DOC: Remove invalid ndarray option from colormap docstrings by Gnefil · Pull Request #13797 · mne-tools/mne-python

Gnefil · 2026-03-29T16:21:23Z

Reference issue

What does this implement/fix?

This PR solves the conflict between the documentation and the actual signature of mne.viz.plot_source_estimates, which doesn't accept a numpy array for colormap.

Additional information

A possible future minor enhancement would be to include a numpy array option and transform to colormap using matplotlib as suggested by larsoner in comments. If agreed, that could be my next PR.

Additionally, this is my first time contributing. I looked at the contributing guidelines, played with the code, and viewed how others create issues and PRs. But still, I might miss something, so don't hesitate to point out any mistakes! Finally, this is a work by Lifeng, a 2026 GSoC applicant for project 2.

Copilot

Pull request overview

Updates MNE-Python documentation to match the actual accepted types for the colormap parameter (fixing a mismatch where docs claimed np.ndarray was allowed, but runtime validation rejects it), and adds new-contributor attribution for the changelog.

Changes:

Update the shared colormap parameter docstring template to remove np.ndarray and document Matplotlib Colormap objects instead.
Add a Towncrier dev changelog entry describing the documentation fix.
Add the contributor name/link to doc/changes/names.inc.

Reviewed changes

Copilot reviewed 3 out of 3 changed files in this pull request and generated 3 comments.

File	Description
`mne/utils/docs.py`	Adjusts the canonical `colormap` parameter doc snippet to reflect accepted types.
`doc/changes/dev/13797.other.rst`	Adds a changelog entry for the documentation correction.
`doc/changes/names.inc`	Registers the new contributor for changelog attribution.

CarinaFo · 2026-03-30T06:13:19Z

Hi Gnefil,

thank you for your contribution.

If you sign up for a free account on circleci and link it to your github repo, the workflows related to documentation building will run (they are currently failing).

Gnefil · 2026-03-30T15:37:53Z

Hii @CarinaFo, thanks for replying!

If you sign up for a free account on circleci and link it to your github repo, the workflows related to documentation building will run (they are currently failing).

I have successfully signed up for CircleCI, however I am stucked in "No CircleCI organizations found" and "Join via invite". Account integration doesn't show GitHub, so I presume it is linked. This is after Join via GitHub option after signing up. Could you clarify what should be the next steps?

Thanks in advance!

JiwaniZakir

The docdict["colormap"] entry in mne/utils/docs.py is a shared docstring used across multiple functions, not just plot_source_estimates — so the changelog entry in 13797.other.rst likely understates the scope of this change. It would be worth auditing all callers of this docdict key (e.g., with a grep for "colormap" in the codebase) to confirm they all accept matplotlib.colors.Colormap and no longer accept raw np.ndarray inputs.

More critically, this PR updates documentation without a corresponding code change to the underlying implementation. If any of the functions that use this docstring still accept and handle np.ndarray arguments internally (as the old docstring described), the new docstring is now inaccurate and will silently mislead users who pass arrays — a behavioral regression in documentation fidelity. Conversely, if ndarray support was already broken or unimplemented, a deprecation notice or explicit error with a clear message would be more user-friendly than silently dropping it from the docs.

Also, 13797.other.rst is missing a newline at end of file, which may cause formatting issues in the rendered changelog.

Gnefil · 2026-03-31T04:47:21Z

Hii Zakir,

Thanks for your critical comments!

so the changelog entry in 13797.other.rst likely understates the scope of this change
a behavioral regression in documentation fidelity.

I see, then I am going to audit colormap callers in the whole codebase to see whether updating colormap documentation is enough, or fixing mne.viz.plot_source_estimates to accept ndarray instead.

a deprecation notice or explicit error with a clear message would be more user-friendly...

I beg to politely differ, aligning documentation with the actual behaviour should be the priority, then, raising an extra error for a type that is not accepted seems redundant. Anyways, I would check the previous step to see what action is suitable.

Also, 13797.other.rst is missing a newline at end of file, which may cause formatting issues in the rendered changelog.

Got it, will fix it in the next commit.

Thanks again for your extensive thoughts, really appreciate it!

Aniketsy · 2026-03-31T06:46:14Z

Also, 13797.other.rst is missing a newline at end of file, which may cause formatting issues in the rendered changelog.

@JiwaniZakir we don't need new line in changelog entry
Also my suggestion @Gnefil please wait for the review from maintainers if anything is unclear for you. Thanks!

Gnefil · 2026-03-31T15:23:05Z

Also my suggestion @Gnefil please wait for the review from maintainers if anything is unclear for you. Thanks!

Hii Aniket, I think you have a point as well. Sure, I will wait for a bit. Thanks for your suggestion!

