Merge branch 'main' into main

Author: mathias-sm

.circleci/config.yml

@@ -131,7 +131,8 @@ jobs:
       - run:
           name: Check Qt
           command: |
-            ./tools/check_qt_import.sh PyQt6
+            set -x
+            ./tools/check_qt_import.sh ${MNE_QT_BACKEND}
       # Load tiny cache so that ~/.mne does not need to be created below
       - restore_cache:
           keys:

.github/workflows/codeql-analysis.yml

@@ -44,7 +44,7 @@ jobs:
 
     # Initializes the CodeQL tools for scanning.
     - name: Initialize CodeQL
-      uses: github/codeql-action/init@v4.35.2
+      uses: github/codeql-action/init@v4.35.4
       with:
         languages: ${{ matrix.language }}
         # If you wish to specify custom queries, you can do so here or in a config file.
@@ -58,7 +58,7 @@ jobs:
     # Autobuild attempts to build any compiled languages  (C/C++, C#, or Java).
     # If this step fails, then you should remove it and run the build manually (see below)
     - name: Autobuild
-      uses: github/codeql-action/autobuild@v4.35.2
+      uses: github/codeql-action/autobuild@v4.35.4
 
     # ℹ️ Command-line programs to run using the OS shell.
     # 📚 See https://docs.github.com/en/actions/using-workflows/workflow-syntax-for-github-actions#jobsjob_idstepsrun
@@ -71,4 +71,4 @@ jobs:
     #   ./location_of_script_within_repo/buildscript.sh
 
     - name: Perform CodeQL Analysis
-      uses: github/codeql-action/analyze@v4.35.2
+      uses: github/codeql-action/analyze@v4.35.4

.pre-commit-config.yaml

@@ -1,7 +1,7 @@
 repos:
   # Ruff mne
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.15.12
+    rev: v0.15.13
     hooks:
       - id: ruff-check
         name: ruff lint mne
@@ -74,7 +74,7 @@ repos:
 
   # zizmor
   - repo: https://github.com/woodruffw/zizmor-pre-commit
-    rev: v1.24.1
+    rev: v1.25.2
     hooks:
       - id: zizmor
         args: [--fix]

azure-pipelines.yml

@@ -38,34 +38,27 @@ stages:
       - job: All
         pool:
           vmImage: 'ubuntu-latest'
-        variables:
-          PYTHON_VERSION: '3.11'
-          PYTHON_ARCH: 'x64'
         steps:
-          - bash: echo $(COMMIT_MSG)
           - task: UsePythonVersion@0
             inputs:
-              versionSpec: $(PYTHON_VERSION)
-              architecture: $(PYTHON_ARCH)
+              versionSpec: '3.14'
+              architecture: 'x64'
               addToPath: true
-            displayName: 'Get Python'
+            displayName: Get Python
           - bash: |
               set -eo pipefail
               python -m pip install --progress-bar off --upgrade pip build
-              python -m pip install --progress-bar off -ve .[hdf5] --group=test
+              python -m pip install --only-binary=":all:" --progress-bar off -ve .[hdf5] --group=test
               python -m pip uninstall -yq pytest-qt  # don't want to set up display, etc. for this
               pre-commit install --install-hooks
             displayName: Install dependencies
-          - bash: |
-              make pre-commit
+          - bash: make pre-commit
             displayName: make pre-commit
             condition: always()
-          - bash: |
-              make nesting
+          - bash: make nesting
             displayName: make nesting
             condition: always()
-          - bash: |
-              make check-readme
+          - bash: make check-readme
             displayName: make check-readme
             condition: always()
           - bash: mypy
@@ -75,7 +68,6 @@ stages:
             displayName: vulture
             condition: always()
 
