test_suite #5419
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| name: test_suite | |
| concurrency: | |
| group: ${{ github.workflow }}-${{ github.event.number }}-${{ github.event.ref }} | |
| cancel-in-progress: true | |
| on: | |
| push: | |
| branches: ['**'] | |
| tags: ['**'] | |
| pull_request: | |
| branches: ['**'] | |
| schedule: | |
| - cron: "0 4 * * *" | |
| jobs: | |
| style: | |
| runs-on: ubuntu-latest | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| python-version: ["3.12"] | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - uses: actions/cache@v4 | |
| with: | |
| path: ${{ env.pythonLocation }} | |
| key: style-0-${{ env.pythonLocation }}-${{ hashFiles('pyproject.toml') }} | |
| - name: Install dependencies | |
| run: | | |
| python -m pip install --upgrade pip | |
| python -m pip install ruff | |
| - name: Display versions and environment information | |
| run: | | |
| python --version | |
| which python | |
| - name: Run style & documentation tests | |
| run: make pep | |
| build: | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| os: [ubuntu-latest] | |
| python-version: ["3.10", "3.12"] # Oldest and newest supported versions | |
| steps: | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - uses: actions/cache@v4 | |
| with: | |
| path: ${{ env.pythonLocation }} | |
| key: build-1-${{ env.pythonLocation }}-${{ hashFiles('pyproject.toml') }} | |
| - name: Install dependencies | |
| run: | | |
| python -m pip install --upgrade pip | |
| python -m pip install build twine | |
| - uses: actions/checkout@v4 | |
| - name: Build sdist | |
| run: python -m build --sdist | |
| - name: Check sdist | |
| run: twine check --strict dist/* | |
| - name: Install sdist | |
| run: python -m pip install ./dist/mne_bids-* | |
| - name: Clean up working directory | |
| run: rm -rf ./* | |
| - name: Try importing mne_bids | |
| run: python -c 'import mne_bids; print(mne_bids.__version__)' | |
| - name: Try cli mne_bids | |
| run: mne_bids --version | |
| - name: Remove sdist install | |
| run: python -m pip uninstall -y mne-bids | |
| - uses: actions/checkout@v4 | |
| - name: Build wheel | |
| run: python -m build --wheel | |
| - name: Check wheel | |
| run: twine check --strict dist/* | |
| - name: Install wheel | |
| run: python -m pip install ./dist/mne_bids-*.whl | |
| - name: Clean up working directory | |
| run: rm -rf ./* | |
| - name: Try importing mne_bids | |
| run: python -c 'import mne_bids; print(mne_bids.__version__)' | |
| - name: Try cli mne_bids | |
| run: mne_bids --version | |
| - name: Remove wheel install | |
| run: python -m pip uninstall -y mne-bids | |
| - uses: actions/checkout@v4 | |
| - name: Test extras install | |
| run: | | |
| python -m pip install .[full] | |
| python -c 'import mne_bids; print(mne_bids.__version__)' | |
| python -c 'import nibabel; print(nibabel.__version__)' | |
| python -c 'import pybv; print(pybv.__version__)' | |
| python -c 'import eeglabio; print(eeglabio.__version__)' | |
| python -c 'import pymatreader; print(pymatreader.__version__)' | |
| python -c 'import matplotlib; print(matplotlib.__version__)' | |
| python -c 'import pandas; print(pandas.__version__)' | |
| python -c 'import EDFlib; print("EDFlib has no .__version__")' | |
| python -c 'import edfio; print(edfio.__version__)' | |
| test: | |
| # For GitHub "required" CI checks, add in branch protection: | |
| # | |
| # 8 checks: | |
| # for each machine type (ubuntu, macos, macos-13, windows): | |
| # (NOTE: macos-13=x86_64, macos>13=arm64) | |
| # 3.10 / mne-stable / full / validator-stable | |
| # 3.12 / mne-stable / full / validator-stable | |
| # | |
| # 3 additional checks with alternative MNE-Python and BIDS validator versions: | |
| # ubuntu / 3.12 / mne-main / full / validator-main | |
| # ubuntu / 3.10 / mne-prev / full / validator-stable | |
| # ubuntu / 3.12 / mne-stable / minimal / validator-stable | |
| timeout-minutes: 60 | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| os: [ubuntu-latest, macos-latest, macos-13, windows-latest] | |
| python-version: ["3.10", "3.12"] # Oldest and newest supported versions | |
| mne-version: [mne-stable] | |
| mne-bids-install: [full] | |
| bids-validator-version: [validator-stable] | |
| include: | |
| # special test runs running only on single CI systems to save resources | |
| # Test development versions | |
| - os: ubuntu-latest | |
| python-version: "3.12" | |
| mne-version: mne-main | |
| mne-bids-install: full | |
| bids-validator-version: validator-main | |
| # Test previous MNE stable version | |
| - os: ubuntu-latest | |
| python-version: "3.10" | |
| mne-version: mne-prev-stable | |
| mne-bids-install: full | |
| bids-validator-version: validator-stable | |
| # Test minimal mne-bids install | |
| - os: ubuntu-latest | |
| python-version: "3.12" | |
| mne-version: mne-stable | |
| mne-bids-install: minimal | |
| bids-validator-version: validator-stable | |
| env: | |
| TZ: Europe/Berlin | |
| FORCE_COLOR: true | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Set up Node.js | |
| uses: actions/setup-node@v4 | |
| with: | |
| node-version: 20 | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Restore cache | |
| uses: actions/cache@v4 | |
| with: | |
| path: ${{ env.pythonLocation }} | |
| key: test-0-${{ env.pythonLocation }}-${{ env.os }}-${{ hashFiles('pyproject.toml') }} | |
| - name: Install Python dependencies using pip | |
| # This would be nicer once this feature is implemented: https://github.com/pypa/pip/issues/11440 | |
| run: | | |
| python -m pip install --upgrade pip | |
| python -m pip install -e .[test] | |
| - name: Install MNE (stable) | |
| if: matrix.mne-version == 'mne-stable' | |
| run: | | |
| git clone --single-branch --branch maint/1.8 https://github.com/mne-tools/mne-python.git | |
| python -m pip install -e ./mne-python | |
| - name: Install MNE (previous stable) | |
| if: matrix.mne-version == 'mne-prev-stable' | |
| # Have to install NumPy<2.1 here because of a change in positional arg handling + MNE 1.7 | |
| # XXX: drop when mne < 1.8 is no longer supported | |
| run: | | |
| git clone --single-branch --branch maint/1.7 https://github.com/mne-tools/mne-python.git | |
| python -m pip install -e ./mne-python "numpy<2.1" | |
| - name: Install MNE (main) | |
| if: matrix.mne-version == 'mne-main' | |
| run: | | |
| git clone --single-branch --branch main https://github.com/mne-tools/mne-python.git | |
| python -m pip install -e ./mne-python | |
| - name: Install BIDS validator (stable) | |
| if: matrix.bids-validator-version == 'validator-stable' | |
| # XXX: Remove pin once this is solved: https://github.com/bids-standard/bids-validator/issues/2124 | |
| run: | | |
| npm install -g [email protected] | |
| - name: Download BIDS validator (main) | |
| if: matrix.bids-validator-version == 'validator-main' | |
| run: | | |
| pushd .. | |
| git clone --depth 1 https://github.com/bids-standard/bids-validator | |
| popd | |
| - name: Install BIDS validator (main) | |
| if: matrix.bids-validator-version == 'validator-main' | |
| run: | | |
| pushd ../bids-validator | |
| # Generate the full development node_modules | |
| npm install | |
| # Build & bundle the bids-validator CLI package | |
| npm -w bids-validator run build | |
| # Generate a package to install globally | |
| npm -w bids-validator pack | |
| # Install the package globally | |
| npm install -g bids-validator-*.tgz | |
| popd | |
| - name: Display versions and environment information | |
| run: | | |
| echo $TZ | |
| date | |
| echo "npm"; npm --version | |
| echo "node"; node --version | |
| echo "bids-validator"; bids-validator --version | |
| echo "python"; python --version | |
| which python | |
| mne sys_info | |
| - name: Install MNE-BIDS (minimal) | |
| if: matrix.mne-bids-install == 'minimal' | |
| run: python -m pip install -e . | |
| - name: Install MNE-BIDS (full) | |
| if: matrix.mne-bids-install == 'full' | |
| run: python -m pip install -e .[full] | |
| # Only run on a limited set of jobs | |
| - name: Run pytest without testing data | |
| run: make test | |
| if: ${{ matrix.python-version == '3.12' && matrix.os == 'ubuntu-latest' && matrix.mne-version == 'mne-main' }} | |
| # Get testing data | |
| - run: ./tools/get_testing_version.sh | |
| working-directory: mne-python | |
| shell: bash | |
| name: 'Get testing version' | |
| - uses: actions/cache@v4 | |
| with: | |
| key: ${{ env.TESTING_VERSION }} | |
| path: ~/mne_data | |
| name: 'Cache testing data' | |
| - run: ./tools/github_actions_download.sh | |
| shell: bash | |
| working-directory: mne-python | |
| - name: Run pytest | |
| shell: bash | |
| run: make test | |
| - name: Upload coverage stats to codecov | |
| uses: codecov/codecov-action@v4 | |
| with: | |
| files: ./coverage.xml | |
| token: ${{ secrets.CODECOV_TOKEN }} | |
| verbose: true | |
| build_docs: | |
| runs-on: ubuntu-latest | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| python-version: ["3.12"] | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - uses: actions/cache@v4 | |
| with: | |
| path: ${{ env.pythonLocation }} | |
| key: build_docs-0-${{ env.pythonLocation }}-${{ hashFiles('pyproject.toml') }} | |
| - name: Install dependencies | |
| run: | | |
| python -m pip install --upgrade pip | |
| python -m pip install --upgrade https://github.com/mne-tools/mne-python/archive/refs/heads/main.zip | |
| python -m pip install -e .[test,doc] | |
| - name: Build the documentation | |
| run: | | |
| make build-doc | |
| - name: Upload artifacts | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: documentation | |
| path: doc/_build/html |