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

* upstream/main: (230 commits)
  FIX: Fix ICA.apply when fitted including marked bad channels (mne-tools#13478)
  FIX: Correctly set the calibration factor in Nihon Kohden reader (mne-tools#13468)
  [pre-commit.ci] pre-commit autoupdate (mne-tools#13479)
  MAINT: Update code credit (mne-tools#13477)
  Fix `versionadded` directive formatting (mne-tools#13471)
  typo in mailmap (mne-tools#13475)
  FIX: Fix _plot_topomap channel names plotting when using a mask (mne-tools#13470)
  FIX: Handle an Eyelink File with blank lines injected throughout file (mne-tools#13469)
  ENH: adds annotation filtering to raw and ica source figures (mne-tools#13460)
  MAINT: Restore VTK nightly wheel on Linux and bump changelog checker (mne-tools#13436)
  [pre-commit.ci] pre-commit autoupdate (mne-tools#13465)
  FIX: Fix add_reference_channels for passing two channels names (mne-tools#13466)
  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)
  ...

Author: larsoner

.circleci/config.yml

@@ -36,7 +36,8 @@ jobs:
       - restore_cache:
           keys:
             - source-cache
-      - checkout
+      - checkout:
+          method: full
       - run:
           name: Complete checkout
           command: |
@@ -93,11 +94,6 @@ jobs:
           name: Set BASH_ENV
           command: ./tools/circleci_bash_env.sh
 
-      - run:
-          name: check neuromag2ft
-          command: |
-            neuromag2ft --version
-
       - run:
           name: Install fonts needed for diagrams
           command: |
@@ -218,6 +214,9 @@ jobs:
       - restore_cache:
           keys:
             - data-cache-phantom-kit
+      - restore_cache:
+          keys:
+            - data-cache-ds004388
       - run:
           name: Get data
           # This limit could be increased, but this is helpful for finding slow ones
@@ -241,6 +240,7 @@ jobs:
               make test-doc;
               mkdir -p doc/_build/test-results/test-doc;
               cp junit-results.xml doc/_build/test-results/test-doc/junit.xml;
+              cp coverage.xml doc/_build/test-results/test-doc/coverage.xml;
             fi;
       # Build docs
       - run:
@@ -252,7 +252,7 @@ jobs:
           name: Check sphinx log for warnings (which are treated as errors)
           when: always
           command: |
-            ! grep "^.* (WARNING|ERROR): .*$" sphinx_log.txt
+            ! grep "^.*\(WARNING\|ERROR\): " sphinx_log.txt
       - run:
           name: Show profiling output
           when: always
@@ -285,6 +285,15 @@ jobs:
       - store_artifacts:
           path: doc/_build/test-results
           destination: test-results
+      # Upload test results to Codecov
+      - run:
+          name: Upload test results to Codecov
+          environment:
+            CODECOV_TOKEN: fb4c4a94-72d7-4743-bb08-af25b623a29a
+          command: |
+            if [[ -f doc/_build/test-results/test-doc/coverage.xml ]]; then
+              bash <(curl -s https://codecov.io/bash) -f doc/_build/test-results/test-doc/coverage.xml || true
+            fi
       # Save the SG RST
       - store_artifacts:
           path: doc/auto_examples.zip
@@ -393,6 +402,10 @@ jobs:
           key: data-cache-phantom-kit
           paths:
             - ~/mne_data/MNE-phantom-KIT-data  # (1 G)
+      - save_cache:
+          key: data-cache-ds004388
+          paths:
+            - ~/mne_data/ds004388  # (1.8 G)
 
 
   linkcheck:
@@ -449,7 +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: |
@@ -477,6 +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
@@ -498,9 +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/CODEOWNERS

@@ -38,13 +38,13 @@
 # Core sensor-space classes
 /mne/epochs.py @drammock @agramfort @mscheltienne @dengemann
 /mne/evoked.py @drammock @agramfort @mscheltienne @dengemann
-/mne/io/*.* @drammock @cbrnr @agramfort @mscheltienne @dengemann
+/mne/io/*.* @drammock @agramfort @mscheltienne @dengemann
 
 # Current-source density
 /mne/preprocessing/_csd.py  @alexrockhill @dengemann
 
 # Decoding
-/mne/decoding/csp.py @cbrnr @agramfort @dengemann
+/mne/decoding/csp.py @agramfort @dengemann
 /mne/decoding/*.py @jasmainak
 
