Merge branch 'main' into manzt/hoist-2

.github/ISSUE_TEMPLATE/bug_report.yml

@@ -0,0 +1,50 @@
+name: "\U0001F41E Bug report"
+description: Report an issue with anywidget
+labels: ['bug']
+body:
+  - type: markdown
+    attributes:
+      value: |
+        Thanks for taking the time to fill out this bug report!
+  - type: textarea
+    id: bug-description
+    attributes:
+      label: Describe the bug
+      description: A clear and concise description of what the bug is. If you intend to submit a PR for this issue, tell us in the description. Thanks!
+      placeholder: Bug description
+    validations:
+      required: true
+  - type: textarea
+    id: reproduction
+    attributes:
+      label: Reproduction
+      description: Please provide a link to a repo or gist that can reproduce the problem you ran into. If a report is vague (e.g. just a generic error message) and has no reproduction, it will receive a "need reproduction" label. If no reproduction is provided within a reasonable time-frame, the issue will be closed.
+      placeholder: Reproduction
+    validations:
+      required: true
+  - type: textarea
+    id: logs
+    attributes:
+      label: Logs
+      description: 'Please include browser console and/or Python logs around the time this bug occurred. Optional if provided reproduction. Please try not to insert an image but copy paste the log text.'
+      render: shell
+  - type: textarea
+    id: system-info
+    attributes:
+      label: System Info
+      description: Output of `npx envinfo --system --browsers` and `pip freeze | grep -E "anywidget|jupyter|notebook"`. And please, other relevant package versions.
+      render: shell
+      placeholder: System, Binaries, Browsers
+    validations:
+      required: true
+  - type: dropdown
+    id: severity
+    attributes:
+      label: Severity
+      description: Select the severity of this issue
+      options:
+        - annoyance
+        - blocking an upgrade
+        - blocking all usage of anywidget
+    validations:
+      required: true

.github/ISSUE_TEMPLATE/config.yml

@@ -0,0 +1,5 @@
+blank_issues_enabled: true
+contact_links:
+  - name: Discord Chat
+    url: https://discord.gg/W5h4vPMbDQ
+    about: Ask questions and discuss with other anywidget devs/users in real time.

.github/ISSUE_TEMPLATE/documentation.yml

@@ -0,0 +1,31 @@
+---
+name: Documentation
+description: Create a report to help us improve the documentation
+labels: [docs]
+body:
+  - type: input
+    id: link
+    attributes:
+      label: Documentation Link
+      description: >-
+        Link to any documentation or examples that you are referencing.
+      placeholder: https://anywidget.dev/...
+  - type: textarea
+    id: issue
+    attributes:
+      label: Issue
+      description: What is lacking, unclear, or incorrect in the documentation?
+      placeholder: |
+        * The section on [...] is confusing because [...]
+        * [...] gives the impression that [...] whereas it should be [...]
+        * An example demonstrating [...] is missing
+    validations:
+      required: true
+  - type: textarea
+    id: recommendation
+    attributes:
+      label: Recommended improvement
+      placeholder: |
+        * Change this line to [...]
+        * Add a paragraph that explains [...]
+        * Add a new section with [...]

.github/ISSUE_TEMPLATE/feature_request.yml

@@ -0,0 +1,35 @@
+name: 'Feature Request'
+description: Request a new anywidget feature
+labels: [enhancement]
+body:
+  - type: markdown
+    attributes:
+      value: |
+        Thanks for taking the time to request this feature!
+  - type: textarea
+    id: problem
+    attributes:
+      label: Describe the problem
+      description: Please provide a clear and concise description the problem this feature would solve. The more information you can provide here, the better.
+      placeholder: I'm always frustrated when...
+    validations:
+      required: true
+  - type: textarea
+    id: solution
+    attributes:
+      label: Describe the proposed solution
+      description: Please provide a clear and concise description of what you would like to happen.
+      placeholder: I would like to see...
+    validations:
+      required: true
+  - type: dropdown
+    id: importance
+    attributes:
+      label: Importance
+      description: How important is this feature to you?
+      options:
+        - nice to have
+        - would make my life easier
+        - i cannot use anywidget without it
+    validations:
+      required: true

