suggest changes within repositories on GitHub and across repositories (pull request).

  • +
  • Repositories that are forked or cloned do not automatically synchronize themselves: +We will learn how to update forks (by pulling from the “central” repository).

  • +
  • A main difference between cloning a repository and forking a repository is that the former is a general operation for generating copies of a repository to different computers, whereas forking is a particular operation implemented on GitHub/GitLab.

  • +
+
+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/branch/main/collaboration/demo-discussion/index.html b/branch/main/collaboration/demo-discussion/index.html new file mode 100644 index 0000000..2570af7 --- /dev/null +++ b/branch/main/collaboration/demo-discussion/index.html @@ -0,0 +1,158 @@ + + + + + + + Conclict resolution, rebasing, and organizational strategies — Reproducible research software development using Python documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/branch/main/collaboration/forking-workflow/index.html b/branch/main/collaboration/forking-workflow/index.html new file mode 100644 index 0000000..a36c862 --- /dev/null +++ b/branch/main/collaboration/forking-workflow/index.html @@ -0,0 +1,374 @@ + + + + + + + How to contribute changes to repositories that belong to others — Reproducible research software development using Python documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

How to contribute changes to repositories that belong to others

+

In this episode we prepare you to suggest and contribute changes to +repositories that belong to others. These might be open source projects that +you use in your work.

+

We will see how Git and services like GitHub or GitLab can be used to suggest +modification without having to ask for write access to the repository and +accept modifications without having to grant write access to others.

+
+

Exercise

+
+

Exercise preparation

+
    +
  • The exercise repository is now different: +https://github.com/workshop-material/recipe-book-forking-exercise (note the -forking-exercise).

  • +
  • First fork the exercise repository to your GitHub account.

  • +
  • Then clone your fork to your computer (if you wish to work locally).

  • +
  • Double-check that you have forked the correct repository.

  • +
+
+
+

Exercise: Collaborating within the same repository (25 min)

+

Technical requirements:

+ +

What is familiar from previous lessons:

+
    +
  • Forking a repository.

  • +
  • Creating a branch.

  • +
  • Committing a change on the new branch.

  • +
  • Opening and merging pull requests.

  • +
+

What will be new in this exercise:

+
    +
  • Opening a pull request towards the upstream repository.

  • +
  • Pull requests can be coupled with automated testing.

  • +
  • Learning that your fork can get out of date.

  • +
  • After the pull requests are merged, updating your fork with the changes.

  • +
  • Learn how to approach other people’s repositories with ideas, changes, and requests.

  • +
+

Exercise tasks:

+
    +
  1. Open an issue in the upstream exercise repository where you describe the +change you want to make. Take note of the issue number.

  2. +
  3. Create a new branch in your fork of the repository.

  4. +
  5. Make a change to the recipe book on the new branch and in the commit cross-reference the issue you opened. +See the walk-through below for how to do this.

  6. +
  7. Open a pull request towards the upstream repository.

  8. +
  9. The instructor will review and merge the pull requests. +During the review, pay attention to the automated test step (here for +demonstration purposes, we test whether the recipe contains an ingredients +and an instructions sections).

  10. +
  11. After few pull requests are merged, update your fork with the changes.

  12. +
  13. Check that in your fork you can see changes from other people’s pull requests.

  14. +
+
+
+
+

Help and discussion

+
+

Help! I don’t have permissions to push my local changes

+

Maybe you see an error like this one:

+
Please make sure you have the correct access rights
+and the repository exists.
+
+
+

Or like this one:

+
failed to push some refs to workshop-material/recipe-book-forking-exercise.git
+
+
+

In this case you probably try to push the changes not to your fork but to the original repository +and in this exercise you do not have write access to the original repository.

+

The simpler solution is to clone again but this time your fork.

+ +
+
+

Opening a pull request towards the upstream repository

+

We have learned in the previous episode that pull requests are always from +branch to branch. But the branch can be in a different repository.

+

When you open a pull request in a fork, by default GitHub will suggest to +direct it towards the default branch of the upstream repository.

+

This can be changed and it should always be verified, but in this case this is +exactly what we want to do, from fork towards upstream:

+
+Screenshot of a pull request from fork towards upstream +
+
+
+

Pull requests can be coupled with automated testing

+

We added an automated test here just for fun and so that you see that this is +possible to do.

+

In this exercise, the test is silly. It will check whether the recipe contains +both an ingredients and an instructions section.

+

In this example the test failed:

+
+Screenshot of a failed test in a pull request +
+

Click on the “Details” link to see the details of the failed test:

+
+Screenshot of details why the test failed +
+

How can this be useful?

+
    +
  • The project can define what kind of tests are expected to pass before a pull +request can be merged.

  • +
  • The reviewer can see the results of the tests, without having to run them +locally.

  • +
+

How does it work?

+
    +
  • We added a GitHub Actions workflow +to automatically run on each push or pull request towards the main branch.

  • +
+

What tests or steps can you image for your project to run automatically with +each pull request?

+
+
+

How to update your fork with changes from upstream

+

This used to be difficult but now it is two mouse clicks.

+

Navigate to your fork and notice how GitHub tells you that your fork is behind. +In my case, it is 9 commits behind upstream. To fix this, click on “Sync fork” +and then “Update branch”:

+
+Screenshot on GitHub fork page showing that the fork is behind +
+

After the update my “branch is up to date” with the upstream repository:

+
+Screenshot on GitHub after fork has been updated +
+
+
+

How to approach other people’s repositories with ideas, changes, and requests

+

Contributing very minor changes

+
    +
  • Clone or fork+clone repository

  • +
  • Create a branch

  • +
  • Commit and push change

  • +
  • Open a pull request or merge request

  • +
+

If you observe an issue and have an idea how to fix it

+
    +
  • Open an issue in the repository you wish to contribute to

  • +
  • Describe the problem

  • +
  • If you have a suggestion on how to fix it, describe your suggestion

  • +
  • Possibly discuss and get feedback

  • +
  • If you are working on the fix, indicate it in the issue so that others know that somebody is working on it and who is working on it

  • +
  • Submit your fix as pull request or merge request which references/closes the issue

  • +
+
+

Motivation

+
    +
  • Inform others about an observed problem

  • +
  • Make it clear whether this issue is up for grabs or already being worked on

  • +
+
+

If you have an idea for a new feature

+
    +
  • Open an issue in the repository you wish to contribute to

  • +
  • In the issue, write a short proposal for your suggested change or new feature

  • +
  • Motivate why and how you wish to do this

  • +
  • Also indicate where you are unsure and where you would like feedback

  • +
  • Discuss and get feedback before you code

  • +
  • Once you start coding, indicate that you are working on it

  • +
  • Once you are done, submit your new feature as pull request or merge request which references/closes the issue/proposal

  • +
+
+

Motivation

+
    +
  • Get agreement and feedback before writing 5000 lines of code which might be rejected

  • +
  • If we later wonder why something was done, we have the issue/proposal as +reference and can read up on the reasoning behind a code change

  • +
+
+
+
+
+

Summary

+
    +
  • This forking workflow lets you propose changes to repositories for +which you have no write access.

  • +
  • This is the way that much modern open-source software works.

  • +
  • You can now contribute to any project you can view.

  • +
+
+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/branch/main/collaboration/index.html b/branch/main/collaboration/index.html new file mode 100644 index 0000000..b4aa30e --- /dev/null +++ b/branch/main/collaboration/index.html @@ -0,0 +1,165 @@ + + + + + + + Collaborative version control and code review — Reproducible research software development using Python documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/branch/main/collaboration/same-repository/index.html b/branch/main/collaboration/same-repository/index.html new file mode 100644 index 0000000..1f9d83f --- /dev/null +++ b/branch/main/collaboration/same-repository/index.html @@ -0,0 +1,421 @@ + + + + + + + Collaborating within the same repository — Reproducible research software development using Python documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

Collaborating within the same repository

+

In this episode, we will learn how to collaborate within the same repository. +We will learn how to cross-reference issues and pull requests, how to review +pull requests, and how to use draft pull requests.

+

This exercise will form a good basis for collaboration that is suitable for +most research groups.

+
+

Note

+

When you read or hear pull request, please think of a change proposal.

+
+
+

Exercise

+

In this exercise, we will contribute to a repository via a pull request. +This means that you propose some change, and then it is accepted (or not).

+
+

Exercise preparation

+
    +
  • First we need to get access to the exercise repository to which we will +contribute.

    +
      +
    • Instructor collects GitHub usernames from learners and adds them as collaborators to the exercise repository +(Settings -> Collaborators and teams -> Manage access -> Add people).

    • +
    +
  • +
  • Don’t forget to accept the invitation

    +
      +
    • Check https://github.com/settings/organizations/

    • +
    • Alternatively check the inbox for the email account you registered with +GitHub. GitHub emails you an invitation link, but if you don’t receive it +you can go to your GitHub notifications in the top right corner. The +maintainer can also “copy invite link” and share it within the group.

    • +
    +
  • +
  • Watching and unwatching repositories

    +
      +
    • Now that you are a collaborator, you get notified about new issues and pull +requests via email.

    • +
    • If you do not wish this, you can “unwatch” a repository (top of +the project page).

    • +
    • However, we recommend watching repositories you are interested +in. You can learn things from experts just by watching the +activity that come through a popular project.

    • +
    +
    +Unwatching a repository +
    +

    Unwatch a repository by clicking “Unwatch” in the repository view, +then “Participating and @mentions” - this way, you will get +notifications about your own interactions.

    +
    +
    +
  • +
+
+
+

Exercise: Collaborating within the same repository (25 min)

+

Technical requirements (from installation instructions):

+ +

What is familiar from the previous workshop day (not repeated here):

+
    +
  • Cloning a repository.

  • +
  • Creating a branch.

  • +
  • Committing a change on the new branch.

  • +
  • Submit a pull request towards the main branch.

  • +
+

What will be new in this exercise:

+
    +
  • If you create the changes locally, you will need to push them to the remote repository.

  • +
  • Learning what a protected branch is and how to modify a protected branch: using a pull request.

  • +
  • Cross-referencing issues and pull requests.

  • +
  • Practice to review a pull request.

  • +
  • Learn about the value of draft pull requests.

  • +
+

Exercise tasks:

+
    +
  1. Start in the exercise +repository and open an +issue where you describe the change you want to make. Note down the issue +number since you will need it later.

  2. +
  3. Create a new branch.

  4. +
  5. Make a change to the recipe book on the new branch and in the commit +cross-reference the issue you opened (see the walk-through below +for how to do that).

  6. +
  7. Push your new branch (with the new commit) to the repository you +are working on.

  8. +
  9. Open a pull request towards the main branch.

  10. +
  11. Review somebody else’s pull request and give constructive feedback. Merge their pull request.

  12. +
  13. Try to create a new branch with some half-finished work and open a draft +pull request. Verify that the draft pull request cannot be merged since it +is not meant to be merged yet.

  14. +
+
+
+
+

Solution and hints

+
+

(1) Opening an issue

+

This is done through the GitHub web interface. For example, you could +give the name of the recipe you want to add (so that others don’t add +the same one). It is the “Issues” tab.

+
+
+

(2) Create a new branch.

+

If on GitHub, you can make the branch in the web interface.

+
+
+

(3) Make a change adding the recipe

+

Add a new file with the recipe in it. Commit the file. In the commit +message, include the note about the issue number, saying that this +will close that issue.

+
+

Cross-referencing issues and pull requests

+

Each issue and each pull request gets a number and you can cross-reference them.

+

When you open an issue, note down the issue number (in this case it is #2):

+
+Each issue gets a number +
+

You can reference this issue number in a commit message or in a pull request, like in this +commit message:

+
this is the new recipe; fixes #2
+
+
+

If you forget to do that in your commit message, you can also reference the issue +in the pull request description. And instead of fixes you can also use closes or resolves +or fix or close or resolve (case insensitive).

+

Here are all the keywords that GitHub recognizes: +https://help.github.com/en/articles/closing-issues-using-keywords

+

Then observe what happens in the issue once your commit gets merged: it will +automatically close the issue and create a link between the issue and the +commit. This is very useful for tracking what changes were made in response to +which issue and to know from when until when precisely the issue was open.

+
+
+
+

(4) Push to GitHub as a new branch

+

Push the branch to the repository. You should end up with a branch +visible in the GitHub web view.

+

This is only necessary if you created the changes locally. If you created the +changes directly on GitHub, you can skip this step.

+
+

In VS Code, you can “publish the branch” to the remote repository by clicking +the cloud icon in the bottom left corner of the window:

+
+Publishing a branch in VS Code +
+
+
+
+

(5) Open a pull request towards the main branch

+

This is done through the GitHub web interface.

+
+
+

(6) Reviewing pull requests

+

You review through the GitHub web interface.

+

Checklist for reviewing a pull request:

+
    +
  • Be kind, on the other side is a human who has put effort into this.

  • +
  • Be constructive: if you see a problem, suggest a solution.

  • +
  • Towards which branch is this directed?

  • +
  • Is the title descriptive?

  • +
  • Is the description informative?

  • +
  • Scroll down to see commits.

  • +
  • Scroll down to see the changes.

  • +
  • If you get incredibly many changes, also consider the license or copyright +and ask where all that code is coming from.

  • +
  • Again, be kind and constructive.

  • +
  • Later we will learn how to suggest changes directly in the pull request.

  • +
+

If someone is new, it’s often nice to say something encouraging in the +comments before merging (even if it’s just “thanks”). If all is good +and there’s not much else to say, you could merge directly.

+
+
+

(7) Draft pull requests

+

Try to create a draft pull request:

+
+Creating a draft pull request +
+

Verify that the draft pull request cannot be merged until it is marked as ready +for review:

+
+Draft pull request cannot be merged +
+

Draft pull requests can be useful for:

+
    +
  • Feedback: You can open a pull request early to get feedback on your work without +signaling that it is ready to merge.

  • +
  • Information: They can help communicating to others that a change is coming up and in +progress.

  • +
+
+
+

What is a protected branch? And how to modify it?

+

A protected branch on GitHub or GitLab is a branch that cannot (accidentally) +deleted or force-pushed to. It is also possible to require that a branch cannot +be directly pushed to or modified, but that changes must be submitted via a +pull request.

+

To protect a branch in your own repository, go to “Settings” -> “Branches”.

+
+
+

Summary

+
    +
  • We used all the same pieces that we’ve learned previously.

  • +
  • But we successfully contributed to a collaborative project!

  • +
  • The pull request allowed us to contribute without changing directly: +this is very good when it’s not mainly our project.

  • +
+
+
+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/branch/main/credit/index.html b/branch/main/credit/index.html new file mode 100644 index 0000000..1adbd54 --- /dev/null +++ b/branch/main/credit/index.html @@ -0,0 +1,154 @@ + + + + + + + Credit — Reproducible research software development using Python documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

Credit

+

The following material (all CC-BY) was reused to create this workshop material:

+ +

(I will also summarize what changes have been made to the original material)

+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/branch/main/documentation/index.html b/branch/main/documentation/index.html new file mode 100644 index 0000000..67d8df7 --- /dev/null +++ b/branch/main/documentation/index.html @@ -0,0 +1,172 @@ + + + + + + + Code documentation — Reproducible research software development using Python documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

Code documentation

+
    +
  • 15 min: What makes good documentation? Also https://diataxis.fr/

  • +
  • 15 min: Writing good README files

  • +
  • 30 min: Exercise: Set up a Sphinx documentation and add API documentation

  • +
  • 15 min: Building documentation with GitHub Actions

  • +
+

requirements.txt:

+
sphinx
+sphinx_rtd_theme >= 2.0
+sphinx_autobuild
+sphinx_autoapi
+myst_parser
+
+
+

conf.py:

+
extensions = [
+    "myst_parser",
+    "autoapi.extension",
+]
+
+autoapi_dirs = ['..']
+
+
+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/branch/main/example/index.html b/branch/main/example/index.html new file mode 100644 index 0000000..236ddb1 --- /dev/null +++ b/branch/main/example/index.html @@ -0,0 +1,235 @@ + + + + + + + Example project: Simulating the motion of planets — Reproducible research software development using Python documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+
    +
  • + +
  • + Edit on GitHub +
  • +
+
+
+
+
+ +
+

Example project: Simulating the motion of planets

+

The example code that we will study +is a hopefully simple N-body simulation written in Python. It is not important +or expected that we understand the code in any detail.

+

The big picture is that the code simulates the motion of a number of +planets:

+
    +
  • We can choose the number of planets.

  • +
  • Each planet starts with a random position, velocity, and mass.

  • +
  • At each time step, the code calculates the gravitational force between each +pair of planets.

  • +
  • The forces accelerate each planet, the acceleration modifies the velocity, +the velocity modifies the position of each planet.

  • +
  • We can choose the number of time steps.

  • +
  • The units were chosen to make numbers easy to read.

  • +
+
+

Example run

+
+

Instructor note

+

The instructor demonstrates running the code on their computer.

+
+

The code is written to accept command-line arguments to specify the number +of planets and the number of time steps.

+

We first generate starting data:

+
$ python generate-data.py --num-planets 10 --output-file initial.csv
+
+
+

The generated file (initial.csv) could look like this:

+
px,py,pz,vx,vy,vz,mass
+-46.88,-42.51,88.33,-0.86,-0.18,0.55,6.70
+-5.29,17.09,-96.13,0.66,0.45,-0.17,3.51
+83.53,-92.83,-68.77,-0.26,-0.48,0.24,6.84
+-36.31,25.48,64.16,0.85,0.75,-0.56,1.53
+-68.38,-17.21,-97.07,0.60,0.26,0.69,6.63
+-48.37,-48.74,3.92,-0.92,-0.33,-0.93,8.60
+40.53,-75.50,44.18,-0.62,-0.31,-0.53,8.04
+-27.21,10.78,-78.82,-0.09,-0.55,-0.03,5.35
+88.42,-74.95,-45.85,0.81,0.68,0.56,5.36
+39.09,53.12,-59.54,-0.54,0.56,0.07,8.98
+
+
+

Then we can simulate their motion (in this case for 20 steps):

+
$ python simulate.py --num-steps 20 \
+                     --input-file initial.csv \
+                     --output-file final.csv
+
+
+

The --output-file (final.csv) is again a CSV file (comma-separated values) +and contains the final positions of all planets.

+

It is possible to run on multiple cores and to animate the result. +Here is an example with 100 planets:

+
$ python generate-data.py --num-planets 100 --output-file initial.csv
+
+$ python simulate.py --num-steps 50 \
+                     --input-file initial.csv \
+                     --output-file final.csv \
+                     --trajectories-file trajectories.npz \
+                     --num-cores 8
+
+$ python animate.py --initial-file initial.csv \
+                    --trajectories-file trajectories.npz \
+                    --output-file animation.mp4
+
+
+
+

Learning goals

+
    +
  • What are the most important steps to make this code reusable by others +and our future selves?

  • +
  • Be able to apply these techniques to your own code/script.

  • +
+
+
+

We will not focus on …

+
    +
  • … how the code works internally in detail.

  • +
  • … whether this is the most efficient algorithm.

  • +
  • … whether the code is numerically stable.

  • +
  • … how to code scales with the number of cores.

  • +
  • … whether it is portable to other operating systems (we will discuss this later).

  • +
+
+
+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/branch/main/genindex/index.html b/branch/main/genindex/index.html new file mode 100644 index 0000000..4978e0b --- /dev/null +++ b/branch/main/genindex/index.html @@ -0,0 +1,147 @@ + + + + + + Index — Reproducible research software development using Python documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/branch/main/index.html b/branch/main/index.html new file mode 100644 index 0000000..7e4b10d --- /dev/null +++ b/branch/main/index.html @@ -0,0 +1,310 @@ + + + + + + + Reproducible research software development using Python — Reproducible research software development using Python documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+
    +
  • + +
  • + Edit on GitHub +
  • +
+
+
+
+
+ +
+

Reproducible research software development using Python

+
+

Big-picture goal

+

This is a hands-on course on research software engineering. In this +workshop we assume that most workshop participants use Python in their work or +a leading a group which uses Python. Therefore, some of the examples will use +Python as the example language.

+

We will work with an example project and go through all the steps of a typical +software project. Once we have seen the building blocks, we will try to apply +them to own projects. Workshop participants will receive and also learn to give +constructive code feedback.

+
+
+

Prerequisites

+
+

Preparation

+
    +
  1. Get a GitHub account following these instructions.

  2. +
  3. You will need a text editor. If you don’t have a favorite one, we recommend +VS Code.

  4. +
  5. If you prefer to work in the terminal and not in VS Code, set up these two (skip this if you use VS Code):

    + +
  6. +
  7. One of these two software environments (if you are not sure which one to +choose or have no preference, choose Conda):

    + +
  8. +
  9. Optional and only on Linux: Apptainer following +these instructions.

  10. +
+
+
+
+

Schedule

+
+

Note

+

The schedule will very soon contain links to lesson material and exercises.

+
+
+

Day 1

+
    +
  • 13:00-13:30 - Welcome and introduction

    + +
  • +
  • 13:30-14:45 (1.25h) - Introduction to version control with Git and GitHub (1/2)

    +
      +
    • Creating a repository and porting your project to Git and GitHub

    • +
    • Basic commands

    • +
    +
  • +
  • 15:00-16:30 (1.5h) - Introduction to version control with Git and GitHub (2/2)

    +
      +
    • Branching and merging

    • +
    • Recovering from typical mistakes

    • +
    +
  • +
  • 16:45-18:00 - Code documentation

    +
      +
    • In-code documentation including docstrings

    • +
    • Writing good README files

    • +
    • Markdown

    • +
    • Sphinx

    • +
    • Building documentation with GitHub Actions

    • +
    • Jupyter Notebooks

    • +
    +
  • +
+
+
+

Day 2

+ +
+
+

Day 3

+
    +
  • 09:00-10:30 - Automated testing

    +
      +
    • Unit tests

    • +
    • End-to-end tests

    • +
    • pytest

    • +
    • GitHub Actions

    • +
    +
  • +
  • 10:45-12:15 - How to make the project more reusable

    +
      +
    • Tracking dependencies with requirements.txt and environment.yml

    • +
    • Recording environments in containers

    • +
    +
  • +
  • 13:00-14:45 - Code quality and good practices

    +
      +
    • Naming (and other) conventions, project organization, modularity

    • +
    • Refactoring (explained through examples)

    • +
    • Design patterns: functional design vs. object-oriented design

    • +
    • How to design your code before writing it

    • +
    • Structuring larger software projects in a modular way

    • +
    • Command-line interfaces

    • +
    • Workflows with Snakemake

    • +
    +
  • +
  • 15:00-16:30 - How to release and publish your code

    +
      +
    • Licenses

    • +
    • Publishing the code via Zenodo

    • +
    • Packaging the code

    • +
    • Sharing the code via PyPI

    • +
    +
  • +
  • 16:45-18:00 - Debriefing and Q&A

    +
      +
    • Participants work on their projects

    • +
    • Together we study actual codes that participants wrote or work on

    • +
    • Constructively we discuss possible improvements

    • +
    • Give individual feedback on code projects

    • +
    +
  • +
+
+
+

If we have time left

+ +
+
+
+
+
+
+
+
+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/branch/main/installation/conda/index.html b/branch/main/installation/conda/index.html new file mode 100644 index 0000000..7f0b7c6 --- /dev/null +++ b/branch/main/installation/conda/index.html @@ -0,0 +1,255 @@ + + + + + + + Conda environment — Reproducible research software development using Python documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

Conda environment

+

A Conda environment is an isolated software environment that is used to manage dependencies for a project +and you decide where it is located.

+

You will need a environment.yml file that documents the dependencies:

+
name: coderefinery
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - python >= 3.10
+  - black
+  - click
+  - flit
+  - ipywidgets
+  - isort
+  - jupyterlab
+  - jupyterlab_code_formatter
+  - jupyterlab-git
+  - matplotlib
+  - myst-parser
+  - nbdime
+  - numpy
+  - pandas
+  - pytest
+  - pytest-cov
+  - scalene
+  - seaborn
+  - snakemake-minimal
+  - sphinx
+  - sphinx-autoapi
+  - sphinx-autobuild
+  - sphinx_rtd_theme >= 2.0
+  - vulture
+  - scikit-image
+
+
+
+

Before you create a virtual environment

+
    +
  1. Create a new directory for this course.

  2. +
  3. In this directory, create an environment.yml file and copy-paste the dependencies above into it.

  4. +
+
+
+

Choose the tool to manage the environment

+

If you are already using one of these tools, please continue using the tool that you like and know. +If you are new to this, we recommend using Miniconda or Miniforge.

+
    +
  • Anaconda

    +
      +
    • Advantages: easy to install, easy to use, good for beginners

    • +
    • Disadvantages: large download, installs more than we will need, license restrictions

    • +
    +
  • +
  • Miniconda

    +
      +
    • Advantages: small size, installs only what you need

    • +
    • Disadvantages: no graphical interface, license restrictions

    • +
    +
  • +
  • Miniforge

    +
      +
    • Advantages: small size, no license restrictions

    • +
    • Disadvantages: no graphical interface

    • +
    +
  • +
  • Micromamba

    +
      +
    • Advantages: fast, small size

    • +
    • Disadvantages: no graphical interface

    • +
    +
  • +
  • Pixi

    +
      +
    • Advantages: fast and new

    • +
    • Disadvantages: new and less tested and not documented here

    • +
    +
  • +
+
+
+

Creating the virtual environment

+
    +
  1. Open your terminal shell (e.g. Bash or Zsh).

  2. +
  3. Activate conda using conda activate or source ~/miniconda3/bin/activate.

  4. +
  5. Run the following command:

    +
    $ conda env create --file environment.yml
    +
    +
    +
  6. +
  7. Make sure that you see “coderefinery” in the output when you ask for a list of all available environments:

    +
    $ conda env list
    +
    +
    +
  8. +
+
+
+

How to verify that this worked

+

(this will be added)

+
+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/branch/main/installation/virtual-environment/index.html b/branch/main/installation/virtual-environment/index.html new file mode 100644 index 0000000..6cf88ee --- /dev/null +++ b/branch/main/installation/virtual-environment/index.html @@ -0,0 +1,220 @@ + + + + + + + Virtual environment — Reproducible research software development using Python documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

Virtual environment

+

A virtual environment is an isolated software environment that is used to manage dependencies for a project +and you decide where it is located.

+

You will need a requirements.txt file that documents the dependencies:

+
black
+click
+flit
+ipywidgets
+isort
+jupyterlab
+jupyterlab-code-formatter
+jupyterlab-git
+matplotlib
+myst-parser
+nbdime
+numpy
+pandas
+pytest
+pytest-cov
+scalene
+seaborn
+sphinx
+sphinx-autoapi
+sphinx-autobuild
+sphinx_rtd_theme >= 2.0
+vulture
+scikit-image
+
+
+
+

Before you create a virtual environment

+
    +
  1. Create a new directory for this course.

  2. +
  3. In this directory, create a requirements.txt file and copy-paste the dependencies above into it.

  4. +
+
+
+

Creating the virtual environment

+

Now create a virtual environment in this directory either using pip and +venv +(more traditional and safer) or using uv (more modern but also less tested):

+
+

Create a new virtual environment and activate it:

+
$ python3 -m venv coderefinery-environment
+$ source coderefinery-environment/bin/activate
+
+
+

Install the dependencies into the environment:

+
$ python3 -m pip install -r requirements.txt
+
+
+
+
+
+

How to verify that this worked

+

(this will be added)

+
+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/branch/main/lesson.pdf b/branch/main/lesson.pdf new file mode 100644 index 0000000..96348bb Binary files /dev/null and b/branch/main/lesson.pdf differ diff --git a/branch/main/objects.inv b/branch/main/objects.inv new file mode 100644 index 0000000..1523d5d --- /dev/null +++ b/branch/main/objects.inv @@ -0,0 +1,7 @@ +# Sphinx inventory version 2 +# Project: Reproducible research software development using Python +# Version: +# The remainder of this file is compressed using zlib. +xڭV=0 +FۊCv(ɢ+ɥ)vZ\$#H(!pVpaG͏Y - +M!&X=;X.ʔ,$K|"DqKƞg`g.oQ3n֍$)70j̥ruNlVC}?rG*=hKnH5 +\)U=hEMrmTmvئ_?5;}!B';-Lp]c끉\Zh)V:Ih:C_Q-2q齮ۉ,ɳ 2X@N\/eߛ{4T8 30IYY45 RBwYۀA:umb[qKcf7Fl2` 3&j+4|8(W=]Ӈ8)9 =Àk4l{:|'mx )Hw>E{UF8,h{̮ڸ94S*tw&vd"U‰umznwREi=,9satt QӚ@||K9f,wxVƨX.z򜽳;;D`[5j9H;)[3ȝg9ʊ \ No newline at end of file diff --git a/branch/main/profiling/index.html b/branch/main/profiling/index.html new file mode 100644 index 0000000..32e95d4 --- /dev/null +++ b/branch/main/profiling/index.html @@ -0,0 +1,161 @@ + + + + + + + Profiling memory and CPU usage — Reproducible research software development using Python documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

Profiling memory and CPU usage

+

Profilers:

+
    +
  • cProfile or profile

  • +
  • line_profiler

  • +
  • viztracer

  • +
  • scalene

  • +
  • Intel VTune

  • +
  • PyInstrument

  • +
  • py-spy

  • +
  • Pyflame

  • +
  • timeit

  • +
+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/branch/main/publishing/index.html b/branch/main/publishing/index.html new file mode 100644 index 0000000..810737e --- /dev/null +++ b/branch/main/publishing/index.html @@ -0,0 +1,159 @@ + + + + + + + How to release and publish your code — Reproducible research software development using Python documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

How to release and publish your code

+

Part 1:

+
    +
  • 30 min: Overview over software licenses and code publishing

  • +
  • 15 min: We add a license, CFF file, and publish to Zenodo (sandbox)

  • +
+

Part 2:

+
    +
  • 30 min: Creating a Python package with the help of flit

  • +
  • 15 min: Deploy the package to test-PyPI using GitHub Actions

  • +
+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/branch/main/refactoring/index.html b/branch/main/refactoring/index.html new file mode 100644 index 0000000..1322aa6 --- /dev/null +++ b/branch/main/refactoring/index.html @@ -0,0 +1,234 @@ + + + + + + + Code quality and good practices — Reproducible research software development using Python documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

Code quality and good practices

+

In this episode we will explore code quality and good practices in Python using +a hands-on approach. We will together build up a small project and improve it +step by step.

+

We will start from a relatively simple image processing script which can read a +telescope image of stars and our goal is to count the number of stars in +the image. Later we will want to be able to process many such images.

+

The (fictional) telescope images look like the one below here (in this +repository we can find more):

+
+Generated image representing a telescope image of stars +
+

Generated image representing a telescope image of stars.

+
+
+ +

Part 1:

+
    +
  • 15 min: Discuss how we would solve the problem, run example code, and make it work +as part of a Jupyter notebook.

  • +
  • 15 min: Refactor the positioning code into a function and a module

  • +
  • 15 min: Now we wish to process many images - discuss how we would approach this

  • +
  • 15 min: Introduce CLI and discuss the benefits

  • +
+

Part 2:

+
    +
  • 30 min: From a script to a workflow (using Snakemake)

  • +
  • 15 min: Discuss concepts

    +
      +
    • Pure functions

    • +
    • Design patterns: functional design vs. object-oriented design

    • +
    • How to design your code before writing it: document-driven development

    • +
    +
  • +
+

Bonus:

+
    +
  • Move it under Git

  • +
  • Document dependencies

  • +
  • Show nbdime, black, vulture, ruff

  • +
+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/branch/main/reusable/index.html b/branch/main/reusable/index.html new file mode 100644 index 0000000..3558af4 --- /dev/null +++ b/branch/main/reusable/index.html @@ -0,0 +1,161 @@ + + + + + + + How to make the project more reusable — Reproducible research software development using Python documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

How to make the project more reusable

+

Part 1:

+
    +
  • 15 min: Motivation

  • +
  • 15 min: Best practices for managing dependencies in Python

  • +
  • 20 min: Exercise

  • +
+

Part 2:

+
    +
  • 10 min: Introduction to containers

  • +
  • 20 min: Demonstration

  • +
  • 10 min: Discussion

  • +
+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/branch/main/search/index.html b/branch/main/search/index.html new file mode 100644 index 0000000..815f5aa --- /dev/null +++ b/branch/main/search/index.html @@ -0,0 +1,161 @@ + + + + + + Search — Reproducible research software development using Python documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+
    +
  • + +
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+
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+
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+ + + + +
+ +
+ +
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+ +
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+
+ + + + + + + + + \ No newline at end of file diff --git a/branch/main/searchindex.js b/branch/main/searchindex.js new file mode 100644 index 0000000..d91106a --- /dev/null +++ b/branch/main/searchindex.js @@ -0,0 +1 @@ +Search.setIndex({"alltitles": {"(1) Opening an issue": [[5, "opening-an-issue"]], "(2) Create a new branch.": [[5, "create-a-new-branch"]], "(3) Make a change adding the recipe": [[5, "make-a-change-adding-the-recipe"]], "(4) Push to GitHub as a new branch": [[5, "push-to-github-as-a-new-branch"]], "(5) Open a pull request towards the main branch": [[5, "open-a-pull-request-towards-the-main-branch"]], "(6) Reviewing pull requests": [[5, "reviewing-pull-requests"]], "(7) Draft pull requests": [[5, "draft-pull-requests"]], "Automated testing": [[16, null]], "Before you create a virtual environment": [[10, "before-you-create-a-virtual-environment"], [11, "before-you-create-a-virtual-environment"]], "Big-picture goal": [[9, "big-picture-goal"]], "Choose the tool to manage the environment": [[10, "choose-the-tool-to-manage-the-environment"]], "Cloning a repository": [[2, "cloning-a-repository"]], "Code documentation": [[7, null]], "Code quality and good practices": [[14, null]], "Collaborating within the same repository": [[5, null]], "Collaborative version control and code review": [[0, null]], "Commits, branches, repositories, forks, clones": [[2, "commits-branches-repositories-forks-clones"]], "Concepts around collaboration": [[2, null]], "Conclict resolution, rebasing, and organizational strategies": [[3, null]], "Conda environment": [[10, null]], "Creating the virtual environment": [[10, "creating-the-virtual-environment"], [11, "creating-the-virtual-environment"]], "Credit": [[6, null]], "Cross-referencing issues and pull requests": [[5, "cross-referencing-issues-and-pull-requests"]], "Day 1": [[9, "day-1"]], "Day 2": [[9, "day-2"]], "Day 3": [[9, "day-3"]], "Example project: Simulating the motion of planets": [[8, null]], "Example run": [[8, "example-run"]], "Exercise": [[1, "exercise"], [4, "exercise"], [5, "exercise"]], "Exercise preparation": [[1, "prerequisites-0"], [4, "prerequisites-0"], [5, "prerequisites-0"]], "Exercise: Collaborating within the same repository (25 min)": [[4, "exercise-0"], [5, "exercise-0"]], "Exercise: Practicing code review (25 min)": [[1, "exercise-0"]], "Forking a repository": [[2, "forking-a-repository"]], "Help and discussion": [[1, "help-and-discussion"], [4, "help-and-discussion"]], "Help! I don\u2019t have permissions to push my local changes": [[4, "help-i-don-t-have-permissions-to-push-my-local-changes"]], "How to approach other people\u2019s repositories with ideas, changes, and requests": [[4, "how-to-approach-other-peoples-repositories-with-ideas-changes-and-requests"]], "How to ask for changes in a pull request": [[1, "how-to-ask-for-changes-in-a-pull-request"]], "How to contribute changes to repositories that belong to others": [[4, null]], "How to make the project more reusable": [[15, null]], "How to modify a pull request to address the review comments": [[1, "how-to-modify-a-pull-request-to-address-the-review-comments"]], "How to release and publish your code": [[13, null]], "How to suggest a change in a pull request as a reviewer": [[1, "how-to-suggest-a-change-in-a-pull-request-as-a-reviewer"]], "How to update your fork with changes from upstream": [[4, "how-to-update-your-fork-with-changes-from-upstream"]], "How to verify that this worked": [[10, "how-to-verify-that-this-worked"], [11, "how-to-verify-that-this-worked"]], "If we have time left": [[9, "if-we-have-time-left"]], "Instructor note": [[8, "instructor-note-0"]], "Learning goals": [[8, null]], "Motivation": [[4, null], [4, null]], "Objectives": [[2, "objectives-0"]], "Opening a pull request towards the upstream repository": [[4, "opening-a-pull-request-towards-the-upstream-repository"]], "Practicing code review": [[1, null]], "Preparation": [[9, "prerequisites-0"]], "Prerequisites": [[9, "prerequisites"]], "Profiling memory and CPU usage": [[12, null]], "Pull requests can be coupled with automated testing": [[4, "pull-requests-can-be-coupled-with-automated-testing"]], "Recovery": [[4, "solution-0"]], "Reproducible research software development using Python": [[9, null]], "Schedule": [[9, "schedule"]], "Solution and hints": [[5, "solution-and-hints"]], "Starting point (spoiler alert)": [[14, "solution-0"]], "Summary": [[1, "summary"], [4, "summary"], [5, "summary"]], "Synchronizing changes between repositories": [[2, "synchronizing-changes-between-repositories"]], "Virtual environment": [[11, null]], "We will not focus on \u2026": [[8, null]], "What is a protected branch? 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jQuery and underscores.js. + * + * Copyright Sphinx contributors + * Released under the two clause BSD licence + */ + +/** + * small helper function to urldecode strings + * + * See https://developer.mozilla.org/en-US/docs/Web/JavaScript/Reference/Global_Objects/decodeURIComponent#Decoding_query_parameters_from_a_URL + */ +jQuery.urldecode = function(x) { + if (!x) { + return x + } + return decodeURIComponent(x.replace(/\+/g, ' ')); +}; + +/** + * small helper function to urlencode strings + */ +jQuery.urlencode = encodeURIComponent; + +/** + * This function returns the parsed url parameters of the + * current request. Multiple values per key are supported, + * it will always return arrays of strings for the value parts. + */ +jQuery.getQueryParameters = function(s) { + if (typeof s === 'undefined') + s = document.location.search; + var parts = s.substr(s.indexOf('?') + 1).split('&'); + var result = {}; + for (var i = 0; i < parts.length; i++) { + var tmp = parts[i].split('=', 2); + var key = jQuery.urldecode(tmp[0]); + var value = jQuery.urldecode(tmp[1]); + if (key in result) + result[key].push(value); + else + result[key] = [value]; + } + return result; +}; + +/** + * highlight a given string on a jquery object by wrapping it in + * span elements with the given class name. + */ +jQuery.fn.highlightText = function(text, className) { + function highlight(node, addItems) { + if (node.nodeType === 3) { + var val = node.nodeValue; + var pos = val.toLowerCase().indexOf(text); + if (pos >= 0 && + !jQuery(node.parentNode).hasClass(className) && + !jQuery(node.parentNode).hasClass("nohighlight")) { + var span; + var isInSVG = jQuery(node).closest("body, svg, foreignObject").is("svg"); + if (isInSVG) { + span = document.createElementNS("http://www.w3.org/2000/svg", "tspan"); + } else { + span = document.createElement("span"); + span.className = className; + } + span.appendChild(document.createTextNode(val.substr(pos, text.length))); + node.parentNode.insertBefore(span, node.parentNode.insertBefore( + document.createTextNode(val.substr(pos + text.length)), + node.nextSibling)); + node.nodeValue = val.substr(0, pos); + if (isInSVG) { + var rect = document.createElementNS("http://www.w3.org/2000/svg", "rect"); + var bbox = node.parentElement.getBBox(); + rect.x.baseVal.value = bbox.x; + rect.y.baseVal.value = bbox.y; + rect.width.baseVal.value = bbox.width; + rect.height.baseVal.value = bbox.height; + rect.setAttribute('class', className); + addItems.push({ + "parent": node.parentNode, + "target": rect}); + } + } + } + else if (!jQuery(node).is("button, select, textarea")) { + jQuery.each(node.childNodes, function() { + highlight(this, addItems); + }); + } + } + var addItems = []; + var result = this.each(function() { + highlight(this, addItems); + }); + for (var i = 0; i < addItems.length; ++i) { + jQuery(addItems[i].parent).before(addItems[i].target); + } + return result; +}; + +/* + * backward compatibility for jQuery.browser + * This will be supported until firefox bug is fixed. + */ +if (!jQuery.browser) { + jQuery.uaMatch = function(ua) { + ua = ua.toLowerCase(); + + var match = /(chrome)[ \/]([\w.]+)/.exec(ua) || + /(webkit)[ \/]([\w.]+)/.exec(ua) || + /(opera)(?:.*version|)[ \/]([\w.]+)/.exec(ua) || + /(msie) ([\w.]+)/.exec(ua) || + ua.indexOf("compatible") < 0 && /(mozilla)(?:.*? rv:([\w.]+)|)/.exec(ua) || + []; + + return { + browser: match[ 1 ] || "", + version: match[ 2 ] || "0" + }; + }; + jQuery.browser = {}; + jQuery.browser[jQuery.uaMatch(navigator.userAgent).browser] = true; +} diff --git a/branch/main/singlehtml/_static/basic.css b/branch/main/singlehtml/_static/basic.css new file mode 100644 index 0000000..f316efc --- /dev/null +++ b/branch/main/singlehtml/_static/basic.css @@ -0,0 +1,925 @@ +/* + * basic.css + * ~~~~~~~~~ + * + * Sphinx stylesheet -- basic theme. + * + * :copyright: Copyright 2007-2024 by the Sphinx team, see AUTHORS. + * :license: BSD, see LICENSE for details. + * + */ + +/* -- main layout ----------------------------------------------------------- */ + +div.clearer { + clear: both; +} + +div.section::after { + display: block; + content: ''; + clear: left; +} + +/* -- relbar ---------------------------------------------------------------- */ + +div.related { + width: 100%; + font-size: 90%; +} + +div.related h3 { + display: none; +} + +div.related ul { + margin: 0; + padding: 0 0 0 10px; + list-style: none; +} + +div.related li { + display: inline; +} + +div.related li.right { + float: right; + margin-right: 5px; +} + +/* -- sidebar --------------------------------------------------------------- */ + +div.sphinxsidebarwrapper { + padding: 10px 5px 0 10px; +} + +div.sphinxsidebar { + float: left; + width: 230px; + margin-left: -100%; + font-size: 90%; + word-wrap: break-word; + overflow-wrap : break-word; +} + +div.sphinxsidebar ul { + list-style: none; +} + +div.sphinxsidebar ul ul, +div.sphinxsidebar ul.want-points { + margin-left: 20px; + list-style: square; +} + +div.sphinxsidebar ul ul { + margin-top: 0; + margin-bottom: 0; +} + +div.sphinxsidebar form { + margin-top: 10px; +} + +div.sphinxsidebar input { + border: 1px solid #98dbcc; + font-family: sans-serif; + font-size: 1em; +} + +div.sphinxsidebar #searchbox form.search { + overflow: hidden; +} + +div.sphinxsidebar #searchbox input[type="text"] { + float: left; + width: 80%; + padding: 0.25em; + box-sizing: border-box; +} + +div.sphinxsidebar #searchbox input[type="submit"] { + float: left; + width: 20%; + border-left: none; + padding: 0.25em; + box-sizing: border-box; +} + + +img { + border: 0; + max-width: 100%; +} + +/* -- search page ----------------------------------------------------------- */ + +ul.search { + margin: 10px 0 0 20px; + padding: 0; +} + +ul.search li { + padding: 5px 0 5px 20px; + background-image: url(file.png); + background-repeat: no-repeat; + background-position: 0 7px; +} + +ul.search li a { + font-weight: bold; +} + +ul.search li p.context { + color: #888; + margin: 2px 0 0 30px; + text-align: left; +} + +ul.keywordmatches li.goodmatch a { + font-weight: bold; +} + +/* -- index page ------------------------------------------------------------ */ + +table.contentstable { + width: 90%; + margin-left: auto; + margin-right: auto; +} + +table.contentstable p.biglink { + line-height: 150%; +} + +a.biglink { + font-size: 1.3em; +} + +span.linkdescr { + font-style: italic; + padding-top: 5px; + font-size: 90%; +} + +/* -- general index --------------------------------------------------------- */ + +table.indextable { + width: 100%; +} + +table.indextable td { + text-align: left; + vertical-align: top; +} + +table.indextable ul { + margin-top: 0; + margin-bottom: 0; + list-style-type: none; +} + +table.indextable > tbody > tr > td > ul { + padding-left: 0em; +} + +table.indextable tr.pcap { + height: 10px; +} + +table.indextable tr.cap { + margin-top: 10px; + background-color: #f2f2f2; +} + +img.toggler { + margin-right: 3px; + margin-top: 3px; + cursor: pointer; +} + +div.modindex-jumpbox { + border-top: 1px solid #ddd; + border-bottom: 1px solid #ddd; + margin: 1em 0 1em 0; + padding: 0.4em; +} + +div.genindex-jumpbox { + border-top: 1px solid #ddd; + border-bottom: 1px solid #ddd; + margin: 1em 0 1em 0; + padding: 0.4em; +} + +/* -- domain module index --------------------------------------------------- */ + +table.modindextable td { + padding: 2px; + border-collapse: collapse; +} + +/* -- general body styles --------------------------------------------------- */ + +div.body { + min-width: 360px; + max-width: 800px; +} + +div.body p, div.body dd, div.body li, div.body blockquote { + -moz-hyphens: auto; + -ms-hyphens: auto; + -webkit-hyphens: auto; + hyphens: auto; +} + +a.headerlink { + visibility: hidden; +} + +a:visited { + color: #551A8B; +} + +h1:hover > a.headerlink, +h2:hover > a.headerlink, +h3:hover > a.headerlink, +h4:hover > a.headerlink, +h5:hover > a.headerlink, +h6:hover > a.headerlink, +dt:hover > a.headerlink, +caption:hover > a.headerlink, +p.caption:hover > a.headerlink, +div.code-block-caption:hover > a.headerlink { + visibility: visible; +} + +div.body p.caption { + text-align: inherit; +} + +div.body td { + text-align: left; +} + +.first { + margin-top: 0 !important; +} + +p.rubric { + margin-top: 30px; + font-weight: bold; +} + +img.align-left, figure.align-left, .figure.align-left, object.align-left { + clear: left; + float: left; + margin-right: 1em; +} + +img.align-right, figure.align-right, .figure.align-right, object.align-right { + clear: right; + float: right; + margin-left: 1em; +} + +img.align-center, figure.align-center, .figure.align-center, object.align-center { + display: block; + margin-left: auto; + margin-right: auto; +} + +img.align-default, figure.align-default, .figure.align-default { + display: block; + margin-left: auto; + margin-right: auto; +} + +.align-left { + text-align: left; +} + +.align-center { + text-align: center; +} + +.align-default { + text-align: center; +} + +.align-right { + text-align: right; +} + +/* -- sidebars -------------------------------------------------------------- */ + +div.sidebar, +aside.sidebar { + margin: 0 0 0.5em 1em; + border: 1px solid #ddb; + padding: 7px; + background-color: #ffe; + width: 40%; + float: right; + clear: right; + overflow-x: auto; +} + +p.sidebar-title { + font-weight: bold; +} + +nav.contents, +aside.topic, +div.admonition, div.topic, blockquote { + clear: left; +} + +/* -- topics ---------------------------------------------------------------- */ + +nav.contents, +aside.topic, +div.topic { + border: 1px solid #ccc; + padding: 7px; + margin: 10px 0 10px 0; +} + +p.topic-title { + font-size: 1.1em; + font-weight: bold; + margin-top: 10px; +} + +/* -- admonitions ----------------------------------------------------------- */ + +div.admonition { + margin-top: 10px; + margin-bottom: 10px; + padding: 7px; +} + +div.admonition dt { + font-weight: bold; +} + +p.admonition-title { + margin: 0px 10px 5px 0px; + font-weight: bold; +} + +div.body p.centered { + text-align: center; + margin-top: 25px; +} + +/* -- content of sidebars/topics/admonitions -------------------------------- */ + +div.sidebar > :last-child, +aside.sidebar > :last-child, +nav.contents > :last-child, +aside.topic > :last-child, +div.topic > :last-child, +div.admonition > :last-child { + margin-bottom: 0; +} + +div.sidebar::after, +aside.sidebar::after, +nav.contents::after, +aside.topic::after, +div.topic::after, +div.admonition::after, +blockquote::after { + display: block; + content: ''; + clear: both; +} + +/* -- tables ---------------------------------------------------------------- */ + +table.docutils { + margin-top: 10px; + margin-bottom: 10px; + border: 0; + border-collapse: collapse; +} + +table.align-center { + margin-left: auto; + margin-right: auto; +} + +table.align-default { + margin-left: auto; + margin-right: auto; +} + +table caption span.caption-number { + font-style: italic; +} + +table caption span.caption-text { +} + +table.docutils td, table.docutils th { + padding: 1px 8px 1px 5px; + border-top: 0; + border-left: 0; + border-right: 0; + border-bottom: 1px solid #aaa; +} + +th { + text-align: left; + padding-right: 5px; +} + +table.citation { + border-left: solid 1px gray; + margin-left: 1px; +} + +table.citation td { + border-bottom: none; +} + +th > :first-child, +td > :first-child { + margin-top: 0px; +} + +th > :last-child, +td > :last-child { + margin-bottom: 0px; +} + +/* -- figures --------------------------------------------------------------- */ + +div.figure, figure { + margin: 0.5em; + padding: 0.5em; +} + +div.figure p.caption, figcaption { + padding: 0.3em; +} + +div.figure p.caption span.caption-number, +figcaption span.caption-number { + font-style: italic; +} + +div.figure p.caption span.caption-text, +figcaption span.caption-text { +} + +/* -- field list styles ----------------------------------------------------- */ + +table.field-list td, table.field-list th { + border: 0 !important; +} + +.field-list ul { + margin: 0; + padding-left: 1em; +} + +.field-list p { + margin: 0; +} + +.field-name { + -moz-hyphens: manual; + -ms-hyphens: manual; + -webkit-hyphens: manual; + hyphens: manual; +} + +/* -- hlist styles ---------------------------------------------------------- */ + +table.hlist { + margin: 1em 0; +} + +table.hlist td { + vertical-align: top; +} + +/* -- object description styles --------------------------------------------- */ + +.sig { + font-family: 'Consolas', 'Menlo', 'DejaVu Sans Mono', 'Bitstream Vera Sans Mono', monospace; +} + +.sig-name, code.descname { + background-color: transparent; + font-weight: bold; +} + +.sig-name { + font-size: 1.1em; +} + +code.descname { + font-size: 1.2em; +} + +.sig-prename, code.descclassname { + background-color: transparent; +} + +.optional { + font-size: 1.3em; +} + +.sig-paren { + font-size: larger; +} + +.sig-param.n { + font-style: italic; +} + +/* C++ specific styling */ + +.sig-inline.c-texpr, +.sig-inline.cpp-texpr { + font-family: unset; +} + +.sig.c .k, .sig.c .kt, +.sig.cpp .k, .sig.cpp .kt { + color: #0033B3; +} + +.sig.c .m, +.sig.cpp .m { + color: #1750EB; +} + +.sig.c .s, .sig.c .sc, +.sig.cpp .s, .sig.cpp .sc { + color: #067D17; +} + + +/* -- other body styles ----------------------------------------------------- */ + +ol.arabic { + list-style: decimal; +} + +ol.loweralpha { + list-style: lower-alpha; +} + +ol.upperalpha { + list-style: upper-alpha; +} + +ol.lowerroman { + list-style: lower-roman; +} + +ol.upperroman { + list-style: upper-roman; +} + +:not(li) > ol > li:first-child > :first-child, +:not(li) > ul > li:first-child > :first-child { + margin-top: 0px; +} + +:not(li) > ol > li:last-child > :last-child, +:not(li) > ul > li:last-child > :last-child { + margin-bottom: 0px; +} + +ol.simple ol p, +ol.simple ul p, +ul.simple ol p, +ul.simple ul p { + margin-top: 0; +} + +ol.simple > li:not(:first-child) > p, +ul.simple > li:not(:first-child) > p { + margin-top: 0; +} + +ol.simple p, +ul.simple p { + margin-bottom: 0; +} + +aside.footnote > span, +div.citation > span { + float: left; +} +aside.footnote > span:last-of-type, +div.citation > span:last-of-type { + padding-right: 0.5em; +} +aside.footnote > p { + margin-left: 2em; +} +div.citation > p { + margin-left: 4em; +} +aside.footnote > p:last-of-type, +div.citation > p:last-of-type { + margin-bottom: 0em; +} +aside.footnote > p:last-of-type:after, +div.citation > p:last-of-type:after { + content: ""; + clear: both; +} + +dl.field-list { + display: grid; + grid-template-columns: fit-content(30%) auto; +} + +dl.field-list > dt { + font-weight: bold; + word-break: break-word; + padding-left: 0.5em; + padding-right: 5px; +} + +dl.field-list > dd { + padding-left: 0.5em; + margin-top: 0em; + margin-left: 0em; + margin-bottom: 0em; +} + +dl { + margin-bottom: 15px; +} + +dd > :first-child { + margin-top: 0px; +} + +dd ul, dd table { + margin-bottom: 10px; +} + +dd { + margin-top: 3px; + margin-bottom: 10px; + margin-left: 30px; +} + +.sig dd { + margin-top: 0px; + margin-bottom: 0px; +} + +.sig dl { + margin-top: 0px; + margin-bottom: 0px; +} + +dl > dd:last-child, +dl > dd:last-child > :last-child { + margin-bottom: 0; +} + +dt:target, span.highlighted { + background-color: #fbe54e; +} + +rect.highlighted { + fill: #fbe54e; +} + +dl.glossary dt { + font-weight: bold; + font-size: 1.1em; +} + +.versionmodified { + font-style: italic; +} + +.system-message { + background-color: #fda; + padding: 5px; + border: 3px solid red; +} + +.footnote:target { + background-color: #ffa; +} + +.line-block { + display: block; + margin-top: 1em; + margin-bottom: 1em; +} + +.line-block .line-block { + margin-top: 0; + margin-bottom: 0; + margin-left: 1.5em; +} + +.guilabel, .menuselection { + font-family: sans-serif; +} + +.accelerator { + text-decoration: underline; +} + +.classifier { + font-style: oblique; +} + +.classifier:before { + font-style: normal; + margin: 0 0.5em; + content: ":"; + display: inline-block; +} + +abbr, acronym { + border-bottom: dotted 1px; + cursor: help; +} + +.translated { + background-color: rgba(207, 255, 207, 0.2) +} + +.untranslated { + background-color: rgba(255, 207, 207, 0.2) +} + +/* -- code displays --------------------------------------------------------- */ + +pre { + overflow: auto; + overflow-y: hidden; /* fixes display issues on Chrome browsers */ +} + +pre, div[class*="highlight-"] { + clear: both; +} + +span.pre { + -moz-hyphens: none; + -ms-hyphens: none; + -webkit-hyphens: none; + hyphens: none; + white-space: nowrap; +} + +div[class*="highlight-"] { + margin: 1em 0; +} + +td.linenos pre { + border: 0; + background-color: transparent; + color: #aaa; +} + +table.highlighttable { + display: block; +} + +table.highlighttable tbody { + display: block; +} + +table.highlighttable tr { + display: flex; +} + +table.highlighttable td { + margin: 0; + padding: 0; +} + +table.highlighttable td.linenos { + padding-right: 0.5em; +} + +table.highlighttable td.code { + flex: 1; + overflow: hidden; +} + +.highlight .hll { + display: block; +} + +div.highlight pre, +table.highlighttable pre { + margin: 0; +} + +div.code-block-caption + div { + margin-top: 0; +} + +div.code-block-caption { + margin-top: 1em; + padding: 2px 5px; + font-size: small; +} + +div.code-block-caption code { + background-color: transparent; +} + +table.highlighttable td.linenos, +span.linenos, +div.highlight span.gp { /* gp: Generic.Prompt */ + user-select: none; + -webkit-user-select: text; /* Safari fallback only */ + -webkit-user-select: none; /* Chrome/Safari */ + -moz-user-select: none; /* Firefox */ + -ms-user-select: none; /* IE10+ */ +} + +div.code-block-caption span.caption-number { + padding: 0.1em 0.3em; + font-style: italic; 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+ display: flex; + top: .3em; + right: .3em; + width: 1.7em; + height: 1.7em; + opacity: 0; + transition: opacity 0.3s, border .3s, background-color .3s; + user-select: none; + padding: 0; + border: none; + outline: none; + border-radius: 0.4em; + /* The colors that GitHub uses */ + border: #1b1f2426 1px solid; + background-color: #f6f8fa; + color: #57606a; +} + +button.copybtn.success { + border-color: #22863a; + color: #22863a; +} + +button.copybtn svg { + stroke: currentColor; + width: 1.5em; + height: 1.5em; + padding: 0.1em; +} + +div.highlight { + position: relative; +} + +.highlight:hover button.copybtn { + opacity: 1; +} + +.highlight button.copybtn:hover { + background-color: rgb(235, 235, 235); +} + +.highlight button.copybtn:active { + background-color: rgb(187, 187, 187); +} + +/** + * A minimal CSS-only tooltip copied from: + * https://codepen.io/mildrenben/pen/rVBrpK + * + * To use, write HTML like the following: + * + *

