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

Author: scott-huberty

.circleci/config.yml

@@ -93,11 +93,6 @@ 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 +213,9 @@ 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 +239,7 @@ 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 +251,7 @@ 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
@@ -285,6 +284,15 @@ 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 +401,10 @@ 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:

.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. -->

.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@635ffb0c9798bd160680f18fd73371e355b85f27

.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}}

.github/workflows/check_changelog.yml

@@ -5,9 +5,12 @@ 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

.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

@@ -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: |

.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 \"${{ github.workflow }}\" GitHub action." --label "no-changelog-entry-needed")
+          PR_NUM=$(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'

.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'

.github/workflows/tests.yml

@@ -7,6 +7,14 @@ on:  # yamllint disable-line rule:truthy
     branches: ["main", "maint/*"]
   pull_request:
     branches: ["main", "maint/*"]
+  # adapted from spyder-ide/spyder
+  workflow_dispatch:
+    inputs:
+      ssh:
+        description: 'Enable ssh debugging'
+        required: false
+        default: false
+        type: boolean
 
 permissions:
   contents: read
@@ -18,9 +26,11 @@ jobs:
     timeout-minutes: 3
     steps:
       - uses: actions/checkout@v4
+        with:
+          persist-credentials: false
       - uses: actions/setup-python@v5
         with:
-          python-version: '3.12'
+          python-version: '3.13'
       - uses: pre-commit/action@v3.0.1
       - run: pip install mypy numpy scipy vulture
       - run: mypy
@@ -40,8 +50,7 @@ jobs:
   pytest:
     name: '${{ matrix.os }} / ${{ matrix.kind }} / ${{ matrix.python }}'
     needs: style
-    timeout-minutes: 70
-    continue-on-error: true
+    timeout-minutes: 80
     runs-on: ${{ matrix.os }}
     defaults:
       run:
@@ -54,70 +63,90 @@ jobs:
       MNE_CI_KIND: '${{ matrix.kind }}'
       CI_OS_NAME: '${{ matrix.os }}'
     strategy:
+      fail-fast: false
       matrix:
         include:
           - os: ubuntu-latest
-            python: '3.12'
+            python: '3.13'
+            kind: pip
+          - os: ubuntu-latest
+            python: '3.13'
             kind: pip-pre
           - os: ubuntu-latest
-            python: '3.12'
+            python: '3.13'
             kind: conda
           - os: macos-latest  # arm64 (Apple Silicon)
-            python: '3.12'
+            python: '3.13'
             kind: mamba
           - os: macos-13  # latest Intel release
-            python: '3.12'
+            python: '3.13'
             kind: mamba
           - os: windows-latest
             python: '3.10'
             kind: mamba
           - os: ubuntu-latest
             python: '3.10'
             kind: minimal
-          - os: ubuntu-20.04
+          - os: ubuntu-22.04
             python: '3.10'
             kind: old
     steps:
       - uses: actions/checkout@v4
         with:
           fetch-depth: 0
+          persist-credentials: false
+      - name: Get commit message
+        run: echo "COMMIT_MESSAGE=$(git show -s --format=%s ${{ github.event.pull_request.head.sha || github.sha }})" | tee -a ${GITHUB_ENV}
+      - name: Triage SSH
+        run: |
+          if [[ "${{ 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: 80
+        with:
+          detached: true
       - run: ./tools/github_actions_env_vars.sh
       # Xvfb/OpenGL
-      - uses: pyvista/setup-headless-display-action@main
+      - uses: pyvista/setup-headless-display-action@v4
         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 +155,9 @@ 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()