-
   - stage: Test
     condition: and(succeeded(), eq(dependencies.Check.outputs['Skip.result.start_main'], 'true'))
     dependsOn: ['Style', 'Check']
@@ -89,57 +81,50 @@ stages:
           DISPLAY: ':99'
           OPENBLAS_NUM_THREADS: '1'
           OMP_NUM_THREADS: '1'
-          MNE_TEST_ALLOW_SKIP: '^.*(PySide6 causes segfaults).*$'
+          MNE_TEST_ALLOW_SKIP: '^$'  # nothing
           MNE_BROWSER_PRECOMPUTE: 'false'
         steps:
           - bash: |
-              set -eo pipefail
+              set -xeo pipefail
               ./tools/setup_xvfb.sh
               sudo apt install -yq tcsh
-            displayName: 'Install Ubuntu dependencies'
-          - bash: |
-              source tools/get_minimal_commands.sh
-            displayName: 'Install minimal commands'
+            displayName: Install Ubuntu dependencies
+          - bash: ./tools/get_minimal_commands.sh
+            displayName: Get minimal commands
           - bash: |
               echo $PATH
               mne_surf2bem --version
               fsl_rigid_register --version
-            displayName: 'Test minimal commands'
+            displayName: Test minimal commands
           - task: UsePythonVersion@0
             inputs:
               versionSpec: '3.12'
               architecture: 'x64'
               addToPath: true
-            displayName: 'Get Python'
           - bash: |
-              set -eo pipefail
+              set -xeo pipefail
               python -m pip install --progress-bar off --upgrade pip
-              python -m pip install --progress-bar off "mne-qt-browser[opengl] @ git+https://github.com/mne-tools/mne-qt-browser.git" pyvista scikit-learn python-picard qtpy nibabel sphinx-gallery "PySide6!=6.8.0,!=6.8.0.1,!=6.8.1.1,!=6.9.1" pandas neo pymatreader antio defusedxml curryreader pymef
-              python -m pip uninstall -yq mne
-              python -m pip install --progress-bar off --upgrade -e . --group=test
-            displayName: 'Install dependencies with pip'
+              python -m pip install --progress-bar off --upgrade --only-binary=":all:" -e . --group=test "mne-qt-browser @ https://github.com/mne-tools/mne-qt-browser/archive/refs/heads/main.zip" pyvista scikit-learn python-picard qtpy nibabel sphinx-gallery "PySide6!=6.8.0,!=6.8.0.1,!=6.8.1.1,!=6.9.1" pandas neo pymatreader antio defusedxml curryreader pymef
+            displayName: Install dependencies with pip
+          - bash: ./tools/check_qt_import.sh PySide6
+            displayName: Check Qt import
           - bash: |
-              set -eo pipefail
+              set -xeo pipefail
               mne sys_info -pd
               mne sys_info -pd | grep "qtpy .*(PySide6=.*)$"
             displayName: Print config
-          - bash: |
-              set -eo pipefail
-              LD_DEBUG=libs python -c "from PySide6.QtWidgets import QApplication, QWidget; app = QApplication([]); import matplotlib; matplotlib.use('QtAgg'); import matplotlib.pyplot as plt; plt.figure()"
-          - bash: source tools/get_testing_version.sh
-            displayName: 'Get testing version'
+          - bash: ./tools/get_testing_version.sh
+            displayName: Get testing version
           - task: Cache@2
             inputs:
               key: $(testing_version)
               path: /home/vsts/mne_data
-            displayName: 'Cache testing data'
           - bash: ./tools/github_actions_download.sh
-            displayName: 'Get test data'
+            displayName: Download testing data
           - script: pytest -m "ultraslowtest or pgtest" --tb=short --cov=mne --cov-report=xml -vv mne
-            displayName: 'slow and mne-qt-browser tests'
-          # Coverage
+            displayName: slow and mne-qt-browser tests
           - bash: bash <(curl -s https://codecov.io/bash)
-            displayName: 'Codecov'
+            displayName: Codecov
             condition: succeededOrFailed()
 