Short

+ */ + .o-tooltip--left { + position: relative; + } + + .o-tooltip--left:after { + opacity: 0; + visibility: hidden; + position: absolute; + content: attr(data-tooltip); + padding: .2em; + font-size: .8em; + left: -.2em; + background: grey; + color: white; + white-space: nowrap; + z-index: 2; + border-radius: 2px; + transform: translateX(-102%) translateY(0); + transition: opacity 0.2s cubic-bezier(0.64, 0.09, 0.08, 1), transform 0.2s cubic-bezier(0.64, 0.09, 0.08, 1); +} + +.o-tooltip--left:hover:after { + display: block; + opacity: 1; + visibility: visible; + transform: translateX(-100%) translateY(0); + transition: opacity 0.2s cubic-bezier(0.64, 0.09, 0.08, 1), transform 0.2s cubic-bezier(0.64, 0.09, 0.08, 1); + transition-delay: .5s; +} + +/* By default the copy button shouldn't show up when printing a page */ +@media print { + button.copybtn { + display: none; + } +} diff --git a/branch/main/singlehtml/_static/copybutton.js b/branch/main/singlehtml/_static/copybutton.js new file mode 100644 index 0000000..f3ecd03 --- /dev/null +++ b/branch/main/singlehtml/_static/copybutton.js @@ -0,0 +1,241 @@ +// Localization support +const messages = { + 'en': { + 'copy': 'Copy', + 'copy_to_clipboard': 'Copy to clipboard', + 'copy_success': 'Copied!', + 'copy_failure': 'Failed to copy', + }, + 'es' : { + 'copy': 'Copiar', + 'copy_to_clipboard': 'Copiar al portapapeles', + 'copy_success': '¡Copiado!', + 'copy_failure': 'Error al copiar', + }, + 'de' : { + 'copy': 'Kopieren', + 'copy_to_clipboard': 'In die Zwischenablage kopieren', + 'copy_success': 'Kopiert!', + 'copy_failure': 'Fehler beim Kopieren', + }, + 'fr' : { + 'copy': 'Copier', + 'copy_to_clipboard': 'Copié dans le presse-papier', + 'copy_success': 'Copié !', + 'copy_failure': 'Échec de la copie', + }, + 'ru': { + 'copy': 'Скопировать', + 'copy_to_clipboard': 'Скопировать в буфер', + 'copy_success': 'Скопировано!', + 'copy_failure': 'Не удалось скопировать', + }, + 'zh-CN': { + 'copy': '复制', + 'copy_to_clipboard': '复制到剪贴板', + 'copy_success': '复制成功!', + 'copy_failure': '复制失败', + }, + 'it' : { + 'copy': 'Copiare', + 'copy_to_clipboard': 'Copiato negli appunti', + 'copy_success': 'Copiato!', + 'copy_failure': 'Errore durante la copia', + } +} + +let locale = 'en' +if( document.documentElement.lang !== undefined + && messages[document.documentElement.lang] !== undefined ) { + locale = document.documentElement.lang +} + +let doc_url_root = DOCUMENTATION_OPTIONS.URL_ROOT; +if (doc_url_root == '#') { + doc_url_root = ''; +} + +/** + * SVG files for our copy buttons + */ +let iconCheck = ` + ${messages[locale]['copy_success']} + + +` + +// If the user specified their own SVG use that, otherwise use the default +let iconCopy = ``; +if (!iconCopy) { + iconCopy = ` + ${messages[locale]['copy_to_clipboard']} + + + +` +} + +/** + * Set up copy/paste for code blocks + */ + +const runWhenDOMLoaded = cb => { + if (document.readyState != 'loading') { + cb() + } else if (document.addEventListener) { + document.addEventListener('DOMContentLoaded', cb) + } else { + document.attachEvent('onreadystatechange', function() { + if (document.readyState == 'complete') cb() + }) + } +} + +const codeCellId = index => `codecell${index}` + +// Clears selected text since ClipboardJS will select the text when copying +const clearSelection = () => { + if (window.getSelection) { + window.getSelection().removeAllRanges() + } else if (document.selection) { + document.selection.empty() + } +} + +// Changes tooltip text for two seconds, then changes it back +const temporarilyChangeTooltip = (el, oldText, newText) => { + el.setAttribute('data-tooltip', newText) + el.classList.add('success') + setTimeout(() => el.setAttribute('data-tooltip', oldText), 2000) + setTimeout(() => el.classList.remove('success'), 2000) +} + +// Changes the copy button icon for two seconds, then changes it back +const temporarilyChangeIcon = (el) => { + el.innerHTML = iconCheck; + setTimeout(() => {el.innerHTML = iconCopy}, 2000) +} + +const addCopyButtonToCodeCells = () => { + // If ClipboardJS hasn't loaded, wait a bit and try again. This + // happens because we load ClipboardJS asynchronously. + if (window.ClipboardJS === undefined) { + setTimeout(addCopyButtonToCodeCells, 250) + return + } + + // Add copybuttons to all of our code cells + const COPYBUTTON_SELECTOR = 'div.highlight pre'; + const codeCells = document.querySelectorAll(COPYBUTTON_SELECTOR) + codeCells.forEach((codeCell, index) => { + const id = codeCellId(index) + codeCell.setAttribute('id', id) + + const clipboardButton = id => + `` + codeCell.insertAdjacentHTML('afterend', clipboardButton(id)) + }) + +function escapeRegExp(string) { + return string.replace(/[.*+?^${}()|[\]\\]/g, '\\$&'); // $& means the whole matched string +} + +/** + * Removes excluded text from a Node. + * + * @param {Node} target Node to filter. + * @param {string} exclude CSS selector of nodes to exclude. + * @returns {DOMString} Text from `target` with text removed. + */ +function filterText(target, exclude) { + const clone = target.cloneNode(true); // clone as to not modify the live DOM + if (exclude) { + // remove excluded nodes + clone.querySelectorAll(exclude).forEach(node => node.remove()); + } + return clone.innerText; +} + +// Callback when a copy button is clicked. Will be passed the node that was clicked +// should then grab the text and replace pieces of text that shouldn't be used in output +function formatCopyText(textContent, copybuttonPromptText, isRegexp = false, onlyCopyPromptLines = true, removePrompts = true, copyEmptyLines = true, lineContinuationChar = "", hereDocDelim = "") { + var regexp; + var match; + + // Do we check for line continuation characters and "HERE-documents"? + var useLineCont = !!lineContinuationChar + var useHereDoc = !!hereDocDelim + + // create regexp to capture prompt and remaining line + if (isRegexp) { + regexp = new RegExp('^(' + copybuttonPromptText + ')(.*)') + } else { + regexp = new RegExp('^(' + escapeRegExp(copybuttonPromptText) + ')(.*)') + } + + const outputLines = []; + var promptFound = false; + var gotLineCont = false; + var gotHereDoc = false; + const lineGotPrompt = []; + for (const line of textContent.split('\n')) { + match = line.match(regexp) + if (match || gotLineCont || gotHereDoc) { + promptFound = regexp.test(line) + lineGotPrompt.push(promptFound) + if (removePrompts && promptFound) { + outputLines.push(match[2]) + } else { + outputLines.push(line) + } + gotLineCont = line.endsWith(lineContinuationChar) & useLineCont + if (line.includes(hereDocDelim) & useHereDoc) + gotHereDoc = !gotHereDoc + } else if (!onlyCopyPromptLines) { + outputLines.push(line) + } else if (copyEmptyLines && line.trim() === '') { + outputLines.push(line) + } + } + + // If no lines with the prompt were found then just use original lines + if (lineGotPrompt.some(v => v === true)) { + textContent = outputLines.join('\n'); + } + + // Remove a trailing newline to avoid auto-running when pasting + if (textContent.endsWith("\n")) { + textContent = textContent.slice(0, -1) + } + return textContent +} + + +var copyTargetText = (trigger) => { + var target = document.querySelector(trigger.attributes['data-clipboard-target'].value); + + // get filtered text + let exclude = '.linenos, .gp'; + + let text = filterText(target, exclude); + return formatCopyText(text, '', false, true, true, true, '', '') +} + + // Initialize with a callback so we can modify the text before copy + const clipboard = new ClipboardJS('.copybtn', {text: copyTargetText}) + + // Update UI with error/success messages + clipboard.on('success', event => { + clearSelection() + temporarilyChangeTooltip(event.trigger, messages[locale]['copy'], messages[locale]['copy_success']) + temporarilyChangeIcon(event.trigger) + }) + + clipboard.on('error', event => { + temporarilyChangeTooltip(event.trigger, messages[locale]['copy'], messages[locale]['copy_failure']) + }) +} + +runWhenDOMLoaded(addCopyButtonToCodeCells) \ No newline at end of file diff --git a/branch/main/singlehtml/_static/copybutton_funcs.js b/branch/main/singlehtml/_static/copybutton_funcs.js new file mode 100644 index 0000000..dbe1aaa --- /dev/null +++ b/branch/main/singlehtml/_static/copybutton_funcs.js @@ -0,0 +1,73 @@ +function escapeRegExp(string) { + return string.replace(/[.*+?^${}()|[\]\\]/g, '\\$&'); // $& means the whole matched string +} + +/** + * Removes excluded text from a Node. + * + * @param {Node} target Node to filter. + * @param {string} exclude CSS selector of nodes to exclude. + * @returns {DOMString} Text from `target` with text removed. + */ +export function filterText(target, exclude) { + const clone = target.cloneNode(true); // clone as to not modify the live DOM + if (exclude) { + // remove excluded nodes + clone.querySelectorAll(exclude).forEach(node => node.remove()); + } + return clone.innerText; +} + +// Callback when a copy button is clicked. Will be passed the node that was clicked +// should then grab the text and replace pieces of text that shouldn't be used in output +export function formatCopyText(textContent, copybuttonPromptText, isRegexp = false, onlyCopyPromptLines = true, removePrompts = true, copyEmptyLines = true, lineContinuationChar = "", hereDocDelim = "") { + var regexp; + var match; + + // Do we check for line continuation characters and "HERE-documents"? + var useLineCont = !!lineContinuationChar + var useHereDoc = !!hereDocDelim + + // create regexp to capture prompt and remaining line + if (isRegexp) { + regexp = new RegExp('^(' + copybuttonPromptText + ')(.*)') + } else { + regexp = new RegExp('^(' + escapeRegExp(copybuttonPromptText) + ')(.*)') + } + + const outputLines = []; + var promptFound = false; + var gotLineCont = false; + var gotHereDoc = false; + const lineGotPrompt = []; + for (const line of textContent.split('\n')) { + match = line.match(regexp) + if (match || gotLineCont || gotHereDoc) { + promptFound = regexp.test(line) + lineGotPrompt.push(promptFound) + if (removePrompts && promptFound) { + outputLines.push(match[2]) + } else { + outputLines.push(line) + } + gotLineCont = line.endsWith(lineContinuationChar) & useLineCont + if (line.includes(hereDocDelim) & useHereDoc) + gotHereDoc = !gotHereDoc + } else if (!onlyCopyPromptLines) { + outputLines.push(line) + } else if (copyEmptyLines && line.trim() === '') { + outputLines.push(line) + } + } + + // If no lines with the prompt were found then just use original lines + if (lineGotPrompt.some(v => v === true)) { + textContent = outputLines.join('\n'); + } + + // Remove a trailing newline to avoid auto-running when pasting + if (textContent.endsWith("\n")) { + textContent = textContent.slice(0, -1) + } + return textContent +} diff --git a/branch/main/singlehtml/_static/css/badge_only.css b/branch/main/singlehtml/_static/css/badge_only.css new file mode 100644 index 0000000..c718cee --- /dev/null +++ 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+ return this; // for chaining... + } +})(jQuery); + +// NO good way to do this!. Copy a hack from here +// https://stackoverflow.com/questions/901115/how-can-i-get-query-string-values-in-javascript +// https://stackoverflow.com/a/2880929 +var urlParams; +(window.onpopstate = function () { + var match, + pl = /\+/g, // Regex for replacing addition symbol with a space + search = /([^&=]+)=?([^&]*)/g, + decode = function (s) { return decodeURIComponent(s.replace(pl, " ")); }, + query = window.location.search.substring(1); + urlParams = {}; + while (match = search.exec(query)) + urlParams[decode(match[1])] = decode(match[2]); +})(); + +// Select heading levels +var maxHeading = urlParams['h'] +if (maxHeading === undefined) maxHeading = 2 +var headingLevels = []; +for (h=2 ; h (sections.length-1) ) { + // if we would scroll past bottom, or above top, do nothing + return; + } + + console.log('xxxxxx'); + var targetSection = sections[targetPos]; + console.log(targetSection, typeof(targetSection)); + + // Return targetSection top and height + var secProperties = section_top_and_height(targetSection); + var top = secProperties['top']; + var height = secProperties['height'] + var win_height = window.innerHeight; + //console.info(top, height, win_height) + + var scroll_to = 0; + if (height >= win_height || height == 0) { + scroll_to = top; + } else { + scroll_to = top - (win_height-height)/3.; + } + //console.info(top, height, win_height, scroll_to) + + $('html, body').animate({ + scrollTop: scroll_to //+ 'px' + }, 'fast'); + +} + + +function minipres() { + /* Enable the minipres mode: + - call the hide() function + - set up the scrolling listener + */ + document.addEventListener('keydown', function (event) { + switch(event.which) { + case 37: // left + switch_slide(-1); + event.preventDefault(); + return false; + break; + //case 38: // up + case 39: // right + switch_slide(+1); + event.preventDefault(); + return false; + break; + //case 40: // down + default: + return; // exit this handler for other keys + } + }, true) + + hide() + + // Increase space between sections + //$("div .section").css('margin-bottom', '50%'); 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+} + +/* Math align to the left */ +.cell_output .MathJax_Display { + text-align: left !important; +} + +/* Pandas tables. Pulled from the Jupyter / nbsphinx CSS */ +div.cell_output table { + border: none; + border-collapse: collapse; + border-spacing: 0; + color: black; + font-size: 1em; + table-layout: fixed; +} + +div.cell_output thead { + border-bottom: 1px solid black; + vertical-align: bottom; +} + +div.cell_output tr, +div.cell_output th, +div.cell_output td { + text-align: right; + vertical-align: middle; + padding: 0.5em 0.5em; + line-height: normal; + white-space: normal; + max-width: none; + border: none; +} + +div.cell_output th { + font-weight: bold; +} + +div.cell_output tbody tr:nth-child(odd) { + background: #f5f5f5; +} + +div.cell_output tbody tr:hover { + background: rgba(66, 165, 245, 0.2); +} + +/** source code line numbers **/ +span.linenos { + opacity: 0.5; +} + +/* Inline text from `paste` operation */ + +span.pasted-text { + font-weight: bold; +} + +span.pasted-inline img { + max-height: 2em; +} + +tbody span.pasted-inline img { + max-height: none; +} + +/* Font colors for 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background-color: #E75C58 +} + +div.highlight .-Color[class*=-BGGreen] { + background-color: #00A250 +} + +div.highlight .-Color[class*=-BGYellow] { + background-color: #DDB62B +} + +div.highlight .-Color[class*=-BGBlue] { + background-color: #208FFB +} + +div.highlight .-Color[class*=-BGMagenta] { + background-color: #D160C4 +} + +div.highlight .-Color[class*=-BGCyan] { + background-color: #60C6C8 +} + +div.highlight .-Color[class*=-BGWhite] { + background-color: #C5C1B4 +} + +/* Font colors for 8-bit ANSI */ + +div.highlight .-Color[class*=-C0] { + color: #000000 +} + +div.highlight .-Color[class*=-BGC0] { + background-color: #000000 +} + +div.highlight .-Color[class*=-C1] { + color: #800000 +} + +div.highlight .-Color[class*=-BGC1] { + background-color: #800000 +} + +div.highlight .-Color[class*=-C2] { + color: #008000 +} + +div.highlight .-Color[class*=-BGC2] { + background-color: #008000 +} + +div.highlight .-Color[class*=-C3] { + color: #808000 +} + +div.highlight .-Color[class*=-BGC3] { + background-color: #808000 +} + +div.highlight .-Color[class*=-C4] { + color: #000080 +} + +div.highlight .-Color[class*=-BGC4] { + background-color: #000080 +} + +div.highlight .-Color[class*=-C5] { + color: #800080 +} + +div.highlight .-Color[class*=-BGC5] { + background-color: #800080 +} + +div.highlight .-Color[class*=-C6] { + color: #008080 +} + +div.highlight .-Color[class*=-BGC6] { + background-color: #008080 +} + +div.highlight .-Color[class*=-C7] { + color: #C0C0C0 +} + +div.highlight .-Color[class*=-BGC7] { + background-color: #C0C0C0 +} + +div.highlight .-Color[class*=-C8] { + color: #808080 +} + +div.highlight .-Color[class*=-BGC8] { + background-color: #808080 +} + +div.highlight .-Color[class*=-C9] { + color: #FF0000 +} + +div.highlight .-Color[class*=-BGC9] { + background-color: #FF0000 +} + +div.highlight .-Color[class*=-C10] { + color: #00FF00 +} + +div.highlight .-Color[class*=-BGC10] { + background-color: #00FF00 +} + +div.highlight .-Color[class*=-C11] { + color: #FFFF00 +} + +div.highlight .-Color[class*=-BGC11] { + background-color: #FFFF00 +} + +div.highlight .-Color[class*=-C12] { + color: #0000FF +} + +div.highlight .-Color[class*=-BGC12] { + background-color: #0000FF +} + +div.highlight .-Color[class*=-C13] { + color: #FF00FF +} + +div.highlight .-Color[class*=-BGC13] { + background-color: #FF00FF +} + +div.highlight .-Color[class*=-C14] { + color: #00FFFF +} + +div.highlight .-Color[class*=-BGC14] { + background-color: #00FFFF +} + +div.highlight .-Color[class*=-C15] { + color: #FFFFFF +} + +div.highlight .-Color[class*=-BGC15] { + background-color: #FFFFFF +} + +div.highlight .-Color[class*=-C16] { + color: #000000 +} + +div.highlight .-Color[class*=-BGC16] { + background-color: #000000 +} + +div.highlight .-Color[class*=-C17] { + color: #00005F +} + +div.highlight .-Color[class*=-BGC17] { + background-color: #00005F +} + +div.highlight .-Color[class*=-C18] { + color: #000087 +} + +div.highlight .-Color[class*=-BGC18] { + background-color: #000087 +} + +div.highlight .-Color[class*=-C19] { + color: #0000AF +} + +div.highlight .-Color[class*=-BGC19] { + background-color: #0000AF +} + +div.highlight .-Color[class*=-C20] { + color: #0000D7 +} + +div.highlight .-Color[class*=-BGC20] { + background-color: #0000D7 +} + +div.highlight .-Color[class*=-C21] { + color: #0000FF +} + +div.highlight .-Color[class*=-BGC21] { + background-color: #0000FF +} + +div.highlight .-Color[class*=-C22] { + color: #005F00 +} + +div.highlight .-Color[class*=-BGC22] { + background-color: #005F00 +} + +div.highlight .-Color[class*=-C23] { + color: #005F5F +} + +div.highlight .-Color[class*=-BGC23] { + background-color: #005F5F +} + +div.highlight .-Color[class*=-C24] { + color: #005F87 +} + +div.highlight .-Color[class*=-BGC24] { + background-color: #005F87 +} + +div.highlight .-Color[class*=-C25] { + color: #005FAF +} + +div.highlight .-Color[class*=-BGC25] { + background-color: #005FAF +} + +div.highlight .-Color[class*=-C26] { + color: #005FD7 +} + +div.highlight .-Color[class*=-BGC26] { + background-color: #005FD7 +} + +div.highlight .-Color[class*=-C27] { + color: #005FFF +} + +div.highlight .-Color[class*=-BGC27] { + background-color: #005FFF +} + +div.highlight .-Color[class*=-C28] { + color: #008700 +} + +div.highlight .-Color[class*=-BGC28] { + background-color: #008700 +} + +div.highlight .-Color[class*=-C29] { + color: #00875F +} + +div.highlight .-Color[class*=-BGC29] { + background-color: #00875F +} + +div.highlight .-Color[class*=-C30] { + color: #008787 +} + +div.highlight .-Color[class*=-BGC30] { + background-color: #008787 +} + +div.highlight .-Color[class*=-C31] { + color: #0087AF +} + +div.highlight .-Color[class*=-BGC31] { + background-color: #0087AF +} + +div.highlight .-Color[class*=-C32] { + color: #0087D7 +} + +div.highlight .-Color[class*=-BGC32] { + background-color: #0087D7 +} + +div.highlight .-Color[class*=-C33] { + color: #0087FF +} + +div.highlight .-Color[class*=-BGC33] { + background-color: #0087FF +} + +div.highlight .-Color[class*=-C34] { + color: #00AF00 +} + +div.highlight .-Color[class*=-BGC34] { + background-color: #00AF00 +} + +div.highlight .-Color[class*=-C35] { + color: #00AF5F +} + +div.highlight .-Color[class*=-BGC35] { + background-color: #00AF5F +} + +div.highlight .-Color[class*=-C36] { + color: #00AF87 +} + +div.highlight .-Color[class*=-BGC36] { + background-color: #00AF87 +} + +div.highlight .-Color[class*=-C37] { + color: #00AFAF +} + +div.highlight .-Color[class*=-BGC37] { + background-color: #00AFAF +} + +div.highlight .-Color[class*=-C38] { + color: #00AFD7 +} + +div.highlight .-Color[class*=-BGC38] { + background-color: #00AFD7 +} + +div.highlight .-Color[class*=-C39] { + color: #00AFFF +} + +div.highlight .-Color[class*=-BGC39] { + background-color: #00AFFF +} + +div.highlight .-Color[class*=-C40] { + color: #00D700 +} + +div.highlight .-Color[class*=-BGC40] { + background-color: #00D700 +} + +div.highlight .-Color[class*=-C41] { + color: #00D75F +} + +div.highlight .-Color[class*=-BGC41] { + background-color: #00D75F +} + +div.highlight .-Color[class*=-C42] { + color: #00D787 +} + +div.highlight .-Color[class*=-BGC42] { + background-color: #00D787 +} + +div.highlight .-Color[class*=-C43] { + color: #00D7AF +} + +div.highlight .-Color[class*=-BGC43] { + background-color: #00D7AF +} + +div.highlight .-Color[class*=-C44] { + color: #00D7D7 +} + +div.highlight .-Color[class*=-BGC44] { + background-color: #00D7D7 +} + +div.highlight .-Color[class*=-C45] { + color: #00D7FF +} + +div.highlight .-Color[class*=-BGC45] { + background-color: #00D7FF +} + +div.highlight .-Color[class*=-C46] { + color: #00FF00 +} + +div.highlight .-Color[class*=-BGC46] { + background-color: #00FF00 +} + +div.highlight .-Color[class*=-C47] { + color: #00FF5F +} + +div.highlight .-Color[class*=-BGC47] { + background-color: #00FF5F +} + +div.highlight .-Color[class*=-C48] { + color: #00FF87 +} + +div.highlight .-Color[class*=-BGC48] { + background-color: #00FF87 +} + +div.highlight .-Color[class*=-C49] { + color: #00FFAF +} + +div.highlight .-Color[class*=-BGC49] { + background-color: #00FFAF +} + +div.highlight .-Color[class*=-C50] { + color: #00FFD7 +} + +div.highlight .-Color[class*=-BGC50] { + background-color: #00FFD7 +} + +div.highlight .-Color[class*=-C51] { + color: #00FFFF +} + +div.highlight .-Color[class*=-BGC51] { + background-color: #00FFFF +} + +div.highlight .-Color[class*=-C52] { + color: #5F0000 +} + +div.highlight .-Color[class*=-BGC52] { + background-color: #5F0000 +} + +div.highlight .-Color[class*=-C53] { + color: #5F005F +} + +div.highlight .-Color[class*=-BGC53] { + background-color: #5F005F +} + +div.highlight .-Color[class*=-C54] { + color: #5F0087 +} + +div.highlight .-Color[class*=-BGC54] { + background-color: #5F0087 +} + +div.highlight .-Color[class*=-C55] { + color: #5F00AF +} + +div.highlight .-Color[class*=-BGC55] { + background-color: #5F00AF +} + +div.highlight .-Color[class*=-C56] { + color: #5F00D7 +} + +div.highlight .-Color[class*=-BGC56] { + background-color: #5F00D7 +} + +div.highlight .-Color[class*=-C57] { + color: #5F00FF +} + +div.highlight .-Color[class*=-BGC57] { + background-color: #5F00FF +} + +div.highlight .-Color[class*=-C58] { + color: #5F5F00 +} + +div.highlight .-Color[class*=-BGC58] { + background-color: #5F5F00 +} + +div.highlight .-Color[class*=-C59] { + color: #5F5F5F +} + +div.highlight .-Color[class*=-BGC59] { + background-color: #5F5F5F +} + +div.highlight .-Color[class*=-C60] { + color: #5F5F87 +} + +div.highlight .-Color[class*=-BGC60] { + background-color: #5F5F87 +} + +div.highlight .-Color[class*=-C61] { + color: #5F5FAF +} + +div.highlight .-Color[class*=-BGC61] { + background-color: #5F5FAF +} + +div.highlight .-Color[class*=-C62] { + color: #5F5FD7 +} + +div.highlight .-Color[class*=-BGC62] { + background-color: #5F5FD7 +} + +div.highlight .-Color[class*=-C63] { + color: #5F5FFF +} + +div.highlight .-Color[class*=-BGC63] { + background-color: #5F5FFF +} + +div.highlight .-Color[class*=-C64] { + color: #5F8700 +} + +div.highlight .-Color[class*=-BGC64] { + background-color: #5F8700 +} + +div.highlight .-Color[class*=-C65] { + color: #5F875F +} + +div.highlight .-Color[class*=-BGC65] { + background-color: #5F875F +} + +div.highlight .-Color[class*=-C66] { + color: #5F8787 +} + +div.highlight .-Color[class*=-BGC66] { + background-color: #5F8787 +} + +div.highlight .-Color[class*=-C67] { + color: #5F87AF +} + +div.highlight .-Color[class*=-BGC67] { + background-color: #5F87AF +} + +div.highlight .-Color[class*=-C68] { + color: #5F87D7 +} + +div.highlight .-Color[class*=-BGC68] { + background-color: #5F87D7 +} + +div.highlight .-Color[class*=-C69] { + color: #5F87FF +} + +div.highlight .-Color[class*=-BGC69] { + background-color: #5F87FF +} + +div.highlight .-Color[class*=-C70] { + color: #5FAF00 +} + +div.highlight .-Color[class*=-BGC70] { + background-color: #5FAF00 +} + +div.highlight .-Color[class*=-C71] { + color: #5FAF5F +} + +div.highlight .-Color[class*=-BGC71] { + background-color: #5FAF5F +} + +div.highlight .-Color[class*=-C72] { + color: #5FAF87 +} + +div.highlight .-Color[class*=-BGC72] { + background-color: #5FAF87 +} + +div.highlight .-Color[class*=-C73] { + color: #5FAFAF +} + +div.highlight .-Color[class*=-BGC73] { + background-color: #5FAFAF +} + +div.highlight .-Color[class*=-C74] { + color: #5FAFD7 +} + +div.highlight .-Color[class*=-BGC74] { + background-color: #5FAFD7 +} + +div.highlight .-Color[class*=-C75] { + color: #5FAFFF +} + +div.highlight .-Color[class*=-BGC75] { + background-color: #5FAFFF +} + +div.highlight .-Color[class*=-C76] { + color: #5FD700 +} + +div.highlight .-Color[class*=-BGC76] { + background-color: #5FD700 +} + +div.highlight .-Color[class*=-C77] { + color: #5FD75F +} + +div.highlight .-Color[class*=-BGC77] { + background-color: #5FD75F +} + +div.highlight .-Color[class*=-C78] { + color: #5FD787 +} + +div.highlight .-Color[class*=-BGC78] { + background-color: #5FD787 +} + +div.highlight .-Color[class*=-C79] { + color: #5FD7AF +} + +div.highlight .-Color[class*=-BGC79] { + background-color: #5FD7AF +} + +div.highlight .-Color[class*=-C80] { + color: #5FD7D7 +} + +div.highlight .-Color[class*=-BGC80] { + background-color: #5FD7D7 +} + +div.highlight .-Color[class*=-C81] { + color: #5FD7FF +} + +div.highlight .-Color[class*=-BGC81] { + background-color: #5FD7FF +} + +div.highlight .-Color[class*=-C82] { + color: #5FFF00 +} + +div.highlight .-Color[class*=-BGC82] { + background-color: #5FFF00 +} + +div.highlight .-Color[class*=-C83] { + color: #5FFF5F +} + +div.highlight .-Color[class*=-BGC83] { + background-color: #5FFF5F +} + +div.highlight .-Color[class*=-C84] { + color: #5FFF87 +} + +div.highlight .-Color[class*=-BGC84] { + background-color: #5FFF87 +} + +div.highlight .-Color[class*=-C85] { + color: #5FFFAF +} + +div.highlight .-Color[class*=-BGC85] { + background-color: #5FFFAF +} + +div.highlight .-Color[class*=-C86] { + color: #5FFFD7 +} + +div.highlight .-Color[class*=-BGC86] { + background-color: #5FFFD7 +} + +div.highlight .-Color[class*=-C87] { + color: #5FFFFF +} + +div.highlight .-Color[class*=-BGC87] { + background-color: #5FFFFF +} + +div.highlight .-Color[class*=-C88] { + color: #870000 +} + +div.highlight .-Color[class*=-BGC88] { + background-color: #870000 +} + +div.highlight .-Color[class*=-C89] { + color: #87005F +} + +div.highlight .-Color[class*=-BGC89] { + background-color: #87005F +} + +div.highlight .-Color[class*=-C90] { + color: #870087 +} + +div.highlight .-Color[class*=-BGC90] { + background-color: #870087 +} + +div.highlight .-Color[class*=-C91] { + color: #8700AF +} + +div.highlight .-Color[class*=-BGC91] { + background-color: #8700AF +} + +div.highlight .-Color[class*=-C92] { + color: #8700D7 +} + +div.highlight .-Color[class*=-BGC92] { + background-color: #8700D7 +} + +div.highlight .-Color[class*=-C93] { + color: #8700FF +} + +div.highlight .-Color[class*=-BGC93] { + background-color: #8700FF +} + +div.highlight .-Color[class*=-C94] { + color: #875F00 +} + +div.highlight .-Color[class*=-BGC94] { + background-color: #875F00 +} + +div.highlight .-Color[class*=-C95] { + color: #875F5F +} + +div.highlight .-Color[class*=-BGC95] { + background-color: #875F5F +} + +div.highlight .-Color[class*=-C96] { + color: #875F87 +} + +div.highlight .-Color[class*=-BGC96] { + background-color: #875F87 +} + +div.highlight .-Color[class*=-C97] { + color: #875FAF +} + +div.highlight .-Color[class*=-BGC97] { + background-color: #875FAF +} + +div.highlight .-Color[class*=-C98] { + color: #875FD7 +} + +div.highlight .-Color[class*=-BGC98] { + background-color: #875FD7 +} + +div.highlight .-Color[class*=-C99] { + color: #875FFF +} + +div.highlight .-Color[class*=-BGC99] { + background-color: #875FFF +} + +div.highlight .-Color[class*=-C100] { + color: #878700 +} + +div.highlight .-Color[class*=-BGC100] { + background-color: #878700 +} + +div.highlight .-Color[class*=-C101] { + color: #87875F +} + +div.highlight .-Color[class*=-BGC101] { + background-color: #87875F +} + +div.highlight .-Color[class*=-C102] { + color: #878787 +} + +div.highlight .-Color[class*=-BGC102] { + background-color: #878787 +} + +div.highlight .-Color[class*=-C103] { + color: #8787AF +} + +div.highlight .-Color[class*=-BGC103] { + background-color: #8787AF +} + +div.highlight .-Color[class*=-C104] { + color: #8787D7 +} + +div.highlight .-Color[class*=-BGC104] { + background-color: #8787D7 +} + +div.highlight .-Color[class*=-C105] { + color: #8787FF +} + +div.highlight .-Color[class*=-BGC105] { + background-color: #8787FF +} + +div.highlight .-Color[class*=-C106] { + color: #87AF00 +} + +div.highlight .-Color[class*=-BGC106] { + background-color: #87AF00 +} + +div.highlight .-Color[class*=-C107] { + color: #87AF5F +} + +div.highlight .-Color[class*=-BGC107] { + background-color: #87AF5F +} + +div.highlight .-Color[class*=-C108] { + color: #87AF87 +} + +div.highlight .-Color[class*=-BGC108] { + background-color: #87AF87 +} + +div.highlight .-Color[class*=-C109] { + color: #87AFAF +} + +div.highlight .-Color[class*=-BGC109] { + background-color: #87AFAF +} + +div.highlight .-Color[class*=-C110] { + color: #87AFD7 +} + +div.highlight .-Color[class*=-BGC110] { + background-color: #87AFD7 +} + +div.highlight .-Color[class*=-C111] { + color: #87AFFF +} + +div.highlight .-Color[class*=-BGC111] { + background-color: #87AFFF +} + +div.highlight .-Color[class*=-C112] { + color: #87D700 +} + +div.highlight .-Color[class*=-BGC112] { + background-color: #87D700 +} + +div.highlight .-Color[class*=-C113] { + color: #87D75F +} + +div.highlight .-Color[class*=-BGC113] { + background-color: #87D75F +} + +div.highlight .-Color[class*=-C114] { + color: #87D787 +} + +div.highlight .-Color[class*=-BGC114] { + background-color: #87D787 +} + +div.highlight .-Color[class*=-C115] { + color: #87D7AF +} + +div.highlight .-Color[class*=-BGC115] { + background-color: #87D7AF +} + +div.highlight .-Color[class*=-C116] { + color: #87D7D7 +} + +div.highlight .-Color[class*=-BGC116] { + background-color: #87D7D7 +} + +div.highlight .-Color[class*=-C117] { + color: #87D7FF +} + +div.highlight .-Color[class*=-BGC117] { + background-color: #87D7FF +} + +div.highlight .-Color[class*=-C118] { + color: #87FF00 +} + +div.highlight .-Color[class*=-BGC118] { + background-color: #87FF00 +} + +div.highlight .-Color[class*=-C119] { + color: #87FF5F +} + +div.highlight .-Color[class*=-BGC119] { + background-color: #87FF5F +} + +div.highlight .-Color[class*=-C120] { + color: #87FF87 +} + +div.highlight .-Color[class*=-BGC120] { + background-color: #87FF87 +} + +div.highlight .-Color[class*=-C121] { + color: #87FFAF +} + +div.highlight .-Color[class*=-BGC121] { + background-color: #87FFAF +} + +div.highlight .-Color[class*=-C122] { + color: #87FFD7 +} + +div.highlight .-Color[class*=-BGC122] { + background-color: #87FFD7 +} + +div.highlight .-Color[class*=-C123] { + color: #87FFFF +} + +div.highlight .-Color[class*=-BGC123] { + background-color: #87FFFF +} + +div.highlight .-Color[class*=-C124] { + color: #AF0000 +} + +div.highlight .-Color[class*=-BGC124] { + background-color: #AF0000 +} + +div.highlight .-Color[class*=-C125] { + color: #AF005F +} + +div.highlight .-Color[class*=-BGC125] { + background-color: #AF005F +} + +div.highlight .-Color[class*=-C126] { + color: #AF0087 +} + +div.highlight .-Color[class*=-BGC126] { + background-color: #AF0087 +} + +div.highlight .-Color[class*=-C127] { + color: #AF00AF +} + +div.highlight .-Color[class*=-BGC127] { + background-color: #AF00AF +} + +div.highlight .-Color[class*=-C128] { + color: #AF00D7 +} + +div.highlight .-Color[class*=-BGC128] { + background-color: #AF00D7 +} + +div.highlight .-Color[class*=-C129] { + color: #AF00FF +} + +div.highlight .-Color[class*=-BGC129] { + background-color: #AF00FF +} + +div.highlight .-Color[class*=-C130] { + color: #AF5F00 +} + +div.highlight .-Color[class*=-BGC130] { + background-color: #AF5F00 +} + +div.highlight .-Color[class*=-C131] { + color: #AF5F5F +} + +div.highlight .-Color[class*=-BGC131] { + background-color: #AF5F5F +} + +div.highlight .-Color[class*=-C132] { + color: #AF5F87 +} + +div.highlight .-Color[class*=-BGC132] { + background-color: #AF5F87 +} + +div.highlight .-Color[class*=-C133] { + color: #AF5FAF +} + +div.highlight .-Color[class*=-BGC133] { + background-color: #AF5FAF +} + +div.highlight .-Color[class*=-C134] { + color: #AF5FD7 +} + +div.highlight .-Color[class*=-BGC134] { + background-color: #AF5FD7 +} + +div.highlight .-Color[class*=-C135] { + color: #AF5FFF +} + +div.highlight .-Color[class*=-BGC135] { + background-color: #AF5FFF +} + +div.highlight .-Color[class*=-C136] { + color: #AF8700 +} + +div.highlight .-Color[class*=-BGC136] { + background-color: #AF8700 +} + +div.highlight .-Color[class*=-C137] { + color: #AF875F +} + +div.highlight .-Color[class*=-BGC137] { + background-color: #AF875F +} + +div.highlight .-Color[class*=-C138] { + color: #AF8787 +} + +div.highlight .-Color[class*=-BGC138] { + background-color: #AF8787 +} + +div.highlight .-Color[class*=-C139] { + color: #AF87AF +} + +div.highlight .-Color[class*=-BGC139] { + background-color: #AF87AF +} + +div.highlight .-Color[class*=-C140] { + color: #AF87D7 +} + +div.highlight .-Color[class*=-BGC140] { + background-color: #AF87D7 +} + +div.highlight .-Color[class*=-C141] { + color: #AF87FF +} + +div.highlight .-Color[class*=-BGC141] { + background-color: #AF87FF +} + +div.highlight .-Color[class*=-C142] { + color: #AFAF00 +} + +div.highlight .-Color[class*=-BGC142] { + background-color: #AFAF00 +} + +div.highlight .-Color[class*=-C143] { + color: #AFAF5F +} + +div.highlight .-Color[class*=-BGC143] { + background-color: #AFAF5F +} + +div.highlight .-Color[class*=-C144] { + color: #AFAF87 +} + +div.highlight .-Color[class*=-BGC144] { + background-color: #AFAF87 +} + +div.highlight .-Color[class*=-C145] { + color: #AFAFAF +} + +div.highlight .-Color[class*=-BGC145] { + background-color: #AFAFAF +} + +div.highlight .-Color[class*=-C146] { + color: #AFAFD7 +} + +div.highlight .-Color[class*=-BGC146] { + background-color: #AFAFD7 +} + +div.highlight .-Color[class*=-C147] { + color: #AFAFFF +} + +div.highlight .-Color[class*=-BGC147] { + background-color: #AFAFFF +} + +div.highlight .-Color[class*=-C148] { + color: #AFD700 +} + +div.highlight .-Color[class*=-BGC148] { + background-color: #AFD700 +} + +div.highlight .-Color[class*=-C149] { + color: #AFD75F +} + +div.highlight .-Color[class*=-BGC149] { + background-color: #AFD75F +} + +div.highlight .-Color[class*=-C150] { + color: #AFD787 +} + +div.highlight .-Color[class*=-BGC150] { + background-color: #AFD787 +} + +div.highlight .-Color[class*=-C151] { + color: #AFD7AF +} + +div.highlight .-Color[class*=-BGC151] { + background-color: #AFD7AF +} + +div.highlight .-Color[class*=-C152] { + color: #AFD7D7 +} + +div.highlight .-Color[class*=-BGC152] { + background-color: #AFD7D7 +} + +div.highlight .-Color[class*=-C153] { + color: #AFD7FF +} + +div.highlight .-Color[class*=-BGC153] { + background-color: #AFD7FF +} + +div.highlight .-Color[class*=-C154] { + color: #AFFF00 +} + +div.highlight .-Color[class*=-BGC154] { + background-color: #AFFF00 +} + +div.highlight .-Color[class*=-C155] { + color: #AFFF5F +} + +div.highlight .-Color[class*=-BGC155] { + background-color: #AFFF5F +} + +div.highlight .-Color[class*=-C156] { + color: #AFFF87 +} + +div.highlight .-Color[class*=-BGC156] { + background-color: #AFFF87 +} + +div.highlight .-Color[class*=-C157] { + color: #AFFFAF +} + +div.highlight .-Color[class*=-BGC157] { + background-color: #AFFFAF +} + +div.highlight .-Color[class*=-C158] { + color: #AFFFD7 +} + +div.highlight .-Color[class*=-BGC158] { + background-color: #AFFFD7 +} + +div.highlight .-Color[class*=-C159] { + color: #AFFFFF +} + +div.highlight .-Color[class*=-BGC159] { + background-color: #AFFFFF +} + +div.highlight .-Color[class*=-C160] { + color: #D70000 +} + +div.highlight .-Color[class*=-BGC160] { + background-color: #D70000 +} + +div.highlight .-Color[class*=-C161] { + color: #D7005F +} + +div.highlight .-Color[class*=-BGC161] { + background-color: #D7005F +} + +div.highlight .-Color[class*=-C162] { + color: #D70087 +} + +div.highlight .-Color[class*=-BGC162] { + background-color: #D70087 +} + +div.highlight .-Color[class*=-C163] { + color: #D700AF +} + +div.highlight .-Color[class*=-BGC163] { + background-color: #D700AF +} + +div.highlight .-Color[class*=-C164] { + color: #D700D7 +} + +div.highlight .-Color[class*=-BGC164] { + background-color: #D700D7 +} + +div.highlight .-Color[class*=-C165] { + color: #D700FF +} + +div.highlight .-Color[class*=-BGC165] { + background-color: #D700FF +} + +div.highlight .-Color[class*=-C166] { + color: #D75F00 +} + +div.highlight .-Color[class*=-BGC166] { + background-color: #D75F00 +} + +div.highlight .-Color[class*=-C167] { + color: #D75F5F +} + +div.highlight .-Color[class*=-BGC167] { + background-color: #D75F5F +} + +div.highlight .-Color[class*=-C168] { + color: #D75F87 +} + +div.highlight .-Color[class*=-BGC168] { + background-color: #D75F87 +} + +div.highlight .-Color[class*=-C169] { + color: #D75FAF +} + +div.highlight .-Color[class*=-BGC169] { + background-color: #D75FAF +} + +div.highlight .-Color[class*=-C170] { + color: #D75FD7 +} + +div.highlight .-Color[class*=-BGC170] { + background-color: #D75FD7 +} + +div.highlight .-Color[class*=-C171] { + color: #D75FFF +} + +div.highlight .-Color[class*=-BGC171] { + background-color: #D75FFF +} + +div.highlight .-Color[class*=-C172] { + color: #D78700 +} + +div.highlight .-Color[class*=-BGC172] { + background-color: #D78700 +} + +div.highlight .-Color[class*=-C173] { + color: #D7875F +} + +div.highlight .-Color[class*=-BGC173] { + background-color: #D7875F +} + +div.highlight .-Color[class*=-C174] { + color: #D78787 +} + +div.highlight .-Color[class*=-BGC174] { + background-color: #D78787 +} + +div.highlight .-Color[class*=-C175] { + color: #D787AF +} + +div.highlight .-Color[class*=-BGC175] { + background-color: #D787AF +} + +div.highlight .-Color[class*=-C176] { + color: #D787D7 +} + +div.highlight .-Color[class*=-BGC176] { + background-color: #D787D7 +} + +div.highlight .-Color[class*=-C177] { + color: #D787FF +} + +div.highlight .-Color[class*=-BGC177] { + background-color: #D787FF +} + +div.highlight .-Color[class*=-C178] { + color: #D7AF00 +} + +div.highlight .-Color[class*=-BGC178] { + background-color: #D7AF00 +} + +div.highlight .-Color[class*=-C179] { + color: #D7AF5F +} + +div.highlight .-Color[class*=-BGC179] { + background-color: #D7AF5F +} + +div.highlight .-Color[class*=-C180] { + color: #D7AF87 +} + +div.highlight .-Color[class*=-BGC180] { + background-color: #D7AF87 +} + +div.highlight .-Color[class*=-C181] { + color: #D7AFAF +} + +div.highlight .-Color[class*=-BGC181] { + background-color: #D7AFAF +} + +div.highlight .-Color[class*=-C182] { + color: #D7AFD7 +} + +div.highlight .-Color[class*=-BGC182] { + background-color: #D7AFD7 +} + +div.highlight .-Color[class*=-C183] { + color: #D7AFFF +} + +div.highlight .-Color[class*=-BGC183] { + background-color: #D7AFFF +} + +div.highlight .-Color[class*=-C184] { + color: #D7D700 +} + +div.highlight .-Color[class*=-BGC184] { + background-color: #D7D700 +} + +div.highlight .-Color[class*=-C185] { + color: #D7D75F +} + +div.highlight .-Color[class*=-BGC185] { + background-color: #D7D75F +} + +div.highlight .-Color[class*=-C186] { + color: #D7D787 +} + +div.highlight .-Color[class*=-BGC186] { + background-color: #D7D787 +} + +div.highlight .-Color[class*=-C187] { + color: #D7D7AF +} + +div.highlight .-Color[class*=-BGC187] { + background-color: #D7D7AF +} + +div.highlight .-Color[class*=-C188] { + color: #D7D7D7 +} + +div.highlight .-Color[class*=-BGC188] { + background-color: #D7D7D7 +} + +div.highlight .-Color[class*=-C189] { + color: #D7D7FF +} + +div.highlight .-Color[class*=-BGC189] { + background-color: #D7D7FF +} + +div.highlight .-Color[class*=-C190] { + color: #D7FF00 +} + +div.highlight .-Color[class*=-BGC190] { + background-color: #D7FF00 +} + +div.highlight .-Color[class*=-C191] { + color: #D7FF5F +} + +div.highlight .-Color[class*=-BGC191] { + background-color: #D7FF5F +} + +div.highlight .-Color[class*=-C192] { + color: #D7FF87 +} + +div.highlight .-Color[class*=-BGC192] { + background-color: #D7FF87 +} + +div.highlight .-Color[class*=-C193] { + color: #D7FFAF +} + +div.highlight .-Color[class*=-BGC193] { + background-color: #D7FFAF +} + +div.highlight .-Color[class*=-C194] { + color: #D7FFD7 +} + +div.highlight .-Color[class*=-BGC194] { + background-color: #D7FFD7 +} + +div.highlight .-Color[class*=-C195] { + color: #D7FFFF +} + +div.highlight .-Color[class*=-BGC195] { + background-color: #D7FFFF +} + +div.highlight .-Color[class*=-C196] { + color: #FF0000 +} + +div.highlight .-Color[class*=-BGC196] { + background-color: #FF0000 +} + +div.highlight .-Color[class*=-C197] { + color: #FF005F +} + +div.highlight .-Color[class*=-BGC197] { + background-color: #FF005F +} + +div.highlight .-Color[class*=-C198] { + color: #FF0087 +} + +div.highlight .-Color[class*=-BGC198] { + background-color: #FF0087 +} + +div.highlight .-Color[class*=-C199] { + color: #FF00AF +} + +div.highlight .-Color[class*=-BGC199] { + background-color: #FF00AF +} + +div.highlight .-Color[class*=-C200] { + color: #FF00D7 +} + +div.highlight .-Color[class*=-BGC200] { + background-color: #FF00D7 +} + +div.highlight .-Color[class*=-C201] { + color: #FF00FF +} + +div.highlight .-Color[class*=-BGC201] { + background-color: #FF00FF +} + +div.highlight .-Color[class*=-C202] { + color: #FF5F00 +} + +div.highlight .-Color[class*=-BGC202] { + background-color: #FF5F00 +} + +div.highlight .-Color[class*=-C203] { + color: #FF5F5F +} + +div.highlight .-Color[class*=-BGC203] { + background-color: #FF5F5F +} + +div.highlight .-Color[class*=-C204] { + color: #FF5F87 +} + +div.highlight .-Color[class*=-BGC204] { + background-color: #FF5F87 +} + +div.highlight .-Color[class*=-C205] { + color: #FF5FAF +} + +div.highlight .-Color[class*=-BGC205] { + background-color: #FF5FAF +} + +div.highlight .-Color[class*=-C206] { + color: #FF5FD7 +} + +div.highlight .-Color[class*=-BGC206] { + background-color: #FF5FD7 +} + +div.highlight .-Color[class*=-C207] { + color: #FF5FFF +} + +div.highlight .-Color[class*=-BGC207] { + background-color: #FF5FFF +} + +div.highlight .-Color[class*=-C208] { + color: #FF8700 +} + +div.highlight .-Color[class*=-BGC208] { + background-color: #FF8700 +} + +div.highlight .-Color[class*=-C209] { + color: #FF875F +} + +div.highlight .-Color[class*=-BGC209] { + background-color: #FF875F +} + +div.highlight .-Color[class*=-C210] { + color: #FF8787 +} + +div.highlight .-Color[class*=-BGC210] { + background-color: #FF8787 +} + +div.highlight .-Color[class*=-C211] { + color: #FF87AF +} + +div.highlight .-Color[class*=-BGC211] { + background-color: #FF87AF +} + +div.highlight .-Color[class*=-C212] { + color: #FF87D7 +} + +div.highlight .-Color[class*=-BGC212] { + background-color: #FF87D7 +} + +div.highlight .-Color[class*=-C213] { + color: #FF87FF +} + +div.highlight .-Color[class*=-BGC213] { + background-color: #FF87FF +} + +div.highlight .-Color[class*=-C214] { + color: #FFAF00 +} + +div.highlight .-Color[class*=-BGC214] { + background-color: #FFAF00 +} + +div.highlight .-Color[class*=-C215] { + color: #FFAF5F +} + +div.highlight .-Color[class*=-BGC215] { + background-color: #FFAF5F +} + +div.highlight .-Color[class*=-C216] { + color: #FFAF87 +} + +div.highlight .-Color[class*=-BGC216] { + background-color: #FFAF87 +} + +div.highlight .-Color[class*=-C217] { + color: #FFAFAF +} + +div.highlight .-Color[class*=-BGC217] { + background-color: #FFAFAF +} + +div.highlight .-Color[class*=-C218] { + color: #FFAFD7 +} + +div.highlight .-Color[class*=-BGC218] { + background-color: #FFAFD7 +} + +div.highlight .-Color[class*=-C219] { + color: #FFAFFF +} + +div.highlight .-Color[class*=-BGC219] { + background-color: #FFAFFF +} + +div.highlight .-Color[class*=-C220] { + color: #FFD700 +} + +div.highlight .-Color[class*=-BGC220] { + background-color: #FFD700 +} + +div.highlight .-Color[class*=-C221] { + color: #FFD75F +} + +div.highlight .-Color[class*=-BGC221] { + background-color: #FFD75F +} + +div.highlight .-Color[class*=-C222] { + color: #FFD787 +} + +div.highlight .-Color[class*=-BGC222] { + background-color: #FFD787 +} + +div.highlight .-Color[class*=-C223] { + color: #FFD7AF +} + +div.highlight .-Color[class*=-BGC223] { + background-color: #FFD7AF +} + +div.highlight .-Color[class*=-C224] { + color: #FFD7D7 +} + +div.highlight .-Color[class*=-BGC224] { + background-color: #FFD7D7 +} + +div.highlight .-Color[class*=-C225] { + color: #FFD7FF +} + +div.highlight .-Color[class*=-BGC225] { + background-color: #FFD7FF +} + +div.highlight .-Color[class*=-C226] { + color: #FFFF00 +} + +div.highlight .-Color[class*=-BGC226] { + background-color: #FFFF00 +} + +div.highlight .-Color[class*=-C227] { + color: #FFFF5F +} + +div.highlight .-Color[class*=-BGC227] { + background-color: #FFFF5F +} + +div.highlight .-Color[class*=-C228] { + color: #FFFF87 +} + +div.highlight .-Color[class*=-BGC228] { + background-color: #FFFF87 +} + +div.highlight .-Color[class*=-C229] { + color: #FFFFAF +} + +div.highlight .-Color[class*=-BGC229] { + background-color: #FFFFAF +} + +div.highlight .-Color[class*=-C230] { + color: #FFFFD7 +} + +div.highlight .-Color[class*=-BGC230] { + background-color: #FFFFD7 +} + +div.highlight .-Color[class*=-C231] { + color: #FFFFFF +} + +div.highlight .-Color[class*=-BGC231] { + background-color: #FFFFFF +} + +div.highlight .-Color[class*=-C232] { + color: #080808 +} + +div.highlight .-Color[class*=-BGC232] { + background-color: #080808 +} + +div.highlight .-Color[class*=-C233] { + color: #121212 +} + +div.highlight .-Color[class*=-BGC233] { + background-color: #121212 +} + +div.highlight .-Color[class*=-C234] { + color: #1C1C1C +} + +div.highlight .-Color[class*=-BGC234] { + background-color: #1C1C1C +} + +div.highlight .-Color[class*=-C235] { + color: #262626 +} + +div.highlight .-Color[class*=-BGC235] { + background-color: #262626 +} + +div.highlight .-Color[class*=-C236] { + color: #303030 +} + +div.highlight .-Color[class*=-BGC236] { + background-color: #303030 +} + +div.highlight .-Color[class*=-C237] { + color: #3A3A3A +} + +div.highlight .-Color[class*=-BGC237] { + background-color: #3A3A3A +} + +div.highlight .-Color[class*=-C238] { + color: #444444 +} + +div.highlight .-Color[class*=-BGC238] { + background-color: #444444 +} + +div.highlight .-Color[class*=-C239] { + color: #4E4E4E +} + +div.highlight .-Color[class*=-BGC239] { + background-color: #4E4E4E +} + +div.highlight .-Color[class*=-C240] { + color: #585858 +} + +div.highlight .-Color[class*=-BGC240] { + background-color: #585858 +} + +div.highlight .-Color[class*=-C241] { + color: #626262 +} + +div.highlight .-Color[class*=-BGC241] { + background-color: #626262 +} + +div.highlight .-Color[class*=-C242] { + color: #6C6C6C +} + +div.highlight .-Color[class*=-BGC242] { + background-color: #6C6C6C +} + +div.highlight .-Color[class*=-C243] { + color: #767676 +} + +div.highlight .-Color[class*=-BGC243] { + background-color: #767676 +} + +div.highlight .-Color[class*=-C244] { + color: #808080 +} + +div.highlight .-Color[class*=-BGC244] { + background-color: #808080 +} + +div.highlight .-Color[class*=-C245] { + color: #8A8A8A +} + +div.highlight .-Color[class*=-BGC245] { + background-color: #8A8A8A +} + +div.highlight .-Color[class*=-C246] { + color: #949494 +} + +div.highlight .-Color[class*=-BGC246] { + background-color: #949494 +} + +div.highlight .-Color[class*=-C247] { + color: #9E9E9E +} + +div.highlight .-Color[class*=-BGC247] { + background-color: #9E9E9E +} + +div.highlight .-Color[class*=-C248] { + color: #A8A8A8 +} + +div.highlight .-Color[class*=-BGC248] { + background-color: #A8A8A8 +} + +div.highlight .-Color[class*=-C249] { + color: #B2B2B2 +} + +div.highlight .-Color[class*=-BGC249] { + background-color: #B2B2B2 +} + +div.highlight .-Color[class*=-C250] { + color: #BCBCBC +} + +div.highlight .-Color[class*=-BGC250] { + background-color: #BCBCBC +} + +div.highlight .-Color[class*=-C251] { + color: #C6C6C6 +} + +div.highlight .-Color[class*=-BGC251] { + background-color: #C6C6C6 +} + +div.highlight .-Color[class*=-C252] { + color: #D0D0D0 +} + +div.highlight .-Color[class*=-BGC252] { + background-color: #D0D0D0 +} + +div.highlight .-Color[class*=-C253] { + color: #DADADA +} + +div.highlight .-Color[class*=-BGC253] { + background-color: #DADADA +} + +div.highlight .-Color[class*=-C254] { + color: #E4E4E4 +} + +div.highlight .-Color[class*=-BGC254] { + background-color: #E4E4E4 +} + +div.highlight .-Color[class*=-C255] { + color: #EEEEEE +} + +div.highlight .-Color[class*=-BGC255] { + background-color: #EEEEEE +} diff --git a/branch/main/singlehtml/_static/plus.png b/branch/main/singlehtml/_static/plus.png new file mode 100644 index 0000000..7107cec Binary files /dev/null and b/branch/main/singlehtml/_static/plus.png differ diff --git a/branch/main/singlehtml/_static/pygments.css b/branch/main/singlehtml/_static/pygments.css new file mode 100644 index 0000000..84ab303 --- /dev/null +++ b/branch/main/singlehtml/_static/pygments.css @@ -0,0 +1,75 @@ +pre { line-height: 125%; } +td.linenos .normal { color: inherit; background-color: transparent; padding-left: 5px; padding-right: 5px; } +span.linenos { color: inherit; background-color: transparent; padding-left: 5px; padding-right: 5px; } +td.linenos .special { color: #000000; background-color: #ffffc0; padding-left: 5px; padding-right: 5px; } +span.linenos.special { color: #000000; background-color: #ffffc0; padding-left: 5px; padding-right: 5px; } +.highlight .hll { background-color: #ffffcc } +.highlight { background: #f8f8f8; } +.highlight .c { color: #3D7B7B; font-style: italic } /* Comment */ +.highlight .err { border: 1px solid #FF0000 } /* Error */ +.highlight .k { color: #008000; font-weight: bold } /* Keyword */ +.highlight .o { color: #666666 } /* Operator */ +.highlight .ch { color: #3D7B7B; font-style: italic } /* Comment.Hashbang */ +.highlight .cm { color: #3D7B7B; font-style: italic } /* Comment.Multiline */ +.highlight .cp { color: #9C6500 } /* Comment.Preproc */ +.highlight .cpf { color: #3D7B7B; font-style: italic } /* Comment.PreprocFile */ +.highlight .c1 { color: #3D7B7B; font-style: italic } /* Comment.Single */ +.highlight .cs { color: #3D7B7B; font-style: italic } /* Comment.Special */ +.highlight .gd { color: #A00000 } /* Generic.Deleted */ +.highlight .ge { font-style: italic } /* Generic.Emph */ +.highlight .ges { font-weight: bold; font-style: italic } /* Generic.EmphStrong */ 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+.highlight .s1 { color: #BA2121 } /* Literal.String.Single */ +.highlight .ss { color: #19177C } /* Literal.String.Symbol */ +.highlight .bp { color: #008000 } /* Name.Builtin.Pseudo */ +.highlight .fm { color: #0000FF } /* Name.Function.Magic */ +.highlight .vc { color: #19177C } /* Name.Variable.Class */ +.highlight .vg { color: #19177C } /* Name.Variable.Global */ +.highlight .vi { color: #19177C } /* Name.Variable.Instance */ +.highlight .vm { color: #19177C } /* Name.Variable.Magic */ +.highlight .il { color: #666666 } /* Literal.Number.Integer.Long */ \ No newline at end of file diff --git a/branch/main/singlehtml/_static/searchtools.js b/branch/main/singlehtml/_static/searchtools.js new file mode 100644 index 0000000..b08d58c --- /dev/null +++ b/branch/main/singlehtml/_static/searchtools.js @@ -0,0 +1,620 @@ +/* + * searchtools.js + * ~~~~~~~~~~~~~~~~ + * + * Sphinx JavaScript utilities for the full-text search. + * + * :copyright: Copyright 2007-2024 by the Sphinx team, see AUTHORS. + * :license: BSD, see LICENSE for details. + * + */ +"use strict"; + +/** + * Simple result scoring code. + */ +if (typeof Scorer === "undefined") { + var Scorer = { + // Implement the following function to further tweak the score for each result + // The function takes a result array [docname, title, anchor, descr, score, filename] + // and returns the new score. + /* + score: result => { + const [docname, title, anchor, descr, score, filename] = result + return score + }, + */ + + // query matches the full name of an object + objNameMatch: 11, + // or matches in the last dotted part of the object name + objPartialMatch: 6, + // Additive scores depending on the priority of the object + objPrio: { + 0: 15, // used to be importantResults + 1: 5, // used to be objectResults + 2: -5, // used to be unimportantResults + }, + // Used when the priority is not in the mapping. + objPrioDefault: 0, + + // query found in title + title: 15, + partialTitle: 7, + // query found in terms + term: 5, + partialTerm: 2, + }; +} + +const _removeChildren = (element) => { + while (element && element.lastChild) element.removeChild(element.lastChild); +}; + +/** + * See https://developer.mozilla.org/en-US/docs/Web/JavaScript/Guide/Regular_Expressions#escaping + */ +const _escapeRegExp = (string) => + string.replace(/[.