Test for MNE-Tools actions

.circleci/config.yml

@@ -137,8 +137,8 @@ jobs:
       - run:
           name: Check Qt
           command: |
-            set -x
-            ./tools/check_qt_import.sh ${MNE_QT_BACKEND}
+            curl https://raw.githubusercontent.com/mne-tools/mne-tools/main/tools/check_qt_import.sh -o check_qt_import.sh
+            bash check_qt_import.sh $MNE_QT_BACKEND
       # Load tiny cache so that ~/.mne does not need to be created below
       - restore_cache:
           keys:

.extended_metadata.yaml

@@ -0,0 +1,55 @@
+# This file contains additional metadata about MNE-Python, beyond what is contained in `pyproject.toml`.
+# This information is used by the actions in MNE-Tools to generate `CITATION.cff` and `codemeta.json`.
+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

@@ -8,7 +8,7 @@ permissions:
   contents: read
 
 jobs:
-  autofix:
+  autofix-changelog-headers:
     name: Autofix and style
     runs-on: ubuntu-latest
     steps:
@@ -24,3 +24,48 @@ jobs:
       - uses: j178/prek-action@v2.0.5
       - uses: autofix-ci/action@c5b2d67aa2274e7b5a18224e8171550871fc7e4a
         if: success() || failure()
+  autofix-dependencies:
+    name: Autoupdate 'old' CI lockfile, README dependencies, and environment file
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v7.0.0
+        with:
+          persist-credentials: false
+      - uses: astral-sh/setup-uv@v8.2.0
+        with:
+          version: ">=0.9"
+          activate-environment: true
+          enable-cache: false
+          python-version: "3.12"
+      - name: Update 'old' CI lockfile
+        # uv pip compile requires setting the python version for the environment 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 \
+          --no-cache
+      - name: Validate 'old' CI lockfile
+        uses: tsbinns/mne-tools/actions/check-lockfile@tools-actions
+        with:
+          project-root: ${{ github.workspace }}
+          lockfile-path: tools/pylock.ci-old.toml
+          groups: lockfile_extras
+      - name: Sync dependencies to README
+        uses: tsbinns/mne-tools/actions/sync-dependencies-to-readme@tools-actions
+        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@tools-actions
+        with:
+          project-root: ${{ github.workspace }}
+          extras: full,full-no-qt,hdf5
+          # manually specify extras groups to sync, as logic for recursion into other groups isn't implemented in the action yet
+          # e.g., `full` includes `mne[full-no-qt]`, but the action won't recognise this, so we need to specify `full-no-qt` explicitly
+          additional-dependencies: pip,mamba,conda,nomkl,noqt5
+          pip-dependencies: pymef
+          requirements-overrides: PySide6==6.11.1,vtk==9.6.2
+      - uses: autofix-ci/action@c5b2d67aa2274e7b5a18224e8171550871fc7e4a
+        if: success() || failure()

.github/workflows/spec_zero.yml

@@ -41,36 +41,19 @@ jobs:
         timeout-minutes: 10
         with:
           detached: true
-      - uses: astral-sh/setup-uv@v8.3.2
-        with:
-          version: ">=0.9"
-          activate-environment: true
-          python-version: "3.12"
+      - name: Setup Python
+        uses: actions/setup-python@v6.2.0
       - name: Install dependencies
-        run: uv pip install -e . packaging requests tomlkit prek
+        run: pip install --upgrade 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
-      - 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: prek auto-update
       - name: check if files changed
         run: |
           git diff && git status --porcelain
           if [[ $(git status --porcelain) ]]; then
             echo "dirty=true" >> $GITHUB_OUTPUT
           fi
         id: status
-      - uses: j178/prek-action@v2.0.5
-        if: steps.status.outputs.dirty == 'true'
       - name: Create PR
         run: |
           set -xeo pipefail
@@ -85,4 +68,4 @@ jobs:
           git push origin spec_zero
           PR_NUM=$(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
-        if: steps.status.outputs.dirty == 'true' && (success() || failure())
+        if: steps.status.outputs.dirty == 'true'

