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Improve type checks - #14036

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larsoner merged 27 commits into
mne-tools:mainfrom
larsoner:types
Jul 14, 2026
Merged

Improve type checks#14036
larsoner merged 27 commits into
mne-tools:mainfrom
larsoner:types

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@larsoner

@larsoner larsoner commented Jul 8, 2026 •
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  1. Move from mypy to ty, including as pre-commit as ty is fast enough 🚀
  2. Add a consistency check for documented types (NumpyDoc) and our types (this check could eventually move to docstub but let's use it here for a bit)
  3. Stricter enforcement (mypy missed some stuff) and checking in epochs.py, evoked.py, and mne/io
  4. Correctly type the io.read_raw_*, but keep their docs/ / website aliases pointing to publicly documented objects
  5. Most typing changes were of the form 1) dict[str, Any], 2) assert x is not None for when x is self._data etc. (places where we know it is by code structure), plus using __getattr__ and __setattr__ to get *Bunch classes to play nicely
  6. Some simplification of ctf/res4.py because type checkers have trouble with NumPy structured arrays
  7. Various minor fixes caught by the tests + checker, like instance of RawEDF where we should have had instance of RawBDF
  8. Switch to prek in CIs instead of pre-commit (pre-commit fails because our pre-commit env is too large now)

Potential other things:

  • Could switch contrib guide from pre-commit to prek if we wanted
  • Could bumpy Python version to 3.11 (3.10 EOL in Oct; 3.11 will be SPEC0-dropped soon actually!), it would simplify a little bit of stuff (no need for typing_extensions)

A follow-up PR can actually fully type hint the public functions + classes, but this is a (I'd argue necessary) prerequisite!

Used Claude Opus 4.8 to help me with the drudgery of assert x is not None etc., but I also made a lot of changes myself, and understand + vouch for all code.

Makes progress toward #12243

larsoner added 3 commits July 8, 2026 17:16
@larsoner
FIX: Count
37fb45e
@larsoner
Merge remote-tracking branch 'upstream/main' into types
03cdf8d 
* upstream/main:
  Fix transition bandwidth reported in 'filter too short' error (mne-tools#11406) (mne-tools#14005)
@larsoner
MAINT: Move to prek
bc6f17c
@larsoner

larsoner commented Jul 8, 2026 •
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Okay too many packages needed for type checking made pre-commit.ci unhappy, so here I move to prek + prek-action in autofix.yml instead. pre-commit.ci will be red here, but once we're happy with this PR we can merge it and disable pre-commit.ci and use prek. (prek uses the preexisting .pre-commit-config.yml and is a nice, faster version of it.) We could also consider other toolsk, but prek is the least invasive to existing dev workflows (people can continue to equvialently continue using pre-commit locally if they want!)

@larsoner

larsoner commented Jul 8, 2026

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A tiny bit of stuff here would get simpler if we dropped 3.10 support. 3.11 is actually almost out of SPEC0 so I don't mind dropping 3.10 now. But not too painful to keep it. It's EOL in October.

@Aniketsy

Aniketsy commented Jul 11, 2026

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nice to see these changes on type check improvement, @larsoner thanks for the work ❤️ , I tried to go through the pr to help with review but it includes many changes so i quit 😁 (leaving for members).

A follow-up PR can actually fully type hint the public functions + classes, but this is a (I'd argue necessary) prerequisite!

happy to help if needed, please feel free to ping 😊

@larsoner
Merge remote-tracking branch 'upstream/main' into types
6a5387c 
* upstream/main:
  Make scrollbar handlers draggable (mne-tools#14040)
  [pre-commit.ci] pre-commit autoupdate (mne-tools#14052)
  Warn when Epochs events fall outside the raw data range (mne-tools#12989) (mne-tools#14004)
  Ensure epochs being concatenated have compatible event ids (mne-tools#14051)
  Widen main content area (mne-tools#14015)
  MAINT: remove dead gain/bits/value_range fields from _read_header in … (mne-tools#14047)
  ENH: replace `_get_blocks` binary reader with mffpy Reader API (mne-tools#14043)
  MAINT: Update dependency specifiers (mne-tools#14048)
  [dependabot]: Bump the actions group with 2 updates (mne-tools#14049)
  Simplify doc building with more refleak (mne-tools#14045)
  ENH: add overlay Brain GUI (mne-tools#14031)
  ENH: support multiple simultaneous overlays in Brain.add_data (mne-tools#13995)
  Add option to show a zero line in browser (mne-tools#14018)
  FIX: pass cmap name string not tuple to interactive topomap slider kwargs (mne-tools#14039)
  Doc/add ai policy pointer (mne-tools#14037)
  Allow subclasses of FigureClass to be passed to plot_raw/plot_epochs (mne-tools#13979)
  MAINT: Replace manual PNS binary block reader in `_read_segment_file` with `mffpy` (mne-tools#14030)
@larsoner

