DOC: Fix apply_function shape description for Epochs (#13118) by bkowshik · Pull Request #13891 · mne-tools/mne-python

bkowshik · 2026-05-08T05:31:17Z

Reference issue (if any)

What does this implement/fix?

The fun parameter docstring for mne.Epochs.apply_function incorrectly stated that the array passed to the user's function when channel_wise=False has shape (len(picks), n_times). The actual shape is (n_epochs, n_channels, n_times). Adds a new fun_applyfun_epochs docdict entry alongside fun_applyfun_evoked and fun_applyfun_stc, leaving the Raw docstring (where (len(picks), n_times) is correct) untouched.

Related (out of scope): https://mne.discourse.group/t/epochs-apply-function-channel-wise-false-picks-silently-ignores-picks/11828 — separate question about whether picks should be honored when channel_wise=False on Epochs.

Documentation post the fix looks like below:

cd doc
make html-noplot
make show

Additional information

Have used Claude Code to understand the issue, identify the location of fix, commands to build locally for testing.

tsbinns

Thanks for opening this PR @bkowshik! I have only a very minor comment.

Please have a look at the instructions for documenting these changes in our contributing guide, so that you can be credited.
For a small documentation change like this, the other change type fits best.

tsbinns · 2026-05-10T17:13:26Z

    " if ``channel_wise=True`` and ``(len(picks), n_times)`` otherwise"
 )
+docdict["fun_applyfun_epochs"] = applyfun_fun_base.format(
+    " if ``channel_wise=True`` and ``(n_epochs, n_channels, n_times)`` otherwise"


Suggested change

" if ``channel_wise=True`` and ``(n_epochs, n_channels, n_times)`` otherwise"

" if ``channel_wise=True`` (because it will apply to 1-D slices along the times axis) and ``(n_epochs, len(picks), n_times)`` otherwise"

Suggest changing n_channels to len(picks) for consistency with the docstring of Raw.apply_function().

Suggest explaining why n_epochs isn't included as a dimension when channel_wise=True (np.apply_along_axis is used to apply the function to 1-D slices along the times axis).

You would need to fix the line length of this suggestion afterwards if applying directly.

Made the change here: 01c233a

Documentation post this change is looking like this.

The fun parameter docstring for mne.Epochs.apply_function incorrectly stated that the array passed to the user's function when channel_wise=False has shape (len(picks), n_times). The actual shape is (n_epochs, n_channels, n_times). Adds a new fun_applyfun_epochs docdict entry alongside fun_applyfun_evoked and fun_applyfun_stc, leaving the Raw docstring (where (len(picks), n_times) is correct) untouched. Per scott-huberty's review suggestion on mne-tools#13136. Fixes mne-tools#13118

@tsbinns

Apply @tsbinns review suggestion (n_channels -> len(picks); explain channel_wise=True shape).

Add 13891.other.rst (other type) and Bhargav Kowshik to names.inc as new contributor.

bkowshik · 2026-05-12T11:39:36Z

Thank you so much for the review, feedback and the PR fixing the issue! 👏

Please have a look at the instructions for documenting these changes in our contributing guide, so that you can be credited. For a small documentation change like this, the other change type fits best.

Made the change in this commit: 3f3793c

tsbinns

Thanks for the changes @bkowshik, looks good!

welcome · 2026-05-13T17:55:10Z

🎉 Congrats on merging your first pull request! 🥳 Looking forward to seeing more from you in the future! 💪

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(mne-tools#13813) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Erica R Peterson <38704848+nordme@users.noreply.github.com> * MAINT: Update dependency specifiers (mne-tools#13899) Co-authored-by: autofix-ci[bot] <114827586+autofix-ci[bot]@users.noreply.github.com> Co-authored-by: Eric Larson <larson.eric.d@gmail.com> * [dependabot]: Bump github/codeql-action from 4.35.3 to 4.35.4 in the actions group (mne-tools#13901) Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: mne[bot] <50266005+mne-bot@users.noreply.github.com> * [pre-commit.ci] pre-commit autoupdate (mne-tools#13902) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: mne[bot] <50266005+mne-bot@users.noreply.github.com> * MAINT: Remove workaround for old PySide6 (mne-tools#13900) * Add spherical montages (mne-tools#13903) * [dependabot]: Bump the actions group with 2 updates (mne-tools#13918) Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: mne[bot] <50266005+mne-bot@users.noreply.github.com> * [pre-commit.ci] pre-commit autoupdate (mne-tools#13919) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: mne[bot] <50266005+mne-bot@users.noreply.github.com> * MAINT: Update dependency specifiers (mne-tools#13916) Co-authored-by: autofix-ci[bot] <114827586+autofix-ci[bot]@users.noreply.github.com> Co-authored-by: Eric Larson <larson.eric.d@gmail.com> * BUG: set_eeg_reference list ch_type now applies per-type CAR by default (mne-tools#13920) * FIX: Avoid iteration errors caused by None when reading Nihon Kohden .LOG files (mne-tools#13915) * Fix drop_log dtype (mne-tools#13923) * Doc: add guidance on taking over a stale pull request (mne-tools#13877) Co-authored-by: Thomas S. 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bkowshik requested review from agramfort, drammock and mscheltienne as code owners May 8, 2026 05:31

tsbinns requested changes May 10, 2026

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bkowshik force-pushed the fix/issue-13118-epochs-applyfun-docstring branch from 93fc229 to 5abd7b1 Compare May 12, 2026 11:10

bkowshik added 2 commits May 12, 2026 17:06

DOC: address review on apply_function Epochs docstring (mne-tools#13891)

01c233a

Apply @tsbinns review suggestion (n_channels -> len(picks); explain channel_wise=True shape).

DOC: add changelog entry for mne-tools#13891

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Add 13891.other.rst (other type) and Bhargav Kowshik to names.inc as new contributor.

bkowshik requested a review from larsoner as a code owner May 12, 2026 11:37

bkowshik requested a review from tsbinns May 12, 2026 11:39

Merge branch 'main' into fix/issue-13118-epochs-applyfun-docstring

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tsbinns approved these changes May 13, 2026

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tsbinns enabled auto-merge (squash) May 13, 2026 17:22

tsbinns merged commit a6fd5cd into mne-tools:main May 13, 2026
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DOC: Fix apply_function shape description for Epochs (#13118)#13891

DOC: Fix apply_function shape description for Epochs (#13118)#13891
tsbinns merged 4 commits into
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bkowshik:fix/issue-13118-epochs-applyfun-docstring

bkowshik commented May 8, 2026 •

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	" if ``channel_wise=True`` and ``(n_epochs, n_channels, n_times)`` otherwise"
	" if ``channel_wise=True`` (because it will apply to 1-D slices along the times axis) and ``(n_epochs, len(picks), n_times)`` otherwise"

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bkowshik commented May 8, 2026 • edited Loading Uh oh! There was an error while loading. Please reload this page.

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bkowshik commented May 8, 2026 •

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