.github/workflows/tests.yml

@@ -109,6 +109,7 @@ jobs:
         if: startswith(matrix.kind, 'pip') && startswith(matrix.os, 'macos')
       # Python (if conda)
       - uses: mamba-org/setup-micromamba@v3
+        id: setup-micromamba
         with:
           environment-file: ${{ env.CONDA_ENV }}
           environment-name: mne
@@ -118,6 +119,9 @@ jobs:
             -v
         if: matrix.kind == 'conda'
         timeout-minutes: 20
+      - name: Make conda python available to later steps
+        run: echo "${{ steps.setup-micromamba.outputs.environment-path }}/bin" >> "$GITHUB_PATH"  # zizmor: ignore[template-injection]
+        if: matrix.kind == 'conda'
       # Python (if old)
       - uses: astral-sh/setup-uv@v8.3.2
         with:
@@ -130,7 +134,11 @@ jobs:
       - run: bash ./tools/github_actions_verify_python.sh "${{ matrix.python }}"
       - run: bash ./tools/github_actions_dependencies.sh
         timeout-minutes: 10
-      - run: python ./tools/github_actions_check_old_env.py
+      - name: Check 'old' CI environment
+        uses: tsbinns/mne-tools/actions/check-environment@tools-actions
+        with:
+          project-root: ${{ github.workspace }}
+          groups: lockfile_extras
         if: matrix.kind == 'old'
       # Minimal commands on Linux (macOS stalls)
       - uses: actions/cache@v6.1.0
@@ -141,8 +149,10 @@ jobs:
       - run: bash ./tools/get_minimal_commands.sh
         if: startswith(matrix.os, 'ubuntu') && matrix.kind != 'minimal' && matrix.kind != 'old' && matrix.kind != 'pip-ft'
       - run: bash ./tools/github_actions_infos.sh
-      # Check Qt
-      - run: bash ./tools/check_qt_import.sh $MNE_QT_BACKEND
+      - name: Check Qt import
+        uses: tsbinns/mne-tools/actions/check-qt-import@tools-actions
+        with:
+          qt-backend: ${{ env.MNE_QT_BACKEND }}
         if: env.MNE_QT_BACKEND != ''
       - name: Run tests with no testing data
         run: MNE_SKIP_TESTING_DATASET_TESTS=true pytest -m "not (ultraslowtest or pgtest)" -n "$PYTEST_XDIST_N" --dist loadscope --timeout=120 --timeout-method=thread -o faulthandler_timeout=110 $COV_ARGS --tb=short -vv -rfE mne/

.pre-commit-config.yaml

@@ -89,15 +89,6 @@ 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: v1.28.0

.yamllint.yml

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

README.rst

@@ -70,20 +70,21 @@ Dependencies
 
 The minimum required dependencies to run MNE-Python are:
 
-.. ↓↓↓ BEGIN CORE DEPS LIST. DO NOT EDIT! HANDLED BY PRE-COMMIT HOOK ↓↓↓
-
-- `Python <https://www.python.org>`__ ≥ 3.10
-- `NumPy <https://numpy.org>`__ ≥ 2.0
-- `SciPy <https://scipy.org>`__ ≥ 1.14
-- `Matplotlib <https://matplotlib.org>`__ ≥ 3.9
-- `Pooch <https://www.fatiando.org/pooch/latest/>`__ ≥ 1.5
+.. ↓↓↓ BEGIN CORE DEPS LIST. DO NOT EDIT! HANDLED BY MNE-TOOLS ↓↓↓
+
+- `python <https://www.python.org>`__ ≥ 3.10
+- `decorator <https://pypi.org/project/decorator/>`__ ≥ 5.1
+- `jinja2 <https://jinja.palletsprojects.com/>`__ ≥ 3.1
+- `lazy_loader <https://pypi.org/project/lazy-loader/>`__ ≥ 0.3
+- `matplotlib <https://matplotlib.org>`__ ≥ 3.9
+- `numpy <https://numpy.org>`__ ≥ 2.0,
+- `packaging <https://packaging.pypa.io/>`__
+- `pooch <https://www.fatiando.org/pooch>`__ ≥ 1.5
+- `scipy <https://scipy.org/>`__ ≥ 1.14
 - `tqdm <https://tqdm.github.io>`__ ≥ 4.66
-- `Jinja2 <https://palletsprojects.com/p/jinja/>`__ ≥ 3.1
-- `decorator <https://github.com/micheles/decorator>`__ ≥ 5.1
-- `lazy-loader <https://pypi.org/project/lazy_loader>`__ ≥ 0.3
-- `packaging <https://packaging.pypa.io/en/stable/>`__
+- `typing-extensions <https://typing-extensions.readthedocs.io/>`__ ≥ 4.15
 
-.. ↑↑↑ END CORE DEPS LIST. DO NOT EDIT! HANDLED BY PRE-COMMIT HOOK ↑↑↑
+.. ↑↑↑ END CORE DEPS LIST. DO NOT EDIT! HANDLED BY MNE-TOOLS ↑↑↑
 
