Pydamage version 0.80 #211
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| 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 |