Move to scanpy 1.9.8 #215
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| name: Python package | |
| on: [pull_request] | |
| defaults: | |
| run: | |
| # for conda env activation | |
| shell: bash -l {0} | |
| jobs: | |
| build: | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| python-version: ["3.12"] | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - name: Setup mamba | |
| uses: mamba-org/setup-micromamba@v1 | |
| with: | |
| environment-file: test-env.yaml | |
| cache-downloads: true | |
| condarc: | | |
| channels: | |
| - conda-forge | |
| - bioconda | |
| - defaults | |
| channel_priority: flexible | |
| extra-specs: | | |
| python=${{ matrix.python-version }} | |
| - name: Debug Micromamba | |
| run: | | |
| micromamba env list | |
| micromamba info | |
| micromamba env export -n test-env | |
| - name: Run black manually | |
| run: | | |
| black --check --verbose ./ | |
| # - name: Install dependencies | |
| # run: | | |
| # sudo apt-get install libhdf5-dev | |
| # pip install -U setuptools>=40.1 wheel 'cmake<3.20' pytest | |
| # pip install $(pwd)/scanpy-scripts | |
| # # python -m pip install $(pwd)/scanpy --no-deps --ignore-installed -vv | |
| - name: Run unit tests | |
| run: | | |
| # needed for __version__ to be available | |
| pip install . --no-deps --ignore-installed | |
| pytest --doctest-modules -v ./ | |
| - name: Test with bats | |
| run: | | |
| ./scanpy-scripts-tests.bats |