Merge branch 'main' into close

mne-tools · Jan 27, 2025 · 18149f2 · 18149f2
2 parents 5901ceb + 3db12ff
commit 18149f2
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diff --git a/.circleci/config.yml b/.circleci/config.yml
@@ -218,6 +218,9 @@ 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
@@ -252,7 +255,7 @@ jobs:
           name: Check sphinx log for warnings (which are treated as errors)
           when: always
           command: |
-            ! grep "^.* WARNING: .*$" sphinx_log.txt
+            ! grep "^.*\(WARNING\|ERROR\): " sphinx_log.txt
       - run:
           name: Show profiling output
           when: always
@@ -393,6 +396,10 @@ 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:

diff --git a/.git-blame-ignore-revs b/.git-blame-ignore-revs
@@ -13,3 +13,4 @@ e39995d9be6fc831c7a4a59f09b7a7c0a41ae315  # 12588, percent formatting
 1c5b39ff1d99bbcb2fc0e0071a989b3f3845ff30  # 12603, ruff UP028
 b8b168088cb474f27833f5f9db9d60abe00dca83  # 12779, PR JSONs
 ee64eba6f345e895e3d5e7d2804fa6aa2dac2e6d  # 12781, Header unification
+362f9330925fb79a6adc19a42243672676dec63e  # 12799, UP038
diff --git a/.github/PULL_REQUEST_TEMPLATE.md b/.github/PULL_REQUEST_TEMPLATE.md
@@ -15,13 +15,20 @@ Again, thanks for contributing!
 
 -->
 
-#### Reference issue
-Example: Fixes #1234.
+#### Reference issue (if any)
+
+<!-- Example:
+
+Fixes #1234.
+
+-->
 
 
 #### What does this implement/fix?
-Explain your changes.
+
+<!-- Explain your changes. -->
 
 
 #### Additional information
-Any additional information you think is important.
+
+<!-- Any additional information you think is important. -->
diff --git a/.github/workflows/autofix.yml b/.github/workflows/autofix.yml
@@ -13,10 +13,12 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v4
+        with:
+          persist-credentials: false
       - uses: actions/setup-python@v5
         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@dd55f44df8f7cdb7a6bf74c78677eb8acd40cd0a
+      - uses: autofix-ci/action@551dded8c6cc8a1054039c8bc0b8b48c51dfc6ef
diff --git a/.github/workflows/automerge.yml b/.github/workflows/automerge.yml
@@ -0,0 +1,17 @@
+name: Bot auto-merge
+on: pull_request  # yamllint disable-line rule:truthy
+
+jobs:
+  autobot:
+    permissions:
+      contents: write
+      pull-requests: write
+    runs-on: ubuntu-latest
+    # Names can be found with gh api /repos/mne-tools/mne-python/pulls/12998 -q .user.login for example
+    if: (github.event.pull_request.user.login == 'dependabot[bot]' || github.event.pull_request.user.login == 'pre-commit-ci[bot]' || github.event.pull_request.user.login == 'github-actions[bot]') && github.repository == 'mne-tools/mne-python'
+    steps:
+      - name: Enable auto-merge for bot PRs
+        run: gh pr merge --auto --squash "$PR_URL"
+        env:
+          PR_URL: ${{github.event.pull_request.html_url}}
+          GH_TOKEN: ${{secrets.GITHUB_TOKEN}}
diff --git a/.github/workflows/check_changelog.yml b/.github/workflows/check_changelog.yml
@@ -5,6 +5,9 @@ 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/

diff --git a/.github/workflows/circle_artifacts.yml b/.github/workflows/circle_artifacts.yml
@@ -1,4 +1,7 @@
 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') }}"

diff --git a/.github/workflows/codeql-analysis.yml b/.github/workflows/codeql-analysis.yml
@@ -39,6 +39,8 @@ jobs:
     steps:
     - name: Checkout repository
       uses: actions/checkout@v4
+      with:
+        persist-credentials: false
 
     # Initializes the CodeQL tools for scanning.
     - name: Initialize CodeQL
@@ -48,11 +50,11 @@ jobs:
         # If you wish to specify custom queries, you can do so here or in a config file.
         # By default, queries listed here will override any specified in a config file.
         # Prefix the list here with "+" to use these queries and those in the config file.
-        
+
         # Details on CodeQL's query packs refer to : https://docs.github.com/en/code-security/code-scanning/automatically-scanning-your-code-for-vulnerabilities-and-errors/configuring-code-scanning#using-queries-in-ql-packs
         # queries: security-extended,security-and-quality
 
-        
+
     # 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
@@ -61,7 +63,7 @@ jobs:
     # 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
 
-    #   If the Autobuild fails above, remove it and uncomment the following three lines. 
+    #   If the Autobuild fails above, remove it and uncomment the following three lines.
     #   modify them (or add more) to build your code if your project, please refer to the EXAMPLE below for guidance.
 
