Add extractor for BioFormats (CXD) #169
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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 |