Merge branch 'main' into add_buttons

Author: WouterKroot

.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

.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: v0.11.9
+    rev: v0.11.13
     hooks:
       - id: ruff
         name: ruff lint mne
@@ -40,7 +40,7 @@ repos:
 
   # 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: v1.7.0
+    rev: v1.9.0
     hooks:
       - id: zizmor
 

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" 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/changes/devel/13228.newfeature.rst

@@ -0,0 +1 @@
+Add an ``extras`` attribute to :class:`mne.Annotations` for storing arbitrary metadata, by `Pierre Guetschel`_.

doc/changes/devel/13241.bugfix.rst

@@ -0,0 +1 @@
+Improved the configuration json to handle with parallel access with file lock configuration by :newcontrib:`Bruno Aristimunha`.

doc/changes/devel/13268.bugfix.rst

@@ -0,0 +1 @@
+Fixed bug where the file_id is not set when the file contains a directory at the end of the file, by `Théodore Papadopoulo`_.

doc/changes/devel/13276.bugfix.rst

@@ -0,0 +1 @@
+Fix bug with :func:`mne.simulation.simulate_raw` and :class:`mne.simulation.SourceSimulator` where using different head positions with ``head_pos`` and a BEM would raise an error, by `Eric Larson`_.

doc/changes/devel/13277.bugfix.rst

@@ -0,0 +1 @@
+Update :func:`mne.viz.plot_alignment` and related functions to support PyVista deprecation of positional arguments by :newcontrib:`user27182`.

doc/changes/devel/13280.bugfix.rst

@@ -0,0 +1 @@
+Fixed bug where :func:`mne.preprocessing.maxwell_filter_prepare_emptyroom` would not reliably identify meg channel types for matching bads across emptyroom and task, by `Harrison Ritz`_.