Move python package so that repo can support multiple python packages #2
Workflow file for this run
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| name: Python Package using Conda | |
| on: | |
| push: | |
| branches: [ "master" ] | |
| pull_request: | |
| branches: [ "master" ] | |
| paths: | |
| - 'src/python/dropseq_hdf5/**' | |
| jobs: | |
| build-linux: | |
| runs-on: ubuntu-latest | |
| strategy: | |
| max-parallel: 5 | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Set up Python | |
| uses: actions/setup-python@v3 | |
| with: | |
| python-version: '3.12' | |
| - name: Add conda to system path | |
| run: | | |
| # $CONDA is an environment variable pointing to the root of the miniconda directory | |
| # https://github.com/actions/runner-images/blob/ff9acc6/images/ubuntu/Ubuntu2204-Readme.md#environment-variables | |
| echo $CONDA/bin >> $GITHUB_PATH | |
| - name: Modify the conda configuration to use conda-forge | |
| run: | | |
| conda config --add channels conda-forge | |
| conda config --remove channels defaults || true | |
| # There are many issues filed regarding: | |
| # > warning libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY | |
| # when using the recommended strict channel priority and creating environments from YAML files, | |
| # but the FOSS conda/mamba community has not been able to fix the issue. | |
| # https://github.com/mamba-org/mamba/issues/2810#issuecomment-1910011988 | |
| conda config --set channel_priority flexible | |
| # Disable lock files to avoid bugs in mamba and libmamba | |
| # https://mamba.readthedocs.io/en/latest/user_guide/troubleshooting.html#hangs-during-package-installation-on-nfs-network-file-systems | |
| # https://github.com/mamba-org/mamba/issues/1993#issuecomment-1268397084 | |
| echo "use_lockfiles: false" >> ~/.mambarc | |
| - name: Install dependencies | |
| run: | | |
| cd src/python/dropseq_hdf5 | |
| conda env update --file environment.yml --name base | |
| - name: Lint with flake8 | |
| run: | | |
| cd src/python/dropseq_hdf5 | |
| # Explicitly using the classic solver to avoid: | |
| # a) "libarchive.so.20: cannot open shared object", and | |
| # b) switching from the miniconda installed in the "ubuntu-latest" image | |
| # https://github.com/actions/runner-images/blob/ff9acc6/images/ubuntu/Ubuntu2204-Readme.md#package-management | |
| # c) upgrading to a working version using the below takes minutes while the tests themselves take seconds | |
| # https://stackoverflow.com/questions/77617946/solve-conda-libmamba-solver-libarchive-so-19-error-after-updating-conda-to-23#answer-78293971 | |
| conda install --solver=classic --override-channels --channel conda-forge flake8 | |
| # stop the build if there are Python syntax errors or undefined names | |
| flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics | |
| # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide | |
| flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics | |
| - name: Test with unittest | |
| run: | | |
| cd src/python/dropseq_hdf5 | |
| PYTHONPATH=src python -m unittest discover -s tests |