diff --git a/.github/CODEOWNERS b/.github/CODEOWNERS new file mode 100644 index 000000000..98cac96b2 --- /dev/null +++ b/.github/CODEOWNERS @@ -0,0 +1 @@ +* @DomInvivo diff --git a/.github/CODE_OF_CONDUCT.md b/.github/CODE_OF_CONDUCT.md new file mode 100644 index 000000000..18c914718 --- /dev/null +++ b/.github/CODE_OF_CONDUCT.md @@ -0,0 +1,128 @@ +# Contributor Covenant Code of Conduct + +## Our Pledge + +We as members, contributors, and leaders pledge to make participation in our +community a harassment-free experience for everyone, regardless of age, body +size, visible or invisible disability, ethnicity, sex characteristics, gender +identity and expression, level of experience, education, socio-economic status, +nationality, personal appearance, race, religion, or sexual identity +and orientation. + +We pledge to act and interact in ways that contribute to an open, welcoming, +diverse, inclusive, and healthy community. + +## Our Standards + +Examples of behavior that contributes to a positive environment for our +community include: + +* Demonstrating empathy and kindness toward other people +* Being respectful of differing opinions, viewpoints, and experiences +* Giving and gracefully accepting constructive feedback +* Accepting responsibility and apologizing to those affected by our mistakes, + and learning from the experience +* Focusing on what is best not just for us as individuals, but for the + overall community + +Examples of unacceptable behavior include: + +* The use of sexualized language or imagery, and sexual attention or + advances of any kind +* Trolling, insulting or derogatory comments, and personal or political attacks +* Public or private harassment +* Publishing others' private information, such as a physical or email + address, without their explicit permission +* Other conduct which could reasonably be considered inappropriate in a + professional setting + +## Enforcement Responsibilities + +Community leaders are responsible for clarifying and enforcing our standards of +acceptable behavior and will take appropriate and fair corrective action in +response to any behavior that they deem inappropriate, threatening, offensive, +or harmful. + +Community leaders have the right and responsibility to remove, edit, or reject +comments, commits, code, wiki edits, issues, and other contributions that are +not aligned to this Code of Conduct, and will communicate reasons for moderation +decisions when appropriate. + +## Scope + +This Code of Conduct applies within all community spaces, and also applies when +an individual is officially representing the community in public spaces. +Examples of representing our community include using an official e-mail address, +posting via an official social media account, or acting as an appointed +representative at an online or offline event. + +## Enforcement + +Instances of abusive, harassing, or otherwise unacceptable behavior may be +reported to the community leaders responsible for enforcement at +. +All complaints will be reviewed and investigated promptly and fairly. + +All community leaders are obligated to respect the privacy and security of the +reporter of any incident. + +## Enforcement Guidelines + +Community leaders will follow these Community Impact Guidelines in determining +the consequences for any action they deem in violation of this Code of Conduct: + +### 1. Correction + +**Community Impact**: Use of inappropriate language or other behavior deemed +unprofessional or unwelcome in the community. + +**Consequence**: A private, written warning from community leaders, providing +clarity around the nature of the violation and an explanation of why the +behavior was inappropriate. A public apology may be requested. + +### 2. Warning + +**Community Impact**: A violation through a single incident or series +of actions. + +**Consequence**: A warning with consequences for continued behavior. No +interaction with the people involved, including unsolicited interaction with +those enforcing the Code of Conduct, for a specified period of time. This +includes avoiding interactions in community spaces as well as external channels +like social media. Violating these terms may lead to a temporary or +permanent ban. + +### 3. Temporary Ban + +**Community Impact**: A serious violation of community standards, including +sustained inappropriate behavior. + +**Consequence**: A temporary ban from any sort of interaction or public +communication with the community for a specified period of time. No public or +private interaction with the people involved, including unsolicited interaction +with those enforcing the Code of Conduct, is allowed during this period. +Violating these terms may lead to a permanent ban. + +### 4. Permanent Ban + +**Community Impact**: Demonstrating a pattern of violation of community +standards, including sustained inappropriate behavior, harassment of an +individual, or aggression toward or disparagement of classes of individuals. + +**Consequence**: A permanent ban from any sort of public interaction within +the community. + +## Attribution + +This Code of Conduct is adapted from the [Contributor Covenant][homepage], +version 2.0, available at +https://www.contributor-covenant.org/version/2/0/code_of_conduct.html. + +Community Impact Guidelines were inspired by [Mozilla's code of conduct +enforcement ladder](https://github.com/mozilla/diversity). + +[homepage]: https://www.contributor-covenant.org + +For answers to common questions about this code of conduct, see the FAQ at +https://www.contributor-covenant.org/faq. Translations are available at +https://www.contributor-covenant.org/translations. diff --git a/.github/PULL_REQUEST_TEMPLATE.md b/.github/PULL_REQUEST_TEMPLATE.md index 56db38d4a..ee1bbedcf 100644 --- a/.github/PULL_REQUEST_TEMPLATE.md +++ b/.github/PULL_REQUEST_TEMPLATE.md @@ -1,5 +1,7 @@ Checklist: -- [ ] Added a `news` entry: _copy `news/TEMPLATE.rst` to `news/my-feature-or-branch.rst`) and edit it._ +- [ ] Was this PR discussed in a issue? It is recommended to first discuss a new feature into a GitHub issue before opening a PR. +- [ ] Add tests to cover the fixed bug(s) or the new introduced feature(s) (if appropriate). +- [ ] Update the API documentation is a new function is added or an existing one is deleted. --- diff --git a/.github/workflows/lint.yml b/.github/workflows/code-check.yml similarity index 57% rename from .github/workflows/lint.yml rename to .github/workflows/code-check.yml index ddaf40412..d5a28b611 100644 --- a/.github/workflows/lint.yml +++ b/.github/workflows/code-check.yml @@ -1,26 +1,26 @@ -name: Lint +name: code-check on: push: - branches: - - "master" + branches: ["main"] + tags: ["*"] pull_request: branches: - "*" + - "!gh-pages" jobs: - lint-source-code: - name: Lint - runs-on: "ubuntu-latest" - + python-format-black: + name: Python lint [black] + runs-on: ubuntu-latest steps: - name: Checkout the code uses: actions/checkout@v3 - name: Set up Python - uses: actions/setup-python@v2 + uses: actions/setup-python@v4 with: - python-version: 3.9 + python-version: "3.10" - name: Install black run: | diff --git a/.github/workflows/doc.yml b/.github/workflows/doc.yml index 27bb74f04..cc9017762 100644 --- a/.github/workflows/doc.yml +++ b/.github/workflows/doc.yml @@ -2,8 +2,9 @@ name: doc on: push: - branches: - - "master" + branches: ["main"] + release: + types: [published] jobs: doc: @@ -18,22 +19,34 @@ jobs: - name: Checkout the code uses: actions/checkout@v3 - - name: Setup Mamba - uses: mamba-org/provision-with-micromamba@v14 + - name: Setup mamba + uses: mamba-org/setup-micromamba@v1 with: environment-file: env.yml - environment-name: goli + environment-name: openfractal + cache-environment: true cache-downloads: true - cache-env: true - channel-priority: strict - name: Install library run: python -m pip install --no-deps . - name: Deploy the doc run: | - # Get the privpage branch + echo "Configure git" + git config --global user.name "${GITHUB_ACTOR}" + git config --global user.email "${GITHUB_ACTOR}@users.noreply.github.com" + + echo "Get the gh-pages branch" git fetch origin gh-pages - # Build and serve the doc - mkdocs gh-deploy --force + TAG_OR_BRANCH_NAME=${GITHUB_REF##*/} + + if [ $TAG_OR_BRANCH_NAME = "main" ]; then + echo "Build and deploy the doc on main" + mike deploy --push --force main + else + echo "Build and deploy the doc on $TAG_OR_BRANCH_NAME" + + mike deploy --push --force stable + mike deploy --push --force $TAG_OR_BRANCH_NAME + fi diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml new file mode 100644 index 000000000..cb8949f16 --- /dev/null +++ b/.github/workflows/release.yml @@ -0,0 +1,112 @@ +name: release + +on: + workflow_dispatch: + inputs: + release-version: + description: "A valid Semver version string" + required: true + +permissions: + contents: write + pull-requests: write + +jobs: + release: + # Do not release if not triggered from the default branch + if: github.ref == format('refs/heads/{0}', github.event.repository.default_branch) + + runs-on: ubuntu-latest + timeout-minutes: 30 + + defaults: + run: + shell: bash -l {0} + + steps: + - name: Checkout the code + uses: actions/checkout@v3 + + - name: Setup mamba + uses: mamba-org/setup-micromamba@v1 + with: + environment-file: env.yml + environment-name: graphium + cache-environment: true + cache-downloads: true + create-args: >- + pip + semver + python-build + setuptools_scm + + - name: Check the version is valid semver + run: | + RELEASE_VERSION="${{ inputs.release-version }}" + + { + pysemver check $RELEASE_VERSION + } || { + echo "The version '$RELEASE_VERSION' is not a valid Semver version string." + echo "Please use a valid semver version string. More details at https://semver.org/" + echo "The release process is aborted." + exit 1 + } + + - name: Check the version is higher than the latest one + run: | + # Retrieve the git tags first + git fetch --prune --unshallow --tags &> /dev/null + + RELEASE_VERSION="${{ inputs.release-version }}" + LATEST_VERSION=$(git describe --abbrev=0 --tags) + + IS_HIGHER_VERSION=$(pysemver compare $RELEASE_VERSION $LATEST_VERSION) + + if [ "$IS_HIGHER_VERSION" != "1" ]; then + echo "The version '$RELEASE_VERSION' is not higher than the latest version '$LATEST_VERSION'." + echo "The release process is aborted." + exit 1 + fi + + - name: Build Changelog + id: github_release + uses: mikepenz/release-changelog-builder-action@v4 + env: + GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} + + - name: Configure git + run: | + git config --global user.name "${GITHUB_ACTOR}" + git config --global user.email "${GITHUB_ACTOR}@users.noreply.github.com" + + - name: Create and push git tag + env: + GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} + run: | + # Tag the release + git tag -a "${{ inputs.release-version }}" -m "Release version ${{ inputs.release-version }}" + + # Push the modified changelogs + git push origin main + + # Push the tags + git push origin "${{ inputs.release-version }}" + + - name: Install library + run: python -m pip install --no-deps . + + - name: Build the wheel and sdist + run: python -m build --no-isolation + + - name: Publish package to PyPI + uses: pypa/gh-action-pypi-publish@release/v1 + with: + password: ${{ secrets.PYPI_API_TOKEN }} + packages-dir: dist/ + + - name: Create GitHub Release + uses: softprops/action-gh-release@de2c0eb89ae2a093876385947365aca7b0e5f844 + with: + tag_name: ${{ inputs.release-version }} + body: ${{steps.github_release.outputs.changelog}} diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml index 920fdb375..434661963 100644 --- a/.github/workflows/test.yml +++ b/.github/workflows/test.yml @@ -2,11 +2,14 @@ name: test on: push: - branches: - - "master" + branches: ["main"] + tags: ["*"] pull_request: branches: - "*" + - "!gh-pages" + schedule: + - cron: "0 4 * * MON" jobs: test: @@ -31,17 +34,16 @@ jobs: - name: Checkout the code uses: actions/checkout@v3 - - name: Setup Mamba - uses: mamba-org/provision-with-micromamba@v15 + - name: Setup mamba + uses: mamba-org/setup-micromamba@v1 with: environment-file: env.yml - environment-name: goli - extra-specs: | + environment-name: graphium + cache-environment: true + cache-downloads: true + create-args: >- python=${{ matrix.python-version }} pytorch=${{ matrix.pytorch-version }} - cache-downloads: true - cache-env: true - channel-priority: strict - name: Install library run: python -m pip install --no-deps . @@ -50,7 +52,7 @@ jobs: run: pytest - name: Test CLI - run: goli --help + run: graphium --help - name: Test building the doc run: mkdocs build diff --git a/MANIFEST.in b/MANIFEST.in deleted file mode 100644 index 36d7eed6d..000000000 --- a/MANIFEST.in +++ /dev/null @@ -1,8 +0,0 @@ -include README.md -include *.py -graft goli/*.yaml -recursive-include goli/ *.csv -recursive-include goli/config/ *.yaml -recursive-exclude * __pycache__ -recursive-exclude * *.py[co] -recursive-exclude * .ipynb_checkpoints/* diff --git a/README.md b/README.md index f32cefae2..16103d454 100644 --- a/README.md +++ b/README.md @@ -1,19 +1,14 @@
-

The Graph Of LIfe Library.

