[WIP] Enhance distance and gpf metrics #187
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| 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) |