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Update CI: drop EOL jobs, test Python 3.11-3.15, add timeouts - #578
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The test workflow was failing for reasons unrelated to the code. - 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). Pass --python to uv run so that every matrix entry actually runs with its own interpreter. - Add a 45 minute timeout to the test job. Slow PhysioNet downloads made jobs hang until GitHub cancelled them after 6 hours. - Update actions/checkout, astral-sh/setup-uv and the Read the Docs build image, and set up Python explicitly in the docs workflow. Add Dependabot to keep GitHub Actions up to date. - Replace the stale Poetry instructions in DEVELOPING.md with the uv equivalent.
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As already expected, jobs fail due to PhysioNet being unreachable. I would still recommend to merge this PR, I'll submit a follow-up PR which skips all tests that rely on the network (PhysioNet in particular) next. |
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Thanks for looking at this @cbrnr. We're working on the PhysioNet slowness/unavailability. In the process of migrating the platform to new infrastructure. |
tompollard
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Thanks @cbrnr, looks good to me
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Thanks @tompollard! I hope everything will be fine and PhysioNet will be available again! |
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This is the second PR of a series that modernizes the project's tooling (see #578 for the first one, which updated the CI workflows and tests Python 3.11-3.15). ## Changes - **Require Python >= 3.11.** Python 3.9 is end-of-life and 3.10 will be soon, and CI no longer tests them. `black`'s target version is updated accordingly. - **Raise the minimum versions of some dependencies.** `soundfile` (0.10.0 -> 0.12.1), `matplotlib` (3.2.2 -> 3.8.0) and `requests` (2.8.1 -> 2.31.0) had lower bounds that are much older than anything we test. The development dependencies `pytest` (8.0.0) and `pytest-xdist` (3.5.0) are raised as well. The minimum versions of `numpy`, `scipy`, `pandas`, `fsspec` and `aiohttp` are unchanged. - **Add a "minimum versions" job.** It runs the tests on Python 3.11 with the lowest allowed versions of all direct dependencies (`uv run --resolution lowest-direct`), so a lower bound cannot silently become unusable. - **Add a changelog entry.** ## Notes - The new job runs the whole test suite, so it is affected by the same slow or unreachable PhysioNet downloads as the other jobs (it has the same 45 minute timeout). A later PR will make the PhysioNet tests skip instead of fail. ## Testing I resolved the lowest-direct environment locally on Python 3.11 (numpy 1.26.4, scipy 1.13.0, pandas 2.2.3, soundfile 0.12.1, matplotlib 3.8.0, requests 2.31.0, fsspec 2023.10.0, aiohttp 3.10.11, pytest 8.0.0, pytest-xdist 3.5.0). With PhysioNet blocked, the test suite there passes except for the same 17 tests that need PhysioNet, and `black --check` passes with the new target version.
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Third PR of the tooling series (after #578 and #580). The project already uses uv for package management, so this switches the build backend to `uv_build` as well. ## Changes - **Build backend:** `uv_build >= 0.13.0, < 0.14` replaces `hatchling`. The package lives in the project root (not in `src/`), so `module-root = ""` is set. - **Static version:** `uv_build` does not support dynamic versions, so the version is now only specified in `pyproject.toml` (the release instructions in `DEVELOPING.md` are updated). `wfdb.__version__` is read from the installed package metadata, and it is `"unknown"` if `wfdb` is imported from a source tree that has not been installed. The documentation reads the version from `pyproject.toml`. - **License:** `uv_build` does not include the license file automatically, so `license-files = ["LICENSE"]` is set. I also switched to the SPDX expression `license = "MIT"` (the old table form is deprecated). - **Changelog entry.** ## What changes in the distributions - **Wheel:** the same files as before, the metadata is the same except for the license field (`License-Expression: MIT` instead of `License: MIT License`). - **sdist:** it now only contains the `wfdb` package, `LICENSE`, `README.md` and `pyproject.toml` (plus `PKG-INFO`). The hatchling sdist also contained `docs/`, `.github/`, `DEVELOPING.md`, `pylintrc` and some dotfiles (tests, sample data and the demo files were already excluded). I think that is fine, but let me know if you would like to keep some of these in the sdist. ## Testing - Built the sdist and wheel with the latest `uv_build` (0.13.6) and with the lowest allowed version (0.13.0), and compared the result with the hatchling build (see above). - Installed the wheel: `wfdb.__version__` is `4.3.1`. In an editable install it is `4.3.1`, and importing from an uninstalled source tree gives `unknown`. - The docs build as before (same warnings) and show version 4.3.1. - The test suite behaves as before (only the 17 tests that need PhysioNet fail when offline), and `black --check` passes.
