MAINT: Add rstcheck to CIs and pre-commit

.pre-commit-config.yaml

@@ -41,3 +41,13 @@ repos:
     hooks:
       - id: yamllint
         args: [--strict, -c, .yamllint.yml]
+
+  # rstcheck
+  - repo: https://github.com/rstcheck/rstcheck.git
+    rev: v6.2.0
+    hooks:
+      - id: rstcheck
+        files: ^doc/.*\.(rst|inc)$
+        # https://github.com/rstcheck/rstcheck/issues/199
+        # https://github.com/rstcheck/rstcheck/issues/200
+        exclude: ^doc/(help/faq|install/manual_install|install/mne_c|install/advanced|install/updating|_includes/channel_interpolation|_includes/inverse|_includes/ssp)\.rst$

doc/_includes/dig_formats.rst

@@ -1,4 +1,5 @@
 :orphan:
+
 .. _dig-formats:
 
 Supported formats for digitized 3D locations

doc/development/contributing.rst

@@ -1111,3 +1111,5 @@ it can serve as a useful example of what to expect from the PR review process.
 
 .. _optipng: http://optipng.sourceforge.net/
 .. _optipng for Windows: http://prdownloads.sourceforge.net/optipng/optipng-0.7.7-win32.zip?download
+
+.. include:: ../links.inc

doc/documentation/design_philosophy.rst

@@ -94,3 +94,5 @@ of data.
 .. LINKS
 
 .. _`method chaining`: https://en.wikipedia.org/wiki/Method_chaining
+
+.. include:: ../links.inc

doc/documentation/index.rst

@@ -59,3 +59,5 @@ Documentation for the related C and MATLAB tools are available here:
    cookbook
    cite
    cited
+
+.. include:: ../links.inc

doc/install/mne_tools_suite.rst

@@ -112,3 +112,5 @@ Help with installation is available through the `MNE Forum`_. See the
 .. _invertmeeg: https://github.com/LukeTheHecker/invert
 .. _MNE-ARI: https://github.com/john-veillette/mne_ari
 .. _niseq: https://github.com/john-veillette/niseq
+
+.. include:: ../links.inc

mne/decoding/tests/test_search_light.py

@@ -2,6 +2,7 @@
 #
 # License: BSD-3-Clause
 
+import platform
 from inspect import signature
 
 import numpy as np
@@ -10,7 +11,7 @@
 
 from mne.decoding.search_light import GeneralizingEstimator, SlidingEstimator
 from mne.decoding.transformer import Vectorizer
-from mne.utils import _record_warnings, use_log_level
+from mne.utils import _record_warnings, check_version, use_log_level
 
 pytest.importorskip("sklearn")
 
@@ -29,6 +30,9 @@ def make_data():
 
 def test_search_light():
     """Test SlidingEstimator."""
+    # https://github.com/scikit-learn/scikit-learn/issues/27711
+    if platform.system() == "Windows" and check_version("numpy", "2.0.0.dev0"):
+        pytest.skip("sklearn int_t / long long mismatch")
     from sklearn.linear_model import LogisticRegression, Ridge
     from sklearn.metrics import make_scorer, roc_auc_score
     from sklearn.pipeline import make_pipeline

pyproject.toml

@@ -140,3 +140,17 @@ exclude = "(dist/)|(build/)|(.*\\.ipynb)"
 
 [tool.bandit.assert_used]
 skips = ["*/test_*.py"] # assert statements are good practice with pytest
+
+[tool.rstcheck]
+report_level = "WARNING"
+ignore_roles = [
+    "func", "class", "term", "ref", "doc", "gh", "file", "samp", "meth", "mod", "kbd",
+    "newcontrib", "footcite", "footcite:t", "eq", "py:mod", "attr", "py:class", "exc",
+]
+ignore_directives = [
+    "rst-class", "tab-set", "grid", "toctree", "footbibliography", "autosummary",
+    "currentmodule", "automodule", "cssclass", "tabularcolumns", "minigallery",
+    "autoclass", "highlight", "dropdown", "graphviz", "glossary", "autofunction",
+    "bibliography",
+]
+ignore_messages = "^.*(Unknown target name|Undefined substitution referenced)[^`]*$"

tools/azure_dependencies.sh

@@ -25,7 +25,7 @@ elif [ "${TEST_MODE}" == "pip-pre" ]; then
 	echo "misc"
 	python -m pip install $STD_ARGS imageio-ffmpeg xlrd mffpy python-picard pillow
 	echo "nibabel with workaround"
-	python -m pip install --progress-bar off git+https://github.com/mscheltienne/nibabel.git@np.sctypes
+	python -m pip install --progress-bar off git+https://github.com/nipy/nibabel.git
 	echo "joblib"
 	python -m pip install --progress-bar off git+https://github.com/joblib/joblib@master
 	echo "EDFlib-Python"

tools/github_actions_dependencies.sh

@@ -44,7 +44,7 @@ else
 	echo "mne-qt-browser"
 	pip install $STD_ARGS git+https://github.com/mne-tools/mne-qt-browser
 	echo "nibabel with workaround"
-	pip install $STD_ARGS git+https://github.com/mscheltienne/nibabel.git@np.sctypes
+	pip install $STD_ARGS git+https://github.com/nipy/nibabel.git
 	echo "joblib"
 	pip install $STD_ARGS git+https://github.com/joblib/joblib@master
 	echo "EDFlib-Python"