*+\-?^${}()|[\]\\]/g, "\\$&"); // $& means the whole matched string + +const _displayItem = (item, searchTerms, highlightTerms) => { + const docBuilder = DOCUMENTATION_OPTIONS.BUILDER; + const docFileSuffix = DOCUMENTATION_OPTIONS.FILE_SUFFIX; + const docLinkSuffix = DOCUMENTATION_OPTIONS.LINK_SUFFIX; + const showSearchSummary = DOCUMENTATION_OPTIONS.SHOW_SEARCH_SUMMARY; + const contentRoot = document.documentElement.dataset.content_root; + + const [docName, title, anchor, descr, score, _filename] = item; + + let listItem = document.createElement("li"); + let requestUrl; + let linkUrl; + if (docBuilder === "dirhtml") { + // dirhtml builder + let dirname = docName + "/"; + if (dirname.match(/\/index\/$/)) + dirname = dirname.substring(0, dirname.length - 6); + else if (dirname === "index/") dirname = ""; + requestUrl = contentRoot + dirname; + linkUrl = requestUrl; + } else { + // normal html builders + requestUrl = contentRoot + docName + docFileSuffix; + linkUrl = docName + docLinkSuffix; + } + let linkEl = listItem.appendChild(document.createElement("a")); + linkEl.href = linkUrl + anchor; + linkEl.dataset.score = score; + linkEl.innerHTML = title; + if (descr) { + listItem.appendChild(document.createElement("span")).innerHTML = + " (" + descr + ")"; + // highlight search terms in the description + if (SPHINX_HIGHLIGHT_ENABLED) // set in sphinx_highlight.js + highlightTerms.forEach((term) => _highlightText(listItem, term, "highlighted")); + } + else if (showSearchSummary) + fetch(requestUrl) + .then((responseData) => responseData.text()) + .then((data) => { + if (data) + listItem.appendChild( + Search.makeSearchSummary(data, searchTerms, anchor) + ); + // highlight search terms in the summary + if (SPHINX_HIGHLIGHT_ENABLED) // set in sphinx_highlight.js + highlightTerms.forEach((term) => _highlightText(listItem, term, "highlighted")); + }); + Search.output.appendChild(listItem); +}; +const _finishSearch = (resultCount) => { + Search.stopPulse(); + Search.title.innerText = _("Search Results"); + if (!resultCount) + Search.status.innerText = Documentation.gettext( + "Your search did not match any documents. Please make sure that all words are spelled correctly and that you've selected enough categories." + ); + else + Search.status.innerText = _( + "Search finished, found ${resultCount} page(s) matching the search query." + ).replace('${resultCount}', resultCount); +}; +const _displayNextItem = ( + results, + resultCount, + searchTerms, + highlightTerms, +) => { + // results left, load the summary and display it + // this is intended to be dynamic (don't sub resultsCount) + if (results.length) { + _displayItem(results.pop(), searchTerms, highlightTerms); + setTimeout( + () => _displayNextItem(results, resultCount, searchTerms, highlightTerms), + 5 + ); + } + // search finished, update title and status message + else _finishSearch(resultCount); +}; +// Helper function used by query() to order search results. +// Each input is an array of [docname, title, anchor, descr, score, filename]. +// Order the results by score (in opposite order of appearance, since the +// `_displayNextItem` function uses pop() to retrieve items) and then alphabetically. +const _orderResultsByScoreThenName = (a, b) => { + const leftScore = a[4]; + const rightScore = b[4]; + if (leftScore === rightScore) { + // same score: sort alphabetically + const leftTitle = a[1].toLowerCase(); + const rightTitle = b[1].toLowerCase(); + if (leftTitle === rightTitle) return 0; + return leftTitle > rightTitle ? -1 : 1; // inverted is intentional + } + return leftScore > rightScore ? 1 : -1; +}; + +/** + * Default splitQuery function. Can be overridden in ``sphinx.search`` with a + * custom function per language. + * + * The regular expression works by splitting the string on consecutive characters + * that are not Unicode letters, numbers, underscores, or emoji characters. + * This is the same as ``\W+`` in Python, preserving the surrogate pair area. + */ +if (typeof splitQuery === "undefined") { + var splitQuery = (query) => query + .split(/[^\p{Letter}\p{Number}_\p{Emoji_Presentation}]+/gu) + .filter(term => term) // remove remaining empty strings +} + +/** + * Search Module + */ +const Search = { + _index: null, + _queued_query: null, + _pulse_status: -1, + + htmlToText: (htmlString, anchor) => { + const htmlElement = new DOMParser().parseFromString(htmlString, 'text/html'); + for (const removalQuery of [".headerlink", "script", "style"]) { + htmlElement.querySelectorAll(removalQuery).forEach((el) => { el.remove() }); + } + if (anchor) { + const anchorContent = htmlElement.querySelector(`[role="main"] ${anchor}`); + if (anchorContent) return anchorContent.textContent; + + console.warn( + `Anchored content block not found. Sphinx search tries to obtain it via DOM query '[role=main] ${anchor}'. Check your theme or template.` + ); + } + + // if anchor not specified or not found, fall back to main content + const docContent = htmlElement.querySelector('[role="main"]'); + if (docContent) return docContent.textContent; + + console.warn( + "Content block not found. Sphinx search tries to obtain it via DOM query '[role=main]'. Check your theme or template." + ); + return ""; + }, + + init: () => { + const query = new URLSearchParams(window.location.search).get("q"); + document + .querySelectorAll('input[name="q"]') + .forEach((el) => (el.value = query)); + if (query) Search.performSearch(query); + }, + + loadIndex: (url) => + (document.body.appendChild(document.createElement("script")).src = url), + + setIndex: (index) => { + Search._index = index; + if (Search._queued_query !== null) { + const query = Search._queued_query; + Search._queued_query = null; + Search.query(query); + } + }, + + hasIndex: () => Search._index !== null, + + deferQuery: (query) => (Search._queued_query = query), + + stopPulse: () => (Search._pulse_status = -1), + + startPulse: () => { + if (Search._pulse_status >= 0) return; + + const pulse = () => { + Search._pulse_status = (Search._pulse_status + 1) % 4; + Search.dots.innerText = ".".repeat(Search._pulse_status); + if (Search._pulse_status >= 0) window.setTimeout(pulse, 500); + }; + pulse(); + }, + + /** + * perform a search for something (or wait until index is loaded) + */ + performSearch: (query) => { + // create the required interface elements + const searchText = document.createElement("h2"); + searchText.textContent = _("Searching"); + const searchSummary = document.createElement("p"); + searchSummary.classList.add("search-summary"); + searchSummary.innerText = ""; + const searchList = document.createElement("ul"); + searchList.classList.add("search"); + + const out = document.getElementById("search-results"); + Search.title = out.appendChild(searchText); + Search.dots = Search.title.appendChild(document.createElement("span")); + Search.status = out.appendChild(searchSummary); + Search.output = out.appendChild(searchList); + + const searchProgress = document.getElementById("search-progress"); + // Some themes don't use the search progress node + if (searchProgress) { + searchProgress.innerText = _("Preparing search..."); + } + Search.startPulse(); + + // index already loaded, the browser was quick! + if (Search.hasIndex()) Search.query(query); + else Search.deferQuery(query); + }, + + _parseQuery: (query) => { + // stem the search terms and add them to the correct list + const stemmer = new Stemmer(); + const searchTerms = new Set(); + const excludedTerms = new Set(); + const highlightTerms = new Set(); + const objectTerms = new Set(splitQuery(query.toLowerCase().trim())); + splitQuery(query.trim()).forEach((queryTerm) => { + const queryTermLower = queryTerm.toLowerCase(); + + // maybe skip this "word" + // stopwords array is from language_data.js + if ( + stopwords.indexOf(queryTermLower) !== -1 || + queryTerm.match(/^\d+$/) + ) + return; + + // stem the word + let word = stemmer.stemWord(queryTermLower); + // select the correct list + if (word[0] === "-") excludedTerms.add(word.substr(1)); + else { + searchTerms.add(word); + highlightTerms.add(queryTermLower); + } + }); + + if (SPHINX_HIGHLIGHT_ENABLED) { // set in sphinx_highlight.js + localStorage.setItem("sphinx_highlight_terms", [...highlightTerms].join(" ")) + } + + // console.debug("SEARCH: searching for:"); + // console.info("required: ", [...searchTerms]); + // console.info("excluded: ", [...excludedTerms]); + + return [query, searchTerms, excludedTerms, highlightTerms, objectTerms]; + }, + + /** + * execute search (requires search index to be loaded) + */ + _performSearch: (query, searchTerms, excludedTerms, highlightTerms, objectTerms) => { + const filenames = Search._index.filenames; + const docNames = Search._index.docnames; + const titles = Search._index.titles; + const allTitles = Search._index.alltitles; + const indexEntries = Search._index.indexentries; + + // Collect multiple result groups to be sorted separately and then ordered. + // Each is an array of [docname, title, anchor, descr, score, filename]. + const normalResults = []; + const nonMainIndexResults = []; + + _removeChildren(document.getElementById("search-progress")); + + const queryLower = query.toLowerCase().trim(); + for (const [title, foundTitles] of Object.entries(allTitles)) { + if (title.toLowerCase().trim().includes(queryLower) && (queryLower.length >= title.length/2)) { + for (const [file, id] of foundTitles) { + const score = Math.round(Scorer.title * queryLower.length / title.length); + const boost = titles[file] === title ? 1 : 0; // add a boost for document titles + normalResults.push([ + docNames[file], + titles[file] !== title ? `${titles[file]} > ${title}` : title, + id !== null ? "#" + id : "", + null, + score + boost, + filenames[file], + ]); + } + } + } + + // search for explicit entries in index directives + for (const [entry, foundEntries] of Object.entries(indexEntries)) { + if (entry.includes(queryLower) && (queryLower.length >= entry.length/2)) { + for (const [file, id, isMain] of foundEntries) { + const score = Math.round(100 * queryLower.length / entry.length); + const result = [ + docNames[file], + titles[file], + id ? "#" + id : "", + null, + score, + filenames[file], + ]; + if (isMain) { + normalResults.push(result); + } else { + nonMainIndexResults.push(result); + } + } + } + } + + // lookup as object + objectTerms.forEach((term) => + normalResults.push(...Search.performObjectSearch(term, objectTerms)) + ); + + // lookup as search terms in fulltext + normalResults.push(...Search.performTermsSearch(searchTerms, excludedTerms)); + + // let the scorer override scores with a custom scoring function + if (Scorer.score) { + normalResults.forEach((item) => (item[4] = Scorer.score(item))); + nonMainIndexResults.forEach((item) => (item[4] = Scorer.score(item))); + } + + // Sort each group of results by score and then alphabetically by name. + normalResults.sort(_orderResultsByScoreThenName); + nonMainIndexResults.sort(_orderResultsByScoreThenName); + + // Combine the result groups in (reverse) order. + // Non-main index entries are typically arbitrary cross-references, + // so display them after other results. + let results = [...nonMainIndexResults, ...normalResults]; + + // remove duplicate search results + // note the reversing of results, so that in the case of duplicates, the highest-scoring entry is kept + let seen = new Set(); + results = results.reverse().reduce((acc, result) => { + let resultStr = result.slice(0, 4).concat([result[5]]).map(v => String(v)).join(','); + if (!seen.has(resultStr)) { + acc.push(result); + seen.add(resultStr); + } + return acc; + }, []); + + return results.reverse(); + }, + + query: (query) => { + const [searchQuery, searchTerms, excludedTerms, highlightTerms, objectTerms] = Search._parseQuery(query); + const results = Search._performSearch(searchQuery, searchTerms, excludedTerms, highlightTerms, objectTerms); + + // for debugging + //Search.lastresults = results.slice(); // a copy + // console.info("search results:", Search.lastresults); + + // print the results + _displayNextItem(results, results.length, searchTerms, highlightTerms); + }, + + /** + * search for object names + */ + performObjectSearch: (object, objectTerms) => { + const filenames = Search._index.filenames; + const docNames = Search._index.docnames; + const objects = Search._index.objects; + const objNames = Search._index.objnames; + const titles = Search._index.titles; + + const results = []; + + const objectSearchCallback = (prefix, match) => { + const name = match[4] + const fullname = (prefix ? prefix + "." : "") + name; + const fullnameLower = fullname.toLowerCase(); + if (fullnameLower.indexOf(object) < 0) return; + + let score = 0; + const parts = fullnameLower.split("."); + + // check for different match types: exact matches of full name or + // "last name" (i.e. last dotted part) + if (fullnameLower === object || parts.slice(-1)[0] === object) + score += Scorer.objNameMatch; + else if (parts.slice(-1)[0].indexOf(object) > -1) + score += Scorer.objPartialMatch; // matches in last name + + const objName = objNames[match[1]][2]; + const title = titles[match[0]]; + + // If more than one term searched for, we require other words to be + // found in the name/title/description + const otherTerms = new Set(objectTerms); + otherTerms.delete(object); + if (otherTerms.size > 0) { + const haystack = `${prefix} ${name} ${objName} ${title}`.toLowerCase(); + if ( + [...otherTerms].some((otherTerm) => haystack.indexOf(otherTerm) < 0) + ) + return; + } + + let anchor = match[3]; + if (anchor === "") anchor = fullname; + else if (anchor === "-") anchor = objNames[match[1]][1] + "-" + fullname; + + const descr = objName + _(", in ") + title; + + // add custom score for some objects according to scorer + if (Scorer.objPrio.hasOwnProperty(match[2])) + score += Scorer.objPrio[match[2]]; + else score += Scorer.objPrioDefault; + + results.push([ + docNames[match[0]], + fullname, + "#" + anchor, + descr, + score, + filenames[match[0]], + ]); + }; + Object.keys(objects).forEach((prefix) => + objects[prefix].forEach((array) => + objectSearchCallback(prefix, array) + ) + ); + return results; + }, + + /** + * search for full-text terms in the index + */ + performTermsSearch: (searchTerms, excludedTerms) => { + // prepare search + const terms = Search._index.terms; + const titleTerms = Search._index.titleterms; + const filenames = Search._index.filenames; + const docNames = Search._index.docnames; + const titles = Search._index.titles; + + const scoreMap = new Map(); + const fileMap = new Map(); + + // perform the search on the required terms + searchTerms.forEach((word) => { + const files = []; + const arr = [ + { files: terms[word], score: Scorer.term }, + { files: titleTerms[word], score: Scorer.title }, + ]; + // add support for partial matches + if (word.length > 2) { + const escapedWord = _escapeRegExp(word); + if (!terms.hasOwnProperty(word)) { + Object.keys(terms).forEach((term) => { + if (term.match(escapedWord)) + arr.push({ files: terms[term], score: Scorer.partialTerm }); + }); + } + if (!titleTerms.hasOwnProperty(word)) { + Object.keys(titleTerms).forEach((term) => { + if (term.match(escapedWord)) + arr.push({ files: titleTerms[term], score: Scorer.partialTitle }); + }); + } + } + + // no match but word was a required one + if (arr.every((record) => record.files === undefined)) return; + + // found search word in contents + arr.forEach((record) => { + if (record.files === undefined) return; + + let recordFiles = record.files; + if (recordFiles.length === undefined) recordFiles = [recordFiles]; + files.push(...recordFiles); + + // set score for the word in each file + recordFiles.forEach((file) => { + if (!scoreMap.has(file)) scoreMap.set(file, {}); + scoreMap.get(file)[word] = record.score; + }); + }); + + // create the mapping + files.forEach((file) => { + if (!fileMap.has(file)) fileMap.set(file, [word]); + else if (fileMap.get(file).indexOf(word) === -1) fileMap.get(file).push(word); + }); + }); + + // now check if the files don't contain excluded terms + const results = []; + for (const [file, wordList] of fileMap) { + // check if all requirements are matched + + // as search terms with length < 3 are discarded + const filteredTermCount = [...searchTerms].filter( + (term) => term.length > 2 + ).length; + if ( + wordList.length !== searchTerms.size && + wordList.length !== filteredTermCount + ) + continue; + + // ensure that none of the excluded terms is in the search result + if ( + [...excludedTerms].some( + (term) => + terms[term] === file || + titleTerms[term] === file || + (terms[term] || []).includes(file) || + (titleTerms[term] || []).includes(file) + ) + ) + break; + + // select one (max) score for the file. + const score = Math.max(...wordList.map((w) => scoreMap.get(file)[w])); + // add result to the result list + results.push([ + docNames[file], + titles[file], + "", + null, + score, + filenames[file], + ]); + } + return results; + }, + + /** + * helper function to return a node containing the + * search summary for a given text. keywords is a list + * of stemmed words. + */ + makeSearchSummary: (htmlText, keywords, anchor) => { + const text = Search.htmlToText(htmlText, anchor); + if (text === "") return null; + + const textLower = text.toLowerCase(); + const actualStartPosition = [...keywords] + .map((k) => textLower.indexOf(k.toLowerCase())) + .filter((i) => i > -1) + .slice(-1)[0]; + const startWithContext = Math.max(actualStartPosition - 120, 0); + + const top = startWithContext === 0 ? "" : "..."; + const tail = startWithContext + 240 < text.length ? "..." : ""; + + let summary = document.createElement("p"); + summary.classList.add("context"); + summary.textContent = top + text.substr(startWithContext, 240).trim() + tail; + + return summary; + }, +}; + +_ready(Search.init); diff --git a/branch/main/singlehtml/_static/sphinx_highlight.js b/branch/main/singlehtml/_static/sphinx_highlight.js new file mode 100644 index 0000000..8a96c69 --- /dev/null +++ b/branch/main/singlehtml/_static/sphinx_highlight.js @@ -0,0 +1,154 @@ +/* Highlighting utilities for Sphinx HTML documentation. */ +"use strict"; + +const SPHINX_HIGHLIGHT_ENABLED = true + +/** + * highlight a given string on a node by wrapping it in + * span elements with the given class name. + */ +const _highlight = (node, addItems, text, className) => { + if (node.nodeType === Node.TEXT_NODE) { + const val = node.nodeValue; + const parent = node.parentNode; + const pos = val.toLowerCase().indexOf(text); + if ( + pos >= 0 && + !parent.classList.contains(className) && + !parent.classList.contains("nohighlight") + ) { + let span; + + const closestNode = parent.closest("body, svg, foreignObject"); + const isInSVG = closestNode && closestNode.matches("svg"); + if (isInSVG) { + span = document.createElementNS("http://www.w3.org/2000/svg", "tspan"); + } else { + span = document.createElement("span"); + span.classList.add(className); + } + + span.appendChild(document.createTextNode(val.substr(pos, text.length))); + const rest = document.createTextNode(val.substr(pos + text.length)); + parent.insertBefore( + span, + parent.insertBefore( + rest, + node.nextSibling + ) + ); + node.nodeValue = val.substr(0, pos); + /* There may be more occurrences of search term in this node. So call this + * function recursively on the remaining fragment. + */ + _highlight(rest, addItems, text, className); + + if (isInSVG) { + const rect = document.createElementNS( + "http://www.w3.org/2000/svg", + "rect" + ); + const bbox = parent.getBBox(); + rect.x.baseVal.value = bbox.x; + rect.y.baseVal.value = bbox.y; + rect.width.baseVal.value = bbox.width; + rect.height.baseVal.value = bbox.height; + rect.setAttribute("class", className); + addItems.push({ parent: parent, target: rect }); + } + } + } else if (node.matches && !node.matches("button, select, textarea")) { + node.childNodes.forEach((el) => _highlight(el, addItems, text, className)); + } +}; +const _highlightText = (thisNode, text, className) => { + let addItems = []; + _highlight(thisNode, addItems, text, className); + addItems.forEach((obj) => + obj.parent.insertAdjacentElement("beforebegin", obj.target) + ); +}; + +/** + * Small JavaScript module for the documentation. + */ +const SphinxHighlight = { + + /** + * highlight the search words provided in localstorage in the text + */ + highlightSearchWords: () => { + if (!SPHINX_HIGHLIGHT_ENABLED) return; // bail if no highlight + + // get and clear terms from localstorage + const url = new URL(window.location); + const highlight = + localStorage.getItem("sphinx_highlight_terms") + || url.searchParams.get("highlight") + || ""; + localStorage.removeItem("sphinx_highlight_terms") + url.searchParams.delete("highlight"); + window.history.replaceState({}, "", url); + + // get individual terms from highlight string + const terms = highlight.toLowerCase().split(/\s+/).filter(x => x); + if (terms.length === 0) return; // nothing to do + + // There should never be more than one element matching "div.body" + const divBody = document.querySelectorAll("div.body"); + const body = divBody.length ? divBody[0] : document.querySelector("body"); + window.setTimeout(() => { + terms.forEach((term) => _highlightText(body, term, "highlighted")); + }, 10); + + const searchBox = document.getElementById("searchbox"); + if (searchBox === null) return; + searchBox.appendChild( + document + .createRange() + .createContextualFragment( + '" + ) + ); + }, + + /** + * helper function to hide the search marks again + */ + hideSearchWords: () => { + document + .querySelectorAll("#searchbox .highlight-link") + .forEach((el) => el.remove()); + document + .querySelectorAll("span.highlighted") + .forEach((el) => el.classList.remove("highlighted")); + localStorage.removeItem("sphinx_highlight_terms") + }, + + initEscapeListener: () => { + // only install a listener if it is really needed + if (!DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS) return; + + document.addEventListener("keydown", (event) => { + // bail for input elements + if (BLACKLISTED_KEY_CONTROL_ELEMENTS.has(document.activeElement.tagName)) return; + // bail with special keys + if (event.shiftKey || event.altKey || event.ctrlKey || event.metaKey) return; + if (DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS && (event.key === "Escape")) { + SphinxHighlight.hideSearchWords(); + event.preventDefault(); + } + }); + }, +}; + +_ready(() => { + /* Do not call highlightSearchWords() when we are on the search page. + * It will highlight words from the *previous* search query. + */ + if (typeof Search === "undefined") SphinxHighlight.highlightSearchWords(); + SphinxHighlight.initEscapeListener(); +}); diff --git a/branch/main/singlehtml/_static/sphinx_lesson.css b/branch/main/singlehtml/_static/sphinx_lesson.css new file mode 100644 index 0000000..14b20c6 --- /dev/null +++ b/branch/main/singlehtml/_static/sphinx_lesson.css @@ -0,0 +1,51 @@ +/* sphinx_lesson.css */ + +body.wy-body-for-nav img.with-border { + border: 2px solid; +} + +.rst-content .admonition-no-content { + padding-bottom: 0px; +} + +.rst-content .demo > .admonition-title::before { + content: "\01F440"; /* Eyes */ } +.rst-content .type-along > .admonition-title::before { + content: "\02328\0FE0F"; /* Keyboard */ } +.rst-content .exercise > .admonition-title::before { + content: "\0270D\0FE0F"; /* Hand */ } +.rst-content .solution > .admonition-title::before { + content: "\02714\0FE0E"; /* Check mark */ } +.rst-content .homework > .admonition-title::before { + content: "\01F4DD"; /* Memo */ } +.rst-content .discussion > .admonition-title::before { + content: "\01F4AC"; /* Speech balloon */ } +.rst-content .questions > .admonition-title::before { + content: "\02753\0FE0E"; /* Question mark */ } +.rst-content .prerequisites > .admonition-title::before { + content: "\02699"; /* Gear */ } +.rst-content .seealso > .admonition-title::before { + content: "\027A1\0FE0E"; /* Question mark */ } + + +/* instructor-note */ +.rst-content .instructor-note { + background: #e7e7e7; +} +.rst-content .instructor-note > .admonition-title { + background: #6a6a6a; +} +.rst-content .instructor-note > .admonition-title::before { + content: ""; +} + + +/* sphinx_toggle_button, make the font white */ +.rst-content .toggle.admonition button.toggle-button { + color: white; +} + +/* sphinx-togglebutton, remove underflow when toggled to hidden mode */ +.rst-content .admonition.toggle-hidden { + padding-bottom: 0px; +} diff --git a/branch/main/singlehtml/_static/sphinx_rtd_theme_ext_color_contrast.css b/branch/main/singlehtml/_static/sphinx_rtd_theme_ext_color_contrast.css new file mode 100644 index 0000000..e68feb8 --- /dev/null +++ b/branch/main/singlehtml/_static/sphinx_rtd_theme_ext_color_contrast.css @@ -0,0 +1,47 @@ +/* The following are for web accessibility of sphinx_rtd_theme: they + * solve some of the most frequent contrast issues. Remove when this + * solved: + * https://github.com/readthedocs/sphinx_rtd_theme/issues/971 + */ +/* background: #fcfcfc, note boxes #E7F2FA */ +a { color: #2573A7; } /* original #2980B9, #1F5C84; */ +body { color: #242424; } /* original #404040, #383838 */ +.wy-side-nav-search>a, .wy-side-nav-search .wy-dropdown>a { + color: #ffffff; +} /* original #fcfcfc */ +footer { color: #737373; } /* original gray=#808080*/ +footer span.commit code, footer span.commit .rst-content tt, .rst-content footer span.commit tt { + color: #737373; +} /* original gray=#808080*/ +.rst-content tt.literal, .rst-content tt.literal, .rst-content code.literal { + color: #AB2314; +} +/* Sidebar background */ +.wy-side-nav-search { background-color: #277CB4;} + +/* Same, but for pygments */ +.highlight .ch { color: #3E7A89; } /* #! line */ +.highlight .c1 { color: #3E7A89; } /* also comments */ +.highlight .nv { color: #AD3ECC; } /* variable */ +.highlight .gp { color: #B45608; } /* prompt character, $*/ +.highlight .si { color: #3975B1; } /* ${} variable text */ +.highlight .nc { color: #0C78A7; } + +/* Sphinx admonitions */ +/* warning */ +.wy-alert.wy-alert-warning .wy-alert-title, .rst-content .wy-alert-warning.note .wy-alert-title, .rst-content .attention .wy-alert-title, .rst-content .caution .wy-alert-title, .rst-content .wy-alert-warning.danger .wy-alert-title, .rst-content .wy-alert-warning.error .wy-alert-title, .rst-content .wy-alert-warning.hint .wy-alert-title, .rst-content .wy-alert-warning.important .wy-alert-title, .rst-content .wy-alert-warning.tip .wy-alert-title, .rst-content .warning .wy-alert-title, .rst-content .wy-alert-warning.seealso .wy-alert-title, .rst-content .admonition-todo .wy-alert-title, .rst-content .wy-alert-warning.admonition .wy-alert-title, .wy-alert.wy-alert-warning .rst-content .admonition-title, .rst-content .wy-alert.wy-alert-warning .admonition-title, .rst-content .wy-alert-warning.note .admonition-title, .rst-content .attention .admonition-title, .rst-content .caution .admonition-title, .rst-content .wy-alert-warning.danger .admonition-title, .rst-content .wy-alert-warning.error .admonition-title, .rst-content .wy-alert-warning.hint .admonition-title, .rst-content .wy-alert-warning.important .admonition-title, .rst-content .wy-alert-warning.tip .admonition-title, .rst-content .warning .admonition-title, .rst-content .wy-alert-warning.seealso .admonition-title, .rst-content .admonition-todo .admonition-title, .rst-content .wy-alert-warning.admonition .admonition-title { + background: #B15E16; } +/* important */ +.wy-alert.wy-alert-success .wy-alert-title, .rst-content .wy-alert-success.note .wy-alert-title, .rst-content .wy-alert-success.attention .wy-alert-title, .rst-content .wy-alert-success.caution .wy-alert-title, .rst-content .wy-alert-success.danger .wy-alert-title, .rst-content .wy-alert-success.error .wy-alert-title, .rst-content .hint .wy-alert-title, .rst-content .important .wy-alert-title, .rst-content .tip .wy-alert-title, .rst-content .wy-alert-success.warning .wy-alert-title, .rst-content .wy-alert-success.seealso .wy-alert-title, .rst-content .wy-alert-success.admonition-todo .wy-alert-title, .rst-content .wy-alert-success.admonition .wy-alert-title, .wy-alert.wy-alert-success .rst-content .admonition-title, .rst-content .wy-alert.wy-alert-success .admonition-title, .rst-content .wy-alert-success.note .admonition-title, .rst-content .wy-alert-success.attention .admonition-title, .rst-content .wy-alert-success.caution .admonition-title, .rst-content .wy-alert-success.danger .admonition-title, .rst-content .wy-alert-success.error .admonition-title, .rst-content .hint .admonition-title, .rst-content .important .admonition-title, .rst-content .tip .admonition-title, .rst-content .wy-alert-success.warning .admonition-title, .rst-content .wy-alert-success.seealso .admonition-title, .rst-content .wy-alert-success.admonition-todo .admonition-title, .rst-content .wy-alert-success.admonition .admonition-title { + background: #12826C; } +/* seealso, note, etc */ +.wy-alert.wy-alert-info .wy-alert-title, .rst-content .note .wy-alert-title, .rst-content .wy-alert-info.attention .wy-alert-title, .rst-content .wy-alert-info.caution .wy-alert-title, .rst-content .wy-alert-info.danger .wy-alert-title, .rst-content .wy-alert-info.error .wy-alert-title, .rst-content .wy-alert-info.hint .wy-alert-title, .rst-content .wy-alert-info.important .wy-alert-title, .rst-content .wy-alert-info.tip .wy-alert-title, .rst-content .wy-alert-info.warning .wy-alert-title, .rst-content .seealso .wy-alert-title, .rst-content .wy-alert-info.admonition-todo .wy-alert-title, .rst-content .wy-alert-info.admonition .wy-alert-title, .wy-alert.wy-alert-info .rst-content .admonition-title, .rst-content .wy-alert.wy-alert-info .admonition-title, .rst-content .note .admonition-title, .rst-content .wy-alert-info.attention .admonition-title, .rst-content .wy-alert-info.caution .admonition-title, .rst-content .wy-alert-info.danger .admonition-title, .rst-content .wy-alert-info.error .admonition-title, .rst-content .wy-alert-info.hint .admonition-title, .rst-content .wy-alert-info.important .admonition-title, .rst-content .wy-alert-info.tip .admonition-title, .rst-content .wy-alert-info.warning .admonition-title, .rst-content .seealso .admonition-title, .rst-content .wy-alert-info.admonition-todo .admonition-title, .rst-content .wy-alert-info.admonition .admonition-title { + background: #277CB4; } +/* error, danger */ +.rst-content .danger .admonition-title, .rst-content .danger .wy-alert-title, .rst-content .error .admonition-title, .rst-content .error .wy-alert-title, .rst-content .wy-alert-danger.admonition-todo .admonition-title, .rst-content .wy-alert-danger.admonition-todo .wy-alert-title, .rst-content .wy-alert-danger.admonition .admonition-title, .rst-content .wy-alert-danger.admonition .wy-alert-title, .rst-content .wy-alert-danger.attention .admonition-title, .rst-content .wy-alert-danger.attention .wy-alert-title, .rst-content .wy-alert-danger.caution .admonition-title, .rst-content .wy-alert-danger.caution .wy-alert-title, .rst-content .wy-alert-danger.hint .admonition-title, .rst-content .wy-alert-danger.hint .wy-alert-title, .rst-content .wy-alert-danger.important .admonition-title, .rst-content .wy-alert-danger.important .wy-alert-title, .rst-content .wy-alert-danger.note .admonition-title, .rst-content .wy-alert-danger.note .wy-alert-title, .rst-content .wy-alert-danger.seealso .admonition-title, .rst-content .wy-alert-danger.seealso .wy-alert-title, .rst-content .wy-alert-danger.tip .admonition-title, .rst-content .wy-alert-danger.tip .wy-alert-title, .rst-content .wy-alert-danger.warning .admonition-title, .rst-content .wy-alert-danger.warning .wy-alert-title, .rst-content .wy-alert.wy-alert-danger .admonition-title, .wy-alert.wy-alert-danger .rst-content .admonition-title, .wy-alert.wy-alert-danger .wy-alert-title { + background: #e31704; +} + +/* Generic admonition titles */ +.wy-alert-title, .rst-content .admonition-title { + background: #277CB4; } diff --git a/branch/main/singlehtml/_static/style.css b/branch/main/singlehtml/_static/style.css new file mode 100644 index 0000000..59e60ee --- /dev/null +++ b/branch/main/singlehtml/_static/style.css @@ -0,0 +1,6 @@ +.rst-content .objectives { + background: #fee0d2; +} +.rst-content .objectives > .admonition-title { + background: #fc9272; +} diff --git a/branch/main/singlehtml/_static/tabs.css b/branch/main/singlehtml/_static/tabs.css new file mode 100644 index 0000000..957ba60 --- /dev/null +++ b/branch/main/singlehtml/_static/tabs.css @@ -0,0 +1,89 @@ +.sphinx-tabs { + margin-bottom: 1rem; +} + +[role="tablist"] { + border-bottom: 1px solid #a0b3bf; +} + +.sphinx-tabs-tab { + position: relative; + font-family: Lato,'Helvetica Neue',Arial,Helvetica,sans-serif; + color: #1D5C87; + line-height: 24px; + margin: 0; + font-size: 16px; + font-weight: 400; + background-color: rgba(255, 255, 255, 0); + border-radius: 5px 5px 0 0; + border: 0; + padding: 1rem 1.5rem; + margin-bottom: 0; +} + +.sphinx-tabs-tab[aria-selected="true"] { + font-weight: 700; + border: 1px solid #a0b3bf; + border-bottom: 1px solid white; + margin: -1px; + background-color: white; +} + +.sphinx-tabs-tab:focus { + z-index: 1; + outline-offset: 1px; +} + +.sphinx-tabs-panel { + position: relative; + padding: 1rem; + border: 1px solid #a0b3bf; + margin: 0px -1px -1px -1px; + border-radius: 0 0 5px 5px; + border-top: 0; + background: white; +} + +.sphinx-tabs-panel.code-tab { + padding: 0.4rem; +} + +.sphinx-tab img { + margin-bottom: 24 px; +} + +/* Dark theme preference styling */ + +@media (prefers-color-scheme: dark) { + body[data-theme="auto"] .sphinx-tabs-panel { + color: white; + background-color: rgb(50, 50, 50); + } + + body[data-theme="auto"] .sphinx-tabs-tab { + color: white; + background-color: rgba(255, 255, 255, 0.05); + } + + body[data-theme="auto"] .sphinx-tabs-tab[aria-selected="true"] { + border-bottom: 1px solid rgb(50, 50, 50); + background-color: rgb(50, 50, 50); + } +} + +/* Explicit dark theme styling */ + +body[data-theme="dark"] .sphinx-tabs-panel { + color: white; + background-color: rgb(50, 50, 50); +} + +body[data-theme="dark"] .sphinx-tabs-tab { + color: white; + background-color: rgba(255, 255, 255, 0.05); +} + +body[data-theme="dark"] .sphinx-tabs-tab[aria-selected="true"] { + border-bottom: 2px solid rgb(50, 50, 50); + background-color: rgb(50, 50, 50); +} diff --git a/branch/main/singlehtml/_static/tabs.js b/branch/main/singlehtml/_static/tabs.js new file mode 100644 index 0000000..48dc303 --- /dev/null +++ b/branch/main/singlehtml/_static/tabs.js @@ -0,0 +1,145 @@ +try { + var session = window.sessionStorage || {}; +} catch (e) { + var session = {}; +} + +window.addEventListener("DOMContentLoaded", () => { + const allTabs = document.querySelectorAll('.sphinx-tabs-tab'); + const tabLists = document.querySelectorAll('[role="tablist"]'); + + allTabs.forEach(tab => { + tab.addEventListener("click", changeTabs); + }); + + tabLists.forEach(tabList => { + tabList.addEventListener("keydown", keyTabs); + }); + + // Restore group tab selection from session + const lastSelected = session.getItem('sphinx-tabs-last-selected'); + if (lastSelected != null) selectNamedTabs(lastSelected); +}); + +/** + * Key focus left and right between sibling elements using arrows + * @param {Node} e the element in focus when key was pressed + */ +function keyTabs(e) { + const tab = e.target; + let nextTab = null; + if (e.keyCode === 39 || e.keyCode === 37) { + tab.setAttribute("tabindex", -1); + // Move right + if (e.keyCode === 39) { + nextTab = tab.nextElementSibling; + if (nextTab === null) { + nextTab = tab.parentNode.firstElementChild; + } + // Move left + } else if (e.keyCode === 37) { + nextTab = tab.previousElementSibling; + if (nextTab === null) { + nextTab = tab.parentNode.lastElementChild; + } + } + } + + if (nextTab !== null) { + nextTab.setAttribute("tabindex", 0); + nextTab.focus(); + } +} + +/** + * Select or deselect clicked tab. If a group tab + * is selected, also select tab in other tabLists. + * @param {Node} e the element that was clicked + */ +function changeTabs(e) { + // Use this instead of the element that was clicked, in case it's a child + const notSelected = this.getAttribute("aria-selected") === "false"; + const positionBefore = this.parentNode.getBoundingClientRect().top; + const notClosable = !this.parentNode.classList.contains("closeable"); + + deselectTabList(this); + + if (notSelected || notClosable) { + selectTab(this); + const name = this.getAttribute("name"); + selectNamedTabs(name, this.id); + + if (this.classList.contains("group-tab")) { + // Persist during session + session.setItem('sphinx-tabs-last-selected', name); + } + } + + const positionAfter = this.parentNode.getBoundingClientRect().top; + const positionDelta = positionAfter - positionBefore; + // Scroll to offset content resizing + window.scrollTo(0, window.scrollY + positionDelta); +} + +/** + * Select tab and show associated panel. + * @param {Node} tab tab to select + */ +function selectTab(tab) { + tab.setAttribute("aria-selected", true); + + // Show the associated panel + document + .getElementById(tab.getAttribute("aria-controls")) + .removeAttribute("hidden"); +} + +/** + * Hide the panels associated with all tabs within the + * tablist containing this tab. + * @param {Node} tab a tab within the tablist to deselect + */ +function deselectTabList(tab) { + const parent = tab.parentNode; + const grandparent = parent.parentNode; + + Array.from(parent.children) + .forEach(t => t.setAttribute("aria-selected", false)); + + Array.from(grandparent.children) + .slice(1) // Skip tablist + .forEach(panel => panel.setAttribute("hidden", true)); +} + +/** + * Select grouped tabs with the same name, but no the tab + * with the given id. + * @param {Node} name name of grouped tab to be selected + * @param {Node} clickedId id of clicked tab + */ +function selectNamedTabs(name, clickedId=null) { + const groupedTabs = document.querySelectorAll(`.sphinx-tabs-tab[name="${name}"]`); + const tabLists = Array.from(groupedTabs).map(tab => tab.parentNode); + + tabLists + .forEach(tabList => { + // Don't want to change the tabList containing the clicked tab + const clickedTab = tabList.querySelector(`[id="${clickedId}"]`); + if (clickedTab === null ) { + // Select first tab with matching name + const tab = tabList.querySelector(`.sphinx-tabs-tab[name="${name}"]`); + deselectTabList(tab); + selectTab(tab); + } + }) +} + +if (typeof exports === 'undefined') { + exports = {}; +} + +exports.keyTabs = keyTabs; +exports.changeTabs = changeTabs; +exports.selectTab = selectTab; +exports.deselectTabList = deselectTabList; +exports.selectNamedTabs = selectNamedTabs; diff --git a/branch/main/singlehtml/_static/term_role_formatting.css b/branch/main/singlehtml/_static/term_role_formatting.css new file mode 100644 index 0000000..0b66095 --- /dev/null +++ b/branch/main/singlehtml/_static/term_role_formatting.css @@ -0,0 +1,4 @@ +/* Make terms bold */ +a.reference span.std-term { + font-weight: bold; +} diff --git a/branch/main/singlehtml/_static/togglebutton.css b/branch/main/singlehtml/_static/togglebutton.css new file mode 100644 index 0000000..54a6787 --- /dev/null +++ b/branch/main/singlehtml/_static/togglebutton.css @@ -0,0 +1,160 @@ +/** + * Admonition-based toggles + */ + +/* Visibility of the target */ +.admonition.toggle .admonition-title ~ * { + transition: opacity .3s, height .3s; +} + +/* Toggle buttons inside admonitions so we see the title */ +.admonition.toggle { + position: relative; +} + +/* Titles should cut off earlier to avoid overlapping w/ button */ +.admonition.toggle .admonition-title { + padding-right: 25%; + cursor: pointer; +} + +/* Hovering will cause a slight shift in color to make it feel interactive */ +.admonition.toggle .admonition-title:hover { + box-shadow: inset 0 0 0px 20px rgb(0 0 0 / 1%); +} + +/* Hovering will cause a slight shift in color to make it feel interactive */ +.admonition.toggle .admonition-title:active { + box-shadow: inset 0 0 0px 20px rgb(0 0 0 / 3%); +} + +/* Remove extra whitespace below the admonition title when hidden */ +.admonition.toggle-hidden { + padding-bottom: 0; +} + +.admonition.toggle-hidden .admonition-title { + margin-bottom: 0; +} + +/* hides all the content of a page until de-toggled */ +.admonition.toggle-hidden .admonition-title ~ * { + height: 0; + margin: 0; + opacity: 0; + visibility: hidden; +} + +/* General button style and position*/ +button.toggle-button { + /** + * Background and shape. By default there's no background + * but users can style as they wish + */ + background: none; + border: none; + outline: none; + + /* Positioning just inside the admonition title */ + position: absolute; + right: 0.5em; + padding: 0px; + border: none; + outline: none; +} + +/* Display the toggle hint on wide screens */ +@media (min-width: 768px) { + button.toggle-button.toggle-button-hidden:before { + content: attr(data-toggle-hint); /* This will be filled in by JS */ + font-size: .8em; + align-self: center; + } +} + +/* Icon behavior */ +.tb-icon { + transition: transform .2s ease-out; + height: 1.5em; + width: 1.5em; + stroke: currentColor; /* So that we inherit the color of other text */ +} + +/* The icon should point right when closed, down when open. */ +/* Open */ +.admonition.toggle button .tb-icon { + transform: rotate(90deg); +} + +/* Closed */ +.admonition.toggle button.toggle-button-hidden .tb-icon { + transform: rotate(0deg); +} + +/* With details toggles, we don't rotate the icon so it points right */ +details.toggle-details .tb-icon { + height: 1.4em; + width: 1.4em; + margin-top: 0.1em; /* To center the button vertically */ +} + + +/** + * Details-based toggles. + * In this case, we wrap elements with `.toggle` in a details block. + */ + +/* Details blocks */ +details.toggle-details { + margin: 1em 0; +} + + +details.toggle-details summary { + display: flex; + align-items: center; + cursor: pointer; + list-style: none; + border-radius: .2em; + border-left: 3px solid #1976d2; + background-color: rgb(204 204 204 / 10%); + padding: 0.2em 0.7em 0.3em 0.5em; /* Less padding on left because the SVG has left margin */ + font-size: 0.9em; +} + +details.toggle-details summary:hover { + background-color: rgb(204 204 204 / 20%); +} + +details.toggle-details summary:active { + background: rgb(204 204 204 / 28%); +} + +.toggle-details__summary-text { + margin-left: 0.2em; +} + +details.toggle-details[open] summary { + margin-bottom: .5em; +} + +details.toggle-details[open] summary .tb-icon { + transform: rotate(90deg); +} + +details.toggle-details[open] summary ~ * { + animation: toggle-fade-in .3s ease-out; +} + +@keyframes toggle-fade-in { + from {opacity: 0%;} + to {opacity: 100%;} +} + +/* Print rules - we hide all toggle button elements at print */ +@media print { + /* Always hide the summary so the button doesn't show up */ + details.toggle-details summary { + display: none; + } +} \ No newline at end of file diff --git a/branch/main/singlehtml/_static/togglebutton.js b/branch/main/singlehtml/_static/togglebutton.js new file mode 100644 index 0000000..215a7ee --- /dev/null +++ b/branch/main/singlehtml/_static/togglebutton.js @@ -0,0 +1,187 @@ +/** + * Add Toggle Buttons to elements + */ + +let toggleChevron = ` + + + +`; + +var initToggleItems = () => { + var itemsToToggle = document.querySelectorAll(togglebuttonSelector); + console.log(`[togglebutton]: Adding toggle buttons to ${itemsToToggle.length} items`) + // Add the button to each admonition and hook up a callback to toggle visibility + itemsToToggle.forEach((item, index) => { + if (item.classList.contains("admonition")) { + // If it's an admonition block, then we'll add a button inside + // Generate unique IDs for this item + var toggleID = `toggle-${index}`; + var buttonID = `button-${toggleID}`; + + item.setAttribute('id', toggleID); + if (!item.classList.contains("toggle")){ + item.classList.add("toggle"); + } + // This is the button that will be added to each item to trigger the toggle + var collapseButton = ` + `; + + title = item.querySelector(".admonition-title") + title.insertAdjacentHTML("beforeend", collapseButton); + thisButton = document.getElementById(buttonID); + + // Add click handlers for the button + admonition title (if admonition) + admonitionTitle = document.querySelector(`#${toggleID} > .admonition-title`) + if (admonitionTitle) { + // If an admonition, then make the whole title block clickable + admonitionTitle.addEventListener('click', toggleClickHandler); + admonitionTitle.dataset.target = toggleID + admonitionTitle.dataset.button = buttonID + } else { + // If not an admonition then we'll listen for the button click + thisButton.addEventListener('click', toggleClickHandler); + } + + // Now hide the item for this toggle button unless explicitly noted to show + if (!item.classList.contains("toggle-shown")) { + toggleHidden(thisButton); + } + } else { + // If not an admonition, wrap the block in a
block + // Define the structure of the details block and insert it as a sibling + var detailsBlock = ` +
+ + ${toggleChevron} + ${toggleHintShow} + +
`; + item.insertAdjacentHTML("beforebegin", detailsBlock); + + // Now move the toggle-able content inside of the details block + details = item.previousElementSibling + details.appendChild(item) + item.classList.add("toggle-details__container") + + // Set up a click trigger to change the text as needed + details.addEventListener('click', (click) => { + let parent = click.target.parentElement; + if (parent.tagName.toLowerCase() == "details") { + summary = parent.querySelector("summary"); + details = parent; + } else { + summary = parent; + details = parent.parentElement; + } + // Update the inner text for the proper hint + if (details.open) { + summary.querySelector("span.toggle-details__summary-text").innerText = toggleHintShow; + } else { + summary.querySelector("span.toggle-details__summary-text").innerText = toggleHintHide; + } + + }); + + // If we have a toggle-shown class, open details block should be open + if (item.classList.contains("toggle-shown")) { + details.click(); + } + } + }) +}; + +// This should simply add / remove the collapsed class and change the button text +var toggleHidden = (button) => { + target = button.dataset['target'] + var itemToToggle = document.getElementById(target); + if (itemToToggle.classList.contains("toggle-hidden")) { + itemToToggle.classList.remove("toggle-hidden"); + button.classList.remove("toggle-button-hidden"); + } else { + itemToToggle.classList.add("toggle-hidden"); + button.classList.add("toggle-button-hidden"); + } +} + +var toggleClickHandler = (click) => { + // Be cause the admonition title is clickable and extends to the whole admonition + // We only look for a click event on this title to trigger the toggle. + + if (click.target.classList.contains("admonition-title")) { + button = click.target.querySelector(".toggle-button"); + } else if (click.target.classList.contains("tb-icon")) { + // We've clicked the icon and need to search up one parent for the button + button = click.target.parentElement; + } else if (click.target.tagName == "polyline") { + // We've clicked the SVG elements inside the button, need to up 2 layers + button = click.target.parentElement.parentElement; + } else if (click.target.classList.contains("toggle-button")) { + // We've clicked the button itself and so don't need to do anything + button = click.target; + } else { + console.log(`[togglebutton]: Couldn't find button for ${click.target}`) + } + target = document.getElementById(button.dataset['button']); + toggleHidden(target); +} + +// If we want to blanket-add toggle classes to certain cells +var addToggleToSelector = () => { + const selector = ""; + if (selector.length > 0) { + document.querySelectorAll(selector).forEach((item) => { + item.classList.add("toggle"); + }) + } +} + +// Helper function to run when the DOM is finished +const sphinxToggleRunWhenDOMLoaded = cb => { + if (document.readyState != 'loading') { + cb() + } else if (document.addEventListener) { + document.addEventListener('DOMContentLoaded', cb) + } else { + document.attachEvent('onreadystatechange', function() { + if (document.readyState == 'complete') cb() + }) + } +} +sphinxToggleRunWhenDOMLoaded(addToggleToSelector) +sphinxToggleRunWhenDOMLoaded(initToggleItems) + +/** Toggle details blocks to be open when printing */ +if (toggleOpenOnPrint == "true") { + window.addEventListener("beforeprint", () => { + // Open the details + document.querySelectorAll("details.toggle-details").forEach((el) => { + el.dataset["togglestatus"] = el.open; + el.open = true; + }); + + // Open the admonitions + document.querySelectorAll(".admonition.toggle.toggle-hidden").forEach((el) => { + console.log(el); + el.querySelector("button.toggle-button").click(); + el.dataset["toggle_after_print"] = "true"; + }); + }); + window.addEventListener("afterprint", () => { + // Re-close the details that were closed + document.querySelectorAll("details.toggle-details").forEach((el) => { + el.open = el.dataset["togglestatus"] == "true"; + delete el.dataset["togglestatus"]; + }); + + // Re-close the admonition toggle buttons + document.querySelectorAll(".admonition.toggle").forEach((el) => { + if (el.dataset["toggle_after_print"] == "true") { + el.querySelector("button.toggle-button").click(); + delete el.dataset["toggle_after_print"]; + } + }); + }); +} diff --git a/branch/main/singlehtml/index.html b/branch/main/singlehtml/index.html new file mode 100644 index 0000000..99e5221 --- /dev/null +++ b/branch/main/singlehtml/index.html @@ -0,0 +1,1399 @@ + + + + + + + Reproducible research software development using Python documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
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    +
  • + +
  • + Edit on GitHub +
  • +
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+ +
+

