Update Python dependencies and fix GitHub Actions workflow by rcmdnk · Pull Request #99 · mne-tools/mne-features

rcmdnk · 2025-10-15T15:36:46Z

ubuntu-20.04 is obsolete and no longer supported. Since this repository does not strongly depend on a specific OS version, it is better to use ubuntu-latest to simplify maintenance.
Update outdated actions:
- actions/checkout, conda-incubator/setup-miniconda, and codecov/codecov-action.
Add Python 3.10 and 3.13 to the matrix strategy.
- Python 3.8 has already reached end of life, and some libraries no longer support it with their latest versions.
- The test suite should therefore include newer Python releases.
- Python 3.9 will also reach end of life at the end of October.
- Although Python 3.14 is the latest version, Numba does not yet support it (numba/numba#9957
  ).
- Hence, Python 3.10 and 3.13 were added to the matrix.
Remove env.PYTHON_VERSION and replace it with matrix.python-version for consistency with the workflow matrix configuration.

All tests will pass once #97 and #98 are merged.
Example test result is here: https://github.com/rcmdnk/mne-features/actions/runs/18524132632

jbschiratti · 2025-10-17T16:51:21Z

Thank you @rcmdnk for this PR! The workflow file has not been updated in a long time.

In my opinion, we should support Python >= 3.12,<3.14:

Python 3.10 will be deprecated in a year (~Oct. 2026)
As you noted, numba does not yet support Python 3.14.

Can you, please, update the workflow file to use 3.12 and 3.13?

rcmdnk · 2025-10-17T18:08:04Z

@jbschiratti
Thank you for the review.

The Python versions in the workflow have been updated to 3.12 and 3.13.

Regarding the Python version requirements, there are a few differences:

python>=3.8: specified in environment.yml for Conda
python_requires='>=3.6': specified in setup.py for the package build (PyPI requirement)

It would be good to align and maintain these versions consistently at some point.

As for merging, it seems I don’t have the permission to merge this PR.
Could you please merge it for me?

rcmdnk · 2025-10-17T18:13:22Z

It may be necessary for all checks to pass before merging this PR.
If that’s the case, I can create a combined PR including #97, #98, and this one (#99).

Would you prefer that I combine these commits into this PR, or open a new PR instead?

jbschiratti · 2025-10-17T19:21:02Z

@hubertjb Thank you for the review.

Be careful, you're tagging someone else on this PR.

The Python versions in the workflow have been updated to 3.12 and 3.13.

I've thought about this and I think that it would make sense to align with what's done in mne-python or scikit-learn.

Therefore, I'd suggest:

requires_python=">=3.10,<3.14" in setup.py
python >=3.10,<3.14 in environment.yaml
python-version: [ "3.10", "3.11", "3.12", "3.13" ] in main.yml

rcmdnk · 2025-10-17T19:43:47Z

I'm sorry for the wrong mention.

Regarding the Python version requirements, I think it’s safer not to set <3.14 for this project.
If we specify <3.14, we’ll need to make a new release as soon as Numba releases a version that supports Python 3.14.
In addition, Python 3.15 is expected to be released next year.

agramfort · 2025-10-19T07:34:28Z

@rcmdnk I just made you a maintainer of the repo. Thanks for helping this project stay usable by the community 🙏

rcmdnk · 2025-10-20T04:55:21Z

Thanks! This library is very useful, and I’ll try to keep it in good shape.

I've rebased this branch onto master (including #97, #98), and all tests are now green.
For this PR, I’ve set the Python version requirement to >=3.8 to minimize the impact.
If you’re okay with that, I’ll go ahead and merge the PR.

Note

The setup-miniconda action sometimes raises a CondaHTTPError.
Such jobs usually succeed when retried.
It seems the issue tends to occur more often at certain times of the day.
Ref: conda-incubator/setup-miniconda#129

To mitigate this, I’ve increased the number of retries and the timeout in the Conda configuration.
However, some jobs may still fail occasionally.
If that happens, simply re-run the failed jobs and they should pass.

jbschiratti · 2025-10-20T06:52:11Z

@rcmdnk Thank you very much for updating the repository.

