Use pytest config in pyproject.toml in CI by lagru · Pull Request #7555 · scikit-image/scikit-image

lagru · 2024-09-27T14:40:53Z

Description

Closes #7554.

This should be safe, as the pytest documentation states that

rootdir is NOT used to modify sys.path/PYTHONPATH

So while the --config-file option affects the rootdir, it's not adding that directory to the PYTHONPATH where it could accidentally overwrite the installed package.

Checklist

A descriptive but concise pull request title
Docstrings for all functions
Unit tests
A gallery example in ./doc/examples for new features
Contribution guide is followed

Release note

For maintainers and optionally contributors, please refer to the instructions on how to document this PR for the release notes.

...

This should be safe, as the pytest documentation [1] states that "rootdir is NOT used to modify sys.path/PYTHONPATH". So while the `--config-file` option affects the `rootdir`, it's not adding that directory to the PYTHONPATH where it could accidentally overwrite the installed package. This solution is somewhat unsatisfying. Personally, I think a better approach would be to switch to the src-layout. [1] https://docs.pytest.org/en/7.1.x/reference/customize.html?highlight=rootdir#initialization-determining-rootdir-and-configfile

I believe this warning disappeared with tifffile 2024.4.24 which added support for NumPy 2.

lagru · 2024-12-17T19:10:41Z

During the meeting @stefanv suggested to use a different approach and just not step out of the project directory. It was suggested that that may be outdated behavior from a long time ago. 😅

lagru · 2025-01-24T17:25:57Z

Close in favor of #7670.

stefanv · 2025-01-31T02:01:29Z

May not look like it, but we're close 😅

stefanv · 2025-01-31T05:28:33Z

The remaining failure is pyamg related.

stefanv · 2025-01-31T05:46:03Z

Looks like pytest is turning the innocuous warning raised by pyamg into an exception.

Leaving this commented is probably an oversight from scikit-imagegh-7576 / a7b54a8.

lagru · 2025-01-31T13:07:22Z

.github/workflows/nightly_wheel_build.yml

      CIBW_TEST_COMMAND: >
        pip list --pre --format=freeze | grep -q 'numpy==2' &&
-        pytest --pyargs skimage
+        (cd .. && $PYTEST --pyargs skimage)


Should check if this actually works after merging this.

lagru · 2025-01-31T13:53:13Z

pyproject.toml

    'sphinx-copybutton',
    'matplotlib>=3.7',
-    'dask[array]>=2022.9.2',
+    'dask[array]>=2023.2.0',


Guessing that this is done in accordance with SPEC0?

lagru · 2025-01-31T14:01:49Z

skimage/data/tests/test_data.py

-@pytest.mark.xfail(
-    Version(np.__version__) >= Version('2.0.0.dev0'),
-    reason='tifffile uses deprecated attribute `ndarray.newbyteorder`',
-)


I guess this issue cgohlke/tifffile#238 was addressed in tifffile 2024.1.30.

Should we update to tifffile 2024.1.30? I guess it might be possible that there are some combinations of our dependencies that still raise this warning or even fail but probably rare and fix-able with bumping tifffile or downgrading NumPy.

So I think we can leave tifffile be.

lagru · 2025-01-31T14:05:29Z

.github/workflows/emscripten.yml

          # Don't use the cache provider plugin, as it doesn't work with Pyodide
          # right now: https://github.com/pypa/cibuildwheel/issues/1966
-          # pytest -svra -p no:cacheprovider --pyargs skimage
+          $PYTEST -svra -p no:cacheprovider --pyargs skimage


I uncommented this line in c3e6af1. Feel free to revert if I missed something here.

lagru

✔️ Approving since I reviewed your changes @stefanv. Thanks for finishing this! 😊

I think this is ready to go in if the CI is happy with me re-enabling testing on the emscripten.

lagru · 2025-01-31T14:24:29Z

Merged since it seems like 2 core devs approved.

