Manage dev and docs dependencies with uv dependency groups

.github/dependabot.yml

@@ -4,3 +4,14 @@ updates:
     directory: "/"
     schedule:
       interval: "monthly"
+    groups:
+      actions:
+        patterns: ["*"]
+  - package-ecosystem: "uv"
+    directory: "/"
+    schedule:
+      interval: "monthly"
+    # Bump exact pins and upper bounds, but leave lower bounds alone
+    versioning-strategy: increase-if-necessary
+    cooldown:
+      default-days: 7

.github/workflows/docs.yml

@@ -13,14 +13,8 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v7
-      - uses: actions/setup-python@v7
-        with:
-          python-version: "3.12"
-      - name: Install dependencies
-        run: |
-          python -m pip install --upgrade pip
-          pip install -r docs/requirements.txt
+      - uses: astral-sh/[email protected]
+      - name: Install Python
+        run: uv python install 3.12
       - name: Build documentation
-        run: |
-          cd docs
-          make html
+        run: uv run --python 3.12 --only-group docs make -C docs html

.github/workflows/style.yml

@@ -19,5 +19,5 @@ jobs:
         run: uv python install 3.11
       - name: Check style
         run: |
-          uv run --extra dev ruff format --check --diff .
-          uv run --extra dev ruff check .
+          uv run ruff format --check --diff .
+          uv run ruff check .

.github/workflows/test.yml

@@ -29,7 +29,7 @@ jobs:
       - name: Run tests
         env:
           MPLBACKEND: Agg
-        run: uv run --python ${{ matrix.python-version }} --extra dev pytest
+        run: uv run --python ${{ matrix.python-version }} pytest
 
   # Make sure the lower bounds of the direct dependencies are actually usable
   test-minimum:
@@ -46,4 +46,4 @@ jobs:
       - name: Run tests
         env:
           MPLBACKEND: Agg
-        run: uv run --python 3.11 --resolution lowest-direct --extra dev pytest
+        run: uv run --python 3.11 --resolution lowest-direct pytest

.gitignore

@@ -72,3 +72,6 @@ target/
 
 # pyenv
 .python-version
+
+# Not committed: CI resolves dependencies fresh
+uv.lock

.readthedocs.yml

@@ -6,12 +6,16 @@ build:
   os: "ubuntu-24.04"
   tools:
     python: "3.12"
+  jobs:
+    pre_create_environment:
+      - asdf plugin add uv
+      - asdf install uv latest
+      - asdf global uv latest
+    create_environment:
+      - uv venv "${READTHEDOCS_VIRTUALENV_PATH}"
+    install:
+      - UV_PROJECT_ENVIRONMENT="${READTHEDOCS_VIRTUALENV_PATH}" uv sync --only-group docs
 
 # Build from the docs/ directory with Sphinx
 sphinx:
   configuration: docs/conf.py
-
-# Explicitly set the version of Python and its requirements
-python:
-  install:
-    - requirements: docs/requirements.txt

DEVELOPING.md

@@ -25,12 +25,14 @@ git config blame.ignoreRevsFile .git-blame-ignore-revs
 
 This project uses [uv](https://docs.astral.sh/uv/) for package management and distribution.
 
-Development dependencies are specified as optional dependencies, at least for now and until [development dependencies](https://docs.astral.sh/uv/concepts/dependencies/#development-dependencies) become more widely used.
+Development dependencies are specified in the `dev` [dependency group](https://docs.astral.sh/uv/concepts/dependencies/#development-dependencies), which `uv run` installs automatically:
 
 ```sh
-uv add <somepackage> --optional <somegroup>
+uv add --dev <somepackage>
 ```
 
+Ruff is pinned to an exact version because new releases can change formatting and lint results. Dependabot opens monthly pull requests to bump it, along with the pinned documentation dependencies, uv-build, and the GitHub Actions.
+
 ## Creating Distributions
 
 1. Bump the version in [pyproject.toml](./pyproject.toml).
@@ -64,12 +66,10 @@ The project's documentation is generated by [Sphinx](https://docs.readthedocs.io
 
 To manage the content on RTD, request yourself to be added to the [wfdb](https://readthedocs.org/projects/wfdb/) project. The project has already been configured to import content from the GitHub repository. Documentation for new releases should be automatically built and uploaded. See the [import guide](https://docs.readthedocs.io/en/stable/intro/import-guide.html) for more details.
 
-There is some redundancy in specifying the Sphinx requirements between pyproject.toml and [docs/requirements.txt](./docs/requirements.txt), the latter of which is used by RTD. Make sure that the content is consistent across the two files.
-
-To generate the HTML content locally, install the required dependencies and run from the `docs` directory:
+The documentation dependencies are specified in the `docs` dependency group in [pyproject.toml](./pyproject.toml), which is used both locally and by RTD. To generate the HTML content locally, run:
 
 ```sh
-make html
+uv run --only-group docs make -C docs html
 ```
 
 ## Tests

README.md

@@ -27,20 +27,26 @@ The distribution is hosted on PyPI at: [https://pypi.python.org/pypi/wfdb/](http
 pip install wfdb
 ```
 
+Alternatively, add it to a project managed with [uv](https://docs.astral.sh/uv/):
+
+```sh
+uv add wfdb
+```
+
 On some less-common systems, you may need to install `libsndfile` separately.  See the [soundfile installation notes](https://pypi.org/project/soundfile/) for more information.
 
 ## Development
 
-The development version is hosted at: [https://github.com/MIT-LCP/wfdb-python](https://github.com/MIT-LCP/wfdb-python). This repository also contains demo scripts and example data. To install the development version, clone or download the repository, navigate to the base directory, and run:
+The development version is hosted at: [https://github.com/MIT-LCP/wfdb-python](https://github.com/MIT-LCP/wfdb-python). This repository also contains demo scripts and example data. To set up a development environment, install [uv](https://docs.astral.sh/uv/), clone the repository, navigate to the base directory, and run:
 
 ```sh
-pip install .
+uv sync
 ```
 
-If you intend to make changes to the repository, you can install additional packages that are useful for development by running:
+This creates a virtual environment in `.venv` containing the package and all development tools. Commands can then be run inside this environment with `uv run`, for example:
 
 ```sh
-pip install ".[dev]"
+uv run pytest
 ```
 
 Please see the [DEVELOPING.md](https://github.com/MIT-LCP/wfdb-python/blob/main/DEVELOPING.md) document for contribution/development instructions.

pyproject.toml

@@ -22,19 +22,24 @@ dependencies = [
     "aiohttp >= 3.10.11",
 ]
 
-[project.optional-dependencies]
-dev = [
-    "pytest >= 8.0.0",
-    "pytest-xdist >= 3.5.0",
-    "ruff >= 0.13.0",
-    "sphinx >= 7.0.0",
-]
-
 [project.urls]
 homepage = "https://github.com/MIT-LCP/wfdb-python/"
 repository = "https://github.com/MIT-LCP/wfdb-python/"
 documentation = "https://wfdb.readthedocs.io/"
 
+[dependency-groups]
+dev = [
+    "pytest >= 8.0.0",
+    "pytest-xdist >= 3.5.0",
+    "ruff == 0.17.3",
+]
+# Heavy dependencies are mocked in docs/conf.py, so the project itself is not needed
+docs = [
+    "fsspec >= 2023.10.0",
+    "numpydoc == 1.7.0",
+    "sphinx == 7.0.0",
+]
+
 [tool.ruff]
 target-version = "py311"
 extend-exclude = ["*.ipynb"]