Merge remote-tracking branch 'upstream/main' into fix-issue-11267

* upstream/main: (46 commits)
  MAINT: Restore edfio git install (mne-tools#13421)
  Support preload=False for the new EEGLAB single .set format (mne-tools#13096)
  [pre-commit.ci] pre-commit autoupdate (mne-tools#13453)
  MAINT: Restore PySide6 6.10.0 testing (mne-tools#13446)
  MAINT: Auth [skip azp] [skip actions]
  MAINT: Deploy [circle deploy] [skip azp] [skip actions]
  Bump github/codeql-action from 3 to 4 in the actions group (mne-tools#13442)
  ENH: Dont constrain fiducial clicks to mesh vertices (mne-tools#13445)
  Use timezone-aware ISO 8601 for website timestamp (mne-tools#13347)
  [pre-commit.ci] pre-commit autoupdate (mne-tools#13443)
  FIX: Update osf.io links to new format (mne-tools#13440)
  MAINT: Ensure full checkout is used (mne-tools#13439)
  Add BDF export (mne-tools#13435)
  [pre-commit.ci] pre-commit autoupdate (mne-tools#13434)
  [pre-commit.ci] pre-commit autoupdate (mne-tools#13431)
  MAINT: Update code credit (mne-tools#13432)
  FIX, TST: Try to get test_export_epochs_eeeglab passing again (mne-tools#13428)
  FIX: Add on_few_samples parameter to core rank estimation (mne-tools#13350)
  MAINT: Reenable mpl nightly (mne-tools#13426)
  [pre-commit.ci] pre-commit autoupdate (mne-tools#13427)
  ...

Author: larsoner

.circleci/config.yml

@@ -36,7 +36,8 @@ jobs:
       - restore_cache:
           keys:
             - source-cache
-      - checkout
+      - checkout:
+          method: full
       - run:
           name: Complete checkout
           command: |
@@ -461,7 +462,11 @@ jobs:
           at: /tmp/build
       - restore_cache:
           keys:
-            - website-cache
+            - website-cache-1
+      - add_ssh_keys:
+          fingerprints:
+            # SHA256:N4qvp6MSbXcTz/27xz96VPsNuTDRT92zoRP8EW0I/8I
+            - "19:fe:1d:c3:c7:af:7e:16:94:4c:e1:e7:0a:56:13:bd"
       - run:
           name: Set BASH_ENV
           command: |
@@ -489,6 +494,7 @@ jobs:
           command: |
             git config --global user.email "[email protected]";
             git config --global user.name "Circle CI";
+            ssh-add -D && ssh-add ~/.ssh/id_rsa_19fe1dc3c7af7e16944ce1e70a5613bd
             cd ~/mne-tools.github.io;
             git checkout main
             git remote -v
@@ -510,9 +516,9 @@ jobs:
             fi;
             git push origin main;
       - save_cache:
-          key: website-cache
+          key: website-cache-1
           paths:
-            - ~/mne_data/MNE-visual_92_categories-data
+            - ~/mne-tools.github.io
 
 workflows:
   default:

.github/workflows/autofix.yml

@@ -12,10 +12,10 @@ jobs:
     name: Autoupdate changelog entry and headers
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v5
         with:
           persist-credentials: false
-      - uses: actions/setup-python@v5
+      - uses: actions/setup-python@v6
         with:
           python-version: '3.12'
       - run: pip install --upgrade towncrier pygithub gitpython numpy

.github/workflows/codeql-analysis.yml

@@ -38,13 +38,13 @@ jobs:
 
     steps:
     - name: Checkout repository
-      uses: actions/checkout@v4
+      uses: actions/checkout@v5
       with:
         persist-credentials: false
 
     # Initializes the CodeQL tools for scanning.
     - name: Initialize CodeQL
-      uses: github/codeql-action/init@v3
+      uses: github/codeql-action/init@v4
       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@v3
+      uses: github/codeql-action/autobuild@v4
 
     # 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@v3
+      uses: github/codeql-action/analyze@v4

.github/workflows/credit.yml

@@ -17,10 +17,10 @@ jobs:
       GH_TOKEN: ${{ github.token }}
       GITHUB_TOKEN: ${{ github.token }}
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v5
         with:
           persist-credentials: true
-      - uses: actions/setup-python@v5
+      - uses: actions/setup-python@v6
         with:
           python-version: '3.12'
       - run: pip install pygithub -e .