JiwaniZakir · 2026-03-31T15:34:27Z

Thanks for the clarification on the newline — noted, I'll keep that in mind for future reviews. On the scope question, auditing colormap callers across the codebase makes sense given the changelog entry currently only references plot_source_estimates; if other functions share the same incorrect docstring pattern, they should be captured in this PR or the changelog updated to reflect the actual breadth of the fix.

Aniketsy · 2026-03-31T19:10:35Z

@JiwaniZakir please don't give fully ai generated comment, I just saw your comment in other PR and member mentioned you there for Ai generated comment, as it can leads to wrong direction .

JiwaniZakir · 2026-03-31T19:59:39Z

The fix looks correct — removing the ndarray option from the docstring aligns the documentation with the actual accepted types in the function signature. The suggestion to add actual ndarray support as a follow-up (converting via matplotlib) is a cleaner approach than keeping misleading docs. Worth tracking that as a separate issue if it's not already.

Gnefil · 2026-04-03T04:12:59Z

Hii all,

Three issues to comment.

The auditing of Colormap callers is over. I have spent some time auditing the callers. For the most appearance of colormap there weren't a problem. Functions in classes like viz.backends._abstract._AbstractRenderer and viz.brain._brain.Brain accept Colormap with its own docstrings. Nonetheless, due to the huge size of search results and caller nets, I am ready to fix it if any problem raises.

Swapping to accept ndarray instead of modifying the documentation and clarify it does not accept, is a pending suggestion. I have intentions to do it, but it needs maintainers word.

Failing CI is still a problem. I have searched and looked into resources, but still can't figure it out. Surprisingly, comments related to this issue would be urgently more helpful. Could someone type a word or two on the matter? How do I initialize documentation building having my GitHub account linked (logged-in then joined via GitHub)? Thanks in advance!

Welcome any follow-ups to the discussions.

JiwaniZakir · 2026-04-03T04:27:58Z

The docstring fix is straightforward and correct — removing a type that was never actually handled avoids misleading users into passing an ndarray and getting a confusing error. For the future enhancement of accepting ndarrays, it would be worth checking whether matplotlib.colors.ListedColormap(array) is sufficient or if normalization handling needs to be considered as well before adding that path.

CarinaFo · 2026-04-06T02:31:53Z

Regarding CircleCI tests failing, don't worry about that for now. We are updating the contributing guide to include some info on failing tests in PRs.
The recommended workflow is to ensure the documentation builds without errors on your local machine.
I suggest trying to build the docs locally.

CarinaFo

Doc changes look good, but need to be tested by building docs locally (see my last comment).

JiwaniZakir · 2026-04-06T03:06:04Z

The towncrier entry should use double backticks for the parameter name (colormap) to match the formatting convention used elsewhere in the changelog. Also worth double-checking that the updated docstring description doesn't retain any language implying array-like inputs are accepted — Copilot's note about "custom look up table" phrasing is worth addressing explicitly before this merges.

Gnefil · 2026-04-06T05:59:10Z

I apologise in advance if I am mistaken.

Could you please stop sending automatically generated messages? It is confusing, annoying, and only wastes energy in conversations. The double backstick and look-up table issues were already fixed in the last commit. The basis of automatically generated comments is not even based on the commits, but only on the messages. You don't even cheat right.

Next time, I will seek report requests.

JiwaniZakir · 2026-04-06T06:06:34Z

The fix looks correct in principle — removing the ndarray option from the docstring to match the actual function signature prevents misleading users. One thing worth verifying: make sure all callsites of colormap across the codebase (not just plot_source_estimates) have been audited, since the issue title says "docstrings" (plural) and the fix should be consistent everywhere that shared docstring snippet is used. If you used a numpydoc extended summary or a shared docdict entry for this parameter, a single change there would cover all functions at once rather than patching them individually.

Gnefil

Hii Carina,

Thanks for getting back. I have compiled the docs and run them locally; it looks fine. Regarding the CI process, got it.

Evidence:

Also, before:

and after:

Gnefil

Requested review accomplished. Could this PR proceed?

CarinaFo · 2026-04-12T06:30:48Z

Hi Gnefil,

Thank you for your contribution and for your patience. Everything looks good from my side.

I’ll be discussing the next steps for your PR with the other maintainers this week. At the moment, we’re unable to merge it as it’s currently awaiting another reviewer’s approval.

Apologies for the delay and any confusion during the review process. Please be assured that we’re actively monitoring the situation and working to move things forward.

Cheers,

Carina

Gnefil · 2026-04-12T08:21:02Z

Hii Carina,

No problem, thanks for keeping me updated! I just wanted to make sure that everything is in place. Your confirmation is reassuring.

I will wait for further instructions.

Kind regards,

welcome · 2026-04-17T19:04:03Z

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

larsoner · 2026-04-17T19:04:04Z

Thanks @Gnefil !

Gnefil · 2026-04-19T09:38:21Z

My pleasure!

…s#13797)

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Binns <[email protected]> * [pre-commit.ci] pre-commit autoupdate (mne-tools#13818) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: mne[bot] <[email protected]> * MAINT: Update code credit [ci skip] (mne-tools#13823) Co-authored-by: Eric Larson <[email protected]> * Update values to int64 (mne-tools#13548) Co-authored-by: Eric Larson <[email protected]> Co-authored-by: autofix-ci[bot] <114827586+autofix-ci[bot]@users.noreply.github.com> Co-authored-by: Daniel McCloy <[email protected]> * FIX: Installer links etc [ci skip] * TST: Doc * FIX: correct mode parameter in get_point_spread and get_cross_talk (mne-tools#13754) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * DOC: Add epoch quality example (mne-tools#13710) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Thomas S. Binns <[email protected]> * Change syncing of dependencies with `README` (mne-tools#13832) * DOC: Fix changelog [circle deploy] (mne-tools#13833) Co-authored-by: Thomas S. Binns <[email protected]> * Exclude private submodules (e.g., _edf) from Credits page (mne-tools#13673) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * BUG: Fix bug with backward compat [circle deploy] (mne-tools#13835) * Fix bug with credit [circle deploy] (mne-tools#13841) * ENH: broaden OPM coil handling for colocated topomaps (mne-tools#13825) * DOC: Add artifact-cleaning note to epoch quality example. (mne-tools#13827) * [pre-commit.ci] pre-commit autoupdate (mne-tools#13839) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: mne[bot] <[email protected]> Co-authored-by: Eric Larson <[email protected]> * FIX: Ref [skip azp] [skip actions] * BUG: Fix bug with logging level (mne-tools#13843) * fix env var in actions (mne-tools#13844) Co-authored-by: Scott Huberty <[email protected]> * TST: Add regression coverage for OPM topomap grouping via `plot_joint()` and `ICA` (mne-tools#13842) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * Customize annotation colors (mne-tools#13838) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * DOC: Remove invalid ndarray option from colormap docstrings (mne-tools#13797) * Fix versionadded for annotation_colors (mne-tools#13853) * [dependabot]: Bump the actions group with 2 updates (mne-tools#13852) Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: mne[bot] <[email protected]> * [pre-commit.ci] pre-commit autoupdate (mne-tools#13854) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: mne[bot] <[email protected]> * MAINT: Links [circle deploy] [skip azp] [skip actions] * MAINT: add OPM overlap grouping helper (mne-tools#13847) * FIX: Correct fNIRS interpolation with reordered picks (mne-tools#13856) * MAINT: Modernize numpydoc checks (mne-tools#13865) * Allow concatenating `BaseRaw` objects (mne-tools#13263) Co-authored-by: Copilot <[email protected]> Co-authored-by: Eric Larson <[email protected]> * Add dark theme to Matplotlib-based raw.plot (mne-tools#13861) Co-authored-by: Copilot <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * FIX: Check [ci skip] * FIX: Sets [ci skip] * Update towncrier change type descriptions (mne-tools#13829) * fix numpydoc (missed YD01 ignore) (mne-tools#13868) * FIX: correct label orientation for 0-90 deg nodes in plot_connectivity_circle (mne-tools#13855) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Daniel McCloy <[email protected]> * [dependabot]: Bump the actions group with 3 updates (mne-tools#13871) Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: mne[bot] <[email protected]> * [pre-commit.ci] pre-commit autoupdate (mne-tools#13873) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: mne[bot] <[email protected]> * Add preload keyward argument to Inst.load_data() method call (mne-tools#13858) * MAINT: Make test dir read-only (mne-tools#13872) * BUG: improve FreeSurfer error message when executable not found (mne-tools#13874) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Eric Larson <[email protected]> * add CI description to contributing guide (mne-tools#13837) Co-authored-by: Daniel McCloy <[email protected]> * Fix grammar [ci skip] (mne-tools#13881) * FIX: handle missing __version__ in check_version (mne-tools#13870) Co-authored-by: Claude Sonnet 4.6 <[email protected]> * apply diataxis to tutorials/inverse/80_brainstorm_phantom_elekta.py (mne-tools#13584) Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * add AI policy (mne-tools#13883) * MAINT: Switch to pip for macOS and minimal jobs (mne-tools#13882) * MAINT: Update code credit (mne-tools#13878) * ENH: Allow passing source detector distances to beer lambert law (mne-tools#13875) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * MAINT: Update for vtk deprecation (mne-tools#13886) * ENH: Add overrides= parameter to read_raw_brainvision for BIDS header repair (mne-tools#13884) * Fix bug with ica.plot_properties (mne-tools#13885) * Fix `picks` being ignored in `Epochs.apply_function()` (mne-tools#13894) * Update describing changes in contributing guide (mne-tools#13895) * Add Zuna to related software list (mne-tools#13849) Co-authored-by: Daniel McCloy <[email protected]> * [dependabot]: Bump github/codeql-action from 4.35.2 to 4.35.3 in the actions group (mne-tools#13897) Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: mne[bot] <[email protected]> Co-authored-by: Eric Larson <[email protected]> * DOC: Fix apply_function shape description for Epochs (mne-tools#13891) Co-authored-by: Eric Larson <[email protected]> * Raise warning and errors when np.nan provided to mne.stats.permutation_t_test(). (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 <[email protected]> * 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 <[email protected]> * [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] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: mne[bot] <[email protected]> * [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] <[email protected]> * 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] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: mne[bot] <[email protected]> * [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] <[email protected]> * 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 <[email protected]> * 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. Binns <[email protected]> Co-authored-by: Daniel McCloy <[email protected]> * FIX: Make set_eeg_reference working with a string for a channel name (mne-tools#13917) --------- Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: mne[bot] <[email protected]> Co-authored-by: Clemens Brunner <[email protected]> Co-authored-by: Aman Srivastava <[email protected]> Co-authored-by: Daniel McCloy <[email protected]> Co-authored-by: Himanshu Mahor <[email protected]> Co-authored-by: Scott Huberty <[email protected]> Co-authored-by: Victor Férat <[email protected]> Co-authored-by: Marijn van Vliet <[email protected]> Co-authored-by: Eric Larson <[email protected]> Co-authored-by: Aniket <[email protected]> Co-authored-by: Carina Forster <[email protected]> Co-authored-by: Thomas S. Binns <[email protected]> Co-authored-by: Erica Peterson <[email protected]> Co-authored-by: Horizon_Architect_07 <[email protected]> Co-authored-by: Pragnya <[email protected]> Co-authored-by: Benedikt Ehinger <[email protected]> Co-authored-by: Kay Robbins <[email protected]> Co-authored-by: Bru <[email protected]> Co-authored-by: Stefan Appelhoff <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Johannes Herforth <[email protected]> Co-authored-by: Hansuja <[email protected]> Co-authored-by: Simon Kern <[email protected]> Co-authored-by: autofix-ci[bot] <114827586+autofix-ci[bot]@users.noreply.github.com> Co-authored-by: Akhilesh <[email protected]> Co-authored-by: CHH <[email protected]> Co-authored-by: Teon L Brooks <[email protected]> Co-authored-by: Lifeng <[email protected]> Co-authored-by: Kalle Mäkelä <[email protected]> Co-authored-by: Copilot <[email protected]> Co-authored-by: Pavel Popov <[email protected]> Co-authored-by: Ayushi Satodiya <[email protected]> Co-authored-by: Seth Bashford <[email protected]> Co-authored-by: Baris <[email protected]> Co-authored-by: Claude Sonnet 4.6 <[email protected]> Co-authored-by: Jonas Mago <[email protected]> Co-authored-by: Bhargav Kowshik <[email protected]> Co-authored-by: Erica R Peterson <[email protected]> Co-authored-by: Ben Tang <[email protected]> Co-authored-by: myd7349 <[email protected]> Co-authored-by: Michael Straube <[email protected]>

Gnefil added 2 commits March 30, 2026 00:04

DOC: Remove invalid ndarray option from colormap docstrings

a3a6e3a

DOC: Add changelog for mne-tools#13797

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Gnefil marked this pull request as ready for review March 29, 2026 17:27

Gnefil requested review from agramfort, drammock and larsoner as code owners March 29, 2026 17:27

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DOC: Update to clearer explanation and apply backticks correctly

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Gnefil requested a review from CarinaFo April 6, 2026 06:21

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tsbinns mentioned this pull request Apr 7, 2026

mne.viz.plot_source_estimates docs incorrectly say colormap can be supplied as an ndarray #13189

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tsbinns mentioned this pull request Apr 7, 2026

DOC: Correct colormap types in global docdict #13822

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Gnefil commented Apr 10, 2026

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CarinaFo mentioned this pull request Apr 14, 2026

add CI description to contributing guide #13837

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larsoner merged commit d862945 into mne-tools:main Apr 17, 2026
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paavalipopov pushed a commit to paavalipopov/mne-python that referenced this pull request Apr 20, 2026

DOC: Remove invalid ndarray option from colormap docstrings (mne-tool…

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…s#13797)

Gnefil deleted the fix-stc-colormap-doc branch May 16, 2026 14:23

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