Reproducible research software development using Python

+
+

Big-picture goal

+

This is a hands-on course on research software engineering. In this +workshop we assume that most workshop participants use Python in their work or +a leading a group which uses Python. Therefore, some of the examples will use +Python as the example language.

+

We will work with an example project and go through all the steps of a typical +software project. Once we have seen the building blocks, we will try to apply +them to own projects. Workshop participants will receive and also learn to give +constructive code feedback.

+
+
+

Prerequisites

+
+

Preparation

+
    +
  1. Get a GitHub account following these instructions.

  2. +
  3. You will need a text editor. If you don’t have a favorite one, we recommend +VS Code.

  4. +
  5. If you prefer to work in the terminal and not in VS Code, set up these two (skip this if you use VS Code):

    + +
  6. +
  7. One of these two software environments (if you are not sure which one to +choose or have no preference, choose Conda):

    + +
  8. +
  9. Optional and only on Linux: Apptainer following +these instructions.

  10. +
+
+
+
+

Schedule

+
+

Note

+

The schedule will very soon contain links to lesson material and exercises.

+
+
+

Day 1

+
    +
  • 13:00-13:30 - Welcome and introduction

    + +
  • +
  • 13:30-14:45 (1.25h) - Introduction to version control with Git and GitHub (1/2)

    +
      +
    • Creating a repository and porting your project to Git and GitHub

    • +
    • Basic commands

    • +
    +
  • +
  • 15:00-16:30 (1.5h) - Introduction to version control with Git and GitHub (2/2)

    +
      +
    • Branching and merging

    • +
    • Recovering from typical mistakes

    • +
    +
  • +
  • 16:45-18:00 - Code documentation

    +
      +
    • In-code documentation including docstrings

    • +
    • Writing good README files

    • +
    • Markdown

    • +
    • Sphinx

    • +
    • Building documentation with GitHub Actions

    • +
    • Jupyter Notebooks

    • +
    +
  • +
+
+
+

Day 2

+ +
+
+

Day 3

+
    +
  • 09:00-10:30 - Automated testing

    +
      +
    • Unit tests

    • +
    • End-to-end tests

    • +
    • pytest

    • +
    • GitHub Actions

    • +
    +
  • +
  • 10:45-12:15 - How to make the project more reusable

    +
      +
    • Tracking dependencies with requirements.txt and environment.yml

    • +
    • Recording environments in containers

    • +
    +
  • +
  • 13:00-14:45 - Code quality and good practices

    +
      +
    • Naming (and other) conventions, project organization, modularity

    • +
    • Refactoring (explained through examples)

    • +
    • Design patterns: functional design vs. object-oriented design

    • +
    • How to design your code before writing it

    • +
    • Structuring larger software projects in a modular way

    • +
    • Command-line interfaces

    • +
    • Workflows with Snakemake

    • +
    +
  • +
  • 15:00-16:30 - How to release and publish your code

    +
      +
    • Licenses

    • +
    • Publishing the code via Zenodo

    • +
    • Packaging the code

    • +
    • Sharing the code via PyPI

    • +
    +
  • +
  • 16:45-18:00 - Debriefing and Q&A

    +
      +
    • Participants work on their projects

    • +
    • Together we study actual codes that participants wrote or work on

    • +
    • Constructively we discuss possible improvements

    • +
    • Give individual feedback on code projects

    • +
    +
  • +
+
+
+

If we have time left

+ +
+
+

Conda environment

+

A Conda environment is an isolated software environment that is used to manage dependencies for a project +and you decide where it is located.

+

You will need a environment.yml file that documents the dependencies:

+
name: coderefinery
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - python >= 3.10
+  - black
+  - click
+  - flit
+  - ipywidgets
+  - isort
+  - jupyterlab
+  - jupyterlab_code_formatter
+  - jupyterlab-git
+  - matplotlib
+  - myst-parser
+  - nbdime
+  - numpy
+  - pandas
+  - pytest
+  - pytest-cov
+  - scalene
+  - seaborn
+  - snakemake-minimal
+  - sphinx
+  - sphinx-autoapi
+  - sphinx-autobuild
+  - sphinx_rtd_theme >= 2.0
+  - vulture
+  - scikit-image
+
+
+
+
Before you create a virtual environment
+
    +
  1. Create a new directory for this course.

  2. +
  3. In this directory, create an environment.yml file and copy-paste the dependencies above into it.

  4. +
+
+
+
Choose the tool to manage the environment
+

If you are already using one of these tools, please continue using the tool that you like and know. +If you are new to this, we recommend using Miniconda or Miniforge.

+
    +
  • Anaconda

    +
      +
    • Advantages: easy to install, easy to use, good for beginners

    • +
    • Disadvantages: large download, installs more than we will need, license restrictions

    • +
    +
  • +
  • Miniconda

    +
      +
    • Advantages: small size, installs only what you need

    • +
    • Disadvantages: no graphical interface, license restrictions

    • +
    +
  • +
  • Miniforge

    +
      +
    • Advantages: small size, no license restrictions

    • +
    • Disadvantages: no graphical interface

    • +
    +
  • +
  • Micromamba

    +
      +
    • Advantages: fast, small size

    • +
    • Disadvantages: no graphical interface

    • +
    +
  • +
  • Pixi

    +
      +
    • Advantages: fast and new

    • +
    • Disadvantages: new and less tested and not documented here

    • +
    +
  • +
+
+
+
Creating the virtual environment
+
    +
  1. Open your terminal shell (e.g. Bash or Zsh).

  2. +
  3. Activate conda using conda activate or source ~/miniconda3/bin/activate.

  4. +
  5. Run the following command:

    +
    $ conda env create --file environment.yml
    +
    +
    +
  6. +
  7. Make sure that you see “coderefinery” in the output when you ask for a list of all available environments:

    +
    $ conda env list
    +
    +
    +
  8. +
+
+
+
How to verify that this worked
+

(this will be added)

+
+
+
+

Virtual environment

+

A virtual environment is an isolated software environment that is used to manage dependencies for a project +and you decide where it is located.

+

You will need a requirements.txt file that documents the dependencies:

+
black
+click
+flit
+ipywidgets
+isort
+jupyterlab
+jupyterlab-code-formatter
+jupyterlab-git
+matplotlib
+myst-parser
+nbdime
+numpy
+pandas
+pytest
+pytest-cov
+scalene
+seaborn
+sphinx
+sphinx-autoapi
+sphinx-autobuild
+sphinx_rtd_theme >= 2.0
+vulture
+scikit-image
+
+
+
+
Before you create a virtual environment
+
    +
  1. Create a new directory for this course.

  2. +
  3. In this directory, create a requirements.txt file and copy-paste the dependencies above into it.

  4. +
+
+
+
Creating the virtual environment
+

Now create a virtual environment in this directory either using pip and +venv +(more traditional and safer) or using uv (more modern but also less tested):

+
+

Create a new virtual environment and activate it:

+
$ python3 -m venv coderefinery-environment
+$ source coderefinery-environment/bin/activate
+
+
+

Install the dependencies into the environment:

+
$ python3 -m pip install -r requirements.txt
+
+
+
+
+
+
How to verify that this worked
+

(this will be added)

+
+
+
+
+
+

Example project: Simulating the motion of planets

+

The example code that we will study +is a hopefully simple N-body simulation written in Python. It is not important +or expected that we understand the code in any detail.

+

The big picture is that the code simulates the motion of a number of +planets:

+
    +
  • We can choose the number of planets.

  • +
  • Each planet starts with a random position, velocity, and mass.

  • +
  • At each time step, the code calculates the gravitational force between each +pair of planets.

  • +
  • The forces accelerate each planet, the acceleration modifies the velocity, +the velocity modifies the position of each planet.

  • +
  • We can choose the number of time steps.

  • +
  • The units were chosen to make numbers easy to read.

  • +
+
+
Example run
+
+

Instructor note

+

The instructor demonstrates running the code on their computer.

+
+

The code is written to accept command-line arguments to specify the number +of planets and the number of time steps.

+

We first generate starting data:

+
$ python generate-data.py --num-planets 10 --output-file initial.csv
+
+
+

The generated file (initial.csv) could look like this:

+
px,py,pz,vx,vy,vz,mass
+-46.88,-42.51,88.33,-0.86,-0.18,0.55,6.70
+-5.29,17.09,-96.13,0.66,0.45,-0.17,3.51
+83.53,-92.83,-68.77,-0.26,-0.48,0.24,6.84
+-36.31,25.48,64.16,0.85,0.75,-0.56,1.53
+-68.38,-17.21,-97.07,0.60,0.26,0.69,6.63
+-48.37,-48.74,3.92,-0.92,-0.33,-0.93,8.60
+40.53,-75.50,44.18,-0.62,-0.31,-0.53,8.04
+-27.21,10.78,-78.82,-0.09,-0.55,-0.03,5.35
+88.42,-74.95,-45.85,0.81,0.68,0.56,5.36
+39.09,53.12,-59.54,-0.54,0.56,0.07,8.98
+
+
+

Then we can simulate their motion (in this case for 20 steps):

+
$ python simulate.py --num-steps 20 \
+                     --input-file initial.csv \
+                     --output-file final.csv
+
+
+

The --output-file (final.csv) is again a CSV file (comma-separated values) +and contains the final positions of all planets.

+

It is possible to run on multiple cores and to animate the result. +Here is an example with 100 planets:

+
$ python generate-data.py --num-planets 100 --output-file initial.csv
+
+$ python simulate.py --num-steps 50 \
+                     --input-file initial.csv \
+                     --output-file final.csv \
+                     --trajectories-file trajectories.npz \
+                     --num-cores 8
+
+$ python animate.py --initial-file initial.csv \
+                    --trajectories-file trajectories.npz \
+                    --output-file animation.mp4
+
+
+
+

Learning goals

+
    +
  • What are the most important steps to make this code reusable by others +and our future selves?

  • +
  • Be able to apply these techniques to your own code/script.

  • +
+
+
+

We will not focus on …

+
    +
  • … how the code works internally in detail.

  • +
  • … whether this is the most efficient algorithm.

  • +
  • … whether the code is numerically stable.

  • +
  • … how to code scales with the number of cores.

  • +
  • … whether it is portable to other operating systems (we will discuss this later).

  • +
+
+
+
+
+

Code documentation

+
    +
  • 15 min: What makes good documentation? Also https://diataxis.fr/

  • +
  • 15 min: Writing good README files

  • +
  • 30 min: Exercise: Set up a Sphinx documentation and add API documentation

  • +
  • 15 min: Building documentation with GitHub Actions

  • +
+

requirements.txt:

+
sphinx
+sphinx_rtd_theme >= 2.0
+sphinx_autobuild
+sphinx_autoapi
+myst_parser
+
+
+

conf.py:

+
extensions = [
+    "myst_parser",
+    "autoapi.extension",
+]
+
+autoapi_dirs = ['..']
+
+
+
+
+

Collaborative version control and code review

+
+
+
Concepts around collaboration
+
+

Objectives

+
    +
  • Be able to decide whether to divide work at the branch level or at the repository level.

  • +
+
+
+
Commits, branches, repositories, forks, clones
+
    +
  • repository: The project, contains all data and history (commits, branches, tags).

  • +
  • commit: Snapshot of the project, gets a unique identifier (e.g. c7f0e8bfc718be04525847fc7ac237f470add76e).

  • +
  • branch: Independent development line. The main development line is often called main.

  • +
  • tag: A pointer to one commit, to be able to refer to it later. Like a commemorative plaque +that you attach to a particular commit (e.g. phd-printed or paper-submitted).

  • +
  • cloning: Copying the whole repository to your laptop - the first time. It is not necessary to download each file one by one.

  • +
  • forking: Taking a copy of a repository (which is typically not yours) - your +copy (fork) stays on GitHub/GitLab and you can make changes to your copy.

  • +
+
+
+
Cloning a repository
+

In order to make a complete copy a whole repository, the git clone command +can be used. When cloning, all the files, of all or selected branches, of a +repository are copied in one operation. Cloning of a repository is of relevance +in a few different situations:

+
    +
  • Working on your own, cloning is the operation that you can use to create +multiple instances of a repository on, for instance, a personal computer, a +server, and a supercomputer.

  • +
  • The parent repository could be a repository that you or your colleague own. A +common use case for cloning is when working together within a smaller team +where everyone has read and write access to the same git repository.

  • +
  • Alternatively, cloning can be made from a public repository of a code that +you would like to use. Perhaps you have no intention to work on the code, but +would like to stay in tune with the latest developments, also in-between +releases of new versions of the code.

  • +
+
+Forking and cloning +
+

Forking and cloning

+
+
+
+
+
Forking a repository
+

When a fork is made on GitHub/GitLab a complete copy, of all or selected +branches, of the repository is made. The copy will reside under a different +account on GitHub/GitLab. Forking of a repository is of high relevance when +working with a git repository to which you do not have write access.

+
    +
  • In the fork repository commits can be made to the base branch (main or +master), and to other branches.

  • +
  • The commits that are made within the branches of the fork repository can be +contributed back to the parent repository by means of pull or merge requests.

  • +
+
+
+
Synchronizing changes between repositories
+
    +
  • We need a mechanism to communicate changes between the repositories.

  • +
  • We will pull or fetch updates from remote repositories (we will soon discuss the difference between pull and fetch).

  • +
  • We will push updates to remote repositories.

  • +
  • We will learn how to suggest changes within repositories on GitHub and across repositories (pull request).

  • +
  • Repositories that are forked or cloned do not automatically synchronize themselves: +We will learn how to update forks (by pulling from the “central” repository).

  • +
  • A main difference between cloning a repository and forking a repository is that the former is a general operation for generating copies of a repository to different computers, whereas forking is a particular operation implemented on GitHub/GitLab.

  • +
+
+
+
+
Collaborating within the same repository
+

In this episode, we will learn how to collaborate within the same repository. +We will learn how to cross-reference issues and pull requests, how to review +pull requests, and how to use draft pull requests.

+

This exercise will form a good basis for collaboration that is suitable for +most research groups.

+
+

Note

+

When you read or hear pull request, please think of a change proposal.

+
+
+
Exercise
+

In this exercise, we will contribute to a repository via a pull request. +This means that you propose some change, and then it is accepted (or not).

+
+

Exercise preparation

+
    +
  • First we need to get access to the exercise repository to which we will +contribute.

    +
      +
    • Instructor collects GitHub usernames from learners and adds them as collaborators to the exercise repository +(Settings -> Collaborators and teams -> Manage access -> Add people).

    • +
    +
  • +
  • Don’t forget to accept the invitation

    +
      +
    • Check https://github.com/settings/organizations/

    • +
    • Alternatively check the inbox for the email account you registered with +GitHub. GitHub emails you an invitation link, but if you don’t receive it +you can go to your GitHub notifications in the top right corner. The +maintainer can also “copy invite link” and share it within the group.

    • +
    +
  • +
  • Watching and unwatching repositories

    +
      +
    • Now that you are a collaborator, you get notified about new issues and pull +requests via email.

    • +
    • If you do not wish this, you can “unwatch” a repository (top of +the project page).

    • +
    • However, we recommend watching repositories you are interested +in. You can learn things from experts just by watching the +activity that come through a popular project.

    • +
    +
    +Unwatching a repository +
    +

    Unwatch a repository by clicking “Unwatch” in the repository view, +then “Participating and @mentions” - this way, you will get +notifications about your own interactions.

    +
    +
    +
  • +
+
+
+

Exercise: Collaborating within the same repository (25 min)

+

Technical requirements (from installation instructions):

+ +

What is familiar from the previous workshop day (not repeated here):

+
    +
  • Cloning a repository.

  • +
  • Creating a branch.

  • +
  • Committing a change on the new branch.

  • +
  • Submit a pull request towards the main branch.

  • +
+

What will be new in this exercise:

+
    +
  • If you create the changes locally, you will need to push them to the remote repository.

  • +
  • Learning what a protected branch is and how to modify a protected branch: using a pull request.

  • +
  • Cross-referencing issues and pull requests.

  • +
  • Practice to review a pull request.

  • +
  • Learn about the value of draft pull requests.

  • +
+

Exercise tasks:

+
    +
  1. Start in the exercise +repository and open an +issue where you describe the change you want to make. Note down the issue +number since you will need it later.

  2. +
  3. Create a new branch.

  4. +
  5. Make a change to the recipe book on the new branch and in the commit +cross-reference the issue you opened (see the walk-through below +for how to do that).

  6. +
  7. Push your new branch (with the new commit) to the repository you +are working on.

  8. +
  9. Open a pull request towards the main branch.

  10. +
  11. Review somebody else’s pull request and give constructive feedback. Merge their pull request.

  12. +
  13. Try to create a new branch with some half-finished work and open a draft +pull request. Verify that the draft pull request cannot be merged since it +is not meant to be merged yet.

  14. +
+
+
+
+
Solution and hints
+
+
(1) Opening an issue
+

This is done through the GitHub web interface. For example, you could +give the name of the recipe you want to add (so that others don’t add +the same one). It is the “Issues” tab.

+
+
+
(2) Create a new branch.
+

If on GitHub, you can make the branch in the web interface.

+
+
+
(3) Make a change adding the recipe
+

Add a new file with the recipe in it. Commit the file. In the commit +message, include the note about the issue number, saying that this +will close that issue.

+
+
Cross-referencing issues and pull requests
+

Each issue and each pull request gets a number and you can cross-reference them.

+

When you open an issue, note down the issue number (in this case it is #2):

+
+Each issue gets a number +
+

You can reference this issue number in a commit message or in a pull request, like in this +commit message:

+
this is the new recipe; fixes #2
+
+
+

If you forget to do that in your commit message, you can also reference the issue +in the pull request description. And instead of fixes you can also use closes or resolves +or fix or close or resolve (case insensitive).

+

Here are all the keywords that GitHub recognizes: +https://help.github.com/en/articles/closing-issues-using-keywords

+

Then observe what happens in the issue once your commit gets merged: it will +automatically close the issue and create a link between the issue and the +commit. This is very useful for tracking what changes were made in response to +which issue and to know from when until when precisely the issue was open.

+
+
+
+
(4) Push to GitHub as a new branch
+

Push the branch to the repository. You should end up with a branch +visible in the GitHub web view.

+

This is only necessary if you created the changes locally. If you created the +changes directly on GitHub, you can skip this step.

+
+

In VS Code, you can “publish the branch” to the remote repository by clicking +the cloud icon in the bottom left corner of the window:

+
+Publishing a branch in VS Code +
+
+
+
+
(5) Open a pull request towards the main branch
+

This is done through the GitHub web interface.

+
+
+
(6) Reviewing pull requests
+

You review through the GitHub web interface.

+

Checklist for reviewing a pull request:

+
    +
  • Be kind, on the other side is a human who has put effort into this.

  • +
  • Be constructive: if you see a problem, suggest a solution.

  • +
  • Towards which branch is this directed?

  • +
  • Is the title descriptive?

  • +
  • Is the description informative?

  • +
  • Scroll down to see commits.

  • +
  • Scroll down to see the changes.

  • +
  • If you get incredibly many changes, also consider the license or copyright +and ask where all that code is coming from.

  • +
  • Again, be kind and constructive.

  • +
  • Later we will learn how to suggest changes directly in the pull request.

  • +
+

If someone is new, it’s often nice to say something encouraging in the +comments before merging (even if it’s just “thanks”). If all is good +and there’s not much else to say, you could merge directly.

+
+
+
(7) Draft pull requests
+

Try to create a draft pull request:

+
+Creating a draft pull request +
+

Verify that the draft pull request cannot be merged until it is marked as ready +for review:

+
+Draft pull request cannot be merged +
+

Draft pull requests can be useful for:

+
    +
  • Feedback: You can open a pull request early to get feedback on your work without +signaling that it is ready to merge.

  • +
  • Information: They can help communicating to others that a change is coming up and in +progress.

  • +
+
+
+
What is a protected branch? And how to modify it?
+

A protected branch on GitHub or GitLab is a branch that cannot (accidentally) +deleted or force-pushed to. It is also possible to require that a branch cannot +be directly pushed to or modified, but that changes must be submitted via a +pull request.

+

To protect a branch in your own repository, go to “Settings” -> “Branches”.

+
+
+
Summary
+
    +
  • We used all the same pieces that we’ve learned previously.

  • +
  • But we successfully contributed to a collaborative project!

  • +
  • The pull request allowed us to contribute without changing directly: +this is very good when it’s not mainly our project.

  • +
+
+
+
+
+
Practicing code review
+

In this episode we will practice the code review process. We will learn how to +ask for changes in a pull request, how to suggest a change in a pull request, +and how to modify a pull request.

+

This will enable research groups to work more collaboratively and to not only +improve the code quality but also to learn from each other.

+
+
Exercise
+
+

Exercise preparation

+

We can continue in the same exercise repository which we have used in the +previous episode.

+
+
+

Exercise: Practicing code review (25 min)

+

Technical requirements:

+ +

What is familiar from previous lessons:

+
    +
  • Creating a branch.

  • +
  • Committing a change on the new branch.

  • +
  • Opening and merging pull requests.

  • +
+

What will be new in this exercise:

+
    +
  • As a reviewer, we will learn how to ask for changes in a pull request.

  • +
  • As a reviewer, we will learn how to suggest a change in a pull request.

  • +
  • As a submitter, we will learn how to modify a pull request without closing +the incomplete one and opening a new one.

  • +
+

Exercise tasks:

+
    +
  1. Create a new branch and one or few commits: in these improve something but also +deliberately introduce a typo and also a larger mistake which we will want to fix during the code review.

  2. +
  3. Open a pull request towards the main branch.

  4. +
  5. As a reviewer to somebody else’s pull request, ask for an improvement and +also directly suggest a change for the small typo. (Hint: +suggestions are possible through the GitHub web interface, view of +a pull request, “Files changed” view, after selecting some lines. +Look for the “±” button.)

  6. +
  7. As the submitter, learn how to accept the suggested change. (Hint: +GitHub web interface, “Files Changed” view.)

  8. +
  9. As the submitter, improve the pull request without having to close and open +a new one: by adding a new commit to the same branch. (Hint: push +to the branch again.)

  10. +
  11. Once the changes are addressed, merge the pull request.

  12. +
+
+
+
+
Help and discussion
+

From here on out, we don’t give detailed steps to the solution. You +need to combine what you know, and the extra info below, in order to +solve the above.

+
+
How to ask for changes in a pull request
+

Technically, there are at least two common ways to ask for changes in a pull +request.

+

Either in the comment field of the pull request:

+
+Screenshot of a pull request comment field +
+

Or by using the “Review changes”:

+
+Screenshot of a pull request navigating to the "Review changes" tab +
+

And always please be kind and constructive in your comments. Remember that the +goal is not gate-keeping but collaborative learning.

+
+
+
How to suggest a change in a pull request as a reviewer
+

If you see a very small problem that is easy to fix, you can suggest a change +as a reviewer.

+

Instead of asking the submitter to tiny problem, you can suggest a change by +clicking on the plus sign next to the line number in the “Files changed” tab:

+
+Screenshot of leaving a comment to a line in a pull request +
+

Here you can comment on specific lines or even line ranges.

+

But now the interesting part is to click on the “Add a suggestion” symbol (the +one that looks like plus and minus). Now you can fix the tiny problem (in this +case a typo) and then click on the “Add single comment” button:

+
+Sequence of clicks to add a suggestion to a line in a pull request +
+

The result is this and the submitter can accept the change with a single click:

+
+Screenshot of a pull request with a suggested change +
+

After accepting with “Commit suggestion”, the improvement gets added to the +pull request.

+
+
+
How to modify a pull request to address the review comments
+

If the reviewer asks for changes, it is not necessary to close the pull request +and later open a new one. It can even be counter-productive to do so: This can +fragment the discussion and the history of the pull request and can make it +harder to understand the context of the changes.

+

A much better mechanism to recognize that pull requests are not implemented +from a specific commit to a specific branch, but always from a branch to a +branch.

+

This means that you can make amendments to the pull request by adding new +commits to the same source branch. This way the pull request will be updated +automatically and the reviewer can see the new changes and comment on them.

+

The fact that pull requests are from branch to branch also strongly suggests +that it is a good practice to create a new branch for each pull request. +Otherwise you could accidentally modify an open pull request by adding new +commits to the source branch.

+
+
+
+
Summary
+
    +
  • Our process isn’t just about code now. It’s about discussion and +working together to make the whole process better.

  • +
  • GitHub discussions and reviewing are quite powerful and can make +small changes easy.

  • +
+
+
+
+
How to contribute changes to repositories that belong to others
+

In this episode we prepare you to suggest and contribute changes to +repositories that belong to others. These might be open source projects that +you use in your work.

+

We will see how Git and services like GitHub or GitLab can be used to suggest +modification without having to ask for write access to the repository and +accept modifications without having to grant write access to others.

+
+
Exercise
+
+

Exercise preparation

+
    +
  • The exercise repository is now different: +https://github.com/workshop-material/recipe-book-forking-exercise (note the -forking-exercise).

  • +
  • First fork the exercise repository to your GitHub account.

  • +
  • Then clone your fork to your computer (if you wish to work locally).

  • +
  • Double-check that you have forked the correct repository.

  • +
+
+
+

Exercise: Collaborating within the same repository (25 min)

+

Technical requirements:

+ +

What is familiar from previous lessons:

+
    +
  • Forking a repository.

  • +
  • Creating a branch.

  • +
  • Committing a change on the new branch.

  • +
  • Opening and merging pull requests.

  • +
+

What will be new in this exercise:

+
    +
  • Opening a pull request towards the upstream repository.

  • +
  • Pull requests can be coupled with automated testing.

  • +
  • Learning that your fork can get out of date.

  • +
  • After the pull requests are merged, updating your fork with the changes.

  • +
  • Learn how to approach other people’s repositories with ideas, changes, and requests.

  • +
+

Exercise tasks:

+
    +
  1. Open an issue in the upstream exercise repository where you describe the +change you want to make. Take note of the issue number.

  2. +
  3. Create a new branch in your fork of the repository.

  4. +
  5. Make a change to the recipe book on the new branch and in the commit cross-reference the issue you opened. +See the walk-through below for how to do this.

  6. +
  7. Open a pull request towards the upstream repository.

  8. +
  9. The instructor will review and merge the pull requests. +During the review, pay attention to the automated test step (here for +demonstration purposes, we test whether the recipe contains an ingredients +and an instructions sections).

  10. +
  11. After few pull requests are merged, update your fork with the changes.

  12. +
  13. Check that in your fork you can see changes from other people’s pull requests.

  14. +
+
+
+
+
Help and discussion
+
+
Help! I don’t have permissions to push my local changes
+

Maybe you see an error like this one:

+
Please make sure you have the correct access rights
+and the repository exists.
+
+
+

Or like this one:

+
failed to push some refs to workshop-material/recipe-book-forking-exercise.git
+
+
+

In this case you probably try to push the changes not to your fork but to the original repository +and in this exercise you do not have write access to the original repository.

+

The simpler solution is to clone again but this time your fork.

+ +
+
+
Opening a pull request towards the upstream repository
+

We have learned in the previous episode that pull requests are always from +branch to branch. But the branch can be in a different repository.

+

When you open a pull request in a fork, by default GitHub will suggest to +direct it towards the default branch of the upstream repository.

+

This can be changed and it should always be verified, but in this case this is +exactly what we want to do, from fork towards upstream:

+
+Screenshot of a pull request from fork towards upstream +
+
+
+
Pull requests can be coupled with automated testing
+

We added an automated test here just for fun and so that you see that this is +possible to do.

+

In this exercise, the test is silly. It will check whether the recipe contains +both an ingredients and an instructions section.

+

In this example the test failed:

+
+Screenshot of a failed test in a pull request +
+

Click on the “Details” link to see the details of the failed test:

+
+Screenshot of details why the test failed +
+

How can this be useful?

+
    +
  • The project can define what kind of tests are expected to pass before a pull +request can be merged.

  • +
  • The reviewer can see the results of the tests, without having to run them +locally.

  • +
+

How does it work?

+
    +
  • We added a GitHub Actions workflow +to automatically run on each push or pull request towards the main branch.

  • +
+

What tests or steps can you image for your project to run automatically with +each pull request?

+
+
+
How to update your fork with changes from upstream
+

This used to be difficult but now it is two mouse clicks.

+

Navigate to your fork and notice how GitHub tells you that your fork is behind. +In my case, it is 9 commits behind upstream. To fix this, click on “Sync fork” +and then “Update branch”:

+
+Screenshot on GitHub fork page showing that the fork is behind +
+

After the update my “branch is up to date” with the upstream repository:

+
+Screenshot on GitHub after fork has been updated +
+
+
+
How to approach other people’s repositories with ideas, changes, and requests
+

Contributing very minor changes

+
    +
  • Clone or fork+clone repository

  • +
  • Create a branch

  • +
  • Commit and push change

  • +
  • Open a pull request or merge request

  • +
+

If you observe an issue and have an idea how to fix it

+
    +
  • Open an issue in the repository you wish to contribute to

  • +
  • Describe the problem

  • +
  • If you have a suggestion on how to fix it, describe your suggestion

  • +
  • Possibly discuss and get feedback

  • +
  • If you are working on the fix, indicate it in the issue so that others know that somebody is working on it and who is working on it

  • +
  • Submit your fix as pull request or merge request which references/closes the issue

  • +
+
+

Motivation

+
    +
  • Inform others about an observed problem

  • +
  • Make it clear whether this issue is up for grabs or already being worked on

  • +
+
+

If you have an idea for a new feature

+
    +
  • Open an issue in the repository you wish to contribute to

  • +
  • In the issue, write a short proposal for your suggested change or new feature

  • +
  • Motivate why and how you wish to do this

  • +
  • Also indicate where you are unsure and where you would like feedback

  • +
  • Discuss and get feedback before you code

  • +
  • Once you start coding, indicate that you are working on it

  • +
  • Once you are done, submit your new feature as pull request or merge request which references/closes the issue/proposal

  • +
+
+

Motivation

+
    +
  • Get agreement and feedback before writing 5000 lines of code which might be rejected

  • +
  • If we later wonder why something was done, we have the issue/proposal as +reference and can read up on the reasoning behind a code change

  • +
+
+
+
+
+
Summary
+
    +
  • This forking workflow lets you propose changes to repositories for +which you have no write access.