       - job: Linux_Qt_Bindings
@@ -148,59 +133,54 @@ stages:
         variables:
           DISPLAY: ':99'
           OPENBLAS_NUM_THREADS: '1'
-          TEST_OPTIONS: "--tb=short --cov=mne --cov-report=xml --cov-append -vv mne/viz/_brain mne/viz/backends mne/viz/tests/test_evoked.py mne/gui mne/report"
-          MNE_TEST_ALLOW_SKIP: '^.*(PySide6 causes segfaults).*$'
+          TEST_OPTIONS: "--tb=short --cov=mne --cov-report=xml --cov-append -vv mne/gui mne/viz/_brain mne/viz/backends mne/viz/tests/test_evoked.py mne/report"
+          MNE_TEST_ALLOW_SKIP: '^$'  # nothing (can be overridden below)
         steps:
           - bash: ./tools/setup_xvfb.sh
-            displayName: 'Install Ubuntu dependencies'
+            displayName: Setup up Xvfb
           - task: UsePythonVersion@0
             inputs:
-              versionSpec: '3.10'
+              versionSpec: '3.14'
               architecture: 'x64'
               addToPath: true
-            displayName: 'Get Python'
           - bash: |
-              set -eo pipefail
+              set -xeo pipefail
               python -m pip install --progress-bar off --upgrade pip
-              python -m pip install --progress-bar off --upgrade --pre --only-binary=\"numpy,scipy,matplotlib,vtk\" numpy scipy matplotlib vtk
+              python -m pip install --progress-bar off --upgrade --only-binary=":all:" -e .[full-pyside6] --group=test_extra "mne-qt-browser @ https://github.com/mne-tools/mne-qt-browser/archive/refs/heads/main.zip"
               python -c "import vtk"
-              python -m pip install --progress-bar off --upgrade -ve .[full] --group=test_extra
-            displayName: 'Install dependencies with pip'
+            displayName: Install dependencies with pip
           - bash: |
-              set -e
+              set -xeo pipefail
               which mne
               mne sys_info -pd
               python ./tools/check_mne_location.py
             displayName: Print config
-          - bash: source tools/get_testing_version.sh
-            displayName: 'Get testing version'
+          - bash: ./tools/get_testing_version.sh
+            displayName: Get testing version
           - task: Cache@2
             inputs:
               key: $(testing_version)
               path: /home/vsts/mne_data
-            displayName: 'Cache testing data'
           - bash: ./tools/github_actions_download.sh
-            displayName: 'Get test data'
+            displayName: Download testing data
+          - bash: ./tools/check_qt_import.sh PySide6
+            displayName: Check Qt import
           - bash: |
-              set -eo pipefail
-              python -m pip install PyQt6
-              LD_DEBUG=libs python -c "from PyQt6.QtWidgets import QApplication, QWidget; app = QApplication([]); import matplotlib; matplotlib.use('QtAgg'); import matplotlib.pyplot as plt; plt.figure()"
-            displayName: 'Check Qt import'
+              set -xeo pipefail
+              mne sys_info -pd
+              mne sys_info -pd | grep "qtpy .* (PySide6=.*)$"
+              export MNE_TEST_ALLOW_SKIP="^.*PySide6 causes segfaults.*$"
+              PYTEST_QT_API=PySide6 pytest -m "not ultraslowtest" ${TEST_OPTIONS}
+              python -m pip uninstall -yq PySide6
+            displayName: PySide6
           - bash: |
-              set -eo pipefail
+              set -xeo pipefail
+              python -m pip install PyQt6
               mne sys_info -pd
               mne sys_info -pd | grep "qtpy .* (PyQt6=.*)$"
               PYTEST_QT_API=PyQt6 pytest -m "not ultraslowtest" ${TEST_OPTIONS}
               python -m pip uninstall -yq PyQt6 PyQt6-sip PyQt6-Qt6
-            displayName: 'PyQt6'
-          - bash: |
-              set -eo pipefail
-              python -m pip install "PySide6!=6.8.0,!=6.8.0.1,!=6.9.1"
-              mne sys_info -pd
-              mne sys_info -pd | grep "qtpy .* (PySide6=.*)$"
-              PYTEST_QT_API=PySide6 pytest -m "not ultraslowtest" ${TEST_OPTIONS}
-              python -m pip uninstall -yq PySide6
-            displayName: 'PySide6'
+            displayName: PyQt6
           # PyQt5 leaves cruft behind, so run it last
           - bash: |
               set -eo pipefail
@@ -209,10 +189,9 @@ stages:
               mne sys_info -pd | grep "qtpy .* (PyQt5=.*)$"
               PYTEST_QT_API=PyQt5 pytest -m "not ultraslowtest" ${TEST_OPTIONS}
               python -m pip uninstall -yq PyQt5 PyQt5-sip PyQt5-Qt5
-            displayName: 'PyQt5'
-          # Coverage
+            displayName: PyQt5
           - bash: bash <(curl -s https://codecov.io/bash)
-            displayName: 'Codecov'
+            displayName: Codecov
             condition: succeededOrFailed()
 