+

Scaling molecular GNNs to infinity.

--- -[![Binder](http://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/valence-discovery/goli/master?urlpath=lab/tree/docs/tutorials/) -[![PyPI](https://img.shields.io/pypi/v/goli)](https://pypi.org/project/goli-life/) -[![Conda](https://img.shields.io/conda/v/conda-forge/goli?label=conda&color=success)](https://anaconda.org/conda-forge/goli) -[![PyPI - Downloads](https://img.shields.io/pypi/dm/goli-life)](https://pypi.org/project/goli/) -[![Conda](https://img.shields.io/conda/dn/conda-forge/goli)](https://anaconda.org/conda-forge/goli) -[![PyPI - Python Version](https://img.shields.io/pypi/pyversions/goli-life)](https://pypi.org/project/goli-life/) -[![license](https://img.shields.io/badge/License-Apache%202.0-blue.svg)](https://github.com/valence-discovery/goli/blob/master/LICENSE) -[![GitHub Repo stars](https://img.shields.io/github/stars/valence-discovery/goli)](https://github.com/valence-discovery/goli/stargazers) -[![GitHub Repo stars](https://img.shields.io/github/forks/valence-discovery/goli)](https://github.com/valence-discovery/goli/network/members) +[![test](https://github.com/datamol-io/graphium/actions/workflows/test.yml/badge.svg)](https://github.com/datamol-io/graphium/actions/workflows/test.yml) +[![release](https://github.com/datamol-io/graphium/actions/workflows/release.yml/badge.svg)](https://github.com/datamol-io/graphium/actions/workflows/release.yml) +[![code-check](https://github.com/datamol-io/graphium/actions/workflows/code-check.yml/badge.svg)](https://github.com/datamol-io/graphium/actions/workflows/code-check.yml) +[![doc](https://github.com/datamol-io/graphium/actions/workflows/doc.yml/badge.svg)](https://github.com/datamol-io/graphium/actions/workflows/doc.yml) A deep learning library focused on graph representation learning for real-world chemical tasks. @@ -24,38 +19,31 @@ A deep learning library focused on graph representation learning for real-world - ⮔ Read-to-use training loop based on [Pytorch Lightning](https://www.pytorchlightning.ai/). - 🔌 Have a new dataset? Goli provides a simple plug-and-play interface. Change the path, the name of the columns to predict, the atomic featurization, and you’re ready to play! -## Try Online - -Visit [![Binder](http://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/valence-discovery/goli/master?urlpath=lab/tree/docs/tutorials/) and try Goli online. - ## Documentation -Visit https://valence-discovery.github.io/goli/. +Visit https://graphium-docs.datamol.io/. ## Installation for developers -### For CPU and GPU developers installs +### For CPU and GPU developers -Use either [`mamba`](https://github.com/mamba-org/mamba) or [`conda`](https://docs.conda.io/en/latest/): +Use [`mamba`](https://github.com/mamba-org/mamba): ```bash -# Install mamba if unavailable -conda install -c conda-forge mamba - -# Install Goli's dependencies in a new environment named `goli_dev` -mamba env create -f env.yml -n goli_dev +# Install Graphium's dependencies in a new environment named `graphium` +mamba env create -f env.yml -n graphium -# Install Goli in dev mode -conda activate goli_dev +# Install Graphium in dev mode +conda activate graphium pip install -e . ``` -### For IPU developers installs +### For IPU developers ```bash -mkdir ~/.venv # Create the folder for the environment -python3 -m venv ~/.venv/goli_ipu # Create the environment -source ~/.venv/goli_ipu/bin/activate # Activate the environment +mkdir ~/.venv # Create the folder for the environment +python3 -m venv ~/.venv/graphium_ipu # Create the environment +source ~/.venv/graphium_ipu/bin/activate # Activate the environment # Installing the poptorch SDK. Make sure to change the path pip install PATH_TO_SDK/poptorch-3.2.0+109946_bb50ce43ab_ubuntu_20_04-cp38-cp38-linux_x86_64.whl @@ -63,41 +51,29 @@ pip install PATH_TO_SDK/poptorch-3.2.0+109946_bb50ce43ab_ubuntu_20_04-cp38-cp38- # Activate poplar SDK. source PATH_TO_SDK/enable -# Install the IPU specific and goli requirements +# Install the IPU specific and graphium requirements PACKAGE_NAME=pytorch pip install -r requirements_ipu.txt -# Install Goli in dev mode +# Install Graphium in dev mode pip install -e . ``` ## Training a model -To learn how to train a model, we invite you to look at the documentation, or the jupyter notebooks available [here](https://github.com/valence-discovery/goli/tree/master/docs/tutorials/model_training). +To learn how to train a model, we invite you to look at the documentation, or the jupyter notebooks available [here](https://github.com/datamol-io/graphium/tree/master/docs/tutorials/model_training). If you are not familiar with [PyTorch](https://pytorch.org/docs) or [PyTorch-Lightning](https://pytorch-lightning.readthedocs.io/en/latest/), we highly recommend going through their tutorial first. -## Changelogs - -See the latest changelogs at [CHANGELOG.rst](./CHANGELOG.rst). - ## License Under the Apache-2.0 license. See [LICENSE](LICENSE). -## Authors - -See [AUTHORS.rst](./AUTHORS.rst). - ## Documentation -* Diagram for data processing in molGPS. - -Data Processing Chart - - - -* Diagram for Muti-task network in molGPS +- Diagram for data processing in molGPS. -Full Graph Multi-task Network +Data Processing Chart +- Diagram for Muti-task network in molGPS +Full Graph Multi-task Network diff --git a/goli/__init__.py b/graphium/__init__.py similarity index 100% rename from goli/__init__.py rename to graphium/__init__.py diff --git a/goli/_version.py b/graphium/_version.py similarity index 100% rename from goli/_version.py rename to graphium/_version.py diff --git a/goli/cli/README.md b/graphium/cli/README.md similarity index 100% rename from goli/cli/README.md rename to graphium/cli/README.md diff --git a/goli/cli/__init__.py b/graphium/cli/__init__.py similarity index 100% rename from goli/cli/__init__.py rename to graphium/cli/__init__.py diff --git a/goli/cli/data.py b/graphium/cli/data.py 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goli/visualization/README.md rename to graphium/visualization/README.md diff --git a/goli/visualization/__init__.py b/graphium/visualization/__init__.py similarity index 100% rename from goli/visualization/__init__.py rename to graphium/visualization/__init__.py diff --git a/goli/visualization/vis_utils.py b/graphium/visualization/vis_utils.py similarity index 100% rename from goli/visualization/vis_utils.py rename to graphium/visualization/vis_utils.py diff --git a/pyproject.toml b/pyproject.toml index 5fe8dfc9c..2635ebf05 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -55,7 +55,7 @@ namespaces = true [tool.black] line-length = 110 -target-version = ['py39', 'py310'] +target-version = ['py310', 'py311'] include = '\.pyi?$' [tool.pytest.ini_options]