Update Suite2pSegmentationExtractor to support multi channel and multi plane outputs
#298
Workflow file for this run
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: Full Tests | |
| on: | |
| pull_request: | |
| workflow_dispatch: | |
| workflow_run: | |
| workflows: [update-testing-data] | |
| types: [completed] | |
| jobs: | |
| on-failure: | |
| name: Notify on failure | |
| runs-on: ${{ matrix.os }} | |
| if: ${{ github.event.workflow_run.conclusion == 'failure' }} | |
| steps: | |
| - run: | | |
| echo 'The triggering workflow failed.' | |
| 0 | |
| on-success: | |
| name: Full tests on ${{ matrix.os }} with Python ${{ matrix.python-version }} | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| python-version: [3.8, 3.9, "3.10", 3.11] | |
| os: [ubuntu-latest, windows-latest, macos-latest] | |
| steps: | |
| - uses: s-weigand/setup-conda@v1 | |
| - uses: actions/checkout@v2 | |
| - run: git fetch --prune --unshallow --tags | |
| - name: Setup Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v2 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Global Setup | |
| run: | | |
| pip install -U pip | |
| pip install pytest-xdist | |
| git config --global user.email "[email protected]" | |
| git config --global user.name "CI Almighty" | |
| pip install wheel==0.41.2 # needed for scanimage | |
| - name: Install roiextractors with minimal requirements | |
| run: pip install .[test] | |
| - name: Run minimal tests | |
| run: pytest tests/test_internals -n auto --dist loadscope | |
| - name: Test full installation (-e needed for codecov report) | |
| run: pip install -e .[full] | |
| - name: Get ophys_testing_data current head hash | |
| id: ophys | |
| run: echo "::set-output name=HASH_OPHYS_DATASET::$(git ls-remote https://gin.g-node.org/CatalystNeuro/ophys_testing_data.git HEAD | cut -f1)" | |
| - name: Cache ophys dataset - ${{ steps.ophys.outputs.HASH_OPHYS_DATASET }} | |
| uses: actions/cache@v2 | |
| id: cache-ophys-datasets | |
| with: | |
| path: ./ophys_testing_data | |
| key: ophys-datasets-042023-${{ matrix.os }}-${{ steps.ophys.outputs.HASH_OPHYS_DATASET }} | |
| - name: Run full pytest with coverage | |
| run: pytest -n auto --dist loadscope --cov=./ --cov-report xml:./codecov.xml | |
| - if: ${{ matrix.python-version == '3.9' && matrix.os == 'ubuntu-latest'}} | |
| name: Upload full coverage to Codecov | |
| uses: codecov/codecov-action@v1 | |
| with: | |
| token: ${{ secrets.CODECOV_TOKEN }} | |
| file: ./codecov.xml | |
| flags: unittests | |
| name: codecov-umbrella | |
| yml: ./codecov.yml |