Tests #651
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| name: Tests | |
| on: | |
| push: | |
| branches: | |
| - main | |
| - dev | |
| pull_request: | |
| branches-ignore: [] | |
| schedule: | |
| - cron: '0 0 13 * *' | |
| jobs: | |
| build-linux: | |
| runs