  • +
  • This is the way that much modern open-source software works.

  • +
  • You can now contribute to any project you can view.

  • +
+
+
+
+
Conclict resolution, rebasing, and organizational strategies
+

(40 min demo and discussion)

+
+
+
+
+

Automated testing

+
    +
  • 15 min: Motivation

  • +
  • 15 min: End-to-end tests

  • +
  • 15 min: Pytest

  • +
  • 15 min: Moving to GitHub Actions

  • +
  • 20 min: Exercise

  • +
  • 10 min: Where to go from here

  • +
+
+
+

How to make the project more reusable

+

Part 1:

+
    +
  • 15 min: Motivation

  • +
  • 15 min: Best practices for managing dependencies in Python

  • +
  • 20 min: Exercise

  • +
+

Part 2:

+
    +
  • 10 min: Introduction to containers

  • +
  • 20 min: Demonstration

  • +
  • 10 min: Discussion

  • +
+
+
+

Code quality and good practices

+

In this episode we will explore code quality and good practices in Python using +a hands-on approach. We will together build up a small project and improve it +step by step.

+

We will start from a relatively simple image processing script which can read a +telescope image of stars and our goal is to count the number of stars in +the image. Later we will want to be able to process many such images.

+

The (fictional) telescope images look like the one below here (in this +repository we can find more):

+
+Generated image representing a telescope image of stars +
+

Generated image representing a telescope image of stars.

+
+
+ +

Part 1:

+
    +
  • 15 min: Discuss how we would solve the problem, run example code, and make it work +as part of a Jupyter notebook.

  • +
  • 15 min: Refactor the positioning code into a function and a module

  • +
  • 15 min: Now we wish to process many images - discuss how we would approach this

  • +
  • 15 min: Introduce CLI and discuss the benefits

  • +
+

Part 2:

+
    +
  • 30 min: From a script to a workflow (using Snakemake)

  • +
  • 15 min: Discuss concepts

    +
      +
    • Pure functions

    • +
    • Design patterns: functional design vs. object-oriented design

    • +
    • How to design your code before writing it: document-driven development

    • +
    +
  • +
+

Bonus:

+
    +
  • Move it under Git

  • +
  • Document dependencies

  • +
  • Show nbdime, black, vulture, ruff

  • +
+
+
+

How to release and publish your code

+

Part 1:

+
    +
  • 30 min: Overview over software licenses and code publishing

  • +
  • 15 min: We add a license, CFF file, and publish to Zenodo (sandbox)

  • +
+

Part 2:

+
    +
  • 30 min: Creating a Python package with the help of flit

  • +
  • 15 min: Deploy the package to test-PyPI using GitHub Actions

  • +
+
+
+

Profiling memory and CPU usage

+

Profilers:

+
    +
  • cProfile or profile

  • +
  • line_profiler

  • +
  • viztracer

  • +
  • scalene

  • +
  • Intel VTune

  • +
  • PyInstrument

  • +
  • py-spy

  • +
  • Pyflame

  • +
  • timeit

  • +
+
+
+
+
+

Credit

+

The following material (all CC-BY) was reused to create this workshop material:

+ +

(I will also summarize what changes have been made to the original material)

+
+
+
+
+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/branch/main/singlehtml/objects.inv b/branch/main/singlehtml/objects.inv new file mode 100644 index 0000000..82d72b9 Binary files /dev/null and b/branch/main/singlehtml/objects.inv differ diff --git a/branch/main/testing/index.html b/branch/main/testing/index.html new file mode 100644 index 0000000..4ee06c1 --- /dev/null +++ b/branch/main/testing/index.html @@ -0,0 +1,157 @@ + + + + + + + Automated testing — Reproducible research software development using Python documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

Automated testing

+
    +
  • 15 min: Motivation

  • +
  • 15 min: End-to-end tests

  • +
  • 15 min: Pytest

  • +
  • 15 min: Moving to GitHub Actions

  • +
  • 20 min: Exercise

  • +
  • 10 min: Where to go from here

  • +
+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/collaboration/code-review/index.html b/collaboration/code-review/index.html new file mode 100644 index 0000000..2186f04 --- /dev/null +++ b/collaboration/code-review/index.html @@ -0,0 +1,287 @@ + + + + + + + Practicing code review — Reproducible research software development using Python documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

Practicing code review

+

In this episode we will practice the code review process. We will learn how to +ask for changes in a pull request, how to suggest a change in a pull request, +and how to modify a pull request.

+

This will enable research groups to work more collaboratively and to not only +improve the code quality but also to learn from each other.

+
+

Exercise

+
+

Exercise preparation

+

We can continue in the same exercise repository which we have used in the +previous episode.

+
+
+

Exercise: Practicing code review (25 min)

+

Technical requirements:

+ +

What is familiar from previous lessons:

+
    +
  • Creating a branch.

  • +
  • Committing a change on the new branch.

  • +
  • Opening and merging pull requests.

  • +
+

What will be new in this exercise:

+
    +
  • As a reviewer, we will learn how to ask for changes in a pull request.

  • +
  • As a reviewer, we will learn how to suggest a change in a pull request.

  • +
  • As a submitter, we will learn how to modify a pull request without closing +the incomplete one and opening a new one.

  • +
+

Exercise tasks:

+
    +
  1. Create a new branch and one or few commits: in these improve something but also +deliberately introduce a typo and also a larger mistake which we will want to fix during the code review.

  2. +
  3. Open a pull request towards the main branch.

  4. +
  5. As a reviewer to somebody else’s pull request, ask for an improvement and +also directly suggest a change for the small typo. (Hint: +suggestions are possible through the GitHub web interface, view of +a pull request, “Files changed” view, after selecting some lines. +Look for the “±” button.)

  6. +
  7. As the submitter, learn how to accept the suggested change. (Hint: +GitHub web interface, “Files Changed” view.)

  8. +
  9. As the submitter, improve the pull request without having to close and open +a new one: by adding a new commit to the same branch. (Hint: push +to the branch again.)

  10. +
  11. Once the changes are addressed, merge the pull request.

  12. +
+
+
+
+

Help and discussion

+

From here on out, we don’t give detailed steps to the solution. You +need to combine what you know, and the extra info below, in order to +solve the above.

+
+

How to ask for changes in a pull request

+

Technically, there are at least two common ways to ask for changes in a pull +request.

+

Either in the comment field of the pull request:

+
+Screenshot of a pull request comment field +
+

Or by using the “Review changes”:

+
+Screenshot of a pull request navigating to the "Review changes" tab +
+

And always please be kind and constructive in your comments. Remember that the +goal is not gate-keeping but collaborative learning.

+
+
+

How to suggest a change in a pull request as a reviewer

+

If you see a very small problem that is easy to fix, you can suggest a change +as a reviewer.

+

Instead of asking the submitter to tiny problem, you can suggest a change by +clicking on the plus sign next to the line number in the “Files changed” tab:

+
+Screenshot of leaving a comment to a line in a pull request +
+

Here you can comment on specific lines or even line ranges.

+

But now the interesting part is to click on the “Add a suggestion” symbol (the +one that looks like plus and minus). Now you can fix the tiny problem (in this +case a typo) and then click on the “Add single comment” button:

+
+Sequence of clicks to add a suggestion to a line in a pull request +
+

The result is this and the submitter can accept the change with a single click:

+
+Screenshot of a pull request with a suggested change +
+

After accepting with “Commit suggestion”, the improvement gets added to the +pull request.

+
+
+

How to modify a pull request to address the review comments

+

If the reviewer asks for changes, it is not necessary to close the pull request +and later open a new one. It can even be counter-productive to do so: This can +fragment the discussion and the history of the pull request and can make it +harder to understand the context of the changes.

+

A much better mechanism to recognize that pull requests are not implemented +from a specific commit to a specific branch, but always from a branch to a +branch.

+

This means that you can make amendments to the pull request by adding new +commits to the same source branch. This way the pull request will be updated +automatically and the reviewer can see the new changes and comment on them.

+

The fact that pull requests are from branch to branch also strongly suggests +that it is a good practice to create a new branch for each pull request. +Otherwise you could accidentally modify an open pull request by adding new +commits to the source branch.

+
+
+
+

Summary

+
    +
  • Our process isn’t just about code now. It’s about discussion and +working together to make the whole process better.

  • +
  • GitHub discussions and reviewing are quite powerful and can make +small changes easy.

  • +
+
+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/collaboration/concepts/index.html b/collaboration/concepts/index.html new file mode 100644 index 0000000..850bb42 --- /dev/null +++ b/collaboration/concepts/index.html @@ -0,0 +1,232 @@ + + + + + + + Concepts around collaboration — Reproducible research software development using Python documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

Concepts around collaboration

+
+

Objectives

+
    +
  • Be able to decide whether to divide work at the branch level or at the repository level.

  • +
+
+
+

Commits, branches, repositories, forks, clones

+
    +
  • repository: The project, contains all data and history (commits, branches, tags).

  • +
  • commit: Snapshot of the project, gets a unique identifier (e.g. c7f0e8bfc718be04525847fc7ac237f470add76e).

  • +
  • branch: Independent development line. The main development line is often called main.

  • +
  • tag: A pointer to one commit, to be able to refer to it later. Like a commemorative plaque +that you attach to a particular commit (e.g. phd-printed or paper-submitted).

  • +
  • cloning: Copying the whole repository to your laptop - the first time. It is not necessary to download each file one by one.

  • +
  • forking: Taking a copy of a repository (which is typically not yours) - your +copy (fork) stays on GitHub/GitLab and you can make changes to your copy.

  • +
+
+
+

Cloning a repository

+

In order to make a complete copy a whole repository, the git clone command +can be used. When cloning, all the files, of all or selected branches, of a +repository are copied in one operation. Cloning of a repository is of relevance +in a few different situations:

+
    +
  • Working on your own, cloning is the operation that you can use to create +multiple instances of a repository on, for instance, a personal computer, a +server, and a supercomputer.

  • +
  • The parent repository could be a repository that you or your colleague own. A +common use case for cloning is when working together within a smaller team +where everyone has read and write access to the same git repository.

  • +
  • Alternatively, cloning can be made from a public repository of a code that +you would like to use. Perhaps you have no intention to work on the code, but +would like to stay in tune with the latest developments, also in-between +releases of new versions of the code.

  • +
+
+Forking and cloning +
+

Forking and cloning

+
+
+
+
+

Forking a repository

+

When a fork is made on GitHub/GitLab a complete copy, of all or selected +branches, of the repository is made. The copy will reside under a different +account on GitHub/GitLab. Forking of a repository is of high relevance when +working with a git repository to which you do not have write access.

+
    +
  • In the fork repository commits can be made to the base branch (main or +master), and to other branches.

  • +
  • The commits that are made within the branches of the fork repository can be +contributed back to the parent repository by means of pull or merge requests.

  • +
+
+
+

Synchronizing changes between repositories

+
    +
  • We need a mechanism to communicate changes between the repositories.

  • +
  • We will pull or fetch updates from remote repositories (we will soon discuss the difference between pull and fetch).

  • +
  • We will push updates to remote repositories.

  • +
  • We will learn how to suggest changes within repositories on GitHub and across repositories (pull request).

  • +
  • Repositories that are forked or cloned do not automatically synchronize themselves: +We will learn how to update forks (by pulling from the “central” repository).

  • +
  • A main difference between cloning a repository and forking a repository is that the former is a general operation for generating copies of a repository to different computers, whereas forking is a particular operation implemented on GitHub/GitLab.

  • +
+
+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/collaboration/demo-discussion/index.html b/collaboration/demo-discussion/index.html new file mode 100644 index 0000000..2570af7 --- /dev/null +++ b/collaboration/demo-discussion/index.html @@ -0,0 +1,158 @@ + + + + + + + Conclict resolution, rebasing, and organizational strategies — Reproducible research software development using Python documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/collaboration/forking-workflow/index.html b/collaboration/forking-workflow/index.html new file mode 100644 index 0000000..a36c862 --- /dev/null +++ b/collaboration/forking-workflow/index.html @@ -0,0 +1,374 @@ + + + + + + + How to contribute changes to repositories that belong to others — Reproducible research software development using Python documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

How to contribute changes to repositories that belong to others

+

In this episode we prepare you to suggest and contribute changes to +repositories that belong to others. These might be open source projects that +you use in your work.

+

We will see how Git and services like GitHub or GitLab can be used to suggest +modification without having to ask for write access to the repository and +accept modifications without having to grant write access to others.

+
+

Exercise

+
+

Exercise preparation

+
    +
  • The exercise repository is now different: +https://github.com/workshop-material/recipe-book-forking-exercise (note the -forking-exercise).

  • +
  • First fork the exercise repository to your GitHub account.

  • +
  • Then clone your fork to your computer (if you wish to work locally).

  • +
  • Double-check that you have forked the correct repository.

  • +
+
+
+

Exercise: Collaborating within the same repository (25 min)

+

Technical requirements:

+ +

What is familiar from previous lessons:

+
    +
  • Forking a repository.

  • +
  • Creating a branch.

  • +
  • Committing a change on the new branch.

  • +
  • Opening and merging pull requests.

  • +
+

What will be new in this exercise:

+
    +
  • Opening a pull request towards the upstream repository.

  • +
  • Pull requests can be coupled with automated testing.

  • +
  • Learning that your fork can get out of date.

  • +
  • After the pull requests are merged, updating your fork with the changes.

  • +
  • Learn how to approach other people’s repositories with ideas, changes, and requests.

  • +
+

Exercise tasks:

+
    +
  1. Open an issue in the upstream exercise repository where you describe the +change you want to make. Take note of the issue number.

  2. +
  3. Create a new branch in your fork of the repository.

  4. +
  5. Make a change to the recipe book on the new branch and in the commit cross-reference the issue you opened. +See the walk-through below for how to do this.

  6. +
  7. Open a pull request towards the upstream repository.

  8. +
  9. The instructor will review and merge the pull requests. +During the review, pay attention to the automated test step (here for +demonstration purposes, we test whether the recipe contains an ingredients +and an instructions sections).

  10. +
  11. After few pull requests are merged, update your fork with the changes.

  12. +
  13. Check that in your fork you can see changes from other people’s pull requests.

  14. +
+
+
+
+

Help and discussion

+
+

Help! I don’t have permissions to push my local changes

+

Maybe you see an error like this one:

+
Please make sure you have the correct access rights
+and the repository exists.
+
+
+

Or like this one:

+
failed to push some refs to workshop-material/recipe-book-forking-exercise.git
+
+
+

In this case you probably try to push the changes not to your fork but to the original repository +and in this exercise you do not have write access to the original repository.

+

The simpler solution is to clone again but this time your fork.

+ +
+
+

Opening a pull request towards the upstream repository

+

We have learned in the previous episode that pull requests are always from +branch to branch. But the branch can be in a different repository.

+

When you open a pull request in a fork, by default GitHub will suggest to +direct it towards the default branch of the upstream repository.

+

This can be changed and it should always be verified, but in this case this is +exactly what we want to do, from fork towards upstream:

+
+Screenshot of a pull request from fork towards upstream +
+
+
+

Pull requests can be coupled with automated testing

+

We added an automated test here just for fun and so that you see that this is +possible to do.

+

In this exercise, the test is silly. It will check whether the recipe contains +both an ingredients and an instructions section.

+

In this example the test failed:

+
+Screenshot of a failed test in a pull request +
+

Click on the “Details” link to see the details of the failed test:

+
+Screenshot of details why the test failed +
+

How can this be useful?

+
    +
  • The project can define what kind of tests are expected to pass before a pull +request can be merged.

  • +
  • The reviewer can see the results of the tests, without having to run them +locally.

  • +
+

How does it work?

+
    +
  • We added a GitHub Actions workflow +to automatically run on each push or pull request towards the main branch.

  • +
+

What tests or steps can you image for your project to run automatically with +each pull request?

+
+
+

How to update your fork with changes from upstream

+

This used to be difficult but now it is two mouse clicks.

+

Navigate to your fork and notice how GitHub tells you that your fork is behind. +In my case, it is 9 commits behind upstream. To fix this, click on “Sync fork” +and then “Update branch”:

+
+Screenshot on GitHub fork page showing that the fork is behind +
+

After the update my “branch is up to date” with the upstream repository:

+
+Screenshot on GitHub after fork has been updated +
+
+
+

How to approach other people’s repositories with ideas, changes, and requests

+

Contributing very minor changes

+
    +
  • Clone or fork+clone repository

  • +
  • Create a branch

  • +
  • Commit and push change

  • +
  • Open a pull request or merge request

  • +
+

If you observe an issue and have an idea how to fix it

+
    +
  • Open an issue in the repository you wish to contribute to

  • +
  • Describe the problem

  • +
  • If you have a suggestion on how to fix it, describe your suggestion

  • +
  • Possibly discuss and get feedback

  • +
  • If you are working on the fix, indicate it in the issue so that others know that somebody is working on it and who is working on it

  • +
  • Submit your fix as pull request or merge request which references/closes the issue

  • +
+
+

Motivation

+
    +
  • Inform others about an observed problem

  • +
  • Make it clear whether this issue is up for grabs or already being worked on

  • +
+
+

If you have an idea for a new feature

+
    +
  • Open an issue in the repository you wish to contribute to

  • +
  • In the issue, write a short proposal for your suggested change or new feature

  • +
  • Motivate why and how you wish to do this

  • +
  • Also indicate where you are unsure and where you would like feedback

  • +
  • Discuss and get feedback before you code

  • +
  • Once you start coding, indicate that you are working on it

  • +
  • Once you are done, submit your new feature as pull request or merge request which references/closes the issue/proposal

  • +
+
+

Motivation

+
    +
  • Get agreement and feedback before writing 5000 lines of code which might be rejected

  • +
  • If we later wonder why something was done, we have the issue/proposal as +reference and can read up on the reasoning behind a code change

  • +
+
+
+
+
+

Summary

+
    +
  • This forking workflow lets you propose changes to repositories for +which you have no write access.

  • +
  • This is the way that much modern open-source software works.

  • +
  • You can now contribute to any project you can view.

  • +
+
+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/collaboration/index.html b/collaboration/index.html new file mode 100644 index 0000000..b4aa30e --- /dev/null +++ b/collaboration/index.html @@ -0,0 +1,165 @@ + + + + + + + Collaborative version control and code review — Reproducible research software development using Python documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/collaboration/same-repository/index.html b/collaboration/same-repository/index.html new file mode 100644 index 0000000..1f9d83f --- /dev/null +++ b/collaboration/same-repository/index.html @@ -0,0 +1,421 @@ + + + + + + + Collaborating within the same repository — Reproducible research software development using Python documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

Collaborating within the same repository

+

In this episode, we will learn how to collaborate within the same repository. +We will learn how to cross-reference issues and pull requests, how to review +pull requests, and how to use draft pull requests.

+

This exercise will form a good basis for collaboration that is suitable for +most research groups.

+
+

Note

+

When you read or hear pull request, please think of a change proposal.

+
+
+

Exercise

+

In this exercise, we will contribute to a repository via a pull request. +This means that you propose some change, and then it is accepted (or not).

+
+

Exercise preparation

+
    +
  • First we need to get access to the exercise repository to which we will +contribute.

    +
      +
    • Instructor collects GitHub usernames from learners and adds them as collaborators to the exercise repository +(Settings -> Collaborators and teams -> Manage access -> Add people).

    • +
    +
  • +
  • Don’t forget to accept the invitation

    +
      +
    • Check https://github.com/settings/organizations/

    • +
    • Alternatively check the inbox for the email account you registered with +GitHub. GitHub emails you an invitation link, but if you don’t receive it +you can go to your GitHub notifications in the top right corner. The +maintainer can also “copy invite link” and share it within the group.

    • +
    +
  • +
  • Watching and unwatching repositories

    +
      +
    • Now that you are a collaborator, you get notified about new issues and pull +requests via email.

    • +
    • If you do not wish this, you can “unwatch” a repository (top of +the project page).

    • +
    • However, we recommend watching repositories you are interested +in. You can learn things from experts just by watching the +activity that come through a popular project.

    • +
    +
    +Unwatching a repository +
    +

    Unwatch a repository by clicking “Unwatch” in the repository view, +then “Participating and @mentions” - this way, you will get +notifications about your own interactions.

    +
    +
    +
  • +
+
+
+

Exercise: Collaborating within the same repository (25 min)

+

Technical requirements (from installation instructions):

+ +

What is familiar from the previous workshop day (not repeated here):

+
    +
  • Cloning a repository.

  • +
  • Creating a branch.

  • +
  • Committing a change on the new branch.

  • +
  • Submit a pull request towards the main branch.

  • +
+

What will be new in this exercise:

+
    +
  • If you create the changes locally, you will need to push them to the remote repository.

  • +
  • Learning what a protected branch is and how to modify a protected branch: using a pull request.

  • +
  • Cross-referencing issues and pull requests.

  • +
  • Practice to review a pull request.

  • +
  • Learn about the value of draft pull requests.

  • +
+

Exercise tasks:

+
    +
  1. Start in the exercise +repository and open an +issue where you describe the change you want to make. Note down the issue +number since you will need it later.

  2. +
  3. Create a new branch.

  4. +
  5. Make a change to the recipe book on the new branch and in the commit +cross-reference the issue you opened (see the walk-through below +for how to do that).

  6. +
  7. Push your new branch (with the new commit) to the repository you +are working on.

  8. +
  9. Open a pull request towards the main branch.

  10. +
  11. Review somebody else’s pull request and give constructive feedback. Merge their pull request.

  12. +
  13. Try to create a new branch with some half-finished work and open a draft +pull request. Verify that the draft pull request cannot be merged since it +is not meant to be merged yet.

  14. +
+
+
+
+

Solution and hints

+
+

(1) Opening an issue

+

This is done through the GitHub web interface. For example, you could +give the name of the recipe you want to add (so that others don’t add +the same one). It is the “Issues” tab.

+
+
+

(2) Create a new branch.

+

If on GitHub, you can make the branch in the web interface.

+
+
+

(3) Make a change adding the recipe

+

Add a new file with the recipe in it. Commit the file. In the commit +message, include the note about the issue number, saying that this +will close that issue.

+
+

Cross-referencing issues and pull requests

+

Each issue and each pull request gets a number and you can cross-reference them.

+

When you open an issue, note down the issue number (in this case it is #2):

+
+Each issue gets a number +
+

You can reference this issue number in a commit message or in a pull request, like in this +commit message:

+
this is the new recipe; fixes #2
+
+
+

If you forget to do that in your commit message, you can also reference the issue +in the pull request description. And instead of fixes you can also use closes or resolves +or fix or close or resolve (case insensitive).

+

Here are all the keywords that GitHub recognizes: +https://help.github.com/en/articles/closing-issues-using-keywords

+

Then observe what happens in the issue once your commit gets merged: it will +automatically close the issue and create a link between the issue and the +commit. This is very useful for tracking what changes were made in response to +which issue and to know from when until when precisely the issue was open.

+
+
+
+

(4) Push to GitHub as a new branch

+

Push the branch to the repository. You should end up with a branch +visible in the GitHub web view.

+

This is only necessary if you created the changes locally. If you created the +changes directly on GitHub, you can skip this step.

+
+

In VS Code, you can “publish the branch” to the remote repository by clicking +the cloud icon in the bottom left corner of the window:

+
+Publishing a branch in VS Code +
+
+
+
+

(5) Open a pull request towards the main branch

+

This is done through the GitHub web interface.

+
+
+

(6) Reviewing pull requests

+

You review through the GitHub web interface.

+

Checklist for reviewing a pull request:

+
    +
  • Be kind, on the other side is a human who has put effort into this.

  • +
  • Be constructive: if you see a problem, suggest a solution.

  • +
  • Towards which branch is this directed?

  • +
  • Is the title descriptive?

  • +
  • Is the description informative?

  • +
  • Scroll down to see commits.

  • +
  • Scroll down to see the changes.

  • +
  • If you get incredibly many changes, also consider the license or copyright +and ask where all that code is coming from.

  • +
  • Again, be kind and constructive.

  • +
  • Later we will learn how to suggest changes directly in the pull request.

  • +
+

If someone is new, it’s often nice to say something encouraging in the +comments before merging (even if it’s just “thanks”). If all is good +and there’s not much else to say, you could merge directly.

+
+
+

(7) Draft pull requests

+

Try to create a draft pull request:

+
+Creating a draft pull request +
+

Verify that the draft pull request cannot be merged until it is marked as ready +for review:

+
+Draft pull request cannot be merged +
+

Draft pull requests can be useful for:

+
    +
  • Feedback: You can open a pull request early to get feedback on your work without +signaling that it is ready to merge.

  • +
  • Information: They can help communicating to others that a change is coming up and in +progress.

  • +
+
+
+

What is a protected branch? And how to modify it?

+

A protected branch on GitHub or GitLab is a branch that cannot (accidentally) +deleted or force-pushed to. It is also possible to require that a branch cannot +be directly pushed to or modified, but that changes must be submitted via a +pull request.

+

To protect a branch in your own repository, go to “Settings” -> “Branches”.

+
+
+

Summary

+
    +
  • We used all the same pieces that we’ve learned previously.

  • +
  • But we successfully contributed to a collaborative project!

  • +
  • The pull request allowed us to contribute without changing directly: +this is very good when it’s not mainly our project.

  • +
+
+
+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/credit/index.html b/credit/index.html new file mode 100644 index 0000000..1adbd54 --- /dev/null +++ b/credit/index.html @@ -0,0 +1,154 @@ + + + + + + + Credit — Reproducible research software development using Python documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

Credit

+

The following material (all CC-BY) was reused to create this workshop material:

+ +

(I will also summarize what changes have been made to the original material)

+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/documentation/index.html b/documentation/index.html new file mode 100644 index 0000000..67d8df7 --- /dev/null +++ b/documentation/index.html @@ -0,0 +1,172 @@ + + + + + + + Code documentation — Reproducible research software development using Python documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

Code documentation

+
    +
  • 15 min: What makes good documentation? Also https://diataxis.fr/

  • +
  • 15 min: Writing good README files

  • +
  • 30 min: Exercise: Set up a Sphinx documentation and add API documentation

  • +
  • 15 min: Building documentation with GitHub Actions

  • +
+

requirements.txt:

+
sphinx
+sphinx_rtd_theme >= 2.0
+sphinx_autobuild
+sphinx_autoapi
+myst_parser
+
+
+

conf.py:

+
extensions = [
+    "myst_parser",
+    "autoapi.extension",
+]
+
+autoapi_dirs = ['..']
+
+
+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/example/index.html b/example/index.html new file mode 100644 index 0000000..236ddb1 --- /dev/null +++ b/example/index.html @@ -0,0 +1,235 @@ + + + + + + + Example project: Simulating the motion of planets — Reproducible research software development using Python documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+
    +
  • + +
  • + Edit on GitHub +
  • +
+
+
+
+
+ +
+

Example project: Simulating the motion of planets

+

The example code that we will study +is a hopefully simple N-body simulation written in Python. It is not important +or expected that we understand the code in any detail.

+

The big picture is that the code simulates the motion of a number of +planets:

+
    +
  • We can choose the number of planets.

  • +
  • Each planet starts with a random position, velocity, and mass.

  • +
  • At each time step, the code calculates the gravitational force between each +pair of planets.

  • +
  • The forces accelerate each planet, the acceleration modifies the velocity, +the velocity modifies the position of each planet.

  • +
  • We can choose the number of time steps.

  • +
  • The units were chosen to make numbers easy to read.

  • +
+
+

Example run

+
+

Instructor note

+

The instructor demonstrates running the code on their computer.

+
+

The code is written to accept command-line arguments to specify the number +of planets and the number of time steps.

+

We first generate starting data:

+
$ python generate-data.py --num-planets 10 --output-file initial.csv
+
+
+

The generated file (initial.csv) could look like this:

+
px,py,pz,vx,vy,vz,mass
+-46.88,-42.51,88.33,-0.86,-0.18,0.55,6.70
+-5.29,17.09,-96.13,0.66,0.45,-0.17,3.51
+83.53,-92.83,-68.77,-0.26,-0.48,0.24,6.84
+-36.31,25.48,64.16,0.85,0.75,-0.56,1.53
+-68.38,-17.21,-97.07,0.60,0.26,0.69,6.63
+-48.37,-48.74,3.92,-0.92,-0.33,-0.93,8.60
+40.53,-75.50,44.18,-0.62,-0.31,-0.53,8.04
+-27.21,10.78,-78.82,-0.09,-0.55,-0.03,5.35
+88.42,-74.95,-45.85,0.81,0.68,0.56,5.36
+39.09,53.12,-59.54,-0.54,0.56,0.07,8.98
+
+
+

Then we can simulate their motion (in this case for 20 steps):

+
$ python simulate.py --num-steps 20 \
+                     --input-file initial.csv \
+                     --output-file final.csv
+
+
+

The --output-file (final.csv) is again a CSV file (comma-separated values) +and contains the final positions of all planets.

+

It is possible to run on multiple cores and to animate the result. +Here is an example with 100 planets:

+
$ python generate-data.py --num-planets 100 --output-file initial.csv
+
+$ python simulate.py --num-steps 50 \
+                     --input-file initial.csv \
+                     --output-file final.csv \
+                     --trajectories-file trajectories.npz \
+                     --num-cores 8
+
+$ python animate.py --initial-file initial.csv \
+                    --trajectories-file trajectories.npz \
+                    --output-file animation.mp4
+
+
+
+

Learning goals

+
    +
  • What are the most important steps to make this code reusable by others +and our future selves?

  • +
  • Be able to apply these techniques to your own code/script.

  • +
+
+
+

We will not focus on …

+
    +
  • … how the code works internally in detail.

  • +
  • … whether this is the most efficient algorithm.

  • +
  • … whether the code is numerically stable.

  • +
  • … how to code scales with the number of cores.

  • +
  • … whether it is portable to other operating systems (we will discuss this later).

  • +
+
+
+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/genindex/index.html b/genindex/index.html new file mode 100644 index 0000000..4978e0b --- /dev/null +++ b/genindex/index.html @@ -0,0 +1,147 @@ + + + + + + Index — Reproducible research software development using Python documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/index.html b/index.html new file mode 100644 index 0000000..7e4b10d --- /dev/null +++ b/index.html @@ -0,0 +1,310 @@ + + + + + + + Reproducible research software development using Python — Reproducible research software development using Python documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+
    +
  • + +
  • + Edit on GitHub +
  • +
+
+
+
+
+ +
+

Reproducible research software development using Python

+
+

Big-picture goal

+

This is a hands-on course on research software engineering. In this +workshop we assume that most workshop participants use Python in their work or +a leading a group which uses Python. Therefore, some of the examples will use +Python as the example language.

+

We will work with an example project and go through all the steps of a typical +software project. Once we have seen the building blocks, we will try to apply +them to own projects. Workshop participants will receive and also learn to give +constructive code feedback.

+
+
+

Prerequisites

+
+

Preparation

+
    +
  1. Get a GitHub account following these instructions.

  2. +
  3. You will need a text editor. If you don’t have a favorite one, we recommend +VS Code.

  4. +
  5. If you prefer to work in the terminal and not in VS Code, set up these two (skip this if you use VS Code):

    + +
  6. +
  7. One of these two software environments (if you are not sure which one to +choose or have no preference, choose Conda):

    + +
  8. +
  9. Optional and only on Linux: Apptainer following +these instructions.

  10. +
+
+
+
+

Schedule

+
+

Note

+

The schedule will very soon contain links to lesson material and exercises.

+
+
+

Day 1

+
    +
  • 13:00-13:30 - Welcome and introduction

    + +
  • +
  • 13:30-14:45 (1.25h) - Introduction to version control with Git and GitHub (1/2)

    +
      +
    • Creating a repository and porting your project to Git and GitHub

    • +
    • Basic commands

    • +
    +
  • +
  • 15:00-16:30 (1.5h) - Introduction to version control with Git and GitHub (2/2)

    +
      +
    • Branching and merging

    • +
    • Recovering from typical mistakes

    • +
    +
  • +
  • 16:45-18:00 - Code documentation

    +
      +
    • In-code documentation including docstrings

    • +
    • Writing good README files

    • +
    • Markdown

    • +
    • Sphinx

    • +
    • Building documentation with GitHub Actions

    • +
    • Jupyter Notebooks

    • +
    +
  • +
+
+
+

Day 2

+ +
+
+

Day 3

+
    +
  • 09:00-10:30 - Automated testing

    +
      +
    • Unit tests

    • +
    • End-to-end tests

    • +
    • pytest

    • +
    • GitHub Actions

    • +
    +
  • +
  • 10:45-12:15 - How to make the project more reusable

    +
      +
    • Tracking dependencies with requirements.txt and environment.yml

    • +
    • Recording environments in containers

    • +
    +
  • +
  • 13:00-14:45 - Code quality and good practices

    +
      +
    • Naming (and other) conventions, project organization, modularity

    • +
    • Refactoring (explained through examples)

    • +
    • Design patterns: functional design vs. object-oriented design

    • +
    • How to design your code before writing it

    • +
    • Structuring larger software projects in a modular way

    • +
    • Command-line interfaces

    • +
    • Workflows with Snakemake

    • +
    +
  • +
  • 15:00-16:30 - How to release and publish your code

    +
      +
    • Licenses

    • +
    • Publishing the code via Zenodo

    • +
    • Packaging the code

    • +
    • Sharing the code via PyPI

    • +
    +
  • +
  • 16:45-18:00 - Debriefing and Q&A

    +
      +
    • Participants work on their projects

    • +
    • Together we study actual codes that participants wrote or work on

    • +
    • Constructively we discuss possible improvements

    • +
    • Give individual feedback on code projects

    • +
    +
  • +
+
+
+

If we have time left

+ +
+
+
+
+
+
+
+
+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/installation/conda/index.html b/installation/conda/index.html new file mode 100644 index 0000000..7f0b7c6 --- /dev/null +++ b/installation/conda/index.html @@ -0,0 +1,255 @@ + + + + + + + Conda environment — Reproducible research software development using Python documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

Conda environment

+

A Conda environment is an isolated software environment that is used to manage dependencies for a project +and you decide where it is located.

+

You will need a environment.yml file that documents the dependencies:

+
name: coderefinery
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - python >= 3.10
+  - black
+  - click
+  - flit
+  - ipywidgets
+  - isort
+  - jupyterlab
+  - jupyterlab_code_formatter
+  - jupyterlab-git
+  - matplotlib
+  - myst-parser
+  - nbdime
+  - numpy
+  - pandas
+  - pytest
+  - pytest-cov
+  - scalene
+  - seaborn
+  - snakemake-minimal
+  - sphinx
+  - sphinx-autoapi
+  - sphinx-autobuild
+  - sphinx_rtd_theme >= 2.0
+  - vulture
+  - scikit-image
+
+
+
+

Before you create a virtual environment

+
    +
  1. Create a new directory for this course.

  2. +
  3. In this directory, create an environment.yml file and copy-paste the dependencies above into it.

  4. +
+
+
+

Choose the tool to manage the environment

+

If you are already using one of these tools, please continue using the tool that you like and know. +If you are new to this, we recommend using Miniconda or Miniforge.

+
    +
  • Anaconda

    +
      +
    • Advantages: easy to install, easy to use, good for beginners

    • +
    • Disadvantages: large download, installs more than we will need, license restrictions

    • +
    +
  • +
  • Miniconda

    +
      +
    • Advantages: small size, installs only what you need

    • +
    • Disadvantages: no graphical interface, license restrictions

    • +
    +
  • +
  • Miniforge

    +
      +
    • Advantages: small size, no license restrictions

    • +
    • Disadvantages: no graphical interface

    • +
    +
  • +
  • Micromamba

    +
      +
    • Advantages: fast, small size

    • +
    • Disadvantages: no graphical interface

    • +
    +
  • +
  • Pixi

    +
      +
    • Advantages: fast and new

    • +
    • Disadvantages: new and less tested and not documented here

    • +
    +
  • +
+
+
+

Creating the virtual environment

+
    +
  1. Open your terminal shell (e.g. Bash or Zsh).

  2. +
  3. Activate conda using conda activate or source ~/miniconda3/bin/activate.

  4. +
  5. Run the following command:

    +
    $ conda env create --file environment.yml
    +
    +
    +
  6. +
  7. Make sure that you see “coderefinery” in the output when you ask for a list of all available environments:

    +
    $ conda env list
    +
    +
    +
  8. +
+
+
+

How to verify that this worked

+

(this will be added)

+
+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/installation/virtual-environment/index.html b/installation/virtual-environment/index.html new file mode 100644 index 0000000..6cf88ee --- /dev/null +++ b/installation/virtual-environment/index.html @@ -0,0 +1,220 @@ + + + + + + + Virtual environment — Reproducible research software development using Python documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

Virtual environment

+

A virtual environment is an isolated software environment that is used to manage dependencies for a project +and you decide where it is located.

+

You will need a requirements.txt file that documents the dependencies:

+
black
+click
+flit
+ipywidgets
+isort
+jupyterlab
+jupyterlab-code-formatter
+jupyterlab-git
+matplotlib
+myst-parser
+nbdime
+numpy
+pandas
+pytest
+pytest-cov
+scalene
+seaborn
+sphinx
+sphinx-autoapi
+sphinx-autobuild
+sphinx_rtd_theme >= 2.0
+vulture
+scikit-image
+
+
+
+

Before you create a virtual environment

+
    +
  1. Create a new directory for this course.

  2. +
  3. In this directory, create a requirements.txt file and copy-paste the dependencies above into it.

  4. +
+
+
+

Creating the virtual environment

+

Now create a virtual environment in this directory either using pip and +venv +(more traditional and safer) or using uv (more modern but also less tested):

+
+

Create a new virtual environment and activate it:

+
$ python3 -m venv coderefinery-environment
+$ source coderefinery-environment/bin/activate
+
+
+

Install the dependencies into the environment:

+
$ python3 -m pip install -r requirements.txt
+
+
+
+
+
+

How to verify that this worked

+

(this will be added)

+
+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/lesson.pdf b/lesson.pdf new file mode 100644 index 0000000..96348bb Binary files /dev/null and b/lesson.pdf differ diff --git a/objects.inv b/objects.inv new file mode 100644 index 0000000..1523d5d --- /dev/null +++ b/objects.inv @@ -0,0 +1,7 @@ +# Sphinx inventory version 2 +# Project: Reproducible research software development using Python +# Version: +# The remainder of this file is compressed using zlib. +xڭV=0 +FۊCv(ɢ+ɥ)vZ\$#H(!pVpaG͏Y - +M!&X=;X.ʔ,$K|"DqKƞg`g.oQ3n֍$)70j̥ruNlVC}?rG*=hKnH5 +\)U=hEMrmTmvئ_?5;}!B';-Lp]c끉\Zh)V:Ih:C_Q-2q齮ۉ,ɳ 2X@N\/eߛ{4T8 30IYY45 RBwYۀA:umb[qKcf7Fl2` 3&j+4|8(W=]Ӈ8)9 =Àk4l{:|'mx )Hw>E{UF8,h{̮ڸ94S*tw&vd"U‰umznwREi=,9satt QӚ@||K9f,wxVƨX.z򜽳;;D`[5j9H;)[3ȝg9ʊ \ No newline at end of file diff --git a/profiling/index.html b/profiling/index.html new file mode 100644 index 0000000..32e95d4 --- /dev/null +++ b/profiling/index.html @@ -0,0 +1,161 @@ + + + + + + + Profiling memory and CPU usage — Reproducible research software development using Python documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

Profiling memory and CPU usage

+

Profilers:

+
    +
  • cProfile or profile

  • +
  • line_profiler

  • +
  • viztracer

  • +
  • scalene

  • +
  • Intel VTune

  • +
  • PyInstrument

  • +
  • py-spy

  • +
  • Pyflame

  • +
  • timeit

  • +
+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/publishing/index.html b/publishing/index.html new file mode 100644 index 0000000..810737e --- /dev/null +++ b/publishing/index.html @@ -0,0 +1,159 @@ + + + + + + + How to release and publish your code — Reproducible research software development using Python documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

How to release and publish your code

+

Part 1:

+
    +
  • 30 min: Overview over software licenses and code publishing

  • +
  • 15 min: We add a license, CFF file, and publish to Zenodo (sandbox)

  • +
+

Part 2:

+
    +
  • 30 min: Creating a Python package with the help of flit

  • +
  • 15 min: Deploy the package to test-PyPI using GitHub Actions

  • +
+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/refactoring/index.html b/refactoring/index.html new file mode 100644 index 0000000..1322aa6 --- /dev/null +++ b/refactoring/index.html @@ -0,0 +1,234 @@ + + + + + + + Code quality and good practices — Reproducible research software development using Python documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

Code quality and good practices

+

In this episode we will explore code quality and good practices in Python using +a hands-on approach. We will together build up a small project and improve it +step by step.

+

We will start from a relatively simple image processing script which can read a +telescope image of stars and our goal is to count the number of stars in +the image. Later we will want to be able to process many such images.

+

The (fictional) telescope images look like the one below here (in this +repository we can find more):

+
+Generated image representing a telescope image of stars +
+

Generated image representing a telescope image of stars.

+
+
+ +

Part 1:

+
    +
  • 15 min: Discuss how we would solve the problem, run example code, and make it work +as part of a Jupyter notebook.