     # - run: |

diff --git a/.github/workflows/credit.yml b/.github/workflows/credit.yml
@@ -6,19 +6,20 @@ on:  # yamllint disable-line rule:truthy
     - cron: '0 0 1 * *'  # At 00:00 on day-of-month 1
   workflow_dispatch:
 
-permissions:
-  contents: write
-  pull-requests: write
-
 jobs:
   update_credit:
+    permissions:
+      contents: write
+      pull-requests: write
     name: Update
     runs-on: ubuntu-latest
     env:
       GH_TOKEN: ${{ github.token }}
       GITHUB_TOKEN: ${{ github.token }}
     steps:
       - uses: actions/checkout@v4
+        with:
+          persist-credentials: true
       - uses: actions/setup-python@v5
         with:
           python-version: '3.12'
@@ -37,8 +38,8 @@ jobs:
           git config --global user.email "41898282+github-actions[bot]@users.noreply.github.com"
           git config --global user.name "github-actions[bot]"
           git checkout -b credit
-          git commit -am "MAINT: Update code credit [ci skip]"
+          git commit -am "MAINT: Update code credit"
           git push origin credit
-          PR_NUM=$(gh pr create --base main --head credit --title "MAINT: Update code credit" --body "Created by \"${{ github.workflow }}\" GitHub action." --label "no-changelog-entry-needed")
-          echo "Opened https://github.com/mne-tools/mne-python/pulls/${PR_NUM}" >> $GITHUB_STEP_SUMMARY
+          PR_NUM=$(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/${{ github.run_id }})." --label "no-changelog-entry-needed")
+          echo "Opened https://github.com/mne-tools/mne-python/pull/${PR_NUM}" >> $GITHUB_STEP_SUMMARY
         if: steps.status.outputs.dirty == 'true'
diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml
@@ -17,6 +17,8 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v4
+        with:
+          persist-credentials: false
       - uses: actions/setup-python@v5
         with:
           python-version: '3.10'

diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
@@ -18,6 +18,8 @@ jobs:
     timeout-minutes: 3
     steps:
       - uses: actions/checkout@v4
+        with:
+          persist-credentials: false
       - uses: actions/setup-python@v5
         with:
           python-version: '3.12'
@@ -40,8 +42,7 @@ jobs:
   pytest:
     name: '${{ matrix.os }} / ${{ matrix.kind }} / ${{ matrix.python }}'
     needs: style
-    timeout-minutes: 70
-    continue-on-error: true
+    timeout-minutes: 80
     runs-on: ${{ matrix.os }}
     defaults:
       run:
@@ -54,8 +55,12 @@ jobs:
       MNE_CI_KIND: '${{ matrix.kind }}'
       CI_OS_NAME: '${{ matrix.os }}'
     strategy:
+      fail-fast: false
       matrix:
         include:
+          - os: ubuntu-latest
+            python: '3.13'
+            kind: pip
           - os: ubuntu-latest
             python: '3.12'
             kind: pip-pre
@@ -81,43 +86,44 @@ jobs:
       - uses: actions/checkout@v4
         with:
           fetch-depth: 0
+          persist-credentials: false
       - run: ./tools/github_actions_env_vars.sh
       # Xvfb/OpenGL
-      - uses: pyvista/setup-headless-display-action@main
+      - uses: pyvista/setup-headless-display-action@v3
         with:
           qt: true
           pyvista: false
+          wm: false
       # Python (if pip)
       - uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python }}
         if: startswith(matrix.kind, 'pip')
       # Python (if conda)
-      - name: Remove numba and dipy
-        run: |  # TODO: Remove when numba 0.59 and dipy 1.8 land on conda-forge
-          sed -i '/numba/d' environment.yml
-          sed -i '/dipy/d' environment.yml
-          sed -i 's/- mne$/- mne-base/' environment.yml
-        if: matrix.os == 'ubuntu-latest' && startswith(matrix.kind, 'conda') && matrix.python == '3.12'
-      - uses: mamba-org/setup-micromamba@v1
+      - name: Fixes for conda
+        run: |
+          # 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
+        if: matrix.kind == 'conda' || matrix.kind == 'mamba'
+      - uses: mamba-org/setup-micromamba@v2
         with:
           environment-file: ${{ env.CONDA_ENV }}
           environment-name: mne
           create-args: >-
             python=${{ env.PYTHON_VERSION }}
-            mamba
         if: ${{ !startswith(matrix.kind, 'pip') }}
-      # Make sure we have the right Python
-      - run: python -c "import platform; assert platform.machine() == 'arm64', platform.machine()"
-        if: matrix.os == 'macos-14'
-      - run: ./tools/github_actions_dependencies.sh
+      - run: bash ./tools/github_actions_dependencies.sh
       # Minimal commands on Linux (macOS stalls)
-      - run: ./tools/get_minimal_commands.sh
-        if: ${{ startswith(matrix.os, 'ubuntu') }}
-      - run: ./tools/github_actions_infos.sh
+      - run: bash ./tools/get_minimal_commands.sh
+        if: startswith(matrix.os, 'ubuntu') && matrix.kind != 'minimal' && matrix.kind != 'old'
+      - run: bash ./tools/github_actions_infos.sh
       # Check Qt
-      - run: ./tools/check_qt_import.sh $MNE_QT_BACKEND
-        if: ${{ env.MNE_QT_BACKEND != '' }}
+      - run: bash ./tools/check_qt_import.sh $MNE_QT_BACKEND
+        if: env.MNE_QT_BACKEND != ''
       - name: Run tests with no testing data
         run: MNE_SKIP_TESTING_DATASET_TESTS=true pytest -m "not (ultraslowtest or pgtest)" --tb=short --cov=mne --cov-report xml -vv -rfE mne/
         if: matrix.kind == 'minimal'
@@ -126,9 +132,9 @@ jobs:
         with:
           key: ${{ env.TESTING_VERSION }}
           path: ~/mne_data
-      - run: ./tools/github_actions_download.sh
-      - run: ./tools/github_actions_test.sh
-      - uses: codecov/codecov-action@v4
+      - run: bash ./tools/github_actions_download.sh
+      - run: bash ./tools/github_actions_test.sh  # for some reason on macOS we need to run "bash X" in order for a failed test run to show up
+      - uses: codecov/codecov-action@v5
         with:
           token: ${{ secrets.CODECOV_TOKEN }}
-        if: success()
+        if: success() || failure()
diff --git a/.mailmap b/.mailmap
@@ -2,6 +2,7 @@ Adam Li <adam2392@gmail.com> Adam Li <adam2392@Adams-MBP-2.home>
 Adam Li <adam2392@gmail.com> Adam Li <adam2392@new-host-2.home>
 Alan Leggitt <leggitta3@gmail.com> leggitta <leggitta3@gmail.com>
 Alessandro Tonin <alessandro.tonin@wysscenter.ch> Lychfindel <58313635+Lychfindel@users.noreply.github.com>
+Alex Lepauvre <alex.lepauvre@ae.mpg.de> Alex lepauvre <alex.lepauvre@ae.mpg.de>
 Alex Rockhill <aprockhill206@gmail.com> Alex <aprockhill206@gmail.com>
 Alex Rockhill <aprockhill206@gmail.com> Alex <aprockhill@mailbox.org>