…ailure * origin/main: Add zizmor to pre-commit; address GH workflow issues raised (scikit-image#7662) Reenable test marked as flaky on Azure. (scikit-image#7694) Simultaneously resolve all dependencies; add pip caching (scikit-image#7690) Copy keypoints if necessary to preserve contiguity (scikit-image#7692) CI cleanup (scikit-image#7693) Port CI testing from Azure to GitHub (scikit-image#7687) Lower CI build verbosity Use pytest config in pyproject.toml in CI (scikit-image#7555) Improve docstring for rolling_ball function. (scikit-image#7682)

lagru added the 🤖 type: Infrastructure CI, packaging, tools and automation label Sep 27, 2024

lagru force-pushed the no-pytest-config branch from 1099802 to 5eb180a Compare September 27, 2024 15:29

lagru changed the title ~~Debug pytest config not being picked up in tests.yml workflow~~ Use pytest config in pyroject.toml in CI Sep 27, 2024

lagru added 5 commits September 27, 2024 17:49

Use correct operator to check if GITHUB_WORKSPACE exists

4832456

Merge branch 'main' into no-pytest-config

6e89255

Merge branch 'main' into no-pytest-config

4b1ea45

Ignore missing dask dependency in cycle_spin

1302660

Don't expect newbyteorder warning caused by tifffile

3d1ee66

I believe this warning disappeared with tifffile 2024.4.24 which added support for NumPy 2.

lagru marked this pull request as ready for review October 4, 2024 13:00

Merge branch 'main' into no-pytest-config

33a760e

stefanv changed the title ~~Use pytest config in pyroject.toml in CI~~ Use pytest config in pyproject.toml in CI Dec 17, 2024

lagru mentioned this pull request Jan 24, 2025

Ensure pytest configuration in pyproject.toml is picked up #7670

Closed

lagru closed this Jan 24, 2025

lagru reopened this Jan 26, 2025

lagru and others added 5 commits January 26, 2025 13:54

Merge branch 'main' into no-pytest-config

e8a0af8

Ignore warning if cg_mg is not available (missing pyamg)

78769af

Merge remote-tracking branch 'origin/main' into no-pytest-config

632ee80

Merge remote-tracking branch 'origin/main' into no-pytest-config

9fa9b21

Update test scripts in new locations

0f86606

stefanv force-pushed the no-pytest-config branch from acc76ca to 0f86606 Compare January 30, 2025 20:05

jarrodmillman mentioned this pull request Jan 30, 2025

Ignore UserWarning for missing pyamg in test #7686

Closed

Pin higher version of pytest

af51522

stefanv force-pushed the no-pytest-config branch from 33840e9 to af51522 Compare January 30, 2025 21:29

Pin newer dask to get rid of distutils warning

30cd057

stefanv force-pushed the no-pytest-config branch from 98ebcc5 to 30cd057 Compare January 30, 2025 22:50

stefanv added 2 commits January 30, 2025 15:34

Expect sparse efficiency warnings until new pyamg

dd41425

Merge remote-tracking branch 'origin/main' into no-pytest-config

6bf3ef1

New dask version requires newer cloudpickle

31392e4

stefanv force-pushed the no-pytest-config branch from c42b347 to 7ddd77f Compare January 31, 2025 00:57

Tell pytest where to find SparseEfficiencyWarning

816328a

stefanv force-pushed the no-pytest-config branch from 7ddd77f to 816328a Compare January 31, 2025 04:21

stefanv added 3 commits January 30, 2025 20:44

Catch additional warnings

50c8466

Up minimum version of SciPy to fix sparse errors

13d0398

Catch additional warning

977de1e

Ignore warnings raised by pyamg internally

e24d4af

stefanv force-pushed the no-pytest-config branch 4 times, most recently from 8564112 to f50c1e2 Compare January 31, 2025 07:20

Use a reasonable range in simpleitk roundtrip test

012137c

stefanv force-pushed the no-pytest-config branch from f50c1e2 to 012137c Compare January 31, 2025 07:42

jarrodmillman approved these changes Jan 31, 2025

View reviewed changes

Re-enable testing in Emscripten/Pyodide job

c3e6af1

Leaving this commented is probably an oversight from scikit-imagegh-7576 / a7b54a8.

lagru commented Jan 31, 2025

View reviewed changes

lagru merged commit 4f02015 into scikit-image:main Jan 31, 2025
25 checks passed

lagru deleted the no-pytest-config branch January 31, 2025 14:23

stefanv added this to the 0.25.2 milestone Feb 4, 2025

agriyakhetarpal mentioned this pull request Feb 20, 2025

Bump to Pyodide 0.27.2 stable and install available optional dependencies for WASM tests #7646

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Use pytest config in pyproject.toml in CI#7555

Use pytest config in pyproject.toml in CI#7555
lagru merged 24 commits intoscikit-image:mainfrom
lagru:no-pytest-config

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