  • +
  • 15 min: Refactor the positioning code into a function and a module

  • +
  • 15 min: Now we wish to process many images - discuss how we would approach this

  • +
  • 15 min: Introduce CLI and discuss the benefits

  • +
+

Part 2:

+
    +
  • 30 min: From a script to a workflow (using Snakemake)

  • +
  • 15 min: Discuss concepts

    +
      +
    • Pure functions

    • +
    • Design patterns: functional design vs. object-oriented design

    • +
    • How to design your code before writing it: document-driven development

    • +
    +
  • +
+

Bonus:

+
    +
  • Move it under Git

  • +
  • Document dependencies

  • +
  • Show nbdime, black, vulture, ruff

  • +
+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/reusable/index.html b/reusable/index.html new file mode 100644 index 0000000..3558af4 --- /dev/null +++ b/reusable/index.html @@ -0,0 +1,161 @@ + + + + + + + How to make the project more reusable — Reproducible research software development using Python documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

How to make the project more reusable

+

Part 1:

+
    +
  • 15 min: Motivation

  • +
  • 15 min: Best practices for managing dependencies in Python

  • +
  • 20 min: Exercise

  • +
+

Part 2:

+
    +
  • 10 min: Introduction to containers

  • +
  • 20 min: Demonstration

  • +
  • 10 min: Discussion

  • +
+
+ + +
+
+ +
+
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+ margin: 1em 0 1em 0; + padding: 0.4em; +} + +/* -- domain module index --------------------------------------------------- */ + +table.modindextable td { + padding: 2px; + border-collapse: collapse; +} + +/* -- general body styles --------------------------------------------------- */ + +div.body { + min-width: 360px; + max-width: 800px; +} + +div.body p, div.body dd, div.body li, div.body blockquote { + -moz-hyphens: auto; + -ms-hyphens: auto; + -webkit-hyphens: auto; + hyphens: auto; +} + +a.headerlink { + visibility: hidden; +} + +a:visited { + color: #551A8B; +} + +h1:hover > a.headerlink, +h2:hover > a.headerlink, +h3:hover > a.headerlink, +h4:hover > a.headerlink, +h5:hover > a.headerlink, +h6:hover > a.headerlink, +dt:hover > a.headerlink, +caption:hover > a.headerlink, +p.caption:hover > a.headerlink, +div.code-block-caption:hover > a.headerlink { + visibility: visible; +} + +div.body p.caption { + text-align: inherit; +} + +div.body td { + text-align: left; +} + +.first { + margin-top: 0 !important; +} + +p.rubric { + margin-top: 30px; + font-weight: bold; +} + +img.align-left, figure.align-left, .figure.align-left, object.align-left { + clear: left; + float: left; + margin-right: 1em; +} + +img.align-right, figure.align-right, .figure.align-right, object.align-right { + clear: right; + float: right; + margin-left: 1em; +} + +img.align-center, figure.align-center, .figure.align-center, object.align-center { + display: block; + margin-left: auto; + margin-right: auto; +} + +img.align-default, figure.align-default, .figure.align-default { + display: block; + margin-left: auto; + margin-right: auto; +} + +.align-left { + text-align: left; +} + +.align-center { + text-align: center; +} + +.align-default { + text-align: center; +} + +.align-right { + text-align: right; +} + +/* -- sidebars -------------------------------------------------------------- */ + +div.sidebar, +aside.sidebar { + margin: 0 0 0.5em 1em; + border: 1px solid #ddb; + padding: 7px; + background-color: #ffe; + width: 40%; + float: right; + clear: right; + overflow-x: auto; +} + +p.sidebar-title { + font-weight: bold; +} + +nav.contents, +aside.topic, +div.admonition, div.topic, blockquote { + clear: left; +} + +/* -- topics ---------------------------------------------------------------- */ + +nav.contents, +aside.topic, +div.topic { + border: 1px solid #ccc; + padding: 7px; + margin: 10px 0 10px 0; +} + +p.topic-title { + font-size: 1.1em; + font-weight: bold; + margin-top: 10px; +} + +/* -- admonitions ----------------------------------------------------------- */ + +div.admonition { + margin-top: 10px; + margin-bottom: 10px; + padding: 7px; +} + +div.admonition dt { + font-weight: bold; +} + +p.admonition-title { + margin: 0px 10px 5px 0px; + font-weight: bold; +} + +div.body p.centered { + text-align: center; + margin-top: 25px; +} + +/* -- content of sidebars/topics/admonitions -------------------------------- */ + +div.sidebar > :last-child, +aside.sidebar > :last-child, +nav.contents > :last-child, +aside.topic > :last-child, +div.topic > :last-child, +div.admonition > :last-child { + margin-bottom: 0; +} + +div.sidebar::after, +aside.sidebar::after, +nav.contents::after, +aside.topic::after, +div.topic::after, +div.admonition::after, +blockquote::after { + display: block; + content: ''; + clear: both; +} + +/* -- tables ---------------------------------------------------------------- */ + +table.docutils { + margin-top: 10px; + margin-bottom: 10px; + border: 0; + border-collapse: collapse; +} + +table.align-center { + margin-left: auto; + margin-right: auto; +} + +table.align-default { + margin-left: auto; + margin-right: auto; +} + +table caption span.caption-number { + font-style: italic; +} + +table caption span.caption-text { +} + +table.docutils td, table.docutils th { + padding: 1px 8px 1px 5px; + border-top: 0; + border-left: 0; + border-right: 0; + border-bottom: 1px solid #aaa; +} + +th { + text-align: left; + padding-right: 5px; +} + +table.citation { + border-left: solid 1px gray; + margin-left: 1px; +} + +table.citation td { + border-bottom: none; +} + +th > :first-child, +td > :first-child { + margin-top: 0px; +} + +th > :last-child, +td > :last-child { + margin-bottom: 0px; +} + +/* -- figures --------------------------------------------------------------- */ + +div.figure, figure { + margin: 0.5em; + padding: 0.5em; +} + +div.figure p.caption, figcaption { + padding: 0.3em; +} + +div.figure p.caption span.caption-number, +figcaption span.caption-number { + font-style: italic; +} + +div.figure p.caption span.caption-text, +figcaption span.caption-text { +} + +/* -- field list styles ----------------------------------------------------- */ + +table.field-list td, table.field-list th { + border: 0 !important; +} + +.field-list ul { + margin: 0; + padding-left: 1em; +} + +.field-list p { + margin: 0; +} + +.field-name { + -moz-hyphens: manual; + -ms-hyphens: manual; + -webkit-hyphens: manual; + hyphens: manual; +} + +/* -- hlist styles ---------------------------------------------------------- */ + +table.hlist { + margin: 1em 0; +} + +table.hlist td { + vertical-align: top; +} + +/* -- object description styles --------------------------------------------- */ + +.sig { + font-family: 'Consolas', 'Menlo', 'DejaVu Sans Mono', 'Bitstream Vera Sans Mono', monospace; +} + +.sig-name, code.descname { + background-color: transparent; + font-weight: bold; +} + +.sig-name { + font-size: 1.1em; +} + +code.descname { + font-size: 1.2em; +} + +.sig-prename, code.descclassname { + background-color: transparent; +} + +.optional { + font-size: 1.3em; +} + +.sig-paren { + font-size: larger; +} + +.sig-param.n { + font-style: italic; +} + +/* C++ specific styling */ + +.sig-inline.c-texpr, +.sig-inline.cpp-texpr { + font-family: unset; +} + +.sig.c .k, .sig.c .kt, +.sig.cpp .k, .sig.cpp .kt { + color: #0033B3; +} + +.sig.c .m, +.sig.cpp .m { + color: #1750EB; +} + +.sig.c .s, .sig.c .sc, +.sig.cpp .s, .sig.cpp .sc { + color: #067D17; +} + + +/* -- other body styles ----------------------------------------------------- */ + +ol.arabic { + list-style: decimal; +} + +ol.loweralpha { + list-style: lower-alpha; +} + +ol.upperalpha { + list-style: upper-alpha; +} + +ol.lowerroman { + list-style: lower-roman; +} + +ol.upperroman { + list-style: upper-roman; +} + +:not(li) > ol > li:first-child > :first-child, +:not(li) > ul > li:first-child > :first-child { + margin-top: 0px; +} + +:not(li) > ol > li:last-child > :last-child, +:not(li) > ul > li:last-child > :last-child { + margin-bottom: 0px; +} + +ol.simple ol p, +ol.simple ul p, +ul.simple ol p, +ul.simple ul p { + margin-top: 0; +} + +ol.simple > li:not(:first-child) > p, +ul.simple > li:not(:first-child) > p { + margin-top: 0; +} + +ol.simple p, +ul.simple p { + margin-bottom: 0; +} + +aside.footnote > span, +div.citation > span { + float: left; +} +aside.footnote > span:last-of-type, +div.citation > span:last-of-type { + padding-right: 0.5em; +} +aside.footnote > p { + margin-left: 2em; +} +div.citation > p { + margin-left: 4em; +} +aside.footnote > p:last-of-type, +div.citation > p:last-of-type { + margin-bottom: 0em; +} +aside.footnote > p:last-of-type:after, +div.citation > p:last-of-type:after { + content: ""; + clear: both; +} + +dl.field-list { + display: grid; + grid-template-columns: fit-content(30%) auto; +} + +dl.field-list > dt { + font-weight: bold; + word-break: break-word; + padding-left: 0.5em; + padding-right: 5px; +} + +dl.field-list > dd { + padding-left: 0.5em; + margin-top: 0em; + margin-left: 0em; + margin-bottom: 0em; +} + +dl { + margin-bottom: 15px; +} + +dd > :first-child { + margin-top: 0px; +} + +dd ul, dd table { + margin-bottom: 10px; +} + +dd { + margin-top: 3px; + margin-bottom: 10px; + margin-left: 30px; +} + +.sig dd { + margin-top: 0px; + margin-bottom: 0px; +} + +.sig dl { + margin-top: 0px; + margin-bottom: 0px; +} + +dl > dd:last-child, +dl > dd:last-child > :last-child { + margin-bottom: 0; +} + +dt:target, span.highlighted { + background-color: #fbe54e; +} + +rect.highlighted { + fill: #fbe54e; +} + +dl.glossary dt { + font-weight: bold; + font-size: 1.1em; +} + +.versionmodified { + font-style: italic; +} + +.system-message { + background-color: #fda; + padding: 5px; + border: 3px solid red; +} + +.footnote:target { + background-color: #ffa; +} + +.line-block { + display: block; + margin-top: 1em; + margin-bottom: 1em; +} + +.line-block .line-block { + margin-top: 0; + margin-bottom: 0; + margin-left: 1.5em; +} + +.guilabel, .menuselection { + font-family: sans-serif; +} + +.accelerator { + text-decoration: underline; +} + +.classifier { + font-style: oblique; +} + +.classifier:before { + font-style: normal; + margin: 0 0.5em; + content: ":"; + display: inline-block; +} + +abbr, acronym { + border-bottom: dotted 1px; + cursor: help; +} + +.translated { + background-color: rgba(207, 255, 207, 0.2) +} + +.untranslated { + background-color: rgba(255, 207, 207, 0.2) +} + +/* -- code displays --------------------------------------------------------- */ + +pre { + overflow: auto; + overflow-y: hidden; /* fixes display issues on Chrome browsers */ +} + +pre, div[class*="highlight-"] { + clear: both; +} + +span.pre { + -moz-hyphens: none; + -ms-hyphens: none; + -webkit-hyphens: none; + hyphens: none; + white-space: nowrap; +} + +div[class*="highlight-"] { + margin: 1em 0; +} + +td.linenos pre { + border: 0; + background-color: transparent; + color: #aaa; +} + +table.highlighttable { + display: block; +} + +table.highlighttable tbody { + display: block; +} + +table.highlighttable tr { + display: flex; +} + +table.highlighttable td { + margin: 0; + padding: 0; +} + +table.highlighttable td.linenos { + padding-right: 0.5em; +} + +table.highlighttable td.code { + flex: 1; + overflow: hidden; +} + +.highlight .hll { + display: block; +} + +div.highlight pre, +table.highlighttable pre { + margin: 0; +} + +div.code-block-caption + div { + margin-top: 0; +} + +div.code-block-caption { + margin-top: 1em; + padding: 2px 5px; + font-size: small; +} + +div.code-block-caption code { + background-color: transparent; +} + +table.highlighttable td.linenos, +span.linenos, +div.highlight span.gp { /* gp: Generic.Prompt */ + user-select: none; + -webkit-user-select: text; /* Safari fallback only */ + -webkit-user-select: none; /* Chrome/Safari */ + -moz-user-select: none; /* Firefox */ + -ms-user-select: none; /* IE10+ */ +} + +div.code-block-caption span.caption-number { + padding: 0.1em 0.3em; + font-style: italic; +} + +div.code-block-caption span.caption-text { +} + +div.literal-block-wrapper { + margin: 1em 0; +} + +code.xref, a code { + background-color: transparent; + font-weight: bold; +} + +h1 code, h2 code, h3 code, h4 code, h5 code, h6 code { + background-color: transparent; +} + +.viewcode-link { + float: right; +} + +.viewcode-back { + float: right; + font-family: sans-serif; +} + +div.viewcode-block:target { + margin: -1px -10px; + padding: 0 10px; +} + +/* -- math display ---------------------------------------------------------- */ + +img.math { + vertical-align: middle; +} + +div.body div.math p { + text-align: center; +} + +span.eqno { + float: right; +} + +span.eqno a.headerlink { + position: absolute; + z-index: 1; +} + +div.math:hover a.headerlink { + visibility: visible; +} + +/* -- printout stylesheet --------------------------------------------------- */ + +@media print { + div.document, + div.documentwrapper, + div.bodywrapper { + margin: 0 !important; + width: 100%; + } + + div.sphinxsidebar, + div.related, + div.footer, + #top-link { + display: none; + } +} \ No newline at end of file diff --git a/singlehtml/_static/check-solid.svg b/singlehtml/_static/check-solid.svg new file mode 100644 index 0000000..92fad4b --- /dev/null +++ b/singlehtml/_static/check-solid.svg @@ -0,0 +1,4 @@ + + + + diff --git a/singlehtml/_static/clipboard.min.js b/singlehtml/_static/clipboard.min.js new file mode 100644 index 0000000..54b3c46 --- /dev/null +++ b/singlehtml/_static/clipboard.min.js @@ -0,0 +1,7 @@ +/*! + * clipboard.js v2.0.8 + * https://clipboardjs.com/ + * + * Licensed MIT © Zeno Rocha + */ +!function(t,e){"object"==typeof exports&&"object"==typeof module?module.exports=e():"function"==typeof define&&define.amd?define([],e):"object"==typeof exports?exports.ClipboardJS=e():t.ClipboardJS=e()}(this,function(){return n={686:function(t,e,n){"use strict";n.d(e,{default:function(){return o}});var e=n(279),i=n.n(e),e=n(370),u=n.n(e),e=n(817),c=n.n(e);function a(t){try{return document.execCommand(t)}catch(t){return}}var f=function(t){t=c()(t);return a("cut"),t};var l=function(t){var e,n,o,r=1 + + + + diff --git a/singlehtml/_static/copybutton.css b/singlehtml/_static/copybutton.css new file mode 100644 index 0000000..40eafe5 --- /dev/null +++ b/singlehtml/_static/copybutton.css @@ -0,0 +1,93 @@ +/* Copy buttons */ +button.copybtn { + position: absolute; + display: flex; + top: .3em; + right: .3em; + width: 1.7em; + height: 1.7em; + opacity: 0; + transition: opacity 0.3s, border .3s, background-color .3s; + user-select: none; + padding: 0; + border: none; + outline: none; + border-radius: 0.4em; + /* The colors that GitHub uses */ + border: #1b1f2426 1px solid; + background-color: #f6f8fa; + color: #57606a; +} + +button.copybtn.success { + border-color: #22863a; + color: #22863a; +} + +button.copybtn svg { + stroke: currentColor; + width: 1.5em; + height: 1.5em; + padding: 0.1em; +} + +div.highlight { + position: relative; +} + +.highlight:hover button.copybtn { + opacity: 1; +} + +.highlight button.copybtn:hover { + background-color: rgb(235, 235, 235); +} + +.highlight button.copybtn:active { + background-color: rgb(187, 187, 187); +} + +/** + * A minimal CSS-only tooltip copied from: + * https://codepen.io/mildrenben/pen/rVBrpK + * + * To use, write HTML like the following: + * + *

