Merge remote-tracking branch 'upstream/main' into feature/TD-nirs_snirf

* upstream/main: (55 commits)
  doc: fix rendering typo rst docstr (mne-tools#13301)
  DOC: fix docstrs around layout functions (mne-tools#13300)
  MAINT: Fix doc build failure due to deprecation (mne-tools#13299)
  Birthday input cast to datetime.date (mne-tools#13284)
  DOC: fix missing space, use f-strings, structure->object (mne-tools#13291)
  [pre-commit.ci] pre-commit autoupdate (mne-tools#13290)
  ENH: channel_indices_by_type now has an exclude param (mne-tools#13293)
  Proj id and proj name access (mne-tools#13261)
  Fix: nearly invisible traces with spatial_colors=True (mne-tools#13286)
  [pre-commit.ci] pre-commit autoupdate (mne-tools#13283)
  Bump autofix-ci/action from 551dded8c6cc8a1054039c8bc0b8b48c51dfc6ef to 635ffb0c9798bd160680f18fd73371e355b85f27 in the actions group (mne-tools#13282)
  fix Maxwell bads filtering (mne-tools#13280)
  fix actionable linkcheck errors (mne-tools#13273)
  MAINT: Use radius keyword with PyVista tube (mne-tools#13277)
  BUG: Fix bug with simulating head pos and BEM (mne-tools#13276)
  [pre-commit.ci] pre-commit autoupdate (mne-tools#13274)
  MAINT: Update code credit (mne-tools#13267)
  Annotations extras (mne-tools#13228)
  Tidy up the directory reading (mne-tools#13268)
  FIX, DOC: Drop bad channel in 10_publication_figure.py (mne-tools#13266)
  ...

Author: larsoner

.circleci/config.yml

@@ -244,6 +244,7 @@ jobs:
               make test-doc;
               mkdir -p doc/_build/test-results/test-doc;
               cp junit-results.xml doc/_build/test-results/test-doc/junit.xml;
+              cp coverage.xml doc/_build/test-results/test-doc/coverage.xml;
             fi;
       # Build docs
       - run:
@@ -288,6 +289,15 @@ jobs:
       - store_artifacts:
           path: doc/_build/test-results
           destination: test-results
+      # Upload test results to Codecov
+      - run:
+          name: Upload test results to Codecov
+          environment:
+            CODECOV_TOKEN: fb4c4a94-72d7-4743-bb08-af25b623a29a
+          command: |
+            if [[ -f doc/_build/test-results/test-doc/coverage.xml ]]; then
+              bash <(curl -s https://codecov.io/bash) -f doc/_build/test-results/test-doc/coverage.xml || true
+            fi
       # Save the SG RST
       - store_artifacts:
           path: doc/auto_examples.zip

.github/workflows/autofix.yml

@@ -21,4 +21,4 @@ jobs:
       - run: pip install --upgrade towncrier pygithub gitpython numpy
       - run: python ./.github/actions/rename_towncrier/rename_towncrier.py
       - run: python ./tools/dev/ensure_headers.py
-      - uses: autofix-ci/action@551dded8c6cc8a1054039c8bc0b8b48c51dfc6ef
+      - uses: autofix-ci/action@635ffb0c9798bd160680f18fd73371e355b85f27

.github/workflows/circle_artifacts.yml

@@ -5,7 +5,7 @@ permissions:
 jobs:
   circleci_artifacts_redirector_job:
     if: "${{ startsWith(github.event.context, 'ci/circleci: build_docs') }}"
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-latest
     name: Run CircleCI artifacts redirector
     steps:
       - name: GitHub Action step

.github/workflows/tests.yml

@@ -79,7 +79,7 @@ jobs:
           - os: ubuntu-latest
             python: '3.10'
             kind: minimal
-          - os: ubuntu-20.04
+          - os: ubuntu-22.04
             python: '3.10'
             kind: old
     steps:
@@ -89,7 +89,7 @@ jobs:
           persist-credentials: false
       - run: ./tools/github_actions_env_vars.sh
       # Xvfb/OpenGL
-      - uses: pyvista/setup-headless-display-action@v3
+      - uses: pyvista/setup-headless-display-action@v4
         with:
           qt: true
           pyvista: false

.github/zizmor.yml

@@ -0,0 +1,5 @@
+rules:
+  unpinned-uses:
+    config:
+      policies:
+        "*": ref-pin

.mailmap

@@ -30,6 +30,7 @@ Asish Panda <asishrocks95@gmail.com> kaichogami <asishrocks95@gmail.com>
 Basile Pinsard <basile.pinsard@umontreal.ca>
 Brad Buran <bburan@galenea.com> Brad Buran <bburan@alum.mit.edu>
 Britta Westner <britta.wstnr@gmail.com> britta-wstnr <britta.wstnr@gmail.com>
+Bruno Aristimunha <b.aristimunha@gmail.com>
 btkcodedev <btk.codedev@gmail.com>
 buildqa <s1152yb68@contbay.com>
 Burkhard Maess <burkhard.maess@arcor.de> Burkhard Maess <bmaess@users.noreply.github.com>