.github/workflows/release.yml

@@ -16,10 +16,10 @@ jobs:
   package:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v5
         with:
           persist-credentials: false
-      - uses: actions/setup-python@v5
+      - uses: actions/setup-python@v6
         with:
           python-version: '3.10'
       - name: Install dependencies

.github/workflows/tests.yml

@@ -25,10 +25,10 @@ jobs:
     runs-on: ubuntu-latest
     timeout-minutes: 3
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v5
         with:
           persist-credentials: false
-      - uses: actions/setup-python@v5
+      - uses: actions/setup-python@v6
         with:
           python-version: '3.13'
       - uses: pre-commit/[email protected]
@@ -50,7 +50,7 @@ jobs:
   pytest:
     name: '${{ matrix.os }} / ${{ matrix.kind }} / ${{ matrix.python }}'
     needs: style
-    timeout-minutes: 90
+    timeout-minutes: 120
     runs-on: ${{ matrix.os }}
     defaults:
       run:
@@ -75,23 +75,23 @@ jobs:
           - os: ubuntu-latest
             python: '3.13'
             kind: conda
-          - os: macos-latest  # arm64 (Apple Silicon)
+          - os: macos-latest  # arm64 (Apple Silicon): Sequoia
             python: '3.13'
             kind: mamba
-          - os: macos-13  # latest Intel release
+          - os: macos-15-intel  # intel: Sequoia
             python: '3.13'
             kind: mamba
           - os: windows-latest
-            python: '3.10'
+            python: '3.11'
             kind: mamba
           - os: ubuntu-latest
-            python: '3.10'
+            python: '3.12'
             kind: minimal
           - os: ubuntu-22.04
             python: '3.10'
             kind: old
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v5
         with:
           fetch-depth: 0
           persist-credentials: false
@@ -118,7 +118,7 @@ jobs:
           pyvista: false
           wm: false
       # Python (if pip)
-      - uses: actions/setup-python@v5
+      - uses: actions/setup-python@v6
         with:
           python-version: ${{ matrix.python }}
         if: startswith(matrix.kind, 'pip')
@@ -128,17 +128,30 @@ jobs:
           # For some reason on Linux we get crashes
           if [[ "$RUNNER_OS" == "Linux" ]]; then
             sed -i "/numba/d" environment.yml
-          elif [[ "$RUNNER_OS" == "macOS" ]]; then
-            sed -i "" "s/  - PySide6 .*/  - PySide6 <6.8/g" environment.yml
+          fi
+          # And on Windows and macOS PySide6.9.0 segfaults
+          if [[ "$RUNNER_OS" == "macOS" ]]; then
+            sed -i "" "s/  - PySide6 .*/  - PySide6 =6.9.2/g" environment.yml
+            sed -i "" "s/  - vtk .*/  - vtk =9.5.1/g" environment.yml
+
+          else
+            sed -i "s/  - PySide6 .*/  - PySide6 =6.9.2/g" environment.yml
+            sed -i "s/  - vtk .*/  - vtk =9.5.1/g" environment.yml
+            if [[ "$RUNNER_OS" == "Windows" ]]; then
+              echo "MNE_IS_OSMESA=true" | tee -a $GITHUB_ENV
+            fi
           fi
         if: matrix.kind == 'conda' || matrix.kind == 'mamba'
       - uses: mamba-org/setup-micromamba@v2
         with:
           environment-file: ${{ env.CONDA_ENV }}
           environment-name: mne
+          log-level: ${{ runner.debug == '1' && 'debug' || 'info' }}
           create-args: >-
             python=${{ env.PYTHON_VERSION }}
+            -v
         if: ${{ !startswith(matrix.kind, 'pip') }}
+        timeout-minutes: 20
       - run: bash ./tools/github_actions_dependencies.sh
       # Minimal commands on Linux (macOS stalls)
       - run: bash ./tools/get_minimal_commands.sh

.pre-commit-config.yaml

@@ -1,7 +1,7 @@
 repos:
   # Ruff mne
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.12.8
+    rev: v0.14.1
     hooks:
       - id: ruff-check
         name: ruff lint mne
@@ -58,7 +58,7 @@ repos:
         args: ["--ignore-case"]
 
   - repo: https://github.com/pappasam/toml-sort
-    rev: v0.24.2
+    rev: v0.24.3
     hooks:
       - id: toml-sort-fix
         files: pyproject.toml
@@ -82,7 +82,7 @@ repos:
 
   # zizmor
   - repo: https://github.com/woodruffw/zizmor-pre-commit
-    rev: v1.11.0
+    rev: v1.15.2
     hooks:
       - id: zizmor
 

doc/_includes/ged.rst

@@ -14,7 +14,7 @@ This section describes the mathematical formulation and application of
 Generalized Eigendecomposition (GED), often used in spatial filtering
 and source separation algorithms, such as :class:`mne.decoding.CSP`, 
 :class:`mne.decoding.SPoC`, :class:`mne.decoding.SSD` and 
-:class:`mne.preprocessing.Xdawn`.
+:class:`mne.decoding.XdawnTransformer`.
 
 The core principle of GED is to find a set of channel weights (spatial filter) 
 that maximizes the ratio of signal power between two data features. 

doc/api/decoding.rst

@@ -30,6 +30,7 @@ Decoding
    SPoC
    SSD
    XdawnTransformer
+   SpatialFilter
 
 Functions that assist with decoding and model fitting:
 
@@ -39,3 +40,4 @@ Functions that assist with decoding and model fitting:
    compute_ems
    cross_val_multiscore
    get_coef
+   get_spatial_filter_from_estimator

doc/changes/dev/13096.newfeature.rst

@@ -0,0 +1 @@
+Support for preloading=False when reading .set files, by `Bruno Aristimunha`_.