Test for MNE-Tools actions

.extended_metadata.yaml

@@ -0,0 +1,53 @@
+package_name: MNE-Python
+date_created: '2010-12-26'
+date_published: '2014-08-04'
+application_category: Neuroscience
+code_doi: 10.5281/zenodo.592483
+compound_surnames:
+  - García Alanis
+  - van Vliet
+  - De Santis
+  - Dupré la Tour
+  - de la Torre
+  - de Jong
+  - de Montalivet
+  - van den Bosch
+  - Van den Bossche
+  - Van Der Donckt
+  - van der Meer
+  - van Harmelen
+  - Visconti di Oleggio Castello
+  - van Es
+preferred_citation:
+  title: MEG and EEG Data Analysis with MNE-Python
+  journal: Frontiers in Neuroscience
+  type: article
+  year: 2013
+  volume: 7
+  issue: 267
+  start: 1
+  end: 13
+  doi: 10.3389/fnins.2013.00267
+  authors:
+    - family-names: Gramfort
+      given-names: Alexandre
+    - family-names: Luessi
+      given-names: Martin
+    - family-names: Larson
+      given-names: Eric
+    - family-names: Engemann
+      given-names: Denis A.
+    - family-names: Strohmeier
+      given-names: Daniel
+    - family-names: Brodbeck
+      given-names: Christian
+    - family-names: Goj
+      given-names: Roman
+    - family-names: Jas
+      given-names: Mainak
+    - family-names: Brooks
+      given-names: Teon
+    - family-names: Parkkonen
+      given-names: Lauri
+    - family-names: Hämäläinen
+      given-names: Matti S.

.github/workflows/autofix.yml

@@ -19,4 +19,27 @@ jobs:
       - run: pip install --upgrade towncrier pygithub gitpython numpy
       - run: python ./.github/actions/rename_towncrier/rename_towncrier.py
       - run: python ./tools/dev/ensure_headers.py
+      - name: Sync dependencies to README
+        uses: tsbinns/mne-tools/actions/sync-dependencies-to-readme@add_tools
+        with:
+          project-root: ${{ github.workspace }}
+          ignore-upper-pins: numpy
+      - name: Sync dependencies to environment file
+        uses: tsbinns/mne-tools/actions/sync-dependencies-to-environment-file@add_tools
+        with:
+          project-root: ${{ github.workspace }}
+          extras: full,full-no-qt,hdf5
+          additional-dependencies: pip,mamba,conda,nomkl,noqt5
+          pip-dependencies: pymef
+          requirements-overrides: PySide6==6.10.2,vtk==9.6.0
+      # - name: Generate citation
+      #  uses: tsbinns/mne-tools/actions/generate-citation@add_tools
+      #  with:
+      #    project-root: ${{ github.workspace }}
+      #    release-version: "1.13.0"
+      - name: Generate codemeta
+        uses: tsbinns/mne-tools/actions/generate-codemeta@add_tools
+        with:
+          project-root: ${{ github.workspace }}
+          release-version: "1.13.0"
       - uses: autofix-ci/action@c5b2d67aa2274e7b5a18224e8171550871fc7e4a

.github/workflows/check_environment.yml

@@ -0,0 +1,33 @@
+name: Check 'old' environment
+
+on:  # yamllint disable-line rule:truthy
+  pull_request:
+
+jobs:
+  check-environment:
+    permissions:
+      contents: write
+    name: Check 'old' environment
+    runs-on: ubuntu-latest
+    defaults:
+      run:
+        shell: bash -el {0}
+    env:
+      MNE_CI_KIND: 'old'
+    steps:
+      - uses: actions/checkout@v6.0.3
+        with:
+          persist-credentials: false
+      - uses: astral-sh/setup-uv@v8.2.0
+        with:
+          version: ">=0.9"
+          activate-environment: true
+          cache-dependency-glob: |
+            **/pylock.ci-old.toml
+          python-version: '3.10'
+      - run: bash ./tools/github_actions_dependencies.sh
+      - name: Run MNE-Tools action
+        uses: tsbinns/mne-tools/actions/check-environment@add_tools
+        with:
+          project-root: ${{ github.workspace }}
+          groups: lockfile_extras

.github/workflows/check_lockfile.yml

@@ -0,0 +1,24 @@
+name: Check 'old' lockfile
+
+on:  # yamllint disable-line rule:truthy
+  pull_request:
+
+jobs:
+  check-lockfile:
+    permissions:
+      contents: write
+    name: Check 'old' lockfile
+    runs-on: ubuntu-latest
+    defaults:
+      run:
+        shell: bash -el {0}
+    steps:
+      - uses: actions/checkout@v6.0.3
+        with:
+          persist-credentials: false
+      - name: Run MNE-Tools action
+        uses: tsbinns/mne-tools/actions/check-lockfile@add_tools
+        with:
+          project-root: ${{ github.workspace }}
+          lockfile-path: tools/pylock.ci-old.toml
+          groups: lockfile_extras