.pre-commit-config.yaml

@@ -1,7 +1,7 @@
 repos:
   # Ruff mne
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.11.0
+    rev: v0.12.0
     hooks:
       - id: ruff
         name: ruff lint mne
@@ -33,14 +33,14 @@ repos:
 
   # yamllint
   - repo: https://github.com/adrienverge/yamllint.git
-    rev: v1.36.2
+    rev: v1.37.1
     hooks:
       - id: yamllint
         args: [--strict, -c, .yamllint.yml]
 
   # rstcheck
   - repo: https://github.com/rstcheck/rstcheck.git
-    rev: v6.2.4
+    rev: v6.2.5
     hooks:
       - id: rstcheck
         additional_dependencies:
@@ -82,7 +82,7 @@ repos:
 
   # zizmor
   - repo: https://github.com/woodruffw/zizmor-pre-commit
-    rev: v1.5.1
+    rev: v1.9.0
     hooks:
       - id: zizmor
 

Makefile

@@ -41,7 +41,7 @@ test-no-testing-data: in
 	$(PYTESTS) mne
 
 test-doc: sample_data testing_data
-	$(PYTESTS) --doctest-modules --doctest-ignore-import-errors --doctest-glob='*.rst' ./doc/ --ignore=./doc/auto_examples --ignore=./doc/auto_tutorials --ignore=./doc/_build --ignore=./doc/conf.py --ignore=doc/sphinxext --fulltrace
+	$(PYTESTS) --tb=short --cov=mne --cov-report=xml --cov-branch --doctest-modules --doctest-ignore-import-errors --doctest-glob='*.rst' ./doc/ --ignore=./doc/auto_examples --ignore=./doc/auto_tutorials --ignore=./doc/_build --ignore=./doc/conf.py --ignore=doc/sphinxext --fulltrace
 
 pre-commit:
 	@pre-commit run -a --show-diff-on-failure

azure-pipelines.yml

@@ -113,7 +113,7 @@ stages:
           - bash: |
               set -e
               python -m pip install --progress-bar off --upgrade pip
-              python -m pip install --progress-bar off "mne-qt-browser[opengl] @ git+https://github.com/mne-tools/mne-qt-browser.git@main" pyvista scikit-learn python-picard qtpy nibabel sphinx-gallery "PySide6!=6.8.0,!=6.8.0.1,!=6.8.1.1" pandas neo pymatreader antio defusedxml
+              python -m pip install --progress-bar off "mne-qt-browser[opengl] @ git+https://github.com/mne-tools/mne-qt-browser.git" pyvista scikit-learn python-picard qtpy nibabel sphinx-gallery "PySide6!=6.8.0,!=6.8.0.1,!=6.8.1.1,!=6.9.1" pandas neo pymatreader antio defusedxml
               python -m pip uninstall -yq mne
               python -m pip install --progress-bar off --upgrade -e .[test]
             displayName: 'Install dependencies with pip'
@@ -203,7 +203,7 @@ stages:
             displayName: 'PyQt6'
           - bash: |
               set -eo pipefail
-              python -m pip install "PySide6!=6.8.0,!=6.8.0.1"
+              python -m pip install "PySide6!=6.8.0,!=6.8.0.1,!=6.9.1"
               mne sys_info -pd
               mne sys_info -pd | grep "qtpy .* (PySide6=.*)$"
               PYTEST_QT_API=PySide6 pytest ${TEST_OPTIONS}

doc/_includes/institutional-partners.rst

@@ -19,7 +19,6 @@ Current partners
 - `Children’s Hospital of Philadelphia Research Institute <https://www.research.chop.edu/imaging/>`_
 - `Donders Institute for Brain, Cognition and Behaviour at Radboud University <https://www.ru.nl/donders/>`_
 - `Harvard Medical School <https://hms.harvard.edu/>`_
-- `Fondation Campus Biotech Geneva <https://fcbg.ch/>`_
 - `Institut national de recherche en informatique et en automatique <https://www.inria.fr/>`_
 - `Karl-Franzens-Universität Graz <https://www.uni-graz.at/>`_
 - `Massachusetts General Hospital <https://www.massgeneral.org/>`_
@@ -34,6 +33,7 @@ Former partners
 - `Berkeley Institute for Data Science <https://bids.berkeley.edu/>`_
 - `Boston University <https://www.bu.edu/>`_
 - `Commissariat à l’énergie atomique et aux énergies alternatives <https://www.cea.fr/>`_
+- `Fondation Campus Biotech Geneva <https://fcbg.ch/>`_
 - `Forschungszentrum Jülich <https://www.fz-juelich.de/>`_
 - `Institut du Cerveau et de la Moelle épinière <https://icm-institute.org/>`_
 - `Institut national de la santé et de la recherche médicale <https://www.inserm.fr/>`_