Merge branch 'master' of github.com:maxibor/pydamage #183
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| 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@v2 | |
| with: | |
| python-version: 3.7 | |
| mamba-version: "*" | |
| channels: conda-forge,bioconda,defaults | |
| channel-priority: true | |
| environment-file: environment.yml | |
| activate-environment: pydamage | |
| - uses: actions/setup-java@v2 | |
| with: | |
| distribution: 'adopt' | |
| java-version: '11' | |
| - name: Lint with flake8 | |
| shell: bash -l {0} | |
| run: | | |
| pip install flake8 | |
| flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics | |
| - 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 |