larsoner commented Jul 14, 2026

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Okay this approach is working in several projects (mne-kit-gui, sphinx-gallery, etc.) and seems to be working here, so I'll go ahead and merge so that we don't get more and more conflicts!

@larsoner
larsoner enabled auto-merge (squash) July 14, 2026 15:32
@larsoner
larsoner merged commit 6bd165d into mne-tools:main Jul 14, 2026
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@larsoner
larsoner deleted the types branch July 14, 2026 16:34
larsoner added a commit to larsoner/mne-python that referenced this pull request Jul 14, 2026
@larsoner @claude
Merge upstream/main into typed-fully
1dac7c8 
Resolve conflicts from the landed ty type-checker PR (mne-tools#14036) and
intervening feature PRs:

- CI (autofix.yml/tests.yml/azure-pipelines.yml): take upstream's canonical
  restructure (vulture moved into the autofix job, mypy->ty, style job removed);
  our preliminary CI edits were superseded.
- Type-checker infra (_typing.py, test_docstring_parameters.py): keep our richer
  doc/api-scoped consistency checker (superset comparison, Color/FileLike
  pseudo-type aliases, Literal handling) which subsumes upstream's simpler one;
  add a `class`->`type` pseudo-type normalization for the new `figure_class`.
- New upstream features merged with our annotations: `on_outside` on
  BaseEpochs/Epochs/EpochsArray, `show_zero_line`/`figure_class` on
  Raw.plot/Epochs.plot (annotated to match their numpydoc types).
- egi: drop the now-dead `_block_r`/`_get_blocks` helpers and take upstream's
  `_get_mff_reader`-based PNS reader; keep our `_get_signalfname` assert fix.

ty pre-commit hook, ruff, and test_type_hints_match_docstrings all pass.

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
larsoner added a commit to sharifhsn/mne-python that referenced this pull request Jul 14, 2026
@larsoner
Merge remote-tracking branch 'upstream/main' into sharifhsn-perf-opt
b07384e 
* upstream/main: (206 commits)
  Improve type checks (mne-tools#14036)
  Make scrollbar handlers draggable (mne-tools#14040)
  [pre-commit.ci] pre-commit autoupdate (mne-tools#14052)
  Warn when Epochs events fall outside the raw data range (mne-tools#12989) (mne-tools#14004)
  Ensure epochs being concatenated have compatible event ids (mne-tools#14051)
  Widen main content area (mne-tools#14015)
  MAINT: remove dead gain/bits/value_range fields from _read_header in … (mne-tools#14047)
  ENH: replace `_get_blocks` binary reader with mffpy Reader API (mne-tools#14043)
  MAINT: Update dependency specifiers (mne-tools#14048)
  [dependabot]: Bump the actions group with 2 updates (mne-tools#14049)
  Simplify doc building with more refleak (mne-tools#14045)
  ENH: add overlay Brain GUI (mne-tools#14031)
  ENH: support multiple simultaneous overlays in Brain.add_data (mne-tools#13995)
  Add option to show a zero line in browser (mne-tools#14018)
  FIX: pass cmap name string not tuple to interactive topomap slider kwargs (mne-tools#14039)
  Doc/add ai policy pointer (mne-tools#14037)
  Allow subclasses of FigureClass to be passed to plot_raw/plot_epochs (mne-tools#13979)
  MAINT: Replace manual PNS binary block reader in `_read_segment_file` with `mffpy` (mne-tools#14030)
  Fix transition bandwidth reported in 'filter too short' error (mne-tools#11406) (mne-tools#14005)
  ENH: Show the current time as a vertical line in plot_evoked_topo (mne-tools#14032)
  ...
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@larsoner @Aniketsy