.github/workflows/ci.yml

@@ -19,67 +19,53 @@ jobs:
     runs-on: macos-14
     steps:
       - uses: actions/checkout@v4
-      - uses: actions/setup-python@v5
+      # Disable jupyter-builder build hook because not needed for linting/formatting, and requires pnpm
+      - run: |
+          sed -i '' 's/\[tool.hatch.build.hooks.\(.*\)\]/\[_tool.hatch.build.hooks.\1\]/' pyproject.toml
+      - uses: astral-sh/setup-uv@v4
         with:
-          python-version: "3.12"
+          version: "0.5.x"
       - run: |
-          pip install uv
-          uv pip install --system ruff
-          ruff check
-          ruff format
+          uv run ruff check
+          uv run ruff format
 
   TypecheckPython:
     name: Python / Typecheck
     runs-on: macos-14
     steps:
       - uses: actions/checkout@v4
-
-      # Disable jupyter-builder build hook because not needed for typechecking, and requires npm
+      # Disable jupyter-builder build hook because not needed for typechecking, and requires pnpm
       - run: |
           sed -i '' 's/\[tool.hatch.build.hooks.\(.*\)\]/\[_tool.hatch.build.hooks.\1\]/' pyproject.toml
-          cat pyproject.toml
-
-      - uses: actions/setup-python@v5
+      - uses: astral-sh/setup-uv@v4
         with:
-          python-version: "3.12"
-      - run: |
-          pip install uv
-          uv pip install --system -e '.[test,dev]'
-      - run: mypy
+          version: "0.5.x"
+      - run: uv run mypy
 
   TestPython:
     name: Python / Test
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ["3.7", "3.8", "3.9", "3.10", "3.11", "3.12"]
-
+        python-version:
+          - "3.8"
+          - "3.9"
+          - "3.10"
+          - "3.11"
+          - "3.12"
     steps:
       - uses: actions/checkout@v4
-
       - uses: pnpm/action-setup@v4
-      - uses: actions/setup-node@v4
         with:
-          node-version: "22.x"
-      - run: pnpm install --frozen-lock
-
-      - uses: actions/setup-python@v5
+          run_install: true
+      - uses: astral-sh/setup-uv@v4
         with:
-          python-version: ${{ matrix.python-version }}
-
-      - if: ${{ matrix.python-version != '3.7' }}
-        run: |
-          pip install uv
-          uv pip install --system -e '.[test,dev]'
-
-      - if: ${{ matrix.python-version == '3.7' }}
-        run: |
-          pip install -e '.[test,dev]'
-
+          version: "0.5.x"
       - name: Run tests
-        run: pytest ./tests --color=yes --cov anywidget --cov-report xml
-
-      - uses: codecov/codecov-action@v4
+        run: uv run --with pytest-cov pytest ./tests --color=yes --cov anywidget --cov-report xml
+        env:
+          UV_PYTHON: ${{ matrix.python-version }}
+      - uses: codecov/codecov-action@v5
 
   LintJavaScript:
     name: JavaScript / Lint
@@ -91,29 +77,22 @@ jobs:
           version: latest
       - run: biome ci .
 
-
   TypecheckJavaScript:
     name: JavaScript / Typecheck
     runs-on: macos-14
     steps:
       - uses: actions/checkout@v4
       - uses: pnpm/action-setup@v4
-      - uses: actions/setup-node@v4
         with:
-          node-version: "22.x"
-      - run: |
-          pnpm install
-          pnpm typecheck
+          run_install: true
+      - run: pnpm typecheck
 
   TestJavaScript:
     name: JavaScript / Test
     runs-on: macos-14
     steps:
       - uses: actions/checkout@v4
       - uses: pnpm/action-setup@v4
-      - uses: actions/setup-node@v4
         with:
-          node-version: "22.x"
-      - run: |
-          pnpm install
-          pnpm test
+          run_install: true
+      - run: pnpm test

.github/workflows/jsr.yml

@@ -23,7 +23,7 @@ jobs:
       id-token: write
     steps:
       - uses: actions/checkout@v4
-      - uses: denoland/setup-deno@v1
+      - uses: denoland/setup-deno@v2
         with:
           deno-version: v1.x
       - run: |