 Contributing
 ^^^^^^^^^^^^

azure-pipelines.yml

@@ -42,12 +42,17 @@ stages:
         pool:
           vmImage: 'ubuntu-latest'
         variables:
+          MNE_TOOLS_DIR: '$(Pipeline.Workspace)/mne-tools'
           DISPLAY: ':99'
           PYTEST_XDIST_N: '2'  # Microsoft-hosted agents have 2 cores
           MNE_TEST_ALLOW_SKIP: '^$'  # nothing
           MNE_BROWSER_PRECOMPUTE: 'false'
         steps:
-          - bash: ./tools/setup_xvfb.sh
+          - bash: |
+              set -xeo pipefail
+              git clone https://github.com/mne-tools/mne-tools.git "$MNE_TOOLS_DIR"
+            displayName: Clone mne-tools
+          - bash: bash $(MNE_TOOLS_DIR)/tools/setup_xvfb.sh
             displayName: Setup up Xvfb
           - task: Cache@2
             inputs:
@@ -66,7 +71,7 @@ stages:
               python -m pip install --progress-bar off --upgrade pip
               python -m pip install --progress-bar off --upgrade --only-binary=":all:" -e . --group=test "mne-qt-browser @ https://github.com/mne-tools/mne-qt-browser/archive/refs/heads/main.zip" 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 curryreader pymef openmeeg
             displayName: Install dependencies with pip
-          - bash: ./tools/check_qt_import.sh PySide6
+          - bash: bash $(MNE_TOOLS_DIR)/tools/check_qt_import.sh PySide6
             displayName: Check Qt import
           - bash: |
               set -xeo pipefail
@@ -95,12 +100,17 @@ stages:
         pool:
           vmImage: 'ubuntu-latest'
         variables:
+          MNE_TOOLS_DIR: '$(Pipeline.Workspace)/mne-tools'
           DISPLAY: ':99'
           PYTEST_XDIST_N: '2'  # Microsoft-hosted agents have 2 cores
           TEST_OPTIONS: "--tb=short --cov=mne --cov-report=xml --cov-append -vv mne/gui mne/viz/_brain mne/viz/backends mne/viz/tests/test_evoked.py mne/report"
           MNE_TEST_ALLOW_SKIP: '^$'  # nothing (can be overridden below)
         steps:
-          - bash: ./tools/setup_xvfb.sh
+          - bash: |
+              set -xeo pipefail
+              git clone https://github.com/mne-tools/mne-tools.git "$MNE_TOOLS_DIR"
+            displayName: Clone mne-tools
+          - bash: bash $(MNE_TOOLS_DIR)/tools/setup_xvfb.sh
             displayName: Setup up Xvfb
           - task: UsePythonVersion@0
             inputs:
@@ -128,7 +138,7 @@ stages:
             displayName: Cache testing data
           - bash: ./tools/github_actions_download.sh
             displayName: Download testing data
-          - bash: ./tools/check_qt_import.sh PySide6
+          - bash: bash $(MNE_TOOLS_DIR)/tools/check_qt_import.sh PySide6
             displayName: Check Qt import
           - bash: |
               set -xeo pipefail

environment.yml

@@ -1,4 +1,4 @@
-# THIS FILE IS AUTO-GENERATED BY tools/hooks/update_environment_file.py AND WILL BE OVERWRITTEN
+# THIS FILE IS AUTO-GENERATED BY MNE-TOOLS AND WILL BE OVERWRITTEN
 name: mne
 channels:
   - conda-forge
@@ -13,15 +13,14 @@ dependencies:
   - dipy >=0.8
   - edfio >=0.4.10
   - eeglabio
-  - ffmpeg =8.1.2
   - filelock >=3.18.0
   - h5io >=0.2.4
   - h5py >=2.4
   - imageio >=2.6.1
   - imageio-ffmpeg >=0.4.1
   - ipyevents
   - ipympl
-  - ipython >=2.0,!=8.7.0
+  - ipython !=8.7.0,>=2.0
   - ipywidgets
   - jinja2 >=3.1
   - joblib >=0.8
@@ -37,10 +36,10 @@ dependencies:
   - nomkl
   - noqt5
   - numba >=0.35
-  - numpy >=2.0,<3
+  - numpy <3,>=2.0
   - openmeeg >=2.5.7
   - packaging
-  - pandas >=2.2,!=3.0.4
+  - pandas !=3.0.4,>=2.2
   - pillow
   - pip
   - pooch >=1.5
@@ -69,5 +68,6 @@ dependencies:
   - vtk ==9.6.2
   - xlrd
   - pip:
+      - typing-extensions>=4.15; python_version < "3.11"
       - pymef
-      - pyobjc-framework-Cocoa >=5.2.0;platform_system=='Darwin'
+      - pyobjc-framework-Cocoa>=5.2.0; platform_system == "Darwin"