Add extractor for BioFormats (CXD) #168
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| name: Dev Testing | |
| on: | |
| pull_request: | |
| workflow_dispatch: | |
| concurrency: | |
| group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }} | |
| cancel-in-progress: true | |
| jobs: | |
| run: | |
| name: Ubuntu tests with Python ${{ matrix.python-version }} | |
| runs-on: ubuntu-latest | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| python-version: ["3.9", "3.10", "3.11", "3.12"] | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - run: git fetch --prune --unshallow --tags | |
| - name: Setup Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Global Setup | |
| run: | | |
| pip install -U pip | |
| pip install pytest-xdist | |
| git config --global user.email "[email protected]" | |
| git config --global user.name "CI Almighty" | |
| pip install wheel==0.41.2 # needed for scanimage | |
| - name: Install full requirements | |
| run: | | |
| pip install .[test] | |
| pip install .[full] | |
| - name: Clone and Install NeuroConv | |
| run: | | |
| git clone https://github.com/catalystneuro/neuroconv.git | |
| cd neuroconv | |
| pip install --no-cache-dir .[full,test] | |
| cd ../ | |
| - name: Get ophys_testing_data current head hash | |
| id: ophys | |
| run: echo "::set-output name=HASH_OPHYS_DATASET::$(git ls-remote https://gin.g-node.org/CatalystNeuro/ophys_testing_data.git HEAD | cut -f1)" | |
| - name: Cache ophys dataset - ${{ steps.ophys.outputs.HASH_OPHYS_DATASET }} | |
| uses: actions/cache@v2 | |
| id: cache-ophys-datasets | |
| with: | |
| path: ./ophys_testing_data | |
| key: ophys-datasets-042023-ubuntu-latest-${{ steps.ophys.outputs.HASH_OPHYS_DATASET }} | |
| - name: Run NeuroConv tests | |
| run: | | |
| pytest -n auto --dist loadscope neuroconv/tests/test_ophys neuroconv/tests/test_on_data/test_imaging_interfaces.py neuroconv/tests/test_on_data/test_segmentation_interfaces.py |