       - job: Windows
@@ -224,53 +203,51 @@ stages:
           OPENBLAS_NUM_THREADS: '2'
           OMP_DYNAMIC: 'false'
           PYTHONUNBUFFERED: 1
-          PYTHONIOENCODING: 'utf-8'
           AZURE_CI_WINDOWS: 'true'
-          PYTHON_ARCH: 'x64'
           MNE_CI_KIND: $(TEST_MODE)
+          MNE_TEST_ALLOW_SKIP: $(MNE_TEST_ALLOW_SKIP)
         timeoutInMinutes: 95
         strategy:
           maxParallel: 4
           matrix:
             3.11 pip:
               TEST_MODE: 'pip'
               PYTHON_VERSION: '3.11'
+              MNE_TEST_ALLOW_SKIP: "^.*(Requires MNE-C|CUDA not| on Windows|MNE_FORCE_SERIAL|PySide6 causes segfaults).*$"
             3.13 pip pre:
               TEST_MODE: 'pip-pre'
               PYTHON_VERSION: '3.13'
+              MNE_TEST_ALLOW_SKIP: "^.*(Requires (spm|brainstorm) dataset|Requires MNE-C|CUDA not|Numba not| on Windows|MNE_FORCE_SERIAL|PySide6 causes segfaults).*$"
         steps:
           - task: UsePythonVersion@0
             inputs:
               versionSpec: $(PYTHON_VERSION)
-              architecture: $(PYTHON_ARCH)
+              architecture: 'x64'
               addToPath: true
-            displayName: 'Get Python'
           - bash: |
-              set -eo pipefail
+              set -xeo pipefail
               git clone --depth 1 https://github.com/pyvista/setup-headless-display-action.git
               MESA3D_VERSION=24.3.0 bash setup-headless-display-action/windows/install_opengl.sh
             displayName: Install OpenGL
           - bash: ./tools/azure_dependencies.sh
-            displayName: Install dependencies with pip
-          - script: pip install -e .
-            displayName: 'Install MNE-Python dev'
+          - script: pip install --only-binary=":all:" -e .
+            displayName: Install mne
           - script: mne sys_info -pd
-            displayName: 'Print config'
+            displayName: Print config
           - script: python -c "import numpy; numpy.show_config()"
             displayName: Print NumPy config
           - script: python -c "import numpy; import scipy.linalg; import sklearn.neighbors; from threadpoolctl import threadpool_info; from pprint import pprint; pprint(threadpool_info())"
             displayName: Print threadpoolctl info
-          - bash: source tools/get_testing_version.sh
-            displayName: 'Get testing version'
+          - bash: ./tools/get_testing_version.sh
           - task: Cache@2
             inputs:
               key: $(testing_version)
               path: C:\Users\VssAdministrator\mne_data
-            displayName: 'Cache testing data'
+            displayName: Cache testing data
           - bash: ./tools/github_actions_download.sh
-            displayName: 'Get test data'
+            displayName: Download testing data
           - script: pytest -m "not (slowtest or pgtest)" --tb=short --cov=mne --cov-report=xml -vv mne
-            displayName: 'Run tests'
+            displayName: Run tests
           - bash: bash <(curl -s https://codecov.io/bash)
-            displayName: 'Codecov'
+            displayName: Codecov
             condition: succeededOrFailed()

doc/changes/dev/13813.other.rst

@@ -0,0 +1 @@
+Adding checks in :func:`mne.stats.permutation_t_test()` to warn the user when provided with bad input values, by `Himanshu Mahor`_.

doc/changes/dev/13891.other.rst

@@ -0,0 +1 @@
+Fixed the ``fun`` shape description in :meth:`mne.Epochs.apply_function`'s docstring, by :newcontrib:`Bhargav Kowshik`.

doc/changes/dev/13894.bugfix.rst

@@ -0,0 +1 @@
+Fix bug where ``picks`` was ignored in :meth:`mne.Epochs.apply_function` when ``channel_wise=False``, by `Thomas Binns`_.

doc/changes/dev/13899.dependency.rst

@@ -0,0 +1,5 @@
+Updated minimum for:
+
+- Core dependency ``matplotlib >= 3.9``
+
+Changes implemented via CI action created by `Thomas Binns`_.

doc/changes/names.inc

@@ -40,6 +40,7 @@
 .. _Beige Jin: https://github.com/BeiGeJin
 .. _Ben Beasley: https://github.com/musicinmybrain
 .. _Benedikt Ehinger: https://www.benediktehinger.de
+.. _Bhargav Kowshik: https://github.com/bkowshik
 .. _Bradley Voytek: https://github.com/voytek
 .. _Britta Westner: https://britta-wstnr.github.io
 .. _Bruno Aristimunha: https://bruaristimunha.github.io

doc/development/contributing.rst

@@ -587,12 +587,14 @@ deprecation period when the stated release is being prepared:
   parameter, and (if found) update them to use the new function / parameter.
 
 
+.. _`changelog-guide`:
+
 Describe your changes in the changelog
 --------------------------------------
 
-Include in your changeset a brief description of the change in the
-:ref:`changelog <whats_new>` using towncrier_ format, which aggregates small,
-properly-named ``.rst`` files to create a changelog. This can be
+Include in your changeset a brief description of the changes, which will appear in the
+:ref:`changelog <whats_new>`, using towncrier_ format. This aggregates small,
+properly named ``.rst`` files to create a changelog. This can be
 skipped for very minor changes like correcting typos in the documentation.
 
 There are six separate sections for changes, based on change type.
@@ -1024,8 +1026,9 @@ down the road. Here are the guidelines:
   you are specifically asked by a maintainer to PR into another branch (e.g.,
   for backports or maintenance bugfixes to the current stable version).
 
-- Don't forget to include in your PR a brief description of the change in the
-  :ref:`changelog <whats_new>` (:file:`doc/whats_new.rst`).
+- Don't forget to include in your PR a brief description of the change in a
+  changelog entry (see :ref:`the changelog section <changelog-guide>` above
+  for instructions).
 
 - Our community uses the following commit tags and conventions: