dep: remove version pinning #195
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@v2 | |
| with: | |
| python-version: 3.10 | |
| 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 |