.github/workflows/release.yml

@@ -22,28 +22,17 @@ jobs:
       issues: read
     steps:
       - uses: actions/checkout@v4
-
       - uses: pnpm/action-setup@v4
-      - uses: actions/setup-node@v4
         with:
-          node-version: "22.x"
-      - run: pnpm install --frozen-lock
-
-      - uses: actions/setup-python@v5
+          run_install: true
+      - uses: astral-sh/setup-uv@v4
         with:
-          python-version: "3.11"
-      - run: |
-          python -m pip install --upgrade pip
-          pip install build twine
-
+          version: "0.5.x"
       - name: Create Release Pull Request or Publish
         id: changesets
         uses: changesets/action@v1
         with:
-          # this expects you to have a npm script called version that runs some logic and then calls `changeset version`.
-          version: npm run version
-          # This expects you to have a script called release which does a build for the packages and calls `changeset publish`
-          publish: npm run release
+          publish: pnpm release
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
           NPM_TOKEN: ${{ secrets.NPM_TOKEN }}

.gitignore

@@ -1,6 +1,6 @@
 __pycache__/
 
-*.egg-info/
+*.tsbuildinfo
 .eggs/*
 
 .ipynb_checkpoints/

CITATION.cff

@@ -29,7 +29,11 @@ preferred-citation:
       family-names: "Gehlenborg"
       affiliation: "Harvard Medical School"
       orcid: "https://orcid.org/0000-0003-0327-8297"
-  doi: "10.31219/osf.io/tw9sg"
-  journal: "OSF preprint"
-  month: 6
+  doi: "10.21105/joss.06939"
+  journal: "Journal of Open Source Software"
+  volume: "9"
+  number: "102"
+  pages: "6939"
   year: 2024
+  publisher:
+    name: "The Open Journal"

CONTRIBUTING.md

@@ -7,31 +7,16 @@ contains both JavaScript and Python components, it requires dual package
 managers:
 
 - [pnpm](https://pnpm.io) for JavaScript
-- [hatch](https://github.com/pypa/hatch) for Python
+- [uv](https://github.com/astral-sh/uv) for Python
 
 You can [install pnpm](https://pnpm.io/installation) and
-[install hatch](https://github.com/pypa/hatch) with:
+[install uv](https://github.com/astral-sh/uv) with:
 
 ```bash
 npm i -g pnpm
-pipx install hatch
+curl -LsSf https://astral.sh/uv/install.sh | sh # for Linux and macOS, see link for Windows
 ```
 
-Then, create a Python virtual environment with `hatch`:
-
-```bash
-hatch shell
-```
-
-This command creates a virtual environment and installs all dependencies
-specified in the `pyproject.toml`. It also installs **anywidget** in development
-mode. The environment setup might take some time during the first run, but
-`hatch` reuses the environment in subsequent runs.
-
-You can deactivate the environment with `Ctrl + D` and reset it using
-`hatch env remove`. For more information, read the
-[hatch docs](https://hatch.pypa.io/latest/).
-
 ## Code structure
 
 Entry points to be aware of:
@@ -60,12 +45,12 @@ Entry points to be aware of:
 Once your environment is set up, you can start making changes to the codebase.
 We recommend using the classic Jupyter Notebook or Jupyter Lab for development.
 
-If you are using the classic Jupyter Notebook you need to install the local
+If you are using the classic Jupyter Notebook (<v7) you need to install the local
 nbextension:
 
 ```bash
-jupyter nbextension install --py --symlink --sys-prefix anywidget
-jupyter nbextension enable --py --sys-prefix anywidget
+uv run jupyter nbextension install --py --symlink --sys-prefix anywidget
+uv run jupyter nbextension enable --py --sys-prefix anywidget
 ```
 
 Note for developers:
@@ -78,7 +63,7 @@ Note for developers:
 For developing with JupyterLab:
 
 ```bash
-jupyter labextension develop --overwrite anywidget
+uv run jupyter labextension develop --overwrite anywidget
 ```
 
 > **Note** If you make changes to the Python code, you'll need to restart the
@@ -94,8 +79,15 @@ There are a few guidelines we follow:
 
 - For JavaScript, internal variables are written with `snake_case` while
   external APIs are written with `camelCase` (if applicable).
-- For Python, ensure `hatch run lint` passes. You can run `hatch run fmt` to
-  format and fix linting errors.
+- For Python, ensure typechecking and linting passes.
+
+Commands to know:
+
+```sh
+uv run ruff check # linting
+uv run ruff format # formatting
+uv run mypy # typechecking
+```
 
 ### Generating changelogs