python-dropseq_hdf5-conda.yml

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