.github/workflows/spec_zero.yml

@@ -1,6 +1,7 @@
 name: SPEC0
 
 on:  # yamllint disable-line rule:truthy
+  pull_request:
   schedule:
     - cron: '0 0 * * 1'  # At 00:00 every Monday
   workflow_dispatch:
@@ -43,44 +44,42 @@ jobs:
           detached: true
       - uses: astral-sh/setup-uv@v8.2.0
         with:
-          version: ">=0.9"
+          version: ">=0.9,<=0.9.26"
           activate-environment: true
           python-version: "3.12"
       - name: Install dependencies
         run: uv pip install -e . packaging requests tomlkit
       - name: Update tracked dependencies
         run: python ./tools/dev/spec_zero_update_versions.py
       - name: Sync updated dependencies to README
-        run: python tools/sync_dependencies.py
+        uses: tsbinns/mne-tools/actions/sync-dependencies-to-readme@add_tools
+        with:
+          project-root: ${{ github.workspace }}
+          ignore-upper-pins: numpy
+      - name: Sync updated dependencies to environment file
+        uses: tsbinns/mne-tools/actions/sync-dependencies-to-environment-file@add_tools
+        with:
+          project-root: ${{ github.workspace }}
+          extras: full,full-no-qt,hdf5
+          additional-dependencies: pip,mamba,conda,nomkl,noqt5
+          pip-dependencies: pymef
+          requirements-overrides: PySide6==6.10.2,vtk==9.6.0
       - name: Create lockfile for old CI
         # uv pip compile requires setting the python version explicitly in the command :(
-        run: |
-          uv pip compile pyproject.toml --python "3.10" --python-platform "x86_64-unknown-linux-gnu" --group test --group lockfile_extras --resolution lowest-direct --format pylock.toml --output-file tools/pylock.ci-old.toml
-          python tools/github_actions_check_old_lockfile.py
+        run: uv pip compile pyproject.toml --python "3.10" --python-platform "x86_64-unknown-linux-gnu" --group test --group lockfile_extras --resolution lowest-direct --format pylock.toml --output-file tools/pylock.ci-old.toml
+      - name: Validate lockfile for old CI
+        uses: tsbinns/mne-tools/actions/check-lockfile@add_tools
+        with:
+          project-root: ${{ github.workspace }}
+          lockfile-path: tools/pylock.ci-old.toml
+          groups: lockfile_extras
       - name: check if files changed
         run: |
           git diff && git status --porcelain
           if [[ $(git status --porcelain) ]]; then
             echo "dirty=true" >> $GITHUB_OUTPUT
           fi
         id: status
-      - name: Run pre-commit hooks to update other files
-        run: |
-          uv pip install pre-commit
-          pre-commit run --all || true
-        if: steps.status.outputs.dirty == 'true'
-      - name: Create PR
-        run: |
-          set -xeo pipefail
-          git diff
-          git config --global user.email "50266005+mne-bot@users.noreply.github.com"
-          git config --global user.name "mne[bot]"
-          git checkout -b spec_zero
-          if [ -f doc/changes/dev/dependency.rst ]; then
-            git add doc/changes/dev/dependency.rst  # one new file, others changed
-          fi
-          git commit -am "mne[bot]: Update dependency specifiers"
-          git push origin spec_zero
-          PR_NUM=$(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/${{ github.run_id }}). <br> <br> *Adjustments may need to be made to shims in \`mne/fixes.py\` and elswhere in this or another PR. \`make -C tools/dev dep\` is a good starting point for finding potential updates.*")
-          echo "Opened https://github.com/mne-tools/mne-python/pull/${PR_NUM}" >> $GITHUB_STEP_SUMMARY
+      - name: Show diff
+        run: git diff -- ':!pylock.ci-old.toml'
         if: steps.status.outputs.dirty == 'true'

.github/workflows/tests.yml

@@ -149,7 +149,11 @@ jobs:
       - run: bash ./tools/github_actions_verify_python.sh "${{ matrix.python }}"
       - run: bash ./tools/github_actions_dependencies.sh
         timeout-minutes: 10
-      - run: python ./tools/github_actions_check_old_env.py
+      - name: Run MNE-Tools action
+        uses: tsbinns/mne-tools/actions/check-environment@add_tools
+        with:
+          project-root: ${{ github.workspace }}
+          groups: lockfile_extras
         if: matrix.kind == 'old'
       # Minimal commands on Linux (macOS stalls)
       - uses: actions/cache@v5.0.5

.pre-commit-config.yaml

@@ -64,15 +64,6 @@ repos:
       - id: toml-sort-fix
         files: pyproject.toml
 
-  # dependencies
-  - repo: local
-    hooks:
-      - id: update-env-file
-        name: Copy dependency changes from pyproject.toml to environment.yml
-        language: python
-        entry: ./tools/hooks/update_environment_file.py
-        files: '^(pyproject.toml|tools/hooks/update_environment_file.py)$'
-
   # zizmor
   - repo: https://github.com/woodruffw/zizmor-pre-commit
     rev: v1.26.1

.yamllint.yml

@@ -8,3 +8,5 @@ rules:
   document-start: disable
   new-lines:
     type: platform
+  indentation:
+    indent-sequences: consistent