[WIP] Enhance distance and gpf metrics #188
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| name: pytest | |
| concurrency: | |
| group: ${{ github.workflow }}-${{ github.event.number }}-${{ github.event.ref }} | |
| cancel-in-progress: true | |
| on: # yamllint disable-line rule:truthy | |
| pull_request: | |
| push: | |
| branches: [main] | |
| workflow_dispatch: | |
| schedule: | |
| - cron: '0 8 * * 1' | |
| jobs: | |
| pytest: | |
| timeout-minutes: 30 | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| os: [ubuntu, macos, windows] | |
| python-version: [3.9, "3.10", "3.11", "3.12"] | |
| name: ${{ matrix.os }} - py${{ matrix.python-version }} | |
| runs-on: ${{ matrix.os }}-latest | |
| defaults: | |
| run: | |
| shell: bash | |
| steps: | |
| - name: Checkout repository | |
| uses: actions/checkout@v4 | |
| - name: Setup Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| architecture: 'x64' | |
| - name: Install package | |
| run: | | |
| python -m pip install --progress-bar off --upgrade pip setuptools | |
| python -m pip install --progress-bar off .[test] | |
| - name: Display system information | |
| run: pycrostates-sys_info --developer | |
| - name: Display MNE info | |
| run: mne sys_info -pd | |
| - name: Get testing dataset version | |
| run: | | |
| curl https://raw.githubusercontent.com/mne-tools/mne-testing-data/master/version.txt -o mne_testing_data_version.txt | |
| - name: Cache testing dataset | |
| id: cache | |
| uses: actions/cache@v4 | |
| with: | |
| key: mne-testing-${{ runner.os }}-${{ hashFiles('mne_testing_data_version.txt') }} | |
| path: ~/mne_data | |
| - name: Download testing dataset | |
| if: steps.cache.outputs.cache-hit != 'true' | |
| run: python -c "import mne; mne.datasets.testing.data_path(verbose=True)" | |
| - name: Remove dataset version file | |
| run: rm mne_testing_data_version.txt | |
| - name: Run pytest | |
| run: pytest pycrostates --cov=pycrostates --cov-report=xml --cov-config=pyproject.toml | |
| - name: Upload to codecov | |
| uses: codecov/codecov-action@v4 | |
| with: | |
| files: ./coverage.xml | |
| flags: unittests # optional | |
| name: codecov-umbrella # optional | |
| token: ${{ secrets.CODECOV_TOKEN }} | |
| verbose: true # optional (default = false) | |
| pytest-pip-pre: | |
| timeout-minutes: 30 | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| python-version: ["3.11"] | |
| name: pip pre-release - py${{ matrix.python-version }} | |
| runs-on: ubuntu-latest | |
| defaults: | |
| run: | |
| shell: bash | |
| steps: | |
| - name: Checkout repository | |
| uses: actions/checkout@v4 | |
| - name: Setup Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| architecture: 'x64' | |
| - name: Install dependencies | |
| run: | | |
| python -m pip install --progress-bar off --upgrade pip setuptools | |
| python -m pip install --progress-bar off .[test] | |
| python -m pip install --progress-bar off --upgrade git+https://github.com/mne-tools/mne-python | |
| python -m pip install matplotlib | |
| python -m pip install --progress-bar off --upgrade --no-deps --pre --only-binary :all: -i https://pypi.anaconda.org/scientific-python-nightly-wheels/simple --timeout=180 matplotlib | |
| python -m pip install --progress-bar off --upgrade --pre --only-binary :all: -i https://pypi.anaconda.org/scientific-python-nightly-wheels/simple --timeout=180 numpy scipy scikit-learn | |
| - name: Display system information | |
| run: pycrostates-sys_info --developer | |
| - name: Display MNE info | |
| run: mne sys_info -pd | |
| - name: Get testing dataset version | |
| run: | | |
| curl https://raw.githubusercontent.com/mne-tools/mne-testing-data/master/version.txt -o mne_testing_data_version.txt | |
| - name: Cache testing dataset | |
| id: cache | |
| uses: actions/cache@v4 | |
| with: | |
| key: mne-testing-${{ runner.os }}-${{ hashFiles('mne_testing_data_version.txt') }} | |
| path: ~/mne_data | |
| - name: Download testing dataset | |
| if: steps.cache.outputs.cache-hit != 'true' | |
| run: python -c "import mne; mne.datasets.testing.data_path(verbose=True)" | |
| - name: Remove dataset version file | |
| run: rm mne_testing_data_version.txt | |
| - name: Run pytest | |
| run: pytest pycrostates --cov=pycrostates --cov-report=xml --cov-config=pyproject.toml | |
| - name: Upload to codecov | |
| uses: codecov/codecov-action@v4 | |
| with: | |
| files: ./coverage.xml | |
| flags: unittests # optional | |
| name: codecov-umbrella # optional | |
| token: ${{ secrets.CODECOV_TOKEN }} | |
| verbose: true # optional (default = false) |