Short

+ */ + .o-tooltip--left { + position: relative; + } + + .o-tooltip--left:after { + opacity: 0; + visibility: hidden; + position: absolute; + content: attr(data-tooltip); + padding: .2em; + font-size: .8em; + left: -.2em; + background: grey; + color: white; + white-space: nowrap; + z-index: 2; + border-radius: 2px; + transform: translateX(-102%) translateY(0); + transition: opacity 0.2s cubic-bezier(0.64, 0.09, 0.08, 1), transform 0.2s cubic-bezier(0.64, 0.09, 0.08, 1); +} + +.o-tooltip--left:hover:after { + display: block; + opacity: 1; + visibility: visible; + transform: translateX(-100%) translateY(0); + transition: opacity 0.2s cubic-bezier(0.64, 0.09, 0.08, 1), transform 0.2s cubic-bezier(0.64, 0.09, 0.08, 1); + transition-delay: .5s; +} + +/* By default the copy button shouldn't show up when printing a page */ +@media print { + button.copybtn { + display: none; + } +} diff --git a/singlehtml/_static/copybutton.js b/singlehtml/_static/copybutton.js new file mode 100644 index 0000000..f3ecd03 --- /dev/null +++ b/singlehtml/_static/copybutton.js @@ -0,0 +1,241 @@ +// Localization support +const messages = { + 'en': { + 'copy': 'Copy', + 'copy_to_clipboard': 'Copy to clipboard', + 'copy_success': 'Copied!', + 'copy_failure': 'Failed to copy', + }, + 'es' : { + 'copy': 'Copiar', + 'copy_to_clipboard': 'Copiar al portapapeles', + 'copy_success': '¡Copiado!', + 'copy_failure': 'Error al copiar', + }, + 'de' : { + 'copy': 'Kopieren', + 'copy_to_clipboard': 'In die Zwischenablage kopieren', + 'copy_success': 'Kopiert!', + 'copy_failure': 'Fehler beim Kopieren', + }, + 'fr' : { + 'copy': 'Copier', + 'copy_to_clipboard': 'Copié dans le presse-papier', + 'copy_success': 'Copié !', + 'copy_failure': 'Échec de la copie', + }, + 'ru': { + 'copy': 'Скопировать', + 'copy_to_clipboard': 'Скопировать в буфер', + 'copy_success': 'Скопировано!', + 'copy_failure': 'Не удалось скопировать', + }, + 'zh-CN': { + 'copy': '复制', + 'copy_to_clipboard': '复制到剪贴板', + 'copy_success': '复制成功!', + 'copy_failure': '复制失败', + }, + 'it' : { + 'copy': 'Copiare', + 'copy_to_clipboard': 'Copiato negli appunti', + 'copy_success': 'Copiato!', + 'copy_failure': 'Errore durante la copia', + } +} + +let locale = 'en' +if( document.documentElement.lang !== undefined + && messages[document.documentElement.lang] !== undefined ) { + locale = document.documentElement.lang +} + +let doc_url_root = DOCUMENTATION_OPTIONS.URL_ROOT; +if (doc_url_root == '#') { + doc_url_root = ''; +} + +/** + * SVG files for our copy buttons + */ +let iconCheck = ` + ${messages[locale]['copy_success']} + + +` + +// If the user specified their own SVG use that, otherwise use the default +let iconCopy = ``; +if (!iconCopy) { + iconCopy = ` + ${messages[locale]['copy_to_clipboard']} + + + +` +} + +/** + * Set up copy/paste for code blocks + */ + +const runWhenDOMLoaded = cb => { + if (document.readyState != 'loading') { + cb() + } else if (document.addEventListener) { + document.addEventListener('DOMContentLoaded', cb) + } else { + document.attachEvent('onreadystatechange', function() { + if (document.readyState == 'complete') cb() + }) + } +} + +const codeCellId = index => `codecell${index}` + +// Clears selected text since ClipboardJS will select the text when copying +const clearSelection = () => { + if (window.getSelection) { + window.getSelection().removeAllRanges() + } else if (document.selection) { + document.selection.empty() + } +} + +// Changes tooltip text for two seconds, then changes it back +const temporarilyChangeTooltip = (el, oldText, newText) => { + el.setAttribute('data-tooltip', newText) + el.classList.add('success') + setTimeout(() => el.setAttribute('data-tooltip', oldText), 2000) + setTimeout(() => el.classList.remove('success'), 2000) +} + +// Changes the copy button icon for two seconds, then changes it back +const temporarilyChangeIcon = (el) => { + el.innerHTML = iconCheck; + setTimeout(() => {el.innerHTML = iconCopy}, 2000) +} + +const addCopyButtonToCodeCells = () => { + // If ClipboardJS hasn't loaded, wait a bit and try again. This + // happens because we load ClipboardJS asynchronously. + if (window.ClipboardJS === undefined) { + setTimeout(addCopyButtonToCodeCells, 250) + return + } + + // Add copybuttons to all of our code cells + const COPYBUTTON_SELECTOR = 'div.highlight pre'; + const codeCells = document.querySelectorAll(COPYBUTTON_SELECTOR) + codeCells.forEach((codeCell, index) => { + const id = codeCellId(index) + codeCell.setAttribute('id', id) + + const clipboardButton = id => + `` + codeCell.insertAdjacentHTML('afterend', clipboardButton(id)) + }) + +function escapeRegExp(string) { + return string.replace(/[.*+?^${}()|[\]\\]/g, '\\$&'); // $& means the whole matched string +} + +/** + * Removes excluded text from a Node. + * + * @param {Node} target Node to filter. + * @param {string} exclude CSS selector of nodes to exclude. + * @returns {DOMString} Text from `target` with text removed. + */ +function filterText(target, exclude) { + const clone = target.cloneNode(true); // clone as to not modify the live DOM + if (exclude) { + // remove excluded nodes + clone.querySelectorAll(exclude).forEach(node => node.remove()); + } + return clone.innerText; +} + +// Callback when a copy button is clicked. Will be passed the node that was clicked +// should then grab the text and replace pieces of text that shouldn't be used in output +function formatCopyText(textContent, copybuttonPromptText, isRegexp = false, onlyCopyPromptLines = true, removePrompts = true, copyEmptyLines = true, lineContinuationChar = "", hereDocDelim = "") { + var regexp; + var match; + + // Do we check for line continuation characters and "HERE-documents"? + var useLineCont = !!lineContinuationChar + var useHereDoc = !!hereDocDelim + + // create regexp to capture prompt and remaining line + if (isRegexp) { + regexp = new RegExp('^(' + copybuttonPromptText + ')(.*)') + } else { + regexp = new RegExp('^(' + escapeRegExp(copybuttonPromptText) + ')(.*)') + } + + const outputLines = []; + var promptFound = false; + var gotLineCont = false; + var gotHereDoc = false; + const lineGotPrompt = []; + for (const line of textContent.split('\n')) { + match = line.match(regexp) + if (match || gotLineCont || gotHereDoc) { + promptFound = regexp.test(line) + lineGotPrompt.push(promptFound) + if (removePrompts && promptFound) { + outputLines.push(match[2]) + } else { + outputLines.push(line) + } + gotLineCont = line.endsWith(lineContinuationChar) & useLineCont + if (line.includes(hereDocDelim) & useHereDoc) + gotHereDoc = !gotHereDoc + } else if (!onlyCopyPromptLines) { + outputLines.push(line) + } else if (copyEmptyLines && line.trim() === '') { + outputLines.push(line) + } + } + + // If no lines with the prompt were found then just use original lines + if (lineGotPrompt.some(v => v === true)) { + textContent = outputLines.join('\n'); + } + + // Remove a trailing newline to avoid auto-running when pasting + if (textContent.endsWith("\n")) { + textContent = textContent.slice(0, -1) + } + return textContent +} + + +var copyTargetText = (trigger) => { + var target = document.querySelector(trigger.attributes['data-clipboard-target'].value); + + // get filtered text + let exclude = '.linenos, .gp'; + + let text = filterText(target, exclude); + return formatCopyText(text, '', false, true, true, true, '', '') +} + + // Initialize with a callback so we can modify the text before copy + const clipboard = new ClipboardJS('.copybtn', {text: copyTargetText}) + + // Update UI with error/success messages + clipboard.on('success', event => { + clearSelection() + temporarilyChangeTooltip(event.trigger, messages[locale]['copy'], messages[locale]['copy_success']) + temporarilyChangeIcon(event.trigger) + }) + + clipboard.on('error', event => { + temporarilyChangeTooltip(event.trigger, messages[locale]['copy'], messages[locale]['copy_failure']) + }) +} + +runWhenDOMLoaded(addCopyButtonToCodeCells) \ No newline at end of file diff --git a/singlehtml/_static/copybutton_funcs.js b/singlehtml/_static/copybutton_funcs.js new file mode 100644 index 0000000..dbe1aaa --- /dev/null +++ b/singlehtml/_static/copybutton_funcs.js @@ -0,0 +1,73 @@ +function escapeRegExp(string) { + return string.replace(/[.*+?^${}()|[\]\\]/g, '\\$&'); // $& means the whole matched string +} + +/** + * Removes excluded text from a Node. + * + * @param {Node} target Node to filter. + * @param {string} exclude CSS selector of nodes to exclude. + * @returns {DOMString} Text from `target` with text removed. + */ +export function filterText(target, exclude) { + const clone = target.cloneNode(true); // clone as to not modify the live DOM + if (exclude) { + // remove excluded nodes + clone.querySelectorAll(exclude).forEach(node => node.remove()); + } + return clone.innerText; +} + +// Callback when a copy button is clicked. Will be passed the node that was clicked +// should then grab the text and replace pieces of text that shouldn't be used in output +export function formatCopyText(textContent, copybuttonPromptText, isRegexp = false, onlyCopyPromptLines = true, removePrompts = true, copyEmptyLines = true, lineContinuationChar = "", hereDocDelim = "") { + var regexp; + var match; + + // Do we check for line continuation characters and "HERE-documents"? + var useLineCont = !!lineContinuationChar + var useHereDoc = !!hereDocDelim + + // create regexp to capture prompt and remaining line + if (isRegexp) { + regexp = new RegExp('^(' + copybuttonPromptText + ')(.*)') + } else { + regexp = new RegExp('^(' + escapeRegExp(copybuttonPromptText) + ')(.*)') + } + + const outputLines = []; + var promptFound = false; + var gotLineCont = false; + var gotHereDoc = false; + const lineGotPrompt = []; + for (const line of textContent.split('\n')) { + match = line.match(regexp) + if (match || gotLineCont || gotHereDoc) { + 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+ return this; // for chaining... + } +})(jQuery); + +// NO good way to do this!. Copy a hack from here +// https://stackoverflow.com/questions/901115/how-can-i-get-query-string-values-in-javascript +// https://stackoverflow.com/a/2880929 +var urlParams; +(window.onpopstate = function () { + var match, + pl = /\+/g, // Regex for replacing addition symbol with a space + search = /([^&=]+)=?([^&]*)/g, + decode = function (s) { return decodeURIComponent(s.replace(pl, " ")); }, + query = window.location.search.substring(1); + urlParams = {}; + while (match = search.exec(query)) + urlParams[decode(match[1])] = decode(match[2]); +})(); + +// Select heading levels +var maxHeading = urlParams['h'] +if (maxHeading === undefined) maxHeading = 2 +var headingLevels = []; +for (h=2 ; h (sections.length-1) ) { + // if we would scroll past bottom, or above top, do nothing + return; + } + + console.log('xxxxxx'); + var targetSection = sections[targetPos]; + console.log(targetSection, typeof(targetSection)); + + // Return targetSection top and height + var secProperties = section_top_and_height(targetSection); 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Pulled from the Jupyter / nbsphinx CSS */ +div.cell_output table { + border: none; + border-collapse: collapse; + border-spacing: 0; + color: black; + font-size: 1em; + table-layout: fixed; +} + +div.cell_output thead { + border-bottom: 1px solid black; + vertical-align: bottom; +} + +div.cell_output tr, +div.cell_output th, +div.cell_output td { + text-align: right; + vertical-align: middle; + padding: 0.5em 0.5em; + line-height: normal; + white-space: normal; + max-width: none; + border: none; +} + +div.cell_output th { + font-weight: bold; +} + +div.cell_output tbody tr:nth-child(odd) { + background: #f5f5f5; +} + +div.cell_output tbody tr:hover { + background: rgba(66, 165, 245, 0.2); +} + +/** source code line numbers **/ +span.linenos { + opacity: 0.5; +} + +/* Inline text from `paste` operation */ + +span.pasted-text { + font-weight: bold; +} + +span.pasted-inline img { + max-height: 2em; +} + +tbody span.pasted-inline img { + max-height: none; +} + +/* Font colors for translated ANSI escape sequences +Color values are copied from Jupyter Notebook +https://github.com/jupyter/notebook/blob/52581f8eda9b319eb0390ac77fe5903c38f81e3e/notebook/static/notebook/less/ansicolors.less#L14-L21 +Background colors from +https://nbsphinx.readthedocs.io/en/latest/code-cells.html#ANSI-Colors +*/ +div.highlight .-Color-Bold { + font-weight: bold; +} + +div.highlight .-Color[class*=-Black] { + color: #3E424D +} + +div.highlight .-Color[class*=-Red] { + color: #E75C58 +} + +div.highlight .-Color[class*=-Green] { + color: #00A250 +} + +div.highlight .-Color[class*=-Yellow] { + color: #DDB62B +} + +div.highlight .-Color[class*=-Blue] { + color: #208FFB +} + +div.highlight .-Color[class*=-Magenta] { + color: #D160C4 +} + +div.highlight .-Color[class*=-Cyan] { + color: #60C6C8 +} + +div.highlight .-Color[class*=-White] { + color: #C5C1B4 +} + +div.highlight .-Color[class*=-BGBlack] { + background-color: #3E424D +} + +div.highlight .-Color[class*=-BGRed] { + background-color: #E75C58 +} + +div.highlight .-Color[class*=-BGGreen] { + background-color: #00A250 +} + +div.highlight .-Color[class*=-BGYellow] { + background-color: #DDB62B +} + +div.highlight .-Color[class*=-BGBlue] { + background-color: #208FFB +} + +div.highlight .-Color[class*=-BGMagenta] { + background-color: #D160C4 +} + +div.highlight .-Color[class*=-BGCyan] { + background-color: #60C6C8 +} + +div.highlight .-Color[class*=-BGWhite] { + background-color: #C5C1B4 +} + +/* Font colors for 8-bit ANSI */ + +div.highlight .-Color[class*=-C0] { + color: #000000 +} + +div.highlight .-Color[class*=-BGC0] { + background-color: #000000 +} + +div.highlight .-Color[class*=-C1] { + color: #800000 +} + +div.highlight .-Color[class*=-BGC1] { + background-color: #800000 +} + +div.highlight .-Color[class*=-C2] { + color: #008000 +} + +div.highlight .-Color[class*=-BGC2] { + background-color: #008000 +} + +div.highlight .-Color[class*=-C3] { + color: #808000 +} + +div.highlight .-Color[class*=-BGC3] { + background-color: #808000 +} + +div.highlight .-Color[class*=-C4] { + color: #000080 +} + +div.highlight .-Color[class*=-BGC4] { + background-color: #000080 +} + +div.highlight .-Color[class*=-C5] { + color: #800080 +} + +div.highlight .-Color[class*=-BGC5] { + background-color: #800080 +} + +div.highlight .-Color[class*=-C6] { + color: #008080 +} + +div.highlight .-Color[class*=-BGC6] { + background-color: #008080 +} + +div.highlight .-Color[class*=-C7] { + color: #C0C0C0 +} + +div.highlight .-Color[class*=-BGC7] { + background-color: #C0C0C0 +} + +div.highlight .-Color[class*=-C8] { + color: #808080 +} + +div.highlight .-Color[class*=-BGC8] { + background-color: #808080 +} + +div.highlight .-Color[class*=-C9] { + color: #FF0000 +} + +div.highlight .-Color[class*=-BGC9] { + background-color: #FF0000 +} + +div.highlight .-Color[class*=-C10] { + color: #00FF00 +} + +div.highlight .-Color[class*=-BGC10] { + background-color: #00FF00 +} + +div.highlight .-Color[class*=-C11] { + color: #FFFF00 +} + +div.highlight .-Color[class*=-BGC11] { + background-color: #FFFF00 +} + +div.highlight .-Color[class*=-C12] { + color: #0000FF +} + +div.highlight .-Color[class*=-BGC12] { + background-color: #0000FF +} + +div.highlight .-Color[class*=-C13] { + color: #FF00FF +} + +div.highlight .-Color[class*=-BGC13] { + background-color: #FF00FF +} + +div.highlight .-Color[class*=-C14] { + color: #00FFFF +} + +div.highlight .-Color[class*=-BGC14] { + background-color: #00FFFF +} + +div.highlight .-Color[class*=-C15] { + color: #FFFFFF +} + +div.highlight .-Color[class*=-BGC15] { + background-color: #FFFFFF +} + +div.highlight .-Color[class*=-C16] { + color: #000000 +} + +div.highlight .-Color[class*=-BGC16] { + background-color: #000000 +} + +div.highlight .-Color[class*=-C17] { + color: #00005F +} + +div.highlight .-Color[class*=-BGC17] { + background-color: #00005F +} + +div.highlight .-Color[class*=-C18] { + color: #000087 +} + +div.highlight .-Color[class*=-BGC18] { + background-color: #000087 +} + +div.highlight .-Color[class*=-C19] { + color: #0000AF +} + +div.highlight .-Color[class*=-BGC19] { + background-color: #0000AF +} + +div.highlight .-Color[class*=-C20] { + color: #0000D7 +} + +div.highlight .-Color[class*=-BGC20] { + background-color: #0000D7 +} + +div.highlight .-Color[class*=-C21] { + color: #0000FF +} + +div.highlight .-Color[class*=-BGC21] { + background-color: #0000FF +} + +div.highlight .-Color[class*=-C22] { + color: #005F00 +} + +div.highlight .-Color[class*=-BGC22] { + background-color: #005F00 +} + +div.highlight .-Color[class*=-C23] { + color: #005F5F +} + +div.highlight .-Color[class*=-BGC23] { + background-color: #005F5F +} + +div.highlight .-Color[class*=-C24] { + color: #005F87 +} + +div.highlight .-Color[class*=-BGC24] { + background-color: #005F87 +} + +div.highlight .-Color[class*=-C25] { + color: #005FAF +} + +div.highlight .-Color[class*=-BGC25] { + background-color: #005FAF +} + +div.highlight .-Color[class*=-C26] { + color: #005FD7 +} + +div.highlight .-Color[class*=-BGC26] { + background-color: #005FD7 +} + +div.highlight .-Color[class*=-C27] { + color: #005FFF +} + +div.highlight .-Color[class*=-BGC27] { + background-color: #005FFF +} + +div.highlight .-Color[class*=-C28] { + color: #008700 +} + +div.highlight .-Color[class*=-BGC28] { + background-color: #008700 +} + +div.highlight .-Color[class*=-C29] { + color: #00875F +} + +div.highlight .-Color[class*=-BGC29] { + background-color: #00875F +} + +div.highlight .-Color[class*=-C30] { + color: #008787 +} + +div.highlight .-Color[class*=-BGC30] { + background-color: #008787 +} + +div.highlight .-Color[class*=-C31] { + color: #0087AF +} + +div.highlight .-Color[class*=-BGC31] { + background-color: #0087AF +} + +div.highlight .-Color[class*=-C32] { + color: #0087D7 +} + +div.highlight .-Color[class*=-BGC32] { + background-color: #0087D7 +} + +div.highlight .-Color[class*=-C33] { + color: #0087FF +} + +div.highlight .-Color[class*=-BGC33] { + background-color: #0087FF +} + +div.highlight .-Color[class*=-C34] { + color: #00AF00 +} + +div.highlight .-Color[class*=-BGC34] { + background-color: #00AF00 +} + +div.highlight .-Color[class*=-C35] { + color: #00AF5F +} + +div.highlight .-Color[class*=-BGC35] { + background-color: #00AF5F +} + +div.highlight .-Color[class*=-C36] { + color: #00AF87 +} + +div.highlight .-Color[class*=-BGC36] { + background-color: #00AF87 +} + +div.highlight .-Color[class*=-C37] { + color: #00AFAF +} + +div.highlight .-Color[class*=-BGC37] { + background-color: #00AFAF +} + +div.highlight .-Color[class*=-C38] { + color: #00AFD7 +} + +div.highlight .-Color[class*=-BGC38] { + background-color: #00AFD7 +} + +div.highlight .-Color[class*=-C39] { + color: #00AFFF +} + +div.highlight .-Color[class*=-BGC39] { + background-color: #00AFFF +} + +div.highlight .-Color[class*=-C40] { + color: #00D700 +} + +div.highlight .-Color[class*=-BGC40] { + background-color: #00D700 +} + +div.highlight .-Color[class*=-C41] { + color: #00D75F +} + +div.highlight .-Color[class*=-BGC41] { + background-color: #00D75F +} + +div.highlight .-Color[class*=-C42] { + color: #00D787 +} + +div.highlight .-Color[class*=-BGC42] { + background-color: #00D787 +} + +div.highlight .-Color[class*=-C43] { + color: #00D7AF +} + +div.highlight .-Color[class*=-BGC43] { + background-color: #00D7AF +} + +div.highlight .-Color[class*=-C44] { + color: #00D7D7 +} + +div.highlight .-Color[class*=-BGC44] { + background-color: #00D7D7 +} + +div.highlight .-Color[class*=-C45] { + color: #00D7FF +} + +div.highlight .-Color[class*=-BGC45] { + background-color: #00D7FF +} + +div.highlight .-Color[class*=-C46] { + color: #00FF00 +} + +div.highlight .-Color[class*=-BGC46] { + background-color: #00FF00 +} + +div.highlight .-Color[class*=-C47] { + color: #00FF5F +} + +div.highlight .-Color[class*=-BGC47] { + background-color: #00FF5F +} + +div.highlight .-Color[class*=-C48] { + color: #00FF87 +} + +div.highlight .-Color[class*=-BGC48] { + background-color: #00FF87 +} + +div.highlight .-Color[class*=-C49] { + color: #00FFAF +} + +div.highlight .-Color[class*=-BGC49] { + background-color: #00FFAF +} + +div.highlight .-Color[class*=-C50] { + color: #00FFD7 +} + +div.highlight .-Color[class*=-BGC50] { + background-color: #00FFD7 +} + +div.highlight .-Color[class*=-C51] { + color: #00FFFF +} + +div.highlight .-Color[class*=-BGC51] { + background-color: #00FFFF +} + +div.highlight .-Color[class*=-C52] { + color: #5F0000 +} + +div.highlight .-Color[class*=-BGC52] { + background-color: #5F0000 +} + +div.highlight .-Color[class*=-C53] { + color: #5F005F +} + +div.highlight .-Color[class*=-BGC53] { + background-color: #5F005F +} + +div.highlight .-Color[class*=-C54] { + color: #5F0087 +} + +div.highlight .-Color[class*=-BGC54] { + background-color: #5F0087 +} + +div.highlight .-Color[class*=-C55] { + color: #5F00AF +} + +div.highlight .-Color[class*=-BGC55] { + background-color: #5F00AF +} + +div.highlight .-Color[class*=-C56] { + color: #5F00D7 +} + +div.highlight .-Color[class*=-BGC56] { + background-color: #5F00D7 +} + +div.highlight .-Color[class*=-C57] { + color: #5F00FF +} + +div.highlight .-Color[class*=-BGC57] { + background-color: #5F00FF +} + +div.highlight .-Color[class*=-C58] { + color: #5F5F00 +} + +div.highlight .-Color[class*=-BGC58] { + background-color: #5F5F00 +} + +div.highlight .-Color[class*=-C59] { + color: #5F5F5F +} + +div.highlight .-Color[class*=-BGC59] { + background-color: #5F5F5F +} + +div.highlight .-Color[class*=-C60] { + color: #5F5F87 +} + +div.highlight .-Color[class*=-BGC60] { + background-color: #5F5F87 +} + +div.highlight .-Color[class*=-C61] { + color: #5F5FAF +} + +div.highlight .-Color[class*=-BGC61] { + background-color: #5F5FAF +} + +div.highlight .-Color[class*=-C62] { + color: #5F5FD7 +} + +div.highlight .-Color[class*=-BGC62] { + background-color: #5F5FD7 +} + +div.highlight .-Color[class*=-C63] { + color: #5F5FFF +} + +div.highlight .-Color[class*=-BGC63] { + background-color: #5F5FFF +} + +div.highlight .-Color[class*=-C64] { + color: #5F8700 +} + +div.highlight .-Color[class*=-BGC64] { + background-color: #5F8700 +} + +div.highlight .-Color[class*=-C65] { + color: #5F875F +} + +div.highlight .-Color[class*=-BGC65] { + background-color: #5F875F +} + +div.highlight .-Color[class*=-C66] { + color: #5F8787 +} + +div.highlight .-Color[class*=-BGC66] { + background-color: #5F8787 +} + +div.highlight .-Color[class*=-C67] { + color: #5F87AF +} + +div.highlight .-Color[class*=-BGC67] { + background-color: #5F87AF +} + +div.highlight .-Color[class*=-C68] { + color: #5F87D7 +} + +div.highlight .-Color[class*=-BGC68] { + background-color: #5F87D7 +} + +div.highlight .-Color[class*=-C69] { + color: #5F87FF +} + +div.highlight .-Color[class*=-BGC69] { + background-color: #5F87FF +} + +div.highlight .-Color[class*=-C70] { + color: #5FAF00 +} + +div.highlight .-Color[class*=-BGC70] { + background-color: #5FAF00 +} + +div.highlight .-Color[class*=-C71] { + color: #5FAF5F +} + +div.highlight .-Color[class*=-BGC71] { + background-color: #5FAF5F +} + +div.highlight .-Color[class*=-C72] { + color: #5FAF87 +} + +div.highlight .-Color[class*=-BGC72] { + background-color: #5FAF87 +} + +div.highlight .-Color[class*=-C73] { + color: #5FAFAF +} + +div.highlight .-Color[class*=-BGC73] { + background-color: #5FAFAF +} + +div.highlight .-Color[class*=-C74] { + color: #5FAFD7 +} + +div.highlight .-Color[class*=-BGC74] { + background-color: #5FAFD7 +} + +div.highlight .-Color[class*=-C75] { + color: #5FAFFF +} + +div.highlight .-Color[class*=-BGC75] { + background-color: #5FAFFF +} + +div.highlight .-Color[class*=-C76] { + color: #5FD700 +} + +div.highlight .-Color[class*=-BGC76] { + background-color: #5FD700 +} + +div.highlight .-Color[class*=-C77] { + color: #5FD75F +} + +div.highlight .-Color[class*=-BGC77] { + background-color: #5FD75F +} + +div.highlight .-Color[class*=-C78] { + color: #5FD787 +} + +div.highlight .-Color[class*=-BGC78] { + background-color: #5FD787 +} + +div.highlight .-Color[class*=-C79] { + color: #5FD7AF +} + +div.highlight .-Color[class*=-BGC79] { + background-color: #5FD7AF +} + +div.highlight .-Color[class*=-C80] { + color: #5FD7D7 +} + +div.highlight .-Color[class*=-BGC80] { + background-color: #5FD7D7 +} + +div.highlight .-Color[class*=-C81] { + color: #5FD7FF +} + +div.highlight .-Color[class*=-BGC81] { + background-color: #5FD7FF +} + +div.highlight .-Color[class*=-C82] { + color: #5FFF00 +} + +div.highlight .-Color[class*=-BGC82] { + background-color: #5FFF00 +} + +div.highlight .-Color[class*=-C83] { + color: #5FFF5F +} + +div.highlight .-Color[class*=-BGC83] { + background-color: #5FFF5F +} + +div.highlight .-Color[class*=-C84] { + color: #5FFF87 +} + +div.highlight .-Color[class*=-BGC84] { + background-color: #5FFF87 +} + +div.highlight .-Color[class*=-C85] { + color: #5FFFAF +} + +div.highlight .-Color[class*=-BGC85] { + background-color: #5FFFAF +} + +div.highlight .-Color[class*=-C86] { + color: #5FFFD7 +} + +div.highlight .-Color[class*=-BGC86] { + background-color: #5FFFD7 +} + +div.highlight .-Color[class*=-C87] { + color: #5FFFFF +} + +div.highlight .-Color[class*=-BGC87] { + background-color: #5FFFFF +} + +div.highlight .-Color[class*=-C88] { + color: #870000 +} + +div.highlight .-Color[class*=-BGC88] { + background-color: #870000 +} + +div.highlight .-Color[class*=-C89] { + color: #87005F +} + +div.highlight .-Color[class*=-BGC89] { + background-color: #87005F +} + +div.highlight .-Color[class*=-C90] { + color: #870087 +} + +div.highlight .-Color[class*=-BGC90] { + background-color: #870087 +} + +div.highlight .-Color[class*=-C91] { + color: #8700AF +} + +div.highlight .-Color[class*=-BGC91] { + background-color: #8700AF +} + +div.highlight .-Color[class*=-C92] { + color: #8700D7 +} + +div.highlight .-Color[class*=-BGC92] { + background-color: #8700D7 +} + +div.highlight .-Color[class*=-C93] { + color: #8700FF +} + +div.highlight .-Color[class*=-BGC93] { + background-color: #8700FF +} + +div.highlight .-Color[class*=-C94] { + color: #875F00 +} + +div.highlight .-Color[class*=-BGC94] { + background-color: #875F00 +} + +div.highlight .-Color[class*=-C95] { + color: #875F5F +} + +div.highlight .-Color[class*=-BGC95] { + background-color: #875F5F +} + +div.highlight .-Color[class*=-C96] { + color: #875F87 +} + +div.highlight .-Color[class*=-BGC96] { + background-color: #875F87 +} + +div.highlight .-Color[class*=-C97] { + color: #875FAF +} + +div.highlight .-Color[class*=-BGC97] { + background-color: #875FAF +} + +div.highlight .-Color[class*=-C98] { + color: #875FD7 +} + +div.highlight .-Color[class*=-BGC98] { + background-color: #875FD7 +} + +div.highlight .-Color[class*=-C99] { + color: #875FFF +} + +div.highlight .-Color[class*=-BGC99] { + background-color: #875FFF +} + +div.highlight .-Color[class*=-C100] { + color: #878700 +} + +div.highlight .-Color[class*=-BGC100] { + background-color: #878700 +} + +div.highlight .-Color[class*=-C101] { + color: #87875F +} + +div.highlight .-Color[class*=-BGC101] { + background-color: #87875F +} + +div.highlight .-Color[class*=-C102] { + color: #878787 +} + +div.highlight .-Color[class*=-BGC102] { + background-color: #878787 +} + +div.highlight .-Color[class*=-C103] { + color: #8787AF +} + +div.highlight .-Color[class*=-BGC103] { + background-color: #8787AF +} + +div.highlight .-Color[class*=-C104] { + color: #8787D7 +} + +div.highlight .-Color[class*=-BGC104] { + background-color: #8787D7 +} + +div.highlight .-Color[class*=-C105] { + color: #8787FF +} + +div.highlight .-Color[class*=-BGC105] { + background-color: #8787FF +} + +div.highlight .-Color[class*=-C106] { + color: #87AF00 +} + +div.highlight .-Color[class*=-BGC106] { + background-color: #87AF00 +} + +div.highlight .-Color[class*=-C107] { + color: #87AF5F +} + +div.highlight .-Color[class*=-BGC107] { + background-color: #87AF5F +} + +div.highlight .-Color[class*=-C108] { + color: #87AF87 +} + +div.highlight .-Color[class*=-BGC108] { + background-color: #87AF87 +} + +div.highlight .-Color[class*=-C109] { + color: #87AFAF +} + +div.highlight .-Color[class*=-BGC109] { + background-color: #87AFAF +} + +div.highlight .-Color[class*=-C110] { + color: #87AFD7 +} + +div.highlight .-Color[class*=-BGC110] { + background-color: #87AFD7 +} + +div.highlight .-Color[class*=-C111] { + color: #87AFFF +} + +div.highlight .-Color[class*=-BGC111] { + background-color: #87AFFF +} + +div.highlight .-Color[class*=-C112] { + color: #87D700 +} + +div.highlight .-Color[class*=-BGC112] { + background-color: #87D700 +} + +div.highlight .-Color[class*=-C113] { + color: #87D75F +} + +div.highlight .-Color[class*=-BGC113] { + background-color: #87D75F +} + +div.highlight .-Color[class*=-C114] { + color: #87D787 +} + +div.highlight .-Color[class*=-BGC114] { + background-color: #87D787 +} + +div.highlight .-Color[class*=-C115] { + color: #87D7AF +} + +div.highlight .-Color[class*=-BGC115] { + background-color: #87D7AF +} + +div.highlight .-Color[class*=-C116] { + color: #87D7D7 +} + +div.highlight .-Color[class*=-BGC116] { + background-color: #87D7D7 +} + +div.highlight .-Color[class*=-C117] { + color: #87D7FF +} + +div.highlight .-Color[class*=-BGC117] { + background-color: #87D7FF +} + +div.highlight .-Color[class*=-C118] { + color: #87FF00 +} + +div.highlight .-Color[class*=-BGC118] { + background-color: #87FF00 +} + +div.highlight .-Color[class*=-C119] { + color: #87FF5F +} + +div.highlight .-Color[class*=-BGC119] { + background-color: #87FF5F +} + +div.highlight .-Color[class*=-C120] { + color: #87FF87 +} + +div.highlight .-Color[class*=-BGC120] { + background-color: #87FF87 +} + +div.highlight .-Color[class*=-C121] { + color: #87FFAF +} + +div.highlight .-Color[class*=-BGC121] { + background-color: #87FFAF +} + +div.highlight .-Color[class*=-C122] { + color: #87FFD7 +} + +div.highlight .-Color[class*=-BGC122] { + background-color: #87FFD7 +} + +div.highlight .-Color[class*=-C123] { + color: #87FFFF +} + +div.highlight .-Color[class*=-BGC123] { + background-color: #87FFFF +} + +div.highlight .-Color[class*=-C124] { + color: #AF0000 +} + +div.highlight .-Color[class*=-BGC124] { + background-color: #AF0000 +} + +div.highlight .-Color[class*=-C125] { + color: #AF005F +} + +div.highlight .-Color[class*=-BGC125] { + background-color: #AF005F +} + +div.highlight .-Color[class*=-C126] { + color: #AF0087 +} + +div.highlight .-Color[class*=-BGC126] { + background-color: #AF0087 +} + +div.highlight .-Color[class*=-C127] { + color: #AF00AF +} + +div.highlight .-Color[class*=-BGC127] { + background-color: #AF00AF +} + +div.highlight .-Color[class*=-C128] { + color: #AF00D7 +} + +div.highlight .-Color[class*=-BGC128] { + background-color: #AF00D7 +} + +div.highlight .-Color[class*=-C129] { + color: #AF00FF +} + +div.highlight .-Color[class*=-BGC129] { + background-color: #AF00FF +} + +div.highlight .-Color[class*=-C130] { + color: #AF5F00 +} + +div.highlight .-Color[class*=-BGC130] { + background-color: #AF5F00 +} + +div.highlight .-Color[class*=-C131] { + color: #AF5F5F +} + +div.highlight .-Color[class*=-BGC131] { + background-color: #AF5F5F +} + +div.highlight .-Color[class*=-C132] { + color: #AF5F87 +} + +div.highlight .-Color[class*=-BGC132] { + background-color: #AF5F87 +} + +div.highlight .-Color[class*=-C133] { + color: #AF5FAF +} + +div.highlight .-Color[class*=-BGC133] { + background-color: #AF5FAF +} + +div.highlight .-Color[class*=-C134] { + color: #AF5FD7 +} + +div.highlight .-Color[class*=-BGC134] { + background-color: #AF5FD7 +} + +div.highlight .-Color[class*=-C135] { + color: #AF5FFF +} + +div.highlight .-Color[class*=-BGC135] { + background-color: #AF5FFF +} + +div.highlight .-Color[class*=-C136] { + color: #AF8700 +} + +div.highlight .-Color[class*=-BGC136] { + background-color: #AF8700 +} + +div.highlight .-Color[class*=-C137] { + color: #AF875F +} + +div.highlight .-Color[class*=-BGC137] { + background-color: #AF875F +} + +div.highlight .-Color[class*=-C138] { + color: #AF8787 +} + +div.highlight .-Color[class*=-BGC138] { + background-color: #AF8787 +} + +div.highlight .-Color[class*=-C139] { + color: #AF87AF +} + +div.highlight .-Color[class*=-BGC139] { + background-color: #AF87AF +} + +div.highlight .-Color[class*=-C140] { + color: #AF87D7 +} + +div.highlight .-Color[class*=-BGC140] { + background-color: #AF87D7 +} + +div.highlight .-Color[class*=-C141] { + color: #AF87FF +} + +div.highlight .-Color[class*=-BGC141] { + background-color: #AF87FF +} + +div.highlight .-Color[class*=-C142] { + color: #AFAF00 +} + +div.highlight .-Color[class*=-BGC142] { + background-color: #AFAF00 +} + +div.highlight .-Color[class*=-C143] { + color: #AFAF5F +} + +div.highlight .-Color[class*=-BGC143] { + background-color: #AFAF5F +} + +div.highlight .-Color[class*=-C144] { + color: #AFAF87 +} + +div.highlight .-Color[class*=-BGC144] { + background-color: #AFAF87 +} + +div.highlight .-Color[class*=-C145] { + color: #AFAFAF +} + +div.highlight .-Color[class*=-BGC145] { + background-color: #AFAFAF +} + +div.highlight .-Color[class*=-C146] { + color: #AFAFD7 +} + +div.highlight .-Color[class*=-BGC146] { + background-color: #AFAFD7 +} + +div.highlight .-Color[class*=-C147] { + color: #AFAFFF +} + +div.highlight .-Color[class*=-BGC147] { + background-color: #AFAFFF +} + +div.highlight .-Color[class*=-C148] { + color: #AFD700 +} + +div.highlight .-Color[class*=-BGC148] { + background-color: #AFD700 +} + +div.highlight .-Color[class*=-C149] { + color: #AFD75F +} + +div.highlight .-Color[class*=-BGC149] { + background-color: #AFD75F +} + +div.highlight .-Color[class*=-C150] { + color: #AFD787 +} + +div.highlight .-Color[class*=-BGC150] { + background-color: #AFD787 +} + +div.highlight .-Color[class*=-C151] { + color: #AFD7AF +} + +div.highlight .-Color[class*=-BGC151] { + background-color: #AFD7AF +} + +div.highlight .-Color[class*=-C152] { + color: #AFD7D7 +} + +div.highlight .-Color[class*=-BGC152] { + background-color: #AFD7D7 +} + +div.highlight .-Color[class*=-C153] { + color: #AFD7FF +} + +div.highlight .-Color[class*=-BGC153] { + background-color: #AFD7FF +} + +div.highlight .-Color[class*=-C154] { + color: #AFFF00 +} + +div.highlight .-Color[class*=-BGC154] { + background-color: #AFFF00 +} + +div.highlight .-Color[class*=-C155] { + color: #AFFF5F +} + +div.highlight .-Color[class*=-BGC155] { + background-color: #AFFF5F +} + +div.highlight .-Color[class*=-C156] { + color: #AFFF87 +} + +div.highlight .-Color[class*=-BGC156] { + background-color: #AFFF87 +} + +div.highlight .-Color[class*=-C157] { + color: #AFFFAF +} + +div.highlight .-Color[class*=-BGC157] { + background-color: #AFFFAF +} + +div.highlight .-Color[class*=-C158] { + color: #AFFFD7 +} + +div.highlight .-Color[class*=-BGC158] { + background-color: #AFFFD7 +} + +div.highlight .-Color[class*=-C159] { + color: #AFFFFF +} + +div.highlight .-Color[class*=-BGC159] { + background-color: #AFFFFF +} + +div.highlight .-Color[class*=-C160] { + color: #D70000 +} + +div.highlight .-Color[class*=-BGC160] { + background-color: #D70000 +} + +div.highlight .-Color[class*=-C161] { + color: #D7005F +} + +div.highlight .-Color[class*=-BGC161] { + background-color: #D7005F +} + +div.highlight .-Color[class*=-C162] { + color: #D70087 +} + +div.highlight .-Color[class*=-BGC162] { + background-color: #D70087 +} + +div.highlight .-Color[class*=-C163] { + color: #D700AF +} + +div.highlight .-Color[class*=-BGC163] { + background-color: #D700AF +} + +div.highlight .-Color[class*=-C164] { + color: #D700D7 +} + +div.highlight .-Color[class*=-BGC164] { + background-color: #D700D7 +} + +div.highlight .-Color[class*=-C165] { + color: #D700FF +} + +div.highlight .-Color[class*=-BGC165] { + background-color: #D700FF +} + +div.highlight .-Color[class*=-C166] { + color: #D75F00 +} + +div.highlight .-Color[class*=-BGC166] { + background-color: #D75F00 +} + +div.highlight .-Color[class*=-C167] { + color: #D75F5F +} + +div.highlight .-Color[class*=-BGC167] { + background-color: #D75F5F +} + +div.highlight .-Color[class*=-C168] { + color: #D75F87 +} + +div.highlight .-Color[class*=-BGC168] { + background-color: #D75F87 +} + +div.highlight .-Color[class*=-C169] { + color: #D75FAF +} + +div.highlight .-Color[class*=-BGC169] { + background-color: #D75FAF +} + +div.highlight .-Color[class*=-C170] { + color: #D75FD7 +} + +div.highlight .-Color[class*=-BGC170] { + background-color: #D75FD7 +} + +div.highlight .-Color[class*=-C171] { + color: #D75FFF +} + +div.highlight .-Color[class*=-BGC171] { + background-color: #D75FFF +} + +div.highlight .-Color[class*=-C172] { + color: #D78700 +} + +div.highlight .-Color[class*=-BGC172] { + background-color: #D78700 +} + +div.highlight .-Color[class*=-C173] { + color: #D7875F +} + +div.highlight .-Color[class*=-BGC173] { + background-color: #D7875F +} + +div.highlight .-Color[class*=-C174] { + color: #D78787 +} + +div.highlight .-Color[class*=-BGC174] { + background-color: #D78787 +} + +div.highlight .-Color[class*=-C175] { + color: #D787AF +} + +div.highlight .-Color[class*=-BGC175] { + background-color: #D787AF +} + +div.highlight .-Color[class*=-C176] { + color: #D787D7 +} + +div.highlight .-Color[class*=-BGC176] { + background-color: #D787D7 +} + +div.highlight .-Color[class*=-C177] { + color: #D787FF +} + +div.highlight .-Color[class*=-BGC177] { + background-color: #D787FF +} + +div.highlight .-Color[class*=-C178] { + color: #D7AF00 +} + +div.highlight .-Color[class*=-BGC178] { + background-color: #D7AF00 +} + +div.highlight .-Color[class*=-C179] { + color: #D7AF5F +} + +div.highlight .-Color[class*=-BGC179] { + background-color: #D7AF5F +} + +div.highlight .-Color[class*=-C180] { + color: #D7AF87 +} + +div.highlight .-Color[class*=-BGC180] { + background-color: #D7AF87 +} + +div.highlight .-Color[class*=-C181] { + color: #D7AFAF +} + +div.highlight .-Color[class*=-BGC181] { + background-color: #D7AFAF +} + +div.highlight .-Color[class*=-C182] { + color: #D7AFD7 +} + +div.highlight .-Color[class*=-BGC182] { + background-color: #D7AFD7 +} + +div.highlight .-Color[class*=-C183] { + color: #D7AFFF +} + +div.highlight .-Color[class*=-BGC183] { + background-color: #D7AFFF +} + +div.highlight .-Color[class*=-C184] { + color: #D7D700 +} + +div.highlight .-Color[class*=-BGC184] { + background-color: #D7D700 +} + +div.highlight .-Color[class*=-C185] { + color: #D7D75F +} + +div.highlight .-Color[class*=-BGC185] { + background-color: #D7D75F +} + +div.highlight .-Color[class*=-C186] { + color: #D7D787 +} + +div.highlight .-Color[class*=-BGC186] { + background-color: #D7D787 +} + +div.highlight .-Color[class*=-C187] { + color: #D7D7AF +} + +div.highlight .-Color[class*=-BGC187] { + background-color: #D7D7AF +} + +div.highlight .-Color[class*=-C188] { + color: #D7D7D7 +} + +div.highlight .-Color[class*=-BGC188] { + background-color: #D7D7D7 +} + +div.highlight .-Color[class*=-C189] { + color: #D7D7FF +} + +div.highlight .-Color[class*=-BGC189] { + background-color: #D7D7FF +} + +div.highlight .-Color[class*=-C190] { + color: #D7FF00 +} + +div.highlight .-Color[class*=-BGC190] { + background-color: #D7FF00 +} + +div.highlight .-Color[class*=-C191] { + color: #D7FF5F +} + +div.highlight .-Color[class*=-BGC191] { + background-color: #D7FF5F +} + +div.highlight .-Color[class*=-C192] { + color: #D7FF87 +} + +div.highlight .-Color[class*=-BGC192] { + background-color: #D7FF87 +} + +div.highlight .-Color[class*=-C193] { + color: #D7FFAF +} + +div.highlight .-Color[class*=-BGC193] { + background-color: #D7FFAF +} + +div.highlight .-Color[class*=-C194] { + color: #D7FFD7 +} + +div.highlight .-Color[class*=-BGC194] { + background-color: #D7FFD7 +} + +div.highlight .-Color[class*=-C195] { + color: #D7FFFF +} + +div.highlight .-Color[class*=-BGC195] { + background-color: #D7FFFF +} + +div.highlight .-Color[class*=-C196] { + color: #FF0000 +} + +div.highlight .-Color[class*=-BGC196] { + background-color: #FF0000 +} + +div.highlight .-Color[class*=-C197] { + color: #FF005F +} + +div.highlight .-Color[class*=-BGC197] { + background-color: #FF005F +} + +div.highlight .-Color[class*=-C198] { + color: #FF0087 +} + +div.highlight .-Color[class*=-BGC198] { + background-color: #FF0087 +} + +div.highlight .-Color[class*=-C199] { + color: #FF00AF +} + +div.highlight .-Color[class*=-BGC199] { + background-color: #FF00AF +} + +div.highlight .-Color[class*=-C200] { + color: #FF00D7 +} + +div.highlight .-Color[class*=-BGC200] { + background-color: #FF00D7 +} + +div.highlight .-Color[class*=-C201] { + color: #FF00FF +} + +div.highlight .-Color[class*=-BGC201] { + background-color: #FF00FF +} + +div.highlight .-Color[class*=-C202] { + color: #FF5F00 +} + +div.highlight .-Color[class*=-BGC202] { + background-color: #FF5F00 +} + +div.highlight .-Color[class*=-C203] { + color: #FF5F5F +} + +div.highlight .-Color[class*=-BGC203] { + background-color: #FF5F5F +} + +div.highlight .-Color[class*=-C204] { + color: #FF5F87 +} + +div.highlight .-Color[class*=-BGC204] { + background-color: #FF5F87 +} + +div.highlight .-Color[class*=-C205] { + color: #FF5FAF +} + +div.highlight .-Color[class*=-BGC205] { + background-color: #FF5FAF +} + +div.highlight .-Color[class*=-C206] { + color: #FF5FD7 +} + +div.highlight .-Color[class*=-BGC206] { + background-color: #FF5FD7 +} + +div.highlight .-Color[class*=-C207] { + color: #FF5FFF +} + +div.highlight .-Color[class*=-BGC207] { + background-color: #FF5FFF +} + +div.highlight .-Color[class*=-C208] { + color: #FF8700 +} + +div.highlight .-Color[class*=-BGC208] { + background-color: #FF8700 +} + +div.highlight .-Color[class*=-C209] { + color: #FF875F +} + +div.highlight .-Color[class*=-BGC209] { + background-color: #FF875F +} + +div.highlight .-Color[class*=-C210] { + color: #FF8787 +} + +div.highlight .-Color[class*=-BGC210] { + background-color: #FF8787 +} + +div.highlight .-Color[class*=-C211] { + color: #FF87AF +} + +div.highlight .-Color[class*=-BGC211] { + background-color: #FF87AF +} + +div.highlight .-Color[class*=-C212] { + color: #FF87D7 +} + +div.highlight .-Color[class*=-BGC212] { + background-color: #FF87D7 +} + +div.highlight .-Color[class*=-C213] { + color: #FF87FF +} + +div.highlight .-Color[class*=-BGC213] { + background-color: #FF87FF +} + +div.highlight .-Color[class*=-C214] { + color: #FFAF00 +} + +div.highlight .-Color[class*=-BGC214] { + background-color: #FFAF00 +} + +div.highlight .-Color[class*=-C215] { + color: #FFAF5F +} + +div.highlight .-Color[class*=-BGC215] { + background-color: #FFAF5F +} + +div.highlight .-Color[class*=-C216] { + color: #FFAF87 +} + +div.highlight .-Color[class*=-BGC216] { + background-color: #FFAF87 +} + +div.highlight .-Color[class*=-C217] { + color: #FFAFAF +} + +div.highlight .-Color[class*=-BGC217] { + background-color: #FFAFAF +} + +div.highlight .-Color[class*=-C218] { + color: #FFAFD7 +} + +div.highlight .-Color[class*=-BGC218] { + background-color: #FFAFD7 +} + +div.highlight .-Color[class*=-C219] { + color: #FFAFFF +} + +div.highlight .-Color[class*=-BGC219] { + background-color: #FFAFFF +} + +div.highlight .-Color[class*=-C220] { + color: #FFD700 +} + +div.highlight .-Color[class*=-BGC220] { + background-color: #FFD700 +} + +div.highlight .-Color[class*=-C221] { + color: #FFD75F +} + +div.highlight .-Color[class*=-BGC221] { + background-color: #FFD75F +} + +div.highlight .-Color[class*=-C222] { + color: #FFD787 +} + +div.highlight .-Color[class*=-BGC222] { + background-color: #FFD787 +} + +div.highlight .-Color[class*=-C223] { + color: #FFD7AF +} + +div.highlight .-Color[class*=-BGC223] { + background-color: #FFD7AF +} + +div.highlight .-Color[class*=-C224] { + color: #FFD7D7 +} + +div.highlight .-Color[class*=-BGC224] { + background-color: #FFD7D7 +} + +div.highlight .-Color[class*=-C225] { + color: #FFD7FF +} + +div.highlight .-Color[class*=-BGC225] { + background-color: #FFD7FF +} + +div.highlight .-Color[class*=-C226] { + color: #FFFF00 +} + +div.highlight .-Color[class*=-BGC226] { + background-color: #FFFF00 +} + +div.highlight .-Color[class*=-C227] { + color: #FFFF5F +} + +div.highlight .-Color[class*=-BGC227] { + background-color: #FFFF5F +} + +div.highlight .-Color[class*=-C228] { + color: #FFFF87 +} + +div.highlight .-Color[class*=-BGC228] { + background-color: #FFFF87 +} + +div.highlight .-Color[class*=-C229] { + color: #FFFFAF +} + +div.highlight .-Color[class*=-BGC229] { + background-color: #FFFFAF +} + +div.highlight .-Color[class*=-C230] { + color: #FFFFD7 +} + +div.highlight .-Color[class*=-BGC230] { + background-color: #FFFFD7 +} + +div.highlight .-Color[class*=-C231] { + color: #FFFFFF +} + +div.highlight .-Color[class*=-BGC231] { + background-color: #FFFFFF +} + +div.highlight .-Color[class*=-C232] { + color: #080808 +} + +div.highlight .-Color[class*=-BGC232] { + background-color: #080808 +} + +div.highlight .-Color[class*=-C233] { + color: #121212 +} + +div.highlight .-Color[class*=-BGC233] { + background-color: #121212 +} + +div.highlight .-Color[class*=-C234] { + color: #1C1C1C +} + +div.highlight .-Color[class*=-BGC234] { + background-color: #1C1C1C +} + +div.highlight .-Color[class*=-C235] { + color: #262626 +} + +div.highlight .-Color[class*=-BGC235] { + background-color: #262626 +} + +div.highlight .-Color[class*=-C236] { + color: #303030 +} + +div.highlight .-Color[class*=-BGC236] { + background-color: #303030 +} + +div.highlight .-Color[class*=-C237] { + color: #3A3A3A +} + +div.highlight .-Color[class*=-BGC237] { + background-color: #3A3A3A +} + +div.highlight .-Color[class*=-C238] { + color: #444444 +} + +div.highlight .-Color[class*=-BGC238] { + background-color: #444444 +} + +div.highlight .-Color[class*=-C239] { + color: #4E4E4E +} + +div.highlight .-Color[class*=-BGC239] { + background-color: #4E4E4E +} + +div.highlight .-Color[class*=-C240] { + color: #585858 +} + +div.highlight .-Color[class*=-BGC240] { + background-color: #585858 +} + +div.highlight .-Color[class*=-C241] { + color: #626262 +} + +div.highlight .-Color[class*=-BGC241] { + background-color: #626262 +} + +div.highlight .-Color[class*=-C242] { + color: #6C6C6C +} + +div.highlight .-Color[class*=-BGC242] { + background-color: #6C6C6C +} + +div.highlight .-Color[class*=-C243] { + color: #767676 +} + +div.highlight .-Color[class*=-BGC243] { + background-color: #767676 +} + +div.highlight .-Color[class*=-C244] { + color: #808080 +} + +div.highlight .-Color[class*=-BGC244] { + background-color: #808080 +} + +div.highlight .-Color[class*=-C245] { + color: #8A8A8A +} + +div.highlight .-Color[class*=-BGC245] { + background-color: #8A8A8A +} + +div.highlight .-Color[class*=-C246] { + color: #949494 +} + +div.highlight .-Color[class*=-BGC246] { + background-color: #949494 +} + +div.highlight .-Color[class*=-C247] { + color: #9E9E9E +} + +div.highlight .-Color[class*=-BGC247] { + background-color: #9E9E9E +} + +div.highlight .-Color[class*=-C248] { + color: #A8A8A8 +} + +div.highlight .-Color[class*=-BGC248] { + background-color: #A8A8A8 +} + +div.highlight .-Color[class*=-C249] { + color: #B2B2B2 +} + +div.highlight .-Color[class*=-BGC249] { + background-color: #B2B2B2 +} + +div.highlight .-Color[class*=-C250] { + color: #BCBCBC +} + +div.highlight .-Color[class*=-BGC250] { + background-color: #BCBCBC +} + +div.highlight .-Color[class*=-C251] { + color: #C6C6C6 +} + +div.highlight .-Color[class*=-BGC251] { + background-color: #C6C6C6 +} + +div.highlight .-Color[class*=-C252] { + color: #D0D0D0 +} + +div.highlight .-Color[class*=-BGC252] { + background-color: #D0D0D0 +} + +div.highlight .-Color[class*=-C253] { + color: #DADADA +} + +div.highlight .-Color[class*=-BGC253] { + background-color: #DADADA +} + +div.highlight .-Color[class*=-C254] { + color: #E4E4E4 +} + +div.highlight .-Color[class*=-BGC254] { + background-color: #E4E4E4 +} + +div.highlight 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(typeof Scorer === "undefined") { + var Scorer = { + // Implement the following function to further tweak the score for each result + // The function takes a result array [docname, title, anchor, descr, score, filename] + // and returns the new score. + /* + score: result => { + const [docname, title, anchor, descr, score, filename] = result + return score + }, + */ + + // query matches the full name of an object + objNameMatch: 11, + // or matches in the last dotted part of the object name + objPartialMatch: 6, + // Additive scores depending on the priority of the object + objPrio: { + 0: 15, // used to be importantResults + 1: 5, // used to be objectResults + 2: -5, // used to be unimportantResults + }, + // Used when the priority is not in the mapping. + objPrioDefault: 0, + + // query found in title + title: 15, + partialTitle: 7, + // query found in terms + term: 5, + partialTerm: 2, + }; +} + +const _removeChildren = (element) => { + while (element && element.lastChild) element.removeChild(element.lastChild); +}; + +/** + * See https://developer.mozilla.org/en-US/docs/Web/JavaScript/Guide/Regular_Expressions#escaping + */ +const _escapeRegExp = (string) => + string.replace(/[.*+\-?^${}()|[\]\\]/g, "\\$&"); // $& means the whole matched string + +const _displayItem = (item, searchTerms, highlightTerms) => { + const docBuilder = DOCUMENTATION_OPTIONS.BUILDER; + const docFileSuffix = DOCUMENTATION_OPTIONS.FILE_SUFFIX; + const docLinkSuffix = DOCUMENTATION_OPTIONS.LINK_SUFFIX; + const showSearchSummary = DOCUMENTATION_OPTIONS.SHOW_SEARCH_SUMMARY; + const contentRoot = document.documentElement.dataset.content_root; + + const [docName, title, anchor, descr, score, _filename] = item; + + let listItem = document.createElement("li"); + let requestUrl; + let linkUrl; + if (docBuilder === "dirhtml") { + // dirhtml builder + let dirname = docName + "/"; + if (dirname.match(/\/index\/$/)) + dirname = dirname.substring(0, dirname.length - 6); + else if (dirname === "index/") dirname = ""; + requestUrl = contentRoot + dirname; + linkUrl = requestUrl; + } else { + // normal html builders + requestUrl = contentRoot + docName + docFileSuffix; + linkUrl = docName + docLinkSuffix; + } + let linkEl = listItem.appendChild(document.createElement("a")); + linkEl.href = linkUrl + anchor; + linkEl.dataset.score = score; + linkEl.innerHTML = title; + if (descr) { + listItem.appendChild(document.createElement("span")).innerHTML = + " (" + descr + ")"; + // highlight search terms in the description + if (SPHINX_HIGHLIGHT_ENABLED) // set in sphinx_highlight.js + highlightTerms.forEach((term) => _highlightText(listItem, term, "highlighted")); + } + else if (showSearchSummary) + fetch(requestUrl) + .then((responseData) => responseData.text()) + .then((data) => { + if (data) + listItem.appendChild( + Search.makeSearchSummary(data, searchTerms, anchor) + ); + // highlight search terms in the summary + if (SPHINX_HIGHLIGHT_ENABLED) // set in sphinx_highlight.js + highlightTerms.forEach((term) => _highlightText(listItem, term, "highlighted")); + }); + Search.output.appendChild(listItem); +}; +const _finishSearch = (resultCount) => { + Search.stopPulse(); + Search.title.innerText = _("Search Results"); + if (!resultCount) + Search.status.innerText = Documentation.gettext( + "Your search did not match any documents. Please make sure that all words are spelled correctly and that you've selected enough categories." + ); + else + Search.status.innerText = _( + "Search finished, found ${resultCount} page(s) matching the search query." + ).replace('${resultCount}', resultCount); +}; +const _displayNextItem = ( + results, + resultCount, + searchTerms, + highlightTerms, +) => { + // results left, load the summary and display it + // this is intended to be dynamic (don't sub resultsCount) + if (results.length) { + _displayItem(results.pop(), searchTerms, highlightTerms); + setTimeout( + () => _displayNextItem(results, resultCount, searchTerms, highlightTerms), + 5 + ); + } + // search finished, update title and status message + else _finishSearch(resultCount); +}; +// Helper function used by query() to order search results. +// Each input is an array of [docname, title, anchor, descr, score, filename]. +// Order the results by score (in opposite order of appearance, since the +// `_displayNextItem` function uses pop() to retrieve items) and then alphabetically. +const _orderResultsByScoreThenName = (a, b) => { + const leftScore = a[4]; + const rightScore = b[4]; + if (leftScore === rightScore) { + // same score: sort alphabetically + const leftTitle = a[1].toLowerCase(); + const rightTitle = b[1].toLowerCase(); + if (leftTitle === rightTitle) return 0; + return leftTitle > rightTitle ? -1 : 1; // inverted is intentional + } + return leftScore > rightScore ? 1 : -1; +}; + +/** + * Default splitQuery function. Can be overridden in ``sphinx.search`` with a + * custom function per language. + * + * The regular expression works by splitting the string on consecutive characters + * that are not Unicode letters, numbers, underscores, or emoji characters. + * This is the same as ``\W+`` in Python, preserving the surrogate pair area. + */ +if (typeof splitQuery === "undefined") { + var splitQuery = (query) => query + .split(/[^\p{Letter}\p{Number}_\p{Emoji_Presentation}]+/gu) + .filter(term => term) // remove remaining empty strings +} + +/** + * Search Module + */ +const Search = { + _index: null, + _queued_query: null, + _pulse_status: -1, + + htmlToText: (htmlString, anchor) => { + const htmlElement = new DOMParser().parseFromString(htmlString, 'text/html'); + for (const removalQuery of [".headerlink", "script", "style"]) { + htmlElement.querySelectorAll(removalQuery).forEach((el) => { el.remove() }); + } + if (anchor) { + const anchorContent = htmlElement.querySelector(`[role="main"] ${anchor}`); + if (anchorContent) return anchorContent.textContent; + + console.warn( + `Anchored content block not found. Sphinx search tries to obtain it via DOM query '[role=main] ${anchor}'. Check your theme or template.` + ); + } + + // if anchor not specified or not found, fall back to main content + const docContent = htmlElement.querySelector('[role="main"]'); + if (docContent) return docContent.textContent; + + console.warn( + "Content block not found. Sphinx search tries to obtain it via DOM query '[role=main]'. Check your theme or template." + ); + return ""; + }, + + init: () => { + const query = new URLSearchParams(window.location.search).get("q"); + document + .querySelectorAll('input[name="q"]') + .forEach((el) => (el.value = query)); + if (query) Search.performSearch(query); + }, + + loadIndex: (url) => + (document.body.appendChild(document.createElement("script")).src = url), + + setIndex: (index) => { + Search._index = index; + if (Search._queued_query !== null) { + const query = Search._queued_query; + Search._queued_query = null; + Search.query(query); + } + }, + + hasIndex: () => Search._index !== null, + + deferQuery: (query) => (Search._queued_query = query), + + stopPulse: () => (Search._pulse_status = -1), + + startPulse: () => { + if (Search._pulse_status >= 0) return; + + const pulse = () => { + Search._pulse_status = (Search._pulse_status + 1) % 4; + Search.dots.innerText = ".".repeat(Search._pulse_status); + if (Search._pulse_status >= 0) window.setTimeout(pulse, 500); + }; + pulse(); + }, + + /** + * perform a search for something (or wait until index is loaded) + */ + performSearch: (query) => { + // create the required interface elements + const searchText = document.createElement("h2"); + searchText.textContent = _("Searching"); + const searchSummary = document.createElement("p"); + searchSummary.classList.add("search-summary"); + searchSummary.innerText = ""; + const searchList = document.createElement("ul"); + searchList.classList.add("search"); + + const out = document.getElementById("search-results"); + Search.title = out.appendChild(searchText); + Search.dots = Search.title.appendChild(document.createElement("span")); + Search.status = out.appendChild(searchSummary); + Search.output = out.appendChild(searchList); + + const searchProgress = document.getElementById("search-progress"); + // Some themes don't use the search progress node + if (searchProgress) { + searchProgress.innerText = _("Preparing search..."); + } + Search.startPulse(); + + // index already loaded, the browser was quick! + if (Search.hasIndex()) Search.query(query); + else Search.deferQuery(query); + }, + + _parseQuery: (query) => { + // stem the search terms and add them to the correct list + const stemmer = new Stemmer(); + const searchTerms = new Set(); + const excludedTerms = new Set(); + const highlightTerms = new Set(); + const objectTerms = new Set(splitQuery(query.toLowerCase().trim())); + splitQuery(query.trim()).forEach((queryTerm) => { + const queryTermLower = queryTerm.toLowerCase(); + + // maybe skip this "word" + // stopwords array is from language_data.js + if ( + stopwords.indexOf(queryTermLower) !== -1 || + queryTerm.match(/^\d+$/) + ) + return; + + // stem the word + let word = stemmer.stemWord(queryTermLower); + // select the correct list + if (word[0] === "-") excludedTerms.add(word.substr(1)); + else { + searchTerms.add(word); + highlightTerms.add(queryTermLower); + } + }); + + if (SPHINX_HIGHLIGHT_ENABLED) { // set in sphinx_highlight.js + localStorage.setItem("sphinx_highlight_terms", [...highlightTerms].join(" ")) + } + + // console.debug("SEARCH: searching for:"); + // console.info("required: ", [...searchTerms]); + // console.info("excluded: ", [...excludedTerms]); + + return [query, searchTerms, excludedTerms, highlightTerms, objectTerms]; + }, + + /** + * execute search (requires search index to be loaded) + */ + _performSearch: (query, searchTerms, excludedTerms, highlightTerms, objectTerms) => { + const filenames = Search._index.filenames; + const docNames = Search._index.docnames; + const titles = Search._index.titles; + const allTitles = Search._index.alltitles; + const indexEntries = Search._index.indexentries; + + // Collect multiple result groups to be sorted separately and then ordered. + // Each is an array of [docname, title, anchor, descr, score, filename]. + const normalResults = []; + const nonMainIndexResults = []; + + _removeChildren(document.getElementById("search-progress")); + + const queryLower = query.toLowerCase().trim(); + for (const [title, foundTitles] of Object.entries(allTitles)) { + if (title.toLowerCase().trim().includes(queryLower) && (queryLower.length >= title.length/2)) { + for (const [file, id] of foundTitles) { + const score = Math.round(Scorer.title * queryLower.length / title.length); + const boost = titles[file] === title ? 1 : 0; // add a boost for document titles + normalResults.push([ + docNames[file], + titles[file] !== title ? `${titles[file]} > ${title}` : title, + id !== null ? "#" + id : "", + null, + score + boost, + filenames[file], + ]); + } + } + } + + // search for explicit entries in index directives + for (const [entry, foundEntries] of Object.entries(indexEntries)) { + if (entry.includes(queryLower) && (queryLower.length >= entry.length/2)) { + for (const [file, id, isMain] of foundEntries) { + const score = Math.round(100 * queryLower.length / entry.length); + const result = [ + docNames[file], + titles[file], + id ? "#" + id : "", + null, + score, + filenames[file], + ]; + if (isMain) { + normalResults.push(result); + } else { + nonMainIndexResults.push(result); + } + } + } + } + + // lookup as object + objectTerms.forEach((term) => + normalResults.push(...Search.performObjectSearch(term, objectTerms)) + ); + + // lookup as search terms in fulltext + normalResults.push(...Search.performTermsSearch(searchTerms, excludedTerms)); + + // let the scorer override scores with a custom scoring function + if (Scorer.score) { + normalResults.forEach((item) => (item[4] = Scorer.score(item))); + nonMainIndexResults.forEach((item) => (item[4] = Scorer.score(item))); + } + + // Sort each group of results by score and then alphabetically by name. + normalResults.sort(_orderResultsByScoreThenName); + nonMainIndexResults.sort(_orderResultsByScoreThenName); + + // Combine the result groups in (reverse) order. + // Non-main index entries are typically arbitrary cross-references, + // so display them after other results. + let results = [...nonMainIndexResults, ...normalResults]; + + // remove duplicate search results + // note the reversing of results, so that in the case of duplicates, the highest-scoring entry is kept + let seen = new Set(); + results = results.reverse().reduce((acc, result) => { + let resultStr = result.slice(0, 4).concat([result[5]]).map(v => String(v)).join(','); + if (!seen.has(resultStr)) { + acc.push(result); + seen.add(resultStr); + } + return acc; + }, []); + + return results.reverse(); + }, + + query: (query) => { + const [searchQuery, searchTerms, excludedTerms, highlightTerms, objectTerms] = Search._parseQuery(query); + const results = Search._performSearch(searchQuery, searchTerms, excludedTerms, highlightTerms, objectTerms); + + // for debugging + //Search.lastresults = results.slice(); // a copy + // console.info("search results:", Search.lastresults); + + // print the results + _displayNextItem(results, results.length, searchTerms, highlightTerms); + }, + + /** + * search for object names + */ + performObjectSearch: (object, objectTerms) => { + const filenames = Search._index.filenames; + const docNames = Search._index.docnames; + const objects = Search._index.objects; + const objNames = Search._index.objnames; + const titles = Search._index.titles; + + const results = []; + + const objectSearchCallback = (prefix, match) => { + const name = match[4] + const fullname = (prefix ? prefix + "." : "") + name; + const fullnameLower = fullname.toLowerCase(); + if (fullnameLower.indexOf(object) < 0) return; + + let score = 0; + const parts = fullnameLower.split("."); + + // check for different match types: exact matches of full name or + // "last name" (i.e. last dotted part) + if (fullnameLower === object || parts.slice(-1)[0] === object) + score += Scorer.objNameMatch; + else if (parts.slice(-1)[0].indexOf(object) > -1) + score += Scorer.objPartialMatch; // matches in last name + + const objName = objNames[match[1]][2]; + const title = titles[match[0]]; + + // If more than one term searched for, we require other words to be + // found in the name/title/description + const otherTerms = new Set(objectTerms); + otherTerms.delete(object); + if (otherTerms.size > 0) { + const haystack = `${prefix} ${name} ${objName} ${title}`.toLowerCase(); + if ( + [...otherTerms].some((otherTerm) => haystack.indexOf(otherTerm) < 0) + ) + return; + } + + let anchor = match[3]; + if (anchor === "") anchor = fullname; + else if (anchor === "-") anchor = objNames[match[1]][1] + "-" + fullname; + + const descr = objName + _(", in ") + title; + + // add custom score for some objects according to scorer + if (Scorer.objPrio.hasOwnProperty(match[2])) + score += Scorer.objPrio[match[2]]; + else score += Scorer.objPrioDefault; + + results.push([ + docNames[match[0]], + fullname, + "#" + anchor, + descr, + score, + filenames[match[0]], + ]); + }; + Object.keys(objects).forEach((prefix) => + objects[prefix].forEach((array) => + objectSearchCallback(prefix, array) + ) + ); + return results; + }, + + /** + * search for full-text terms in the index + */ + performTermsSearch: (searchTerms, excludedTerms) => { + // prepare search + const terms = Search._index.terms; + const titleTerms = Search._index.titleterms; + const filenames = Search._index.filenames; + const docNames = Search._index.docnames; + const titles = Search._index.titles; + + const scoreMap = new Map(); + const fileMap = new Map(); + + // perform the search on the required terms + searchTerms.forEach((word) => { + const files = []; + const arr = [ + { files: terms[word], score: Scorer.term }, + { files: titleTerms[word], score: Scorer.title }, + ]; + // add support for partial matches + if (word.length > 2) { + const escapedWord = _escapeRegExp(word); + if (!terms.hasOwnProperty(word)) { + Object.keys(terms).forEach((term) => { + if (term.match(escapedWord)) + arr.push({ files: terms[term], score: Scorer.partialTerm }); + }); + } + if (!titleTerms.hasOwnProperty(word)) { + Object.keys(titleTerms).forEach((term) => { + if (term.match(escapedWord)) + arr.push({ files: titleTerms[term], score: Scorer.partialTitle }); + }); + } + } + + // no match but word was a required one + if (arr.every((record) => record.files === undefined)) return; + + // found search word in contents + arr.forEach((record) => { + if (record.files === undefined) return; + + let recordFiles = record.files; + if (recordFiles.length === undefined) recordFiles = [recordFiles]; + files.push(...recordFiles); + + // set score for the word in each file + recordFiles.forEach((file) => { + if (!scoreMap.has(file)) scoreMap.set(file, {}); + scoreMap.get(file)[word] = record.score; + }); + }); + + // create the mapping + files.forEach((file) => { + if (!fileMap.has(file)) fileMap.set(file, [word]); + else if (fileMap.get(file).indexOf(word) === -1) fileMap.get(file).push(word); + }); + }); + + // now check if the files don't contain excluded terms + const results = []; + for (const [file, wordList] of fileMap) { + // check if all requirements are matched + + // as search terms with length < 3 are discarded + const filteredTermCount = [...searchTerms].filter( + (term) => term.length > 2 + ).length; + if ( + wordList.length !== searchTerms.size && + wordList.length !== filteredTermCount + ) + continue; + + // ensure that none of the excluded terms is in the search result + if ( + [...excludedTerms].some( + (term) => + terms[term] === file || + titleTerms[term] === file || + (terms[term] || []).includes(file) || + (titleTerms[term] || []).includes(file) + ) + ) + break; + + // select one (max) score for the file. + const score = Math.max(...wordList.map((w) => scoreMap.get(file)[w])); + // add result to the result list + results.push([ + docNames[file], + titles[file], + "", + null, + score, + filenames[file], + ]); + } + return results; + }, + + /** + * helper function to return a node containing the + * search summary for a given text. keywords is a list + * of stemmed words. + */ + makeSearchSummary: (htmlText, keywords, anchor) => { + const text = Search.htmlToText(htmlText, anchor); + if (text === "") return null; + + const textLower = text.toLowerCase(); + const actualStartPosition = [...keywords] + .map((k) => textLower.indexOf(k.toLowerCase())) + .filter((i) => i > -1) + .slice(-1)[0]; + const startWithContext = Math.max(actualStartPosition - 120, 0); + + const top = startWithContext === 0 ? "" : "..."; + const tail = startWithContext + 240 < text.length ? "..." : ""; + + let summary = document.createElement("p"); + summary.classList.add("context"); + summary.textContent = top + text.substr(startWithContext, 240).trim() + tail; + + return summary; + }, +}; + +_ready(Search.init); diff --git a/singlehtml/_static/sphinx_highlight.js b/singlehtml/_static/sphinx_highlight.js new file mode 100644 index 0000000..8a96c69 --- /dev/null +++ b/singlehtml/_static/sphinx_highlight.js @@ -0,0 +1,154 @@ +/* Highlighting utilities for Sphinx HTML documentation. */ +"use strict"; + +const SPHINX_HIGHLIGHT_ENABLED = true + +/** + * highlight a given string on a node by wrapping it in + * span elements with the given class name. + */ +const _highlight = (node, addItems, text, className) => { + if (node.nodeType === Node.TEXT_NODE) { + const val = node.nodeValue; + const parent = node.parentNode; + const pos = val.toLowerCase().indexOf(text); + if ( + pos >= 0 && + !parent.classList.contains(className) && + !parent.classList.contains("nohighlight") + ) { + let span; + + const closestNode = parent.closest("body, svg, foreignObject"); + const isInSVG = closestNode && closestNode.matches("svg"); + if (isInSVG) { + span = document.createElementNS("http://www.w3.org/2000/svg", "tspan"); + } else { + span = document.createElement("span"); + span.classList.add(className); + } + + span.appendChild(document.createTextNode(val.substr(pos, text.length))); + const rest = document.createTextNode(val.substr(pos + text.length)); + parent.insertBefore( + span, + parent.insertBefore( + rest, + node.nextSibling + ) + ); + node.nodeValue = val.substr(0, pos); + /* There may be more occurrences of search term in this node. So call this + * function recursively on the remaining fragment. + */ + _highlight(rest, addItems, text, className); + + if (isInSVG) { + const rect = document.createElementNS( + "http://www.w3.org/2000/svg", + "rect" + ); + const bbox = parent.getBBox(); + rect.x.baseVal.value = bbox.x; + rect.y.baseVal.value = bbox.y; + rect.width.baseVal.value = bbox.width; + rect.height.baseVal.value = bbox.height; + rect.setAttribute("class", className); + addItems.push({ parent: parent, target: rect }); + } + } + } else if (node.matches && !node.matches("button, select, textarea")) { + node.childNodes.forEach((el) => _highlight(el, addItems, text, className)); + } +}; +const _highlightText = (thisNode, text, className) => { + let addItems = []; + _highlight(thisNode, addItems, text, className); + addItems.forEach((obj) => + obj.parent.insertAdjacentElement("beforebegin", obj.target) + ); +}; + +/** + * Small JavaScript module for the documentation. + */ +const SphinxHighlight = { + + /** + * highlight the search words provided in localstorage in the text + */ + highlightSearchWords: () => { + if (!SPHINX_HIGHLIGHT_ENABLED) return; // bail if no highlight + + // get and clear terms from localstorage + const url = new URL(window.location); + const highlight = + localStorage.getItem("sphinx_highlight_terms") + || url.searchParams.get("highlight") + || ""; + localStorage.removeItem("sphinx_highlight_terms") + url.searchParams.delete("highlight"); + window.history.replaceState({}, "", url); + + // get individual terms from highlight string + const terms = highlight.toLowerCase().split(/\s+/).filter(x => x); + if (terms.length === 0) return; // nothing to do + + // There should never be more than one element matching "div.body" + const divBody = document.querySelectorAll("div.body"); + const body = divBody.length ? divBody[0] : document.querySelector("body"); + window.setTimeout(() => { + terms.forEach((term) => _highlightText(body, term, "highlighted")); + }, 10); + + const searchBox = document.getElementById("searchbox"); + if (searchBox === null) return; + searchBox.appendChild( + document + .createRange() + .createContextualFragment( + '" + ) + ); + }, + + /** + * helper function to hide the search marks again + */ + hideSearchWords: () => { + document + .querySelectorAll("#searchbox .highlight-link") + .forEach((el) => el.remove()); + document + .querySelectorAll("span.highlighted") + .forEach((el) => el.classList.remove("highlighted")); + localStorage.removeItem("sphinx_highlight_terms") + }, + + initEscapeListener: () => { + // only install a listener if it is really needed + if (!DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS) return; + + document.addEventListener("keydown", (event) => { + // bail for input elements + if (BLACKLISTED_KEY_CONTROL_ELEMENTS.has(document.activeElement.tagName)) return; + // bail with special keys + if (event.shiftKey || event.altKey || event.ctrlKey || event.metaKey) return; + if (DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS && (event.key === "Escape")) { + SphinxHighlight.hideSearchWords(); + event.preventDefault(); + } + }); + }, +}; + +_ready(() => { + /* Do not call highlightSearchWords() when we are on the search page. + * It will highlight words from the *previous* search query. + */ + if (typeof Search === "undefined") SphinxHighlight.highlightSearchWords(); + SphinxHighlight.initEscapeListener(); +}); diff --git a/singlehtml/_static/sphinx_lesson.css b/singlehtml/_static/sphinx_lesson.css new file mode 100644 index 0000000..14b20c6 --- /dev/null +++ b/singlehtml/_static/sphinx_lesson.css @@ -0,0 +1,51 @@ +/* sphinx_lesson.css */ + +body.wy-body-for-nav img.with-border { + border: 2px solid; +} + +.rst-content .admonition-no-content { + padding-bottom: 0px; +} + +.rst-content .demo > .admonition-title::before { + content: "\01F440"; /* Eyes */ } +.rst-content .type-along > .admonition-title::before { + content: "\02328\0FE0F"; /* Keyboard */ } +.rst-content .exercise > .admonition-title::before { + content: "\0270D\0FE0F"; /* Hand */ } +.rst-content .solution > .admonition-title::before { + content: "\02714\0FE0E"; /* Check mark */ } +.rst-content .homework > .admonition-title::before { + content: "\01F4DD"; /* Memo */ } +.rst-content .discussion > .admonition-title::before { + content: "\01F4AC"; /* Speech balloon */ } +.rst-content .questions > .admonition-title::before { + content: "\02753\0FE0E"; /* Question mark */ } +.rst-content .prerequisites > .admonition-title::before { + content: "\02699"; /* Gear */ } +.rst-content .seealso > .admonition-title::before { + content: "\027A1\0FE0E"; /* Question mark */ } + + +/* instructor-note */ +.rst-content .instructor-note { + background: #e7e7e7; +} +.rst-content .instructor-note > .admonition-title { + background: #6a6a6a; +} +.rst-content .instructor-note > .admonition-title::before { + content: ""; +} + + +/* sphinx_toggle_button, make the font white */ +.rst-content .toggle.admonition button.toggle-button { + color: white; +} + +/* sphinx-togglebutton, remove underflow when toggled to hidden mode */ +.rst-content .admonition.toggle-hidden { + padding-bottom: 0px; +} diff --git a/singlehtml/_static/sphinx_rtd_theme_ext_color_contrast.css b/singlehtml/_static/sphinx_rtd_theme_ext_color_contrast.css new file mode 100644 index 0000000..e68feb8 --- /dev/null +++ b/singlehtml/_static/sphinx_rtd_theme_ext_color_contrast.css @@ -0,0 +1,47 @@ +/* The following are for web accessibility of sphinx_rtd_theme: they + * solve some of the most frequent contrast issues. Remove when this + * solved: + * https://github.com/readthedocs/sphinx_rtd_theme/issues/971 + */ +/* background: #fcfcfc, note boxes #E7F2FA */ +a { color: #2573A7; } /* original #2980B9, #1F5C84; */ +body { color: #242424; } /* original #404040, #383838 */ +.wy-side-nav-search>a, .wy-side-nav-search .wy-dropdown>a { + color: #ffffff; +} /* original #fcfcfc */ +footer { color: #737373; } /* original gray=#808080*/ +footer span.commit code, footer span.commit .rst-content tt, .rst-content footer span.commit tt { + color: #737373; +} /* original gray=#808080*/ +.rst-content tt.literal, .rst-content tt.literal, .rst-content code.literal { + color: #AB2314; +} +/* Sidebar background */ +.wy-side-nav-search { background-color: #277CB4;} + +/* Same, but for pygments */ +.highlight .ch { color: #3E7A89; } /* #! line */ +.highlight .c1 { color: #3E7A89; } /* also comments */ +.highlight .nv { color: #AD3ECC; } /* variable */ +.highlight .gp { color: #B45608; } /* prompt character, $*/ +.highlight .si { color: #3975B1; } /* ${} variable text */ +.highlight .nc { color: #0C78A7; } + +/* Sphinx admonitions */ +/* warning */ +.wy-alert.wy-alert-warning .wy-alert-title, .rst-content .wy-alert-warning.note .wy-alert-title, .rst-content .attention .wy-alert-title, .rst-content .caution .wy-alert-title, .rst-content .wy-alert-warning.danger .wy-alert-title, .rst-content .wy-alert-warning.error .wy-alert-title, .rst-content .wy-alert-warning.hint .wy-alert-title, .rst-content .wy-alert-warning.important .wy-alert-title, .rst-content .wy-alert-warning.tip .wy-alert-title, .rst-content .warning .wy-alert-title, .rst-content .wy-alert-warning.seealso .wy-alert-title, .rst-content .admonition-todo .wy-alert-title, .rst-content .wy-alert-warning.admonition .wy-alert-title, .wy-alert.wy-alert-warning .rst-content .admonition-title, .rst-content .wy-alert.wy-alert-warning .admonition-title, .rst-content .wy-alert-warning.note .admonition-title, .rst-content .attention .admonition-title, .rst-content .caution .admonition-title, .rst-content .wy-alert-warning.danger .admonition-title, .rst-content .wy-alert-warning.error .admonition-title, .rst-content .wy-alert-warning.hint .admonition-title, .rst-content .wy-alert-warning.important .admonition-title, .rst-content .wy-alert-warning.tip .admonition-title, .rst-content .warning .admonition-title, .rst-content .wy-alert-warning.seealso .admonition-title, .rst-content .admonition-todo .admonition-title, .rst-content .wy-alert-warning.admonition .admonition-title { + background: #B15E16; } +/* important */ +.wy-alert.wy-alert-success .wy-alert-title, .rst-content .wy-alert-success.note .wy-alert-title, .rst-content .wy-alert-success.attention .wy-alert-title, .rst-content .wy-alert-success.caution .wy-alert-title, .rst-content .wy-alert-success.danger .wy-alert-title, .rst-content .wy-alert-success.error .wy-alert-title, .rst-content .hint .wy-alert-title, .rst-content .important .wy-alert-title, .rst-content .tip .wy-alert-title, .rst-content .wy-alert-success.warning .wy-alert-title, .rst-content .wy-alert-success.seealso .wy-alert-title, .rst-content .wy-alert-success.admonition-todo .wy-alert-title, .rst-content .wy-alert-success.admonition .wy-alert-title, .wy-alert.wy-alert-success .rst-content .admonition-title, .rst-content .wy-alert.wy-alert-success .admonition-title, .rst-content .wy-alert-success.note .admonition-title, .rst-content .wy-alert-success.attention .admonition-title, .rst-content .wy-alert-success.caution .admonition-title, .rst-content .wy-alert-success.danger .admonition-title, .rst-content .wy-alert-success.error .admonition-title, .rst-content .hint .admonition-title, .rst-content .important .admonition-title, .rst-content .tip .admonition-title, .rst-content .wy-alert-success.warning .admonition-title, .rst-content .wy-alert-success.seealso .admonition-title, .rst-content .wy-alert-success.admonition-todo .admonition-title, .rst-content .wy-alert-success.admonition .admonition-title { + background: #12826C; } +/* seealso, note, etc */ +.wy-alert.wy-alert-info .wy-alert-title, .rst-content .note .wy-alert-title, .rst-content .wy-alert-info.attention .wy-alert-title, .rst-content .wy-alert-info.caution .wy-alert-title, .rst-content .wy-alert-info.danger .wy-alert-title, .rst-content .wy-alert-info.error .wy-alert-title, .rst-content .wy-alert-info.hint .wy-alert-title, .rst-content .wy-alert-info.important .wy-alert-title, .rst-content .wy-alert-info.tip .wy-alert-title, .rst-content .wy-alert-info.warning .wy-alert-title, .rst-content .seealso .wy-alert-title, .rst-content .wy-alert-info.admonition-todo .wy-alert-title, .rst-content .wy-alert-info.admonition .wy-alert-title, .wy-alert.wy-alert-info .rst-content .admonition-title, .rst-content .wy-alert.wy-alert-info .admonition-title, .rst-content .note .admonition-title, .rst-content .wy-alert-info.attention .admonition-title, .rst-content .wy-alert-info.caution .admonition-title, .rst-content .wy-alert-info.danger .admonition-title, .rst-content .wy-alert-info.error .admonition-title, .rst-content .wy-alert-info.hint .admonition-title, .rst-content .wy-alert-info.important .admonition-title, .rst-content .wy-alert-info.tip .admonition-title, .rst-content .wy-alert-info.warning .admonition-title, .rst-content .seealso .admonition-title, .rst-content .wy-alert-info.admonition-todo .admonition-title, .rst-content .wy-alert-info.admonition .admonition-title { + background: #277CB4; } +/* error, danger */ +.rst-content .danger .admonition-title, .rst-content .danger .wy-alert-title, .rst-content .error .admonition-title, .rst-content .error .wy-alert-title, .rst-content .wy-alert-danger.admonition-todo .admonition-title, .rst-content .wy-alert-danger.admonition-todo .wy-alert-title, .rst-content .wy-alert-danger.admonition .admonition-title, .rst-content .wy-alert-danger.admonition .wy-alert-title, .rst-content .wy-alert-danger.attention .admonition-title, .rst-content .wy-alert-danger.attention .wy-alert-title, .rst-content .wy-alert-danger.caution .admonition-title, .rst-content .wy-alert-danger.caution .wy-alert-title, .rst-content .wy-alert-danger.hint .admonition-title, .rst-content .wy-alert-danger.hint .wy-alert-title, .rst-content .wy-alert-danger.important .admonition-title, .rst-content .wy-alert-danger.important .wy-alert-title, .rst-content .wy-alert-danger.note .admonition-title, .rst-content .wy-alert-danger.note .wy-alert-title, .rst-content .wy-alert-danger.seealso .admonition-title, .rst-content .wy-alert-danger.seealso .wy-alert-title, .rst-content .wy-alert-danger.tip .admonition-title, .rst-content .wy-alert-danger.tip .wy-alert-title, .rst-content .wy-alert-danger.warning .admonition-title, .rst-content .wy-alert-danger.warning .wy-alert-title, .rst-content .wy-alert.wy-alert-danger .admonition-title, .wy-alert.wy-alert-danger .rst-content .admonition-title, .wy-alert.wy-alert-danger .wy-alert-title { + background: #e31704; +} + +/* Generic admonition titles */ +.wy-alert-title, .rst-content .admonition-title { + background: #277CB4; } diff --git a/singlehtml/_static/style.css b/singlehtml/_static/style.css new file mode 100644 index 0000000..59e60ee --- /dev/null +++ b/singlehtml/_static/style.css @@ -0,0 +1,6 @@ +.rst-content .objectives { + background: #fee0d2; +} +.rst-content .objectives > .admonition-title { + background: #fc9272; +} diff --git a/singlehtml/_static/tabs.css b/singlehtml/_static/tabs.css new file mode 100644 index 0000000..957ba60 --- /dev/null +++ b/singlehtml/_static/tabs.css @@ -0,0 +1,89 @@ +.sphinx-tabs { + margin-bottom: 1rem; +} + +[role="tablist"] { + border-bottom: 1px solid #a0b3bf; +} + +.sphinx-tabs-tab { + position: relative; + font-family: Lato,'Helvetica Neue',Arial,Helvetica,sans-serif; + color: #1D5C87; + line-height: 24px; + margin: 0; + font-size: 16px; + font-weight: 400; + background-color: rgba(255, 255, 255, 0); + border-radius: 5px 5px 0 0; + border: 0; + padding: 1rem 1.5rem; + margin-bottom: 0; +} + +.sphinx-tabs-tab[aria-selected="true"] { + font-weight: 700; + border: 1px solid #a0b3bf; + border-bottom: 1px solid white; + margin: -1px; + background-color: white; +} + +.sphinx-tabs-tab:focus { + z-index: 1; + outline-offset: 1px; +} + +.sphinx-tabs-panel { + position: relative; + padding: 1rem; + border: 1px solid #a0b3bf; + margin: 0px -1px -1px -1px; + border-radius: 0 0 5px 5px; + border-top: 0; + background: white; +} + +.sphinx-tabs-panel.code-tab { + padding: 0.4rem; +} + +.sphinx-tab img { + margin-bottom: 24 px; +} + +/* Dark theme preference styling */ + +@media (prefers-color-scheme: dark) { + body[data-theme="auto"] .sphinx-tabs-panel { + color: white; + background-color: rgb(50, 50, 50); + } + + body[data-theme="auto"] .sphinx-tabs-tab { + color: white; + background-color: rgba(255, 255, 255, 0.05); + } + + body[data-theme="auto"] .sphinx-tabs-tab[aria-selected="true"] { + border-bottom: 1px solid rgb(50, 50, 50); + background-color: rgb(50, 50, 50); + } +} + +/* Explicit dark theme styling */ + +body[data-theme="dark"] .sphinx-tabs-panel { + color: white; + background-color: rgb(50, 50, 50); +} + +body[data-theme="dark"] .sphinx-tabs-tab { + color: white; + background-color: rgba(255, 255, 255, 0.05); +} + +body[data-theme="dark"] .sphinx-tabs-tab[aria-selected="true"] { + border-bottom: 2px solid rgb(50, 50, 50); + background-color: rgb(50, 50, 50); +} diff --git a/singlehtml/_static/tabs.js b/singlehtml/_static/tabs.js new file mode 100644 index 0000000..48dc303 --- /dev/null +++ b/singlehtml/_static/tabs.js @@ -0,0 +1,145 @@ +try { + var session = window.sessionStorage || {}; +} catch (e) { + var session = {}; +} + +window.addEventListener("DOMContentLoaded", () => { + const allTabs = document.querySelectorAll('.sphinx-tabs-tab'); + const tabLists = document.querySelectorAll('[role="tablist"]'); + + allTabs.forEach(tab => { + tab.addEventListener("click", changeTabs); + }); + + tabLists.forEach(tabList => { + tabList.addEventListener("keydown", keyTabs); + }); + + // Restore group tab selection from session + const lastSelected = session.getItem('sphinx-tabs-last-selected'); + if (lastSelected != null) selectNamedTabs(lastSelected); +}); + +/** + * Key focus left and right between sibling elements using arrows + * @param {Node} e the element in focus when key was pressed + */ +function keyTabs(e) { + const tab = e.target; + let nextTab = null; + if (e.keyCode === 39 || e.keyCode === 37) { + tab.setAttribute("tabindex", -1); + // Move right + if (e.keyCode === 39) { + nextTab = tab.nextElementSibling; + if (nextTab === null) { + nextTab = tab.parentNode.firstElementChild; + } + // Move left + } else if (e.keyCode === 37) { + nextTab = tab.previousElementSibling; + if (nextTab === null) { + nextTab = tab.parentNode.lastElementChild; + } + } + } + + if (nextTab !== null) { + nextTab.setAttribute("tabindex", 0); + nextTab.focus(); + } +} + +/** + * Select or deselect clicked tab. If a group tab + * is selected, also select tab in other tabLists. + * @param {Node} e the element that was clicked + */ +function changeTabs(e) { + // Use this instead of the element that was clicked, in case it's a child + const notSelected = this.getAttribute("aria-selected") === "false"; + const positionBefore = this.parentNode.getBoundingClientRect().top; + const notClosable = !this.parentNode.classList.contains("closeable"); + + deselectTabList(this); + + if (notSelected || notClosable) { + selectTab(this); + const name = this.getAttribute("name"); + selectNamedTabs(name, this.id); + + if (this.classList.contains("group-tab")) { + // Persist during session + session.setItem('sphinx-tabs-last-selected', name); + } + } + + const positionAfter = this.parentNode.getBoundingClientRect().top; + const positionDelta = positionAfter - positionBefore; + // Scroll to offset content resizing + window.scrollTo(0, window.scrollY + positionDelta); +} + +/** + * Select tab and show associated panel. + * @param {Node} tab tab to select + */ +function selectTab(tab) { + tab.setAttribute("aria-selected", true); + + // Show the associated panel + document + .getElementById(tab.getAttribute("aria-controls")) + .removeAttribute("hidden"); +} + +/** + * Hide the panels associated with all tabs within the + * tablist containing this tab. + * @param {Node} tab a tab within the tablist to deselect + */ +function deselectTabList(tab) { + const parent = tab.parentNode; + const grandparent = parent.parentNode; + + Array.from(parent.children) + .forEach(t => t.setAttribute("aria-selected", false)); + + Array.from(grandparent.children) + .slice(1) // Skip tablist + .forEach(panel => panel.setAttribute("hidden", true)); +} + +/** + * Select grouped tabs with the same name, but no the tab + * with the given id. + * @param {Node} name name of grouped tab to be selected + * @param {Node} clickedId id of clicked tab + */ +function selectNamedTabs(name, clickedId=null) { + const groupedTabs = document.querySelectorAll(`.sphinx-tabs-tab[name="${name}"]`); + const tabLists = Array.from(groupedTabs).map(tab => tab.parentNode); + + tabLists + .forEach(tabList => { + // Don't want to change the tabList containing the clicked tab + const clickedTab = tabList.querySelector(`[id="${clickedId}"]`); + if (clickedTab === null ) { + // Select first tab with matching name + const tab = tabList.querySelector(`.sphinx-tabs-tab[name="${name}"]`); + deselectTabList(tab); + selectTab(tab); + } + }) +} + +if (typeof exports === 'undefined') { + exports = {}; +} + +exports.keyTabs = keyTabs; +exports.changeTabs = changeTabs; +exports.selectTab = selectTab; +exports.deselectTabList = deselectTabList; +exports.selectNamedTabs = selectNamedTabs; diff --git a/singlehtml/_static/term_role_formatting.css b/singlehtml/_static/term_role_formatting.css new file mode 100644 index 0000000..0b66095 --- /dev/null +++ b/singlehtml/_static/term_role_formatting.css @@ -0,0 +1,4 @@ +/* Make terms bold */ +a.reference span.std-term { + font-weight: bold; +} diff --git a/singlehtml/_static/togglebutton.css b/singlehtml/_static/togglebutton.css new file mode 100644 index 0000000..54a6787 --- /dev/null +++ b/singlehtml/_static/togglebutton.css @@ -0,0 +1,160 @@ +/** + * Admonition-based toggles + */ + +/* Visibility of the target */ +.admonition.toggle .admonition-title ~ * { + transition: opacity .3s, height .3s; +} + +/* Toggle buttons inside admonitions so we see the title */ +.admonition.toggle { + position: relative; +} + +/* Titles should cut off earlier to avoid overlapping w/ button */ +.admonition.toggle .admonition-title { + padding-right: 25%; + cursor: pointer; +} + +/* Hovering will cause a slight shift in color to make it feel interactive */ +.admonition.toggle .admonition-title:hover { + box-shadow: inset 0 0 0px 20px rgb(0 0 0 / 1%); +} + +/* Hovering will cause a slight shift in color to make it feel interactive */ +.admonition.toggle .admonition-title:active { + box-shadow: inset 0 0 0px 20px rgb(0 0 0 / 3%); +} + +/* Remove extra whitespace below the admonition title when hidden */ +.admonition.toggle-hidden { + padding-bottom: 0; +} + +.admonition.toggle-hidden .admonition-title { + margin-bottom: 0; +} + +/* hides all the content of a page until de-toggled */ +.admonition.toggle-hidden .admonition-title ~ * { + height: 0; + margin: 0; + opacity: 0; + visibility: hidden; +} + +/* General button style and position*/ +button.toggle-button { + /** + * Background and shape. By default there's no background + * but users can style as they wish + */ + background: none; + border: none; + outline: none; + + /* Positioning just inside the admonition title */ + position: absolute; + right: 0.5em; + padding: 0px; + border: none; + outline: none; +} + +/* Display the toggle hint on wide screens */ +@media (min-width: 768px) { + button.toggle-button.toggle-button-hidden:before { + content: attr(data-toggle-hint); /* This will be filled in by JS */ + font-size: .8em; + align-self: center; + } +} + +/* Icon behavior */ +.tb-icon { + transition: transform .2s ease-out; + height: 1.5em; + width: 1.5em; + stroke: currentColor; /* So that we inherit the color of other text */ +} + +/* The icon should point right when closed, down when open. */ +/* Open */ +.admonition.toggle button .tb-icon { + transform: rotate(90deg); +} + +/* Closed */ +.admonition.toggle button.toggle-button-hidden .tb-icon { + transform: rotate(0deg); +} + +/* With details toggles, we don't rotate the icon so it points right */ +details.toggle-details .tb-icon { + height: 1.4em; + width: 1.4em; + margin-top: 0.1em; /* To center the button vertically */ +} + + +/** + * Details-based toggles. + * In this case, we wrap elements with `.toggle` in a details block. + */ + +/* Details blocks */ +details.toggle-details { + margin: 1em 0; +} + + +details.toggle-details summary { + display: flex; + align-items: center; + cursor: pointer; + list-style: none; + border-radius: .2em; + border-left: 3px solid #1976d2; + background-color: rgb(204 204 204 / 10%); + padding: 0.2em 0.7em 0.3em 0.5em; /* Less padding on left because the SVG has left margin */ + font-size: 0.9em; +} + +details.toggle-details summary:hover { + background-color: rgb(204 204 204 / 20%); +} + +details.toggle-details summary:active { + background: rgb(204 204 204 / 28%); +} + +.toggle-details__summary-text { + margin-left: 0.2em; +} + +details.toggle-details[open] summary { + margin-bottom: .5em; +} + +details.toggle-details[open] summary .tb-icon { + transform: rotate(90deg); +} + +details.toggle-details[open] summary ~ * { + animation: toggle-fade-in .3s ease-out; +} + +@keyframes toggle-fade-in { + from {opacity: 0%;} + to {opacity: 100%;} +} + +/* Print rules - we hide all toggle button elements at print */ +@media print { + /* Always hide the summary so the button doesn't show up */ + details.toggle-details summary { + display: none; + } +} \ No newline at end of file diff --git a/singlehtml/_static/togglebutton.js b/singlehtml/_static/togglebutton.js new file mode 100644 index 0000000..215a7ee --- /dev/null +++ b/singlehtml/_static/togglebutton.js @@ -0,0 +1,187 @@ +/** + * Add Toggle Buttons to elements + */ + +let toggleChevron = ` + + + +`; + +var initToggleItems = () => { + var itemsToToggle = document.querySelectorAll(togglebuttonSelector); + console.log(`[togglebutton]: Adding toggle buttons to ${itemsToToggle.length} items`) + // Add the button to each admonition and hook up a callback to toggle visibility + itemsToToggle.forEach((item, index) => { + if (item.classList.contains("admonition")) { + // If it's an admonition block, then we'll add a button inside + // Generate unique IDs for this item + var toggleID = `toggle-${index}`; + var buttonID = `button-${toggleID}`; + + item.setAttribute('id', toggleID); + if (!item.classList.contains("toggle")){ + item.classList.add("toggle"); + } + // This is the button that will be added to each item to trigger the toggle + var collapseButton = ` + `; + + title = item.querySelector(".admonition-title") + title.insertAdjacentHTML("beforeend", collapseButton); + thisButton = document.getElementById(buttonID); + + // Add click handlers for the button + admonition title (if admonition) + admonitionTitle = document.querySelector(`#${toggleID} > .admonition-title`) + if (admonitionTitle) { + // If an admonition, then make the whole title block clickable + admonitionTitle.addEventListener('click', toggleClickHandler); + admonitionTitle.dataset.target = toggleID + admonitionTitle.dataset.button = buttonID + } else { + // If not an admonition then we'll listen for the button click + thisButton.addEventListener('click', toggleClickHandler); + } + + // Now hide the item for this toggle button unless explicitly noted to show + if (!item.classList.contains("toggle-shown")) { + toggleHidden(thisButton); + } + } else { + // If not an admonition, wrap the block in a
block + // Define the structure of the details block and insert it as a sibling + var detailsBlock = ` +
+ + ${toggleChevron} + ${toggleHintShow} + +
`; + item.insertAdjacentHTML("beforebegin", detailsBlock); + + // Now move the toggle-able content inside of the details block + details = item.previousElementSibling + details.appendChild(item) + item.classList.add("toggle-details__container") + + // Set up a click trigger to change the text as needed + details.addEventListener('click', (click) => { + let parent = click.target.parentElement; + if (parent.tagName.toLowerCase() == "details") { + summary = parent.querySelector("summary"); + details = parent; + } else { + summary = parent; + details = parent.parentElement; + } + // Update the inner text for the proper hint + if (details.open) { + summary.querySelector("span.toggle-details__summary-text").innerText = toggleHintShow; + } else { + summary.querySelector("span.toggle-details__summary-text").innerText = toggleHintHide; + } + + }); + + // If we have a toggle-shown class, open details block should be open + if (item.classList.contains("toggle-shown")) { + details.click(); + } + } + }) +}; + +// This should simply add / remove the collapsed class and change the button text +var toggleHidden = (button) => { + target = button.dataset['target'] + var itemToToggle = document.getElementById(target); + if (itemToToggle.classList.contains("toggle-hidden")) { + itemToToggle.classList.remove("toggle-hidden"); + button.classList.remove("toggle-button-hidden"); + } else { + itemToToggle.classList.add("toggle-hidden"); + button.classList.add("toggle-button-hidden"); + } +} + +var toggleClickHandler = (click) => { + // Be cause the admonition title is clickable and extends to the whole admonition + // We only look for a click event on this title to trigger the toggle. + + if (click.target.classList.contains("admonition-title")) { + button = click.target.querySelector(".toggle-button"); + } else if (click.target.classList.contains("tb-icon")) { + // We've clicked the icon and need to search up one parent for the button + button = click.target.parentElement; + } else if (click.target.tagName == "polyline") { + // We've clicked the SVG elements inside the button, need to up 2 layers + button = click.target.parentElement.parentElement; + } else if (click.target.classList.contains("toggle-button")) { + // We've clicked the button itself and so don't need to do anything + button = click.target; + } else { + console.log(`[togglebutton]: Couldn't find button for ${click.target}`) + } + target = document.getElementById(button.dataset['button']); + toggleHidden(target); +} + +// If we want to blanket-add toggle classes to certain cells +var addToggleToSelector = () => { + const selector = ""; + if (selector.length > 0) { + document.querySelectorAll(selector).forEach((item) => { + item.classList.add("toggle"); + }) + } +} + +// Helper function to run when the DOM is finished +const sphinxToggleRunWhenDOMLoaded = cb => { + if (document.readyState != 'loading') { + cb() + } else if (document.addEventListener) { + document.addEventListener('DOMContentLoaded', cb) + } else { + document.attachEvent('onreadystatechange', function() { + if (document.readyState == 'complete') cb() + }) + } +} +sphinxToggleRunWhenDOMLoaded(addToggleToSelector) +sphinxToggleRunWhenDOMLoaded(initToggleItems) + +/** Toggle details blocks to be open when printing */ +if (toggleOpenOnPrint == "true") { + window.addEventListener("beforeprint", () => { + // Open the details + document.querySelectorAll("details.toggle-details").forEach((el) => { + el.dataset["togglestatus"] = el.open; + el.open = true; + }); + + // Open the admonitions + document.querySelectorAll(".admonition.toggle.toggle-hidden").forEach((el) => { + console.log(el); + el.querySelector("button.toggle-button").click(); + el.dataset["toggle_after_print"] = "true"; + }); + }); + window.addEventListener("afterprint", () => { + // Re-close the details that were closed + document.querySelectorAll("details.toggle-details").forEach((el) => { + el.open = el.dataset["togglestatus"] == "true"; + delete el.dataset["togglestatus"]; + }); + + // Re-close the admonition toggle buttons + document.querySelectorAll(".admonition.toggle").forEach((el) => { + if (el.dataset["toggle_after_print"] == "true") { + el.querySelector("button.toggle-button").click(); + delete el.dataset["toggle_after_print"]; + } + }); + }); +} diff --git a/singlehtml/index.html b/singlehtml/index.html new file mode 100644 index 0000000..99e5221 --- /dev/null +++ b/singlehtml/index.html @@ -0,0 +1,1399 @@ + + + + + + + Reproducible research software development using Python documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+
    +
  • + +
  • + Edit on GitHub +
  • +
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+
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+ +
+

