pydamage_ci.yml

name: pydamage_ci

on: [push, pull_request]


jobs:
  pydamage_ci:
    name: pydamage_testing
    runs-on: 'ubuntu-latest'
    if: "!contains(github.event.head_commit.message, '[skip_ci]')"
    steps:
      - uses: actions/checkout@v2
      - uses: conda-incubator/setup-miniconda@v3
        with:
          auto-update-conda: true
          mamba-version: "*"
          channels: conda-forge,bioconda,defaults
          channel-priority: true
          environment-file: environment.yml
          activate-environment: pydamage
      - name: Test with pytest
        shell: bash -l {0}
        run: |
          pip install -e .
          pip install pytest
          pytest
      - name: Check pydamage help message
        shell: bash -l {0}
        run: |
          pydamage --help
      - name: Check pydamage on test data
        shell: bash -l {0}
        run: |
          pydamage analyze --verbose tests/data/aligned.bam
          pydamage filter pydamage_results/pydamage_results.csv
          pydamage analyze -f -g tests/data/aligned.bam
          pydamage cite