One remark: I'm not sure that we need python >= 3.8 as Python 3.8 has reached end-of-life on October 2024.
If some people are still using Python 3.8, they probably should upgrade to Python 3.10 (or even Python 3.12).
I'd suggest to set python >= 3.10,<3.14. When numba is stable on Python 3.14, we'll allow 3.14 as well.

jbschiratti · 2025-10-20T08:18:58Z

examples/plot_feature_names_analysis.py

+    of auditory vs. visual stimuli).
+
+"""
+# Author: Jean-Baptiste Schiratti <jean.baptiste.schiratti@gmail.com>


You may add your name and e-mail in this list of authors :-)

jbschiratti · 2025-10-20T08:20:04Z

examples/plot_feature_names_analysis.py

Did you check that you can successfully generate the docs with this new example?

jbschiratti · 2025-10-20T08:20:35Z

examples/plot_feature_names_analysis.py

+
+X_train, X_test, y_train, y_test = train_test_split(data, y, test_size=0.2)
+accuracy = pipe.fit(X_train, y_train).score(X_test, y_test)
+print("Accuracy score = %1.3f" % accuracy)


Please use f-string instead

jbschiratti · 2025-10-20T08:22:32Z

mne_features/univariate.py

        return ['ch%s' % ch for ch in range(n_channels)]
    else:
-        return ['ch%s_%s' % (ch, i) for ch in range(n_channels)
+        return ['ch%s__%s' % (ch, i) for ch in range(n_channels)


Please use f-strings instead

The same comment applies to other places of this file.

jbschiratti · 2025-10-20T08:24:55Z

mne_features/feature_extraction.py

+        """Get the feature names"""
+        # trick: use only the first epoch to get the feature names
+        df = extract_features(
+            X[:1],


Suggested change

X[:1],

X[0],

jbschiratti · 2025-10-20T08:26:11Z

mne_features/feature_extraction.py


    feature_names : list of str

+    separator : str


Should list valid separators? Not all strings should be used as separators, right?

For example:

Suggested change

separator : str

separator : Literal["", "_", "__"]

jbschiratti

Thanks a lot @rcmdnk for these changes and updating the unit tests.

A few changes are needed before we merge this

chore: upgrade `actions/checkout` to v5 in .github/workflows/main.yml chore: upgrade `conda-incubator/setup-miniconda` to v3 in .github/workflows/main.yml chore: upgrade `codecov/codecov-action` to v5 in .github/workflows/main.yml chore: update Ubuntu runner to `ubuntu-latest` in .github/workflows/main.yml chore: add Python 3.10,3.11,3.12,3.13 to matrix strategy in .github/workflows/main.yml chore: Configure retries and timeouts for conda downloads in .github/workflows/main.yml chore: update python version (>=3.10,<3.14) in setup.py and environment.yml — 3.9 reaches end of security support in Oct 2025, and 3.14 is not yet supported by Numba (numba/numba#9957)

rcmdnk · 2025-10-20T09:03:57Z

@jbschiratti

Sorry, some previous commit hashes were changed when I rebased histories.
I've not changed examples/plot_feature_names_analysis.py in this PR.
The history was fixed and this PR changes only .github/fowkflows/main.yml, setup.py, and enviroment.yml.

As you mentioned above, I've updated python version as >=3.10,<3.14 in these files.

rcmdnk · 2025-11-20T07:49:49Z

#100 includes these ubuntu/python updates.
Therefore, I close this PR.

This was referenced Oct 15, 2025

Handle single sample output from FeatureFunctionTransformer to support scikit-learn 1.7.2 and later #97

Merged

Replace np.Inf with np.inf in tests #98

Merged

rcmdnk changed the title ~~Update GitHub Actions workflows and dependencies~~ Update Python dependencies (GitHub Actions, environment.yaml, setup.py) Oct 17, 2025

rcmdnk changed the title ~~Update Python dependencies (GitHub Actions, environment.yaml, setup.py)~~ Update Python dependencies and fix GitHub Actions workflow Oct 19, 2025

rcmdnk force-pushed the github_actions branch 3 times, most recently from 7a3ea61 to 3b7a460 Compare October 20, 2025 02:08

rcmdnk force-pushed the github_actions branch from 3b7a460 to a3f0948 Compare October 20, 2025 07:24

jbschiratti reviewed Oct 20, 2025

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Did you check that you can successfully generate the docs with this new example?

jbschiratti reviewed Oct 20, 2025

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rcmdnk force-pushed the github_actions branch from a3f0948 to dadd352 Compare October 20, 2025 08:59

larsoner mentioned this pull request Nov 19, 2025

ENH: Add release workflow and prep 0.3.1 #100

Merged

rcmdnk closed this Nov 20, 2025

bruAristimunha mentioned this pull request Nov 21, 2025

Release new version when numba release compatibility within python 3.14 #103

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rcmdnk deleted the github_actions branch February 1, 2026 03:20

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