 # fNIRS
@@ -66,25 +66,25 @@
 *gamma*.py @agramfort # related tutorials and examples
 
 # IO
-/mne/io/brainvision @sappelhoff @cbrnr @adam2392
+/mne/io/brainvision @sappelhoff @adam2392
 /mne/io/nirx @rob-luke
 /mne/io/snirf @rob-luke
-/mne/export @sappelhoff @cbrnr
+/mne/export @sappelhoff
 /mne/io/eeglab.py @jasmainak
 /mne/io/eeglab/tests/test_eeglab.py @jasmainak
 
 # Minimum Norm
 /mne/minimum_norm @agramfort
 
 # Preprocessing
-/mne/preprocessing/ica.py @cbrnr @adam2392 @agramfort @mscheltienne @dengemann
-/mne/preprocessing/infomax_.py @cbrnr @adam2392 @mscheltienne @dengemann
+/mne/preprocessing/ica.py @adam2392 @agramfort @mscheltienne @dengemann
+/mne/preprocessing/infomax_.py @adam2392 @mscheltienne @dengemann
 /mne/preprocessing/*annotate*.py @mscheltienne
 /mne/preprocessing/bads.py @mscheltienne
 /mne/preprocessing/e*g.py @mscheltienne
 
 # Report
-/mne/report @hoechenberger @dengemann @jasmainak
+/mne/report @dengemann @jasmainak
 
 # Simulation
 /mne/simulation/ @agramfort
@@ -120,9 +120,6 @@
 /doc @larsoner @drammock @agramfort @dengemann
 /logo @drammock
 
-# Installation documentation
-/doc/install @hoechenberger
-
 # Project infrastructure and CIs
 /*.* @larsoner @drammock  # files in the root directory
 /.circleci @larsoner

.github/FUNDING.yml

@@ -0,0 +1,15 @@
+# These are supported funding model platforms
+
+# github:  # Replace with up to 4 GitHub Sponsors-enabled usernames e.g., [user1, user2]
+# patreon:  # Replace with a single Patreon username
+open_collective: mne-python
+# ko_fi:  # Replace with a single Ko-fi username
+# tidelift:  # Replace with a single Tidelift platform-name/package-name e.g., npm/babel
+# community_bridge:  # Replace with a single Community Bridge project-name e.g., cloud-foundry
+# liberapay:  # Replace with a single Liberapay username
+# issuehunt:  # Replace with a single IssueHunt username
+# lfx_crowdfunding:  # Replace with a single LFX Crowdfunding project-name e.g., cloud-foundry
+# polar:  # Replace with a single Polar username
+# buy_me_a_coffee:  # Replace with a single Buy Me a Coffee username
+# thanks_dev:  # Replace with a single thanks.dev username
+# custom:  # Replace with up to 4 custom sponsorship URLs e.g., ['link1', 'link2']

.github/workflows/autofix.yml

@@ -12,13 +12,13 @@ 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
       - run: python ./.github/actions/rename_towncrier/rename_towncrier.py
       - run: python ./tools/dev/ensure_headers.py
-      - uses: autofix-ci/action@ff86a557419858bb967097bfc916833f5647fa8c
+      - uses: autofix-ci/action@635ffb0c9798bd160680f18fd73371e355b85f27

.github/workflows/check_changelog.yml

@@ -5,12 +5,18 @@ on:  # yamllint disable-line rule:truthy
     types: [opened, synchronize, labeled, unlabeled]
     branches: ["main"]
 
+permissions:
+  contents: read
+
 jobs:
   changelog_checker:
-    name: Check towncrier entry in doc/changes/devel/
+    name: Check towncrier entry in doc/changes/dev/
     runs-on: ubuntu-latest
     steps:
-      - uses: scientific-python/action-towncrier-changelog@v1
+      - uses: actions/checkout@v5
+        with:
+          persist-credentials: false
+      - uses: scientific-python/action-towncrier-changelog@v2
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
           BOT_USERNAME: changelog-bot

.github/workflows/circle_artifacts.yml

@@ -1,8 +1,11 @@
 on: [status]  # yamllint disable-line rule:truthy
+permissions:
+  contents: read
+  statuses: write
 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/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: ${{ github.token }}
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v5
         with:
           persist-credentials: true
-      - uses: actions/setup-python@v5
+      - uses: actions/setup-python@v6
         with:
           python-version: '3.12'
       - run: pip install pygithub -e .
@@ -40,6 +40,6 @@ jobs:
           git checkout -b credit
           git commit -am "MAINT: Update code credit"
           git push origin credit
-          PR_NUM=$(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

@@ -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
@@ -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@v4
+      - 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'