Reproducible research software development using Python

+
+

Big-picture goal

+

This is a hands-on course on research software engineering. In this +workshop we assume that most workshop participants use Python in their work or +a leading a group which uses Python. Therefore, some of the examples will use +Python as the example language.

+

We will work with an example project and go through all the steps of a typical +software project. Once we have seen the building blocks, we will try to apply +them to own projects. Workshop participants will receive and also learn to give +constructive code feedback.

+
+
+

Prerequisites

+
+

Preparation

+
    +
  1. Get a GitHub account following these instructions.

  2. +
  3. You will need a text editor. If you don’t have a favorite one, we recommend +VS Code.

  4. +
  5. If you prefer to work in the terminal and not in VS Code, set up these two (skip this if you use VS Code):

    + +
  6. +
  7. One of these two software environments (if you are not sure which one to +choose or have no preference, choose Conda):

    + +
  8. +
  9. Optional and only on Linux: Apptainer following +these instructions.

  10. +
+
+
+
+

Schedule

+
+

Note

+

The schedule will very soon contain links to lesson material and exercises.

+
+
+

Day 1

+
    +
  • 13:00-13:30 - Welcome and introduction

    + +
  • +
  • 13:30-14:45 (1.25h) - Introduction to version control with Git and GitHub (1/2)

    +
      +
    • Creating a repository and porting your project to Git and GitHub

    • +
    • Basic commands

    • +
    +
  • +
  • 15:00-16:30 (1.5h) - Introduction to version control with Git and GitHub (2/2)

    +
      +
    • Branching and merging

    • +
    • Recovering from typical mistakes

    • +
    +
  • +
  • 16:45-18:00 - Code documentation

    +
      +
    • In-code documentation including docstrings

    • +
    • Writing good README files

    • +
    • Markdown

    • +
    • Sphinx

    • +
    • Building documentation with GitHub Actions

    • +
    • Jupyter Notebooks

    • +
    +
  • +
+
+
+

Day 2

+ +
+
+

Day 3

+
    +
  • 09:00-10:30 - Automated testing

    +
      +
    • Unit tests

    • +
    • End-to-end tests

    • +
    • pytest

    • +
    • GitHub Actions

    • +
    +
  • +
  • 10:45-12:15 - How to make the project more reusable

    +
      +
    • Tracking dependencies with requirements.txt and environment.yml

    • +
    • Recording environments in containers

    • +
    +
  • +
  • 13:00-14:45 - Code quality and good practices

    +
      +
    • Naming (and other) conventions, project organization, modularity

    • +
    • Refactoring (explained through examples)

    • +
    • Design patterns: functional design vs. object-oriented design

    • +
    • How to design your code before writing it

    • +
    • Structuring larger software projects in a modular way

    • +
    • Command-line interfaces

    • +
    • Workflows with Snakemake

    • +
    +
  • +
  • 15:00-16:30 - How to release and publish your code

    +
      +
    • Licenses

    • +
    • Publishing the code via Zenodo

    • +
    • Packaging the code

    • +
    • Sharing the code via PyPI

    • +
    +
  • +
  • 16:45-18:00 - Debriefing and Q&A

    +
      +
    • Participants work on their projects

    • +
    • Together we study actual codes that participants wrote or work on

    • +
    • Constructively we discuss possible improvements

    • +
    • Give individual feedback on code projects

    • +
    +
  • +
+
+
+

If we have time left

+ +
+
+

Conda environment

+

A Conda environment is an isolated software environment that is used to manage dependencies for a project +and you decide where it is located.

+

You will need a environment.yml file that documents the dependencies:

+
name: coderefinery
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - python >= 3.10
+  - black
+  - click
+  - flit
+  - ipywidgets
+  - isort
+  - jupyterlab
+  - jupyterlab_code_formatter
+  - jupyterlab-git
+  - matplotlib
+  - myst-parser
+  - nbdime
+  - numpy
+  - pandas
+  - pytest
+  - pytest-cov
+  - scalene
+  - seaborn
+  - snakemake-minimal
+  - sphinx
+  - sphinx-autoapi
+  - sphinx-autobuild
+  - sphinx_rtd_theme >= 2.0
+  - vulture
+  - scikit-image
+
+
+
+
Before you create a virtual environment
+
    +
  1. Create a new directory for this course.

  2. +
  3. In this directory, create an environment.yml file and copy-paste the dependencies above into it.

  4. +
+
+
+
Choose the tool to manage the environment
+

If you are already using one of these tools, please continue using the tool that you like and know. +If you are new to this, we recommend using Miniconda or Miniforge.

+
    +
  • Anaconda

    +
      +
    • Advantages: easy to install, easy to use, good for beginners

    • +
    • Disadvantages: large download, installs more than we will need, license restrictions

    • +
    +
  • +
  • Miniconda

    +
      +
    • Advantages: small size, installs only what you need

    • +
    • Disadvantages: no graphical interface, license restrictions

    • +
    +
  • +
  • Miniforge

    +
      +
    • Advantages: small size, no license restrictions

    • +
    • Disadvantages: no graphical interface

    • +
    +
  • +
  • Micromamba

    +
      +
    • Advantages: fast, small size

    • +
    • Disadvantages: no graphical interface

    • +
    +
  • +
  • Pixi

    +
      +
    • Advantages: fast and new

    • +
    • Disadvantages: new and less tested and not documented here

    • +
    +
  • +
+
+
+
Creating the virtual environment
+
    +
  1. Open your terminal shell (e.g. Bash or Zsh).

  2. +
  3. Activate conda using conda activate or source ~/miniconda3/bin/activate.

  4. +
  5. Run the following command:

    +
    $ conda env create --file environment.yml
    +
    +
    +
  6. +
  7. Make sure that you see “coderefinery” in the output when you ask for a list of all available environments:

    +
    $ conda env list
    +
    +
    +
  8. +
+
+
+
How to verify that this worked
+

(this will be added)

+
+
+
+

Virtual environment

+

A virtual environment is an isolated software environment that is used to manage dependencies for a project +and you decide where it is located.

+

You will need a requirements.txt file that documents the dependencies:

+
black
+click
+flit
+ipywidgets
+isort
+jupyterlab
+jupyterlab-code-formatter
+jupyterlab-git
+matplotlib
+myst-parser
+nbdime
+numpy
+pandas
+pytest
+pytest-cov
+scalene
+seaborn
+sphinx
+sphinx-autoapi
+sphinx-autobuild
+sphinx_rtd_theme >= 2.0
+vulture
+scikit-image
+
+
+
+
Before you create a virtual environment
+
    +
  1. Create a new directory for this course.

  2. +
  3. In this directory, create a requirements.txt file and copy-paste the dependencies above into it.

  4. +
+
+
+
Creating the virtual environment
+

Now create a virtual environment in this directory either using pip and +venv +(more traditional and safer) or using uv (more modern but also less tested):

+
+

Create a new virtual environment and activate it:

+
$ python3 -m venv coderefinery-environment
+$ source coderefinery-environment/bin/activate
+
+
+

Install the dependencies into the environment:

+
$ python3 -m pip install -r requirements.txt
+
+
+
+
+
+
How to verify that this worked
+

(this will be added)

+
+
+
+
+
+

Example project: Simulating the motion of planets

+

The example code that we will study +is a hopefully simple N-body simulation written in Python. It is not important +or expected that we understand the code in any detail.

+

The big picture is that the code simulates the motion of a number of +planets:

+
    +
  • We can choose the number of planets.

  • +
  • Each planet starts with a random position, velocity, and mass.

  • +
  • At each time step, the code calculates the gravitational force between each +pair of planets.

  • +
  • The forces accelerate each planet, the acceleration modifies the velocity, +the velocity modifies the position of each planet.

  • +
  • We can choose the number of time steps.

  • +
  • The units were chosen to make numbers easy to read.

  • +
+
+
Example run
+
+

Instructor note

+

The instructor demonstrates running the code on their computer.

+
+

The code is written to accept command-line arguments to specify the number +of planets and the number of time steps.

+

We first generate starting data:

+
$ python generate-data.py --num-planets 10 --output-file initial.csv
+
+
+

The generated file (initial.csv) could look like this:

+
px,py,pz,vx,vy,vz,mass
+-46.88,-42.51,88.33,-0.86,-0.18,0.55,6.70
+-5.29,17.09,-96.13,0.66,0.45,-0.17,3.51
+83.53,-92.83,-68.77,-0.26,-0.48,0.24,6.84
+-36.31,25.48,64.16,0.85,0.75,-0.56,1.53
+-68.38,-17.21,-97.07,0.60,0.26,0.69,6.63
+-48.37,-48.74,3.92,-0.92,-0.33,-0.93,8.60
+40.53,-75.50,44.18,-0.62,-0.31,-0.53,8.04
+-27.21,10.78,-78.82,-0.09,-0.55,-0.03,5.35
+88.42,-74.95,-45.85,0.81,0.68,0.56,5.36
+39.09,53.12,-59.54,-0.54,0.56,0.07,8.98
+
+
+

Then we can simulate their motion (in this case for 20 steps):

+
$ python simulate.py --num-steps 20 \
+                     --input-file initial.csv \
+                     --output-file final.csv
+
+
+

The --output-file (final.csv) is again a CSV file (comma-separated values) +and contains the final positions of all planets.

+

It is possible to run on multiple cores and to animate the result. +Here is an example with 100 planets:

+
$ python generate-data.py --num-planets 100 --output-file initial.csv
+
+$ python simulate.py --num-steps 50 \
+                     --input-file initial.csv \
+                     --output-file final.csv \
+                     --trajectories-file trajectories.npz \
+                     --num-cores 8
+
+$ python animate.py --initial-file initial.csv \
+                    --trajectories-file trajectories.npz \
+                    --output-file animation.mp4
+
+
+
+

Learning goals

+
    +
  • What are the most important steps to make this code reusable by others +and our future selves?

  • +
  • Be able to apply these techniques to your own code/script.

  • +
+
+
+

We will not focus on …

+
    +
  • … how the code works internally in detail.

  • +
  • … whether this is the most efficient algorithm.

  • +
  • … whether the code is numerically stable.

  • +
  • … how to code scales with the number of cores.

  • +
  • … whether it is portable to other operating systems (we will discuss this later).

  • +
+
+
+
+
+

Code documentation

+
    +
  • 15 min: What makes good documentation? Also https://diataxis.fr/

  • +
  • 15 min: Writing good README files

  • +
  • 30 min: Exercise: Set up a Sphinx documentation and add API documentation

  • +
  • 15 min: Building documentation with GitHub Actions

  • +
+

requirements.txt:

+
sphinx
+sphinx_rtd_theme >= 2.0
+sphinx_autobuild
+sphinx_autoapi
+myst_parser
+
+
+

conf.py:

+
extensions = [
+    "myst_parser",
+    "autoapi.extension",
+]
+
+autoapi_dirs = ['..']
+
+
+
+
+

Collaborative version control and code review

+
+
+
Concepts around collaboration
+
+

Objectives

+
    +
  • Be able to decide whether to divide work at the branch level or at the repository level.

  • +
+
+
+
Commits, branches, repositories, forks, clones
+
    +
  • repository: The project, contains all data and history (commits, branches, tags).

  • +
  • commit: Snapshot of the project, gets a unique identifier (e.g. c7f0e8bfc718be04525847fc7ac237f470add76e).

  • +
  • branch: Independent development line. The main development line is often called main.

  • +
  • tag: A pointer to one commit, to be able to refer to it later. Like a commemorative plaque +that you attach to a particular commit (e.g. phd-printed or paper-submitted).

  • +
  • cloning: Copying the whole repository to your laptop - the first time. It is not necessary to download each file one by one.

  • +
  • forking: Taking a copy of a repository (which is typically not yours) - your +copy (fork) stays on GitHub/GitLab and you can make changes to your copy.

  • +
+
+
+
Cloning a repository
+

In order to make a complete copy a whole repository, the git clone command +can be used. When cloning, all the files, of all or selected branches, of a +repository are copied in one operation. Cloning of a repository is of relevance +in a few different situations:

+
    +
  • Working on your own, cloning is the operation that you can use to create +multiple instances of a repository on, for instance, a personal computer, a +server, and a supercomputer.

  • +
  • The parent repository could be a repository that you or your colleague own. A +common use case for cloning is when working together within a smaller team +where everyone has read and write access to the same git repository.

  • +
  • Alternatively, cloning can be made from a public repository of a code that +you would like to use. Perhaps you have no intention to work on the code, but +would like to stay in tune with the latest developments, also in-between +releases of new versions of the code.

  • +
+
+Forking and cloning +
+

Forking and cloning

+
+
+
+
+
Forking a repository
+

When a fork is made on GitHub/GitLab a complete copy, of all or selected +branches, of the repository is made. The copy will reside under a different +account on GitHub/GitLab. Forking of a repository is of high relevance when +working with a git repository to which you do not have write access.

+
    +
  • In the fork repository commits can be made to the base branch (main or +master), and to other branches.

  • +
  • The commits that are made within the branches of the fork repository can be +contributed back to the parent repository by means of pull or merge requests.

  • +
+
+
+
Synchronizing changes between repositories
+
    +
  • We need a mechanism to communicate changes between the repositories.

  • +
  • We will pull or fetch updates from remote repositories (we will soon discuss the difference between pull and fetch).

  • +
  • We will push updates to remote repositories.

  • +
  • We will learn how to suggest changes within repositories on GitHub and across repositories (pull request).

  • +
  • Repositories that are forked or cloned do not automatically synchronize themselves: +We will learn how to update forks (by pulling from the “central” repository).

  • +
  • A main difference between cloning a repository and forking a repository is that the former is a general operation for generating copies of a repository to different computers, whereas forking is a particular operation implemented on GitHub/GitLab.

  • +
+
+
+
+
Collaborating within the same repository
+

In this episode, we will learn how to collaborate within the same repository. +We will learn how to cross-reference issues and pull requests, how to review +pull requests, and how to use draft pull requests.

+

This exercise will form a good basis for collaboration that is suitable for +most research groups.

+
+

Note

+

When you read or hear pull request, please think of a change proposal.

+
+
+
Exercise
+

In this exercise, we will contribute to a repository via a pull request. +This means that you propose some change, and then it is accepted (or not).

+
+

Exercise preparation

+
    +
  • First we need to get access to the exercise repository to which we will +contribute.

    +
      +
    • Instructor collects GitHub usernames from learners and adds them as collaborators to the exercise repository +(Settings -> Collaborators and teams -> Manage access -> Add people).

    • +
    +
  • +
  • Don’t forget to accept the invitation

    +
      +
    • Check https://github.com/settings/organizations/

    • +
    • Alternatively check the inbox for the email account you registered with +GitHub. GitHub emails you an invitation link, but if you don’t receive it +you can go to your GitHub notifications in the top right corner. The +maintainer can also “copy invite link” and share it within the group.

    • +
    +
  • +
  • Watching and unwatching repositories

    +
      +
    • Now that you are a collaborator, you get notified about new issues and pull +requests via email.

    • +
    • If you do not wish this, you can “unwatch” a repository (top of +the project page).

    • +
    • However, we recommend watching repositories you are interested +in. You can learn things from experts just by watching the +activity that come through a popular project.

    • +
    +
    +Unwatching a repository +
    +

    Unwatch a repository by clicking “Unwatch” in the repository view, +then “Participating and @mentions” - this way, you will get +notifications about your own interactions.

    +
    +
    +
  • +
+
+
+

Exercise: Collaborating within the same repository (25 min)

+

Technical requirements (from installation instructions):

+ +

What is familiar from the previous workshop day (not repeated here):

+
    +
  • Cloning a repository.

  • +
  • Creating a branch.

  • +
  • Committing a change on the new branch.

  • +
  • Submit a pull request towards the main branch.

  • +
+

What will be new in this exercise:

+
    +
  • If you create the changes locally, you will need to push them to the remote repository.

  • +
  • Learning what a protected branch is and how to modify a protected branch: using a pull request.

  • +
  • Cross-referencing issues and pull requests.

  • +
  • Practice to review a pull request.

  • +
  • Learn about the value of draft pull requests.

  • +
+

Exercise tasks:

+
    +
  1. Start in the exercise +repository and open an +issue where you describe the change you want to make. Note down the issue +number since you will need it later.

  2. +
  3. Create a new branch.

  4. +
  5. Make a change to the recipe book on the new branch and in the commit +cross-reference the issue you opened (see the walk-through below +for how to do that).

  6. +
  7. Push your new branch (with the new commit) to the repository you +are working on.

  8. +
  9. Open a pull request towards the main branch.

  10. +
  11. Review somebody else’s pull request and give constructive feedback. Merge their pull request.

  12. +
  13. Try to create a new branch with some half-finished work and open a draft +pull request. Verify that the draft pull request cannot be merged since it +is not meant to be merged yet.

  14. +
+
+
+
+
Solution and hints
+
+
(1) Opening an issue
+

This is done through the GitHub web interface. For example, you could +give the name of the recipe you want to add (so that others don’t add +the same one). It is the “Issues” tab.

+
+
+
(2) Create a new branch.
+

If on GitHub, you can make the branch in the web interface.

+
+
+
(3) Make a change adding the recipe
+

Add a new file with the recipe in it. Commit the file. In the commit +message, include the note about the issue number, saying that this +will close that issue.

+
+
Cross-referencing issues and pull requests
+

Each issue and each pull request gets a number and you can cross-reference them.

+

When you open an issue, note down the issue number (in this case it is #2):

+
+Each issue gets a number +
+

You can reference this issue number in a commit message or in a pull request, like in this +commit message:

+
this is the new recipe; fixes #2
+
+
+

If you forget to do that in your commit message, you can also reference the issue +in the pull request description. And instead of fixes you can also use closes or resolves +or fix or close or resolve (case insensitive).

+

Here are all the keywords that GitHub recognizes: +https://help.github.com/en/articles/closing-issues-using-keywords

+

Then observe what happens in the issue once your commit gets merged: it will +automatically close the issue and create a link between the issue and the +commit. This is very useful for tracking what changes were made in response to +which issue and to know from when until when precisely the issue was open.

+
+
+
+
(4) Push to GitHub as a new branch
+

Push the branch to the repository. You should end up with a branch +visible in the GitHub web view.

+

This is only necessary if you created the changes locally. If you created the +changes directly on GitHub, you can skip this step.

+
+

In VS Code, you can “publish the branch” to the remote repository by clicking +the cloud icon in the bottom left corner of the window:

+
+Publishing a branch in VS Code +
+
+
+
+
(5) Open a pull request towards the main branch
+

This is done through the GitHub web interface.

+
+
+
(6) Reviewing pull requests
+

You review through the GitHub web interface.

+

Checklist for reviewing a pull request:

+
    +
  • Be kind, on the other side is a human who has put effort into this.

  • +
  • Be constructive: if you see a problem, suggest a solution.

  • +
  • Towards which branch is this directed?

  • +
  • Is the title descriptive?

  • +
  • Is the description informative?

  • +
  • Scroll down to see commits.

  • +
  • Scroll down to see the changes.

  • +
  • If you get incredibly many changes, also consider the license or copyright +and ask where all that code is coming from.

  • +
  • Again, be kind and constructive.

  • +
  • Later we will learn how to suggest changes directly in the pull request.

  • +
+

If someone is new, it’s often nice to say something encouraging in the +comments before merging (even if it’s just “thanks”). If all is good +and there’s not much else to say, you could merge directly.

+
+
+
(7) Draft pull requests
+

Try to create a draft pull request:

+
+Creating a draft pull request +
+

Verify that the draft pull request cannot be merged until it is marked as ready +for review:

+
+Draft pull request cannot be merged +
+

Draft pull requests can be useful for:

+
    +
  • Feedback: You can open a pull request early to get feedback on your work without +signaling that it is ready to merge.

  • +
  • Information: They can help communicating to others that a change is coming up and in +progress.

  • +
+
+
+
What is a protected branch? And how to modify it?
+

A protected branch on GitHub or GitLab is a branch that cannot (accidentally) +deleted or force-pushed to. It is also possible to require that a branch cannot +be directly pushed to or modified, but that changes must be submitted via a +pull request.

+

To protect a branch in your own repository, go to “Settings” -> “Branches”.

+
+
+
Summary
+
    +
  • We used all the same pieces that we’ve learned previously.

  • +
  • But we successfully contributed to a collaborative project!

  • +
  • The pull request allowed us to contribute without changing directly: +this is very good when it’s not mainly our project.

  • +
+
+
+
+
+
Practicing code review
+

In this episode we will practice the code review process. We will learn how to +ask for changes in a pull request, how to suggest a change in a pull request, +and how to modify a pull request.

+

This will enable research groups to work more collaboratively and to not only +improve the code quality but also to learn from each other.

+
+
Exercise
+
+

Exercise preparation

+

We can continue in the same exercise repository which we have used in the +previous episode.

+
+
+

Exercise: Practicing code review (25 min)

+

Technical requirements:

+ +

What is familiar from previous lessons:

+
    +
  • Creating a branch.

  • +
  • Committing a change on the new branch.

  • +
  • Opening and merging pull requests.

  • +
+

What will be new in this exercise:

+
    +
  • As a reviewer, we will learn how to ask for changes in a pull request.

  • +
  • As a reviewer, we will learn how to suggest a change in a pull request.

  • +
  • As a submitter, we will learn how to modify a pull request without closing +the incomplete one and opening a new one.

  • +
+

Exercise tasks:

+
    +
  1. Create a new branch and one or few commits: in these improve something but also +deliberately introduce a typo and also a larger mistake which we will want to fix during the code review.

  2. +
  3. Open a pull request towards the main branch.

  4. +
  5. As a reviewer to somebody else’s pull request, ask for an improvement and +also directly suggest a change for the small typo. (Hint: +suggestions are possible through the GitHub web interface, view of +a pull request, “Files changed” view, after selecting some lines. +Look for the “±” button.)

  6. +
  7. As the submitter, learn how to accept the suggested change. (Hint: +GitHub web interface, “Files Changed” view.)

  8. +
  9. As the submitter, improve the pull request without having to close and open +a new one: by adding a new commit to the same branch. (Hint: push +to the branch again.)

  10. +
  11. Once the changes are addressed, merge the pull request.

  12. +
+
+
+
+
Help and discussion
+

From here on out, we don’t give detailed steps to the solution. You +need to combine what you know, and the extra info below, in order to +solve the above.

+
+
How to ask for changes in a pull request
+

Technically, there are at least two common ways to ask for changes in a pull +request.

+

Either in the comment field of the pull request:

+
+Screenshot of a pull request comment field +
+

Or by using the “Review changes”:

+
+Screenshot of a pull request navigating to the "Review changes" tab +
+

And always please be kind and constructive in your comments. Remember that the +goal is not gate-keeping but collaborative learning.

+
+
+
How to suggest a change in a pull request as a reviewer
+

If you see a very small problem that is easy to fix, you can suggest a change +as a reviewer.

+

Instead of asking the submitter to tiny problem, you can suggest a change by +clicking on the plus sign next to the line number in the “Files changed” tab:

+
+Screenshot of leaving a comment to a line in a pull request +
+

Here you can comment on specific lines or even line ranges.

+

But now the interesting part is to click on the “Add a suggestion” symbol (the +one that looks like plus and minus). Now you can fix the tiny problem (in this +case a typo) and then click on the “Add single comment” button:

+
+Sequence of clicks to add a suggestion to a line in a pull request +
+

The result is this and the submitter can accept the change with a single click:

+
+Screenshot of a pull request with a suggested change +
+

After accepting with “Commit suggestion”, the improvement gets added to the +pull request.

+
+
+
How to modify a pull request to address the review comments
+

If the reviewer asks for changes, it is not necessary to close the pull request +and later open a new one. It can even be counter-productive to do so: This can +fragment the discussion and the history of the pull request and can make it +harder to understand the context of the changes.

+

A much better mechanism to recognize that pull requests are not implemented +from a specific commit to a specific branch, but always from a branch to a +branch.

+

This means that you can make amendments to the pull request by adding new +commits to the same source branch. This way the pull request will be updated +automatically and the reviewer can see the new changes and comment on them.

+

The fact that pull requests are from branch to branch also strongly suggests +that it is a good practice to create a new branch for each pull request. +Otherwise you could accidentally modify an open pull request by adding new +commits to the source branch.

+
+
+
+
Summary
+
    +
  • Our process isn’t just about code now. It’s about discussion and +working together to make the whole process better.

  • +
  • GitHub discussions and reviewing are quite powerful and can make +small changes easy.

  • +
+
+
+
+
How to contribute changes to repositories that belong to others
+

In this episode we prepare you to suggest and contribute changes to +repositories that belong to others. These might be open source projects that +you use in your work.

+

We will see how Git and services like GitHub or GitLab can be used to suggest +modification without having to ask for write access to the repository and +accept modifications without having to grant write access to others.

+
+
Exercise
+
+

Exercise preparation

+
    +
  • The exercise repository is now different: +https://github.com/workshop-material/recipe-book-forking-exercise (note the -forking-exercise).

  • +
  • First fork the exercise repository to your GitHub account.

  • +
  • Then clone your fork to your computer (if you wish to work locally).

  • +
  • Double-check that you have forked the correct repository.

  • +
+
+
+

Exercise: Collaborating within the same repository (25 min)

+

Technical requirements:

+ +

What is familiar from previous lessons:

+
    +
  • Forking a repository.

  • +
  • Creating a branch.

  • +
  • Committing a change on the new branch.

  • +
  • Opening and merging pull requests.

  • +
+

What will be new in this exercise:

+
    +
  • Opening a pull request towards the upstream repository.

  • +
  • Pull requests can be coupled with automated testing.

  • +
  • Learning that your fork can get out of date.

  • +
  • After the pull requests are merged, updating your fork with the changes.

  • +
  • Learn how to approach other people’s repositories with ideas, changes, and requests.

  • +
+

Exercise tasks:

+
    +
  1. Open an issue in the upstream exercise repository where you describe the +change you want to make. Take note of the issue number.

  2. +
  3. Create a new branch in your fork of the repository.

  4. +
  5. Make a change to the recipe book on the new branch and in the commit cross-reference the issue you opened. +See the walk-through below for how to do this.

  6. +
  7. Open a pull request towards the upstream repository.

  8. +
  9. The instructor will review and merge the pull requests. +During the review, pay attention to the automated test step (here for +demonstration purposes, we test whether the recipe contains an ingredients +and an instructions sections).

  10. +
  11. After few pull requests are merged, update your fork with the changes.

  12. +
  13. Check that in your fork you can see changes from other people’s pull requests.

  14. +
+
+
+
+
Help and discussion
+
+
Help! I don’t have permissions to push my local changes
+

Maybe you see an error like this one:

+
Please make sure you have the correct access rights
+and the repository exists.
+
+
+

Or like this one:

+
failed to push some refs to workshop-material/recipe-book-forking-exercise.git
+
+
+

In this case you probably try to push the changes not to your fork but to the original repository +and in this exercise you do not have write access to the original repository.

+

The simpler solution is to clone again but this time your fork.

+ +
+
+
Opening a pull request towards the upstream repository
+

We have learned in the previous episode that pull requests are always from +branch to branch. But the branch can be in a different repository.

+

When you open a pull request in a fork, by default GitHub will suggest to +direct it towards the default branch of the upstream repository.

+

This can be changed and it should always be verified, but in this case this is +exactly what we want to do, from fork towards upstream:

+
+Screenshot of a pull request from fork towards upstream +
+
+
+
Pull requests can be coupled with automated testing
+

We added an automated test here just for fun and so that you see that this is +possible to do.

+

In this exercise, the test is silly. It will check whether the recipe contains +both an ingredients and an instructions section.

+

In this example the test failed:

+
+Screenshot of a failed test in a pull request +
+

Click on the “Details” link to see the details of the failed test:

+
+Screenshot of details why the test failed +
+

How can this be useful?

+
    +
  • The project can define what kind of tests are expected to pass before a pull +request can be merged.

  • +
  • The reviewer can see the results of the tests, without having to run them +locally.

  • +
+

How does it work?

+
    +
  • We added a GitHub Actions workflow +to automatically run on each push or pull request towards the main branch.

  • +
+

What tests or steps can you image for your project to run automatically with +each pull request?

+
+
+
How to update your fork with changes from upstream
+

This used to be difficult but now it is two mouse clicks.

+

Navigate to your fork and notice how GitHub tells you that your fork is behind. +In my case, it is 9 commits behind upstream. To fix this, click on “Sync fork” +and then “Update branch”:

+
+Screenshot on GitHub fork page showing that the fork is behind +
+

After the update my “branch is up to date” with the upstream repository:

+
+Screenshot on GitHub after fork has been updated +
+
+
+
How to approach other people’s repositories with ideas, changes, and requests
+

Contributing very minor changes

+
    +
  • Clone or fork+clone repository

  • +
  • Create a branch

  • +
  • Commit and push change

  • +
  • Open a pull request or merge request

  • +
+

If you observe an issue and have an idea how to fix it

+
    +
  • Open an issue in the repository you wish to contribute to

  • +
  • Describe the problem

  • +
  • If you have a suggestion on how to fix it, describe your suggestion

  • +
  • Possibly discuss and get feedback

  • +
  • If you are working on the fix, indicate it in the issue so that others know that somebody is working on it and who is working on it

  • +
  • Submit your fix as pull request or merge request which references/closes the issue

  • +
+
+

Motivation

+
    +
  • Inform others about an observed problem

  • +
  • Make it clear whether this issue is up for grabs or already being worked on

  • +
+
+

If you have an idea for a new feature

+
    +
  • Open an issue in the repository you wish to contribute to

  • +
  • In the issue, write a short proposal for your suggested change or new feature

  • +
  • Motivate why and how you wish to do this

  • +
  • Also indicate where you are unsure and where you would like feedback

  • +
  • Discuss and get feedback before you code

  • +
  • Once you start coding, indicate that you are working on it

  • +
  • Once you are done, submit your new feature as pull request or merge request which references/closes the issue/proposal

  • +
+
+

Motivation

+
    +
  • Get agreement and feedback before writing 5000 lines of code which might be rejected

  • +
  • If we later wonder why something was done, we have the issue/proposal as +reference and can read up on the reasoning behind a code change

  • +
+
+
+
+
+
Summary
+
    +
  • This forking workflow lets you propose changes to repositories for +which you have no write access.

  • +
  • This is the way that much modern open-source software works.

  • +
  • You can now contribute to any project you can view.

  • +
+
+
+
+
Conclict resolution, rebasing, and organizational strategies
+

(40 min demo and discussion)

+
+
+
+
+

Automated testing

+
    +
  • 15 min: Motivation

  • +
  • 15 min: End-to-end tests

  • +
  • 15 min: Pytest

  • +
  • 15 min: Moving to GitHub Actions

  • +
  • 20 min: Exercise

  • +
  • 10 min: Where to go from here

  • +
+
+
+

How to make the project more reusable

+

Part 1:

+
    +
  • 15 min: Motivation

  • +
  • 15 min: Best practices for managing dependencies in Python

  • +
  • 20 min: Exercise

  • +
+

Part 2:

+
    +
  • 10 min: Introduction to containers

  • +
  • 20 min: Demonstration

  • +
  • 10 min: Discussion

  • +
+
+
+

Code quality and good practices

+

In this episode we will explore code quality and good practices in Python using +a hands-on approach. We will together build up a small project and improve it +step by step.

+

We will start from a relatively simple image processing script which can read a +telescope image of stars and our goal is to count the number of stars in +the image. Later we will want to be able to process many such images.

+

The (fictional) telescope images look like the one below here (in this +repository we can find more):

+
+Generated image representing a telescope image of stars +
+

Generated image representing a telescope image of stars.

+
+
+ +

Part 1:

+
    +
  • 15 min: Discuss how we would solve the problem, run example code, and make it work +as part of a Jupyter notebook.

  • +
  • 15 min: Refactor the positioning code into a function and a module

  • +
  • 15 min: Now we wish to process many images - discuss how we would approach this

  • +
  • 15 min: Introduce CLI and discuss the benefits

  • +
+

Part 2:

+
    +
  • 30 min: From a script to a workflow (using Snakemake)

  • +
  • 15 min: Discuss concepts

    +
      +
    • Pure functions

    • +
    • Design patterns: functional design vs. object-oriented design

    • +
    • How to design your code before writing it: document-driven development

    • +
    +
  • +
+

Bonus:

+
    +
  • Move it under Git

  • +
  • Document dependencies

  • +
  • Show nbdime, black, vulture, ruff

  • +
+
+
+

How to release and publish your code

+

Part 1:

+
    +
  • 30 min: Overview over software licenses and code publishing

  • +
  • 15 min: We add a license, CFF file, and publish to Zenodo (sandbox)

  • +
+

Part 2:

+
    +
  • 30 min: Creating a Python package with the help of flit

  • +
  • 15 min: Deploy the package to test-PyPI using GitHub Actions

  • +
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Profiling memory and CPU usage

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Profilers:

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  • cProfile or profile

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  • line_profiler

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  • viztracer

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  • scalene

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  • Intel VTune

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  • PyInstrument

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  • py-spy

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  • Pyflame

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  • timeit

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Credit

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The following material (all CC-BY) was reused to create this workshop material:

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(I will also summarize what changes have been made to the original material)

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Automated testing

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  • 15 min: Motivation

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  • 15 min: End-to-end tests

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  • 15 min: Pytest

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  • 15 min: Moving to GitHub Actions

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  • 20 min: Exercise

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  • 10 min: Where to go from here

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