Merge remote-tracking branch 'upstream/main' into dev-report-src

Author: vferat

.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:

.pre-commit-config.yaml

@@ -1,7 +1,7 @@
 repos:
   # Ruff mne
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.9.10
+    rev: v0.11.4
     hooks:
       - id: ruff
         name: ruff lint mne
@@ -33,7 +33,7 @@ repos:
 
   # yamllint
   - repo: https://github.com/adrienverge/yamllint.git
-    rev: v1.35.1
+    rev: v1.37.0
     hooks:
       - id: yamllint
         args: [--strict, -c, .yamllint.yml]
@@ -82,7 +82,7 @@ repos:
 
   # zizmor
   - repo: https://github.com/woodruffw/zizmor-pre-commit
-    rev: v1.4.1
+    rev: v1.5.2
     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@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" 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'

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/>`_

doc/changes/devel/13172.bugfix.rst

@@ -0,0 +1 @@
+Fix bug in :func:`mne.bem.make_watershed_bem` where function would fail if ``talairach_with_skull.lta`` did not exist due to changes in Freesurfer by `Peter Molfese`_.

doc/changes/devel/13174.bugfix.rst

@@ -0,0 +1 @@
+Fix bug where :func:`mne.export.export_raw` might allocate huge intermediate arrays unnecessarily, when padding data blocks during export to EDF format, by `Daniel McCloy`_.

doc/changes/devel/13178.bugfix.rst

@@ -0,0 +1 @@
+Fix bug with least-squares fitting of head origin using digitization points in :func:`mne.preprocessing.maxwell_filter`, by `Eric Larson`_.

doc/changes/devel/13179.bugfix.rst

@@ -0,0 +1 @@
+Fix bug with :func:`mne.viz.plot_alignment` where ``eeg="projected"`` was not plotted, by `Eric Larson`_.

doc/changes/devel/13179.newfeature.rst

@@ -0,0 +1 @@
+Add ``upsampling`` option to :func:`mne.make_field_map` to allow upsampling MEG helmet surfaces for plotting, by `Eric Larson`_.