Update CI: drop EOL jobs, test Python 3.11-3.15, add timeouts (#578)

The test workflow has been failing for reasons unrelated to the code.
This PR fixes the workflows and brings them up to date. It is the first
of a series of smaller PRs that modernize the project's tooling (the
next ones will raise the minimum Python version, switch the build
backend and replace black/pylint with Ruff).

## Changes

- **Remove the Debian 11 i386 job.** Debian 11 is end-of-life, and its
security repository on deb.debian.org no longer serves the packages it
lists, so `apt-get install` fails with 404s.
- **Test on Python 3.11-3.15** and drop the `numpy==1.26.4` job (NumPy
1.26 is the last release that supports Python 3.9). `uv run` now gets
`--python`, so every matrix entry actually runs with its own interpreter
(previously the interpreter was installed, but not selected).
- **Add a 45 minute timeout to the test job.** Slow PhysioNet downloads
made jobs hang until GitHub cancelled them after 6 hours.
- **Update actions and the Read the Docs image.** `actions/checkout`,
`astral-sh/setup-uv` and the RTD build image (Ubuntu 20.04 is gone) are
updated. The docs workflow sets up Python 3.12 explicitly. Dependabot
keeps GitHub Actions up to date from now on.
- **Replace the stale Poetry instructions** in `DEVELOPING.md` with the
uv equivalent.

## Notes

- `requires-python` still says `>= 3.9`. The next PR raises it to 3.11
to match what CI tests.
- Some tests fail when PhysioNet is slow or unreachable (the failures in
the previous CI run were `ChunkedEncodingError`/`ReadTimeout` from
physionet.org). This PR does not change that, it only makes sure such a
job fails after 45 minutes instead of 6 hours. A later PR makes these
tests skip instead of fail.

## Testing

I could not run the workflows themselves, but I checked that all YAML
files parse, that `uv run --python 3.11` and `--python 3.15` select the
requested interpreter, that the docs build with `docs/requirements.txt`
on Python 3.12, and that the existing test suite on 3.11 and 3.15 only
fails in the 17 tests that need PhysioNet when offline.

Author: tompollard

.github/dependabot.yml

@@ -0,0 +1,6 @@
+version: 2
+updates:
+  - package-ecosystem: "github-actions"
+    directory: "/"
+    schedule:
+      interval: "monthly"

.github/workflows/docs.yml

@@ -10,9 +10,12 @@ on:
 
 jobs:
   docs:
-    runs-on: ubuntu-22.04
+    runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v7
+      - uses: actions/setup-python@v7
+        with:
+          python-version: "3.12"
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip

.github/workflows/style.yml

@@ -13,8 +13,8 @@ jobs:
     name: Style Check
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v4
-      - uses: astral-sh/setup-uv@v3
+      - uses: actions/checkout@v7
+      - uses: astral-sh/setup-uv@v10.2.0
       - name: Install Python
         run: uv python install 3.11
       - name: Check style

.github/workflows/test.yml

@@ -10,21 +10,17 @@ on:
 
 jobs:
   test:
-    name: Python ${{ matrix.python-version }} / ${{ matrix.os }} / ${{ matrix.numpy }}
+    name: Python ${{ matrix.python-version }} / ${{ matrix.os }}
     strategy:
       fail-fast: false
       matrix:
         os: [windows-latest, ubuntu-latest, macos-latest]
-        python-version: ["3.9", "3.10", "3.11", "3.12", "3.13"]
-        numpy: ["numpy"]
-        include:
-          - os: ubuntu-latest
-            python-version: "3.9"
-            numpy: "numpy==1.26.4"
+        python-version: ["3.11", "3.12", "3.13", "3.14", "3.15"]
     runs-on: ${{ matrix.os }}
+    timeout-minutes: 45
     steps:
-      - uses: actions/checkout@v4
-      - uses: astral-sh/setup-uv@v3
+      - uses: actions/checkout@v7
+      - uses: astral-sh/setup-uv@v10.2.0
       - name: Install Python ${{ matrix.python-version }}
         run: uv python install ${{ matrix.python-version }}
       - name: Install libsndfile
@@ -33,34 +29,4 @@ jobs:
       - name: Run tests
         env:
           MPLBACKEND: Agg
-        run: uv run --with ${{ matrix.numpy }} --extra dev pytest
-
-  test-deb11-i386:
-    name: Python 3.7 on Debian 11 i386
-    runs-on: ubuntu-latest
-    container: i386/debian:11
-    env:
-      NPY_PROMOTION_STATE: weak_and_warn
-    steps:
-      - name: Install dependencies
-        run: |
-          apt-get update
-          apt-get install -y --no-install-recommends \
-                  python3-fsspec \
-                  python3-matplotlib \
-                  python3-numpy \
-                  python3-pandas \
-                  python3-pip \
-                  python3-requests \
-                  python3-scipy \
-                  python3-soundfile \
-                  python3-pytest \
-                  git
-          python3 --version
-      # Note: "actions/checkout@v2" requires libstdc++6:amd64 to be
-      # installed in the container.  To keep things simple, use
-      # "actions/checkout@v1" instead.
-      # https://github.com/actions/checkout/issues/334
-      - uses: actions/checkout@v1
-      - name: Run tests
-        run: pytest-3
+        run: uv run --python ${{ matrix.python-version }} --extra dev pytest

.readthedocs.yml

@@ -3,9 +3,9 @@
 version: 2
 
 build:
-  os: "ubuntu-20.04"
+  os: "ubuntu-24.04"
   tools:
-    python: "3.10"
+    python: "3.12"
 
 # Build from the docs/ directory with Sphinx
 sphinx:

DEVELOPING.md

@@ -36,15 +36,10 @@ uv add <somepackage> --optional <somegroup>
 
 It may be useful to publish to testpypi and preview the changes before publishing to PyPi. However, the project dependencies likely will not be available when trying to install from there.
 
-Setup: configure access to repositories:
+Setup: create an API token on PyPI (and on TestPyPI for test uploads) and pass it to uv:
 
 ```sh
-# Create an API token, then add it
-poetry config pypi-token.pypi <my-token>
-
-# For testpypi
-poetry config repositories.test-pypi https://test.pypi.org/legacy/
-poetry config pypi-token.test-pypi <my-testpypi-token>
+export UV_PUBLISH_TOKEN=<my-token>
 ```
 
 To build and upload a new distribution: