Merge remote-tracking branch 'upstream/main' into check

* upstream/main: (23 commits)
  ENH: Add on_missing for combine_channels (mne-tools#13463)
  Bump the actions group with 2 updates (mne-tools#13464)
  Move development dependencies into a dependency group (no more extra) (mne-tools#13452)
  ENH: add on_missing for rename_channels (mne-tools#13456)
  add advisory board to website (mne-tools#13462)
  ENH: Support Nihon Kohden EEG-1200A V01.00 (mne-tools#13448)
  MAINT: Update dependency specifiers (mne-tools#13459)
  ENH: Add encoding parameter to Nihon Kohden reader (mne-tools#13458)
  [MAINT] Automatic SPEC0 dependency version management (mne-tools#13451)
  FIX: Read Nihon Kohden annotation file accurately (mne-tools#13251)
  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)
  ...

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/codeql-analysis.yml

@@ -44,7 +44,7 @@ jobs:
 
     # 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

@@ -40,6 +40,6 @@ jobs:
           git checkout -b credit
           git commit -am "MAINT: Update code credit"
           git push origin credit
-          PR_NUM=$(gh pr create --base main --head credit --title "MAINT: Update code credit" --body "Created by credit [GitHub action](https://github.com/mne-tools/mne-python/actions/runs/${{ github.run_id }})." --label "no-changelog-entry-needed")
+          PR_NUM=$(gh pr create --base main --head credit --title "MAINT: Update code credit" --body "Created by credit [GitHub action](https://github.com/mne-tools/mne-python/actions/runs/${{ github.run_id }}). <br> <br> *Adjustments may need to be made to `doc/changes/credit_tools.py` or `.mailmap` etc. to get CircleCI to pass.*" --label "no-changelog-entry-needed")
           echo "Opened https://github.com/mne-tools/mne-python/pull/${PR_NUM}" >> $GITHUB_STEP_SUMMARY
         if: steps.status.outputs.dirty == 'true'

.github/workflows/release.yml

@@ -28,7 +28,7 @@ jobs:
           pip install build twine
       - run: python -m build --sdist --wheel
       - run: twine check --strict dist/*
-      - uses: actions/upload-artifact@v4
+      - uses: actions/upload-artifact@v5
         with:
           name: dist
           path: dist
@@ -43,7 +43,7 @@ jobs:
       name: pypi
       url: https://pypi.org/p/mne
     steps:
-      - uses: actions/download-artifact@v5
+      - uses: actions/download-artifact@v6
         with:
           name: dist
           path: dist

.github/workflows/spec_zero.yml

@@ -0,0 +1,62 @@
+name: SPEC0
+
+on:  # yamllint disable-line rule:truthy
+  schedule:
+    - cron: '0 0 * * 1'  # At 00:00 every Monday
+  workflow_dispatch:
+    inputs:
+      ssh:
+        description: 'Enable ssh debugging'
+        required: false
+        default: false
+        type: boolean
+
+jobs:
+  update_versions:
+    permissions:
+      contents: write
+      pull-requests: write
+    name: Update dependency versions
+    runs-on: ubuntu-latest
+    env:
+      GH_TOKEN: ${{ github.token }}
+      GITHUB_TOKEN: ${{ github.token }}
+    steps:
+      - uses: actions/checkout@v5
+        with:
+          persist-credentials: true
+      - name: Triage SSH
+        run: |
+          if [[ "${{ inputs.ssh }}" == "true" ]] || [[ "$COMMIT_MESSAGE" == *"[actions ssh]"* ]]; then
+            echo "ENABLE_SSH=true" | tee -a $GITHUB_ENV
+          else
+            echo "ENABLE_SSH=false" | tee -a $GITHUB_ENV
+          fi
+      - name: Setup Remote SSH Connection
+        if: env.ENABLE_SSH == 'true'
+        uses: mxschmitt/action-tmate@v3
+        timeout-minutes: 10
+        with:
+          detached: true
+      - uses: actions/setup-python@v6
+        with:
+          python-version: '3.12'
+      - run: pip install packaging requests tomlkit
+      - run: python tools/dev/spec_zero_update_versions.py
+      - run: |
+          git diff && git status --porcelain
+          if [[ $(git status --porcelain) ]]; then
+            echo "dirty=true" >> $GITHUB_OUTPUT
+          fi
+        id: status
+      - name: Create PR
+        run: |
+          set -xeo pipefail
+          git config --global user.email "41898282+github-actions[bot]@users.noreply.github.com"
+          git config --global user.name "github-actions[bot]"
+          git checkout -b spec_zero
+          git commit -am "MAINT: Update dependency specifiers"
+          git push origin spec_zero
+          PR_NUM=$(gh pr create --base main --head spec_zero --title "MAINT: Update dependency specifiers" --body "Created by spec_zero [GitHub action](https://github.com/mne-tools/mne-python/actions/runs/${{ github.run_id }}). <br> <br> *Adjustments may need to be made to shims in mne/fixes.py in this or another PR. `git grep TODO VERSION` is a good starting point for finding potential updates.*" --label "no-changelog-entry-needed")
+          echo "Opened https://github.com/mne-tools/mne-python/pull/${PR_NUM}" >> $GITHUB_STEP_SUMMARY
+        if: steps.status.outputs.dirty == 'true'

.github/workflows/tests.yml

@@ -59,6 +59,7 @@ jobs:
       PYTHON_VERSION: '${{ matrix.python }}'
       MKL_NUM_THREADS: '1'
       OPENBLAS_NUM_THREADS: '1'
+      OMP_NUM_THREADS: '1'
       PYTHONUNBUFFERED: '1'
       MNE_CI_KIND: '${{ matrix.kind }}'
       CI_OS_NAME: '${{ matrix.os }}'

.pre-commit-config.yaml

@@ -1,7 +1,7 @@
 repos:
   # Ruff mne
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.13.3
+    rev: v0.14.1
     hooks:
       - id: ruff-check
         name: ruff lint mne
@@ -54,7 +54,7 @@ repos:
     rev: v6.0.0
     hooks:
       - id: file-contents-sorter
-        files: ^doc/changes/names.inc|^.mailmap
+        files: ^doc/changes/names.inc|^.mailmap|^doc/sphinxext/related_software.txt
         args: ["--ignore-case"]
 
   - repo: https://github.com/pappasam/toml-sort
@@ -82,7 +82,7 @@ repos:
 
   # zizmor
   - repo: https://github.com/woodruffw/zizmor-pre-commit
-    rev: v1.14.2
+    rev: v1.15.2
     hooks:
       - id: zizmor
 

.yamllint.yml

@@ -6,3 +6,5 @@ ignore: |
 rules:
   line-length: disable
   document-start: disable
+  new-lines:
+    type: platform

azure-pipelines.yml

@@ -52,7 +52,7 @@ stages:
           - bash: |
               set -eo pipefail
               python -m pip install --progress-bar off --upgrade pip build
-              python -m pip install --progress-bar off -ve .[hdf5,test]
+              python -m pip install --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
@@ -88,6 +88,7 @@ stages:
         variables:
           DISPLAY: ':99'
           OPENBLAS_NUM_THREADS: '1'
+          OMP_NUM_THREADS: '1'
           MNE_TEST_ALLOW_SKIP: '^.*(PySide6 causes segfaults).*$'
           MNE_BROWSER_PRECOMPUTE: 'false'
         steps:
@@ -115,7 +116,7 @@ stages:
               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
               python -m pip uninstall -yq mne
-              python -m pip install --progress-bar off --upgrade -e .[test]
+              python -m pip install --progress-bar off --upgrade -e . --group=test
             displayName: 'Install dependencies with pip'
           - bash: |
               set -e
@@ -172,7 +173,7 @@ stages:
               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 -c "import vtk"
-              python -m pip install --progress-bar off --upgrade -ve .[full,test_extra]
+              python -m pip install --progress-bar off --upgrade -ve .[full] --group=test_extra
             displayName: 'Install dependencies with pip'
           - bash: |
               set -e

doc/changes/dev/13096.newfeature.rst

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