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Fourth PR of the tooling series (after #578, #580 and #581). It replaces `black` (formatting) and `pylint` (which was not run anywhere, and had a 560 line config) with [Ruff](https://docs.astral.sh/ruff/), which does both. The PR consists of four commits, and I suggest reviewing them one by one: 1. **Replace black and pylint with Ruff:** the actual configuration. The `dev` extra now contains `ruff >= 0.13.0` (the first version that agrees with the rules below) instead of `black` and `pylint`, the style workflow runs `ruff format --check` and `ruff check`, `pylintrc` is removed, and the developer docs and the changelog are updated. 2. **Fix a test that was never run:** `tests/test_multi_record.py` defines `test_contained_combined_ranges_variable_layout` twice, so the first definition was shadowed and never ran (Ruff reports this as F811). I renamed the second test. Both pass. 3. **Apply ruff formatting and safe lint fixes:** purely mechanical (34 files). You can reproduce it with `ruff check --fix . && ruff format .` on the first two commits. It contains the formatting, plus the safe autofixes of the enabled rules: sorted imports, f-strings instead of `str.format()`, `list[...]`/`X | None` instead of `typing` aliases, `class X:` instead of `class X(object):`, and unused imports. 4. **Ignore the reformatting commit in git blame:** adds `.git-blame-ignore-revs` with commit 3 (GitHub uses this file automatically; locally, run `git config blame.ignoreRevsFile .git-blame-ignore-revs`, which is documented in `DEVELOPING.md`). Note that the hash only stays valid if the commits of this PR are preserved, i.e. with a merge commit (as for the previous PRs), not when squashing or rebasing. ## Configuration - **Line length:** Ruff's default of 88 instead of black's 80 (as configured so far). - **Rules:** `E`, `F`, `W` (pycodestyle/pyflakes), `I` (isort), `UP` (pyupgrade) and `B` (bugbear). `E501` is ignored because the formatter takes care of line lengths, and `F401` is ignored in `__init__.py` files (re-exports). - **Existing violations:** I did not want to change code behavior in this PR, so the rules whose fixes are not safe are ignored for now (about 90 occurrences in total): `E711`, `E721`, `E722`, `E741`, `F841`, `UP031`, `B006`, `B007`, `B020`, `B904`, `B905`. They can be enabled one by one in follow-up PRs. - Jupyter notebooks are not checked (black did not check them either). ## Testing - `ruff check .` and `ruff format --check .` pass (also with the oldest allowed Ruff, 0.13.0), and all modules still import. - The test suite behaves as before on Python 3.11 with the lowest allowed dependency versions and on 3.15 with the latest (65 passed, and only the 17 tests that need PhysioNet fail when offline; the test that was shadowed before is now among the passing ones). - With the ignore file, `git blame` attributes lines changed by commit 3 to their original commits.
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#589) This is the last part of the cleanup that started with #578, #580, #581, #582 and #588. It builds the documentation without warnings, applies one docstring style everywhere, and moves the package to a `src` layout. Each commit can be reviewed on its own. 1. **Fix all Sphinx documentation warnings.** The docs build reported 94 warnings. They are fixed, and the docs workflow now builds with `-W --keep-going` so they stay fixed. - Duplicate object descriptions: repeated `automodule` directives and the classes documented on both the `wfdb` and `io` pages are marked `:no-index:`, so each object is indexed once. - `numpydoc_class_members_toctree = False`, because the autosummary stubs it links to do not exist. - Too short title underlines, and reStructuredText errors in docstrings (lists, literal blocks for the EDF/MATLAB/WAV format descriptions and tables, doctest continuation lines). - The `:no-index:` option needs Sphinx 7.2, so the pinned Sphinx version of the `docs` group goes from 7.0.0 to 7.2.6. 2. **Wrap docstrings and comments at 88 columns**, the same width as the code, and enable W505 in Ruff so it stays that way. This is a mechanical change, and the commit is listed in `.git-blame-ignore-revs`. 3. **Start docstrings on the opening quote line with a one-line summary.** Summaries that were wrapped over several lines or too long for one line are shortened, and the rest of the text moves into the description below. No code changes: comparing the ASTs with docstrings removed shows no difference. A few docstrings were reworded to fit, and the descriptions of `csv_to_wfdb` and `csv2ann` (which described reading a WFDB header) now match what the functions do. Also listed in `.git-blame-ignore-revs`. 4. **Move the package to `src/wfdb`.** This is the default module root of `uv_build`, so the `module-root` setting is removed. The tests now always run against the installed package, and `docs/conf.py` adds `src` to `sys.path`. Files are moved without changes, so `git blame` and `git log --follow` keep working. The wheel and the sdist build as expected. 5. **Ignore the two reformatting commits in git blame**, and add a note about the docstring style to `DEVELOPING.md`. The hashes stay valid with a merge commit, as in #582. 6. **Add `AGENTS.md` and `CLAUDE.md`** with short guidance for coding agents (commands and conventions). `CLAUDE.md` only points to `AGENTS.md`. Checked locally: Ruff lint and format, the docs build with `-W --keep-going`, and the tests that work offline on Python 3.11 with the lowest dependencies and on 3.15. @tompollard this concludes the tooling and infrastructure refresh. Any remaining changes are minor, such as fixing the ignored Ruff rules, which can be done later in follow-up PRs.
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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
apt-get installfails with 404s.numpy==1.26.4job (NumPy 1.26 is the last release that supports Python 3.9).uv runnow gets--python, so every matrix entry actually runs with its own interpreter (previously the interpreter was installed, but not selected).actions/checkout,astral-sh/setup-uvand 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.DEVELOPING.mdwith the uv equivalent.Notes
requires-pythonstill says>= 3.9. The next PR raises it to 3.11 to match what CI tests.ChunkedEncodingError/ReadTimeoutfrom 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 3.11and--python 3.15select the requested interpreter, that the docs build withdocs/requirements.txton 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.