 Alex Rockhill <aprockhill206@gmail.com> Alex Rockhill <aprock@uw.edu>
@@ -118,13 +119,15 @@ Fu-Te Wong <zuxfoucault@gmail.com> zuxfoucault <zuxfoucault@yahoo.com.tw>
 Félix Raimundo <gamaz3ps@gmail.com> Felix Raimundo <gamaz3ps@gmail.com>
 Gansheng Tan <49130176+GanshengT@users.noreply.github.com> Gansheng TAN <49130176+GanshengT@users.noreply.github.com>
 Gennadiy Belonosov <7503709+Genuster@users.noreply.github.com> Gennadiy <7503709+Genuster@users.noreply.github.com>
+Gennadiy Belonosov <7503709+Genuster@users.noreply.github.com> Genuster <7503709+Genuster@users.noreply.github.com>
 Giorgio Marinato <giorgio.marinato@unitn.it> neurogima <76406896+neurogima@users.noreply.github.com>
 Giulio Gabrieli <giulio.gabrieli@iit.it>
 Guillaume Dumas <deep@introspection.eu> deep-introspection <deep@introspection.eu>
 Guillaume Dumas <deep@introspection.eu> Guillaume Dumas <deep-introspection@users.noreply.github.com>
 Hakimeh Aslsardroud <hakimeh.aslsardroud@localhost>
 Hamid Maymandi <46011104+HamidMandi@users.noreply.github.com> Hamid <46011104+HamidMandi@users.noreply.github.com>
 Hasrat Ali Arzoo <hasrat407@gmail.com> hasrat17 <56307533+hasrat17@users.noreply.github.com>
+Hongjiang Ye <rubyyhj@gmail.com> YE Hongjiang <hongjiang.ye@outlook.com>
 Hongjiang Ye <rubyyhj@gmail.com> YE Hongjiang <rubyyhj@gmail.com>
 Hubert Banville <hubert.jbanville@gmail.com> hubertjb <hubert.jbanville@gmail.com>
 Hyonyoung Shin <55095699+mcvain@users.noreply.github.com> mcvain <55095699+mcvain@users.noreply.github.com>
@@ -134,17 +137,18 @@ Ivo de Jong <ivopascal@gmail.com> ivopascal <ivopascal@gmail.com>
 Jaakko Leppakangas <jaeilepp@gmail.com> Jaakko Leppakangas <jaeilepp@student.jyu.fi>
 Jaakko Leppakangas <jaeilepp@gmail.com> jaeilepp <jaeilepp@gmail.com>
 Jaakko Leppakangas <jaeilepp@gmail.com> jaeilepp <jaeilepp@student.jyu.fi>
+Jacob Phelan <jacob.phelan.jp@gmail.com>
 Jair Montoya <montoya.jair.m@gmail.com> jmontoyam <montoya.jair.m@gmail.com>
 Jan Ebert <janpublicebert@posteo.net> janEbert <janpublicebert@posteo.net>
 Jan Sedivy <sedivy@rtsoft.cz>
 Jan Sosulski <mail@jan-sosulski.de> jsosulski <mail@jan-sosulski.de>
 Jean-Baptiste Schiratti <jean.baptiste.schiratti@gmail.com> Jean-Baptiste SCHIRATTI <jean.baptiste.schiratti@gmail.com>
-Jean-Remi King <jeanremi.king+github@gmail.com> Jean-Rémi KING <jeanremi.king@gmail.com>
-Jean-Remi King <jeanremi.king+github@gmail.com> kingjr <jeanremi.kibng+github@gmail.com>
-Jean-Remi King <jeanremi.king+github@gmail.com> kingjr <jeanremi.king+github@gmail.com>
-Jean-Remi King <jeanremi.king+github@gmail.com> kingjr <jeanremi.king@gmail.com>
-Jean-Remi King <jeanremi.king+github@gmail.com> UMR9752 <jeanremi.king+github@gmail.com>
-Jean-Remi King <jeanremi.king+github@gmail.com> UMR9752 <umr9752@umr9752-desktop.(none)>
+Jean-Rémi King <jeanremi.king+github@gmail.com> Jean-Rémi KING <jeanremi.king@gmail.com>
+Jean-Rémi King <jeanremi.king+github@gmail.com> kingjr <jeanremi.kibng+github@gmail.com>
+Jean-Rémi King <jeanremi.king+github@gmail.com> kingjr <jeanremi.king+github@gmail.com>
+Jean-Rémi King <jeanremi.king+github@gmail.com> kingjr <jeanremi.king@gmail.com>
+Jean-Rémi King <jeanremi.king+github@gmail.com> UMR9752 <jeanremi.king+github@gmail.com>
+Jean-Rémi King <jeanremi.king+github@gmail.com> UMR9752 <umr9752@umr9752-desktop.(none)>
 Jeff Stout <stoutjd@nih.gov> jstout211 <jstout211@yahoo.com>
 Jennifer Behnke <jennifer.behnke@localhost>
 Jesper Duemose Nielsen <jdue@dtu.dk> jdue <jdue@dtu.dk>
@@ -288,8 +292,8 @@ Reza Nasri <reza@ddpo.ir> Reza <qablameh13@gmail.com>
 Reza Nasri <reza@ddpo.ir> RezaNasri <rezanasri@outlook.com>
 Riessarius Stargardsky <rie.acad@gmail.com>
 Roan LaPlante <aestrivex@gmail.com> aestrivex <aestrivex@gmail.com>
-Rob Luke <code@robertluke.net> Robert Luke <748691+rob-luke@users.noreply.github.com>
-Rob Luke <code@robertluke.net> Robert Luke <mail@robertluke.net>
+Robert Luke <code@robertluke.net> Robert Luke <748691+rob-luke@users.noreply.github.com>
+Robert Luke <code@robertluke.net> Robert Luke <mail@robertluke.net>
 Robert Seymour <robbyseymour@gmail.com>
 Robin Tibor Schirrmeister <robintibor@gmail.com> robintibor <robintibor@gmail.com>
 Roeland Hancock <rhancock@gmail.com>
@@ -352,3 +356,5 @@ Yousra Bekhti <yousra.bekhti@gmail.com> Yoursa BEKHTI <yousra.bekhti@gmail.com>
 Yousra Bekhti <yousra.bekhti@gmail.com> Yousra BEKHTI <yousra.bekhti@gmail.com>
 Yousra Bekhti <yousra.bekhti@gmail.com> yousrabk <yousra.bekhti@gmail.com>
 Zhi Zhang <850734033@qq.com> ZHANG Zhi <850734033@qq.com>
+Zhi Zhang <850734033@qq.com> ZHANG Zhi <zhi271.zhang@connect.polyu.hk>
+Ziyi ZENG <ziyizeng@link.cuhk.edu.cn> ZIYI ZENG <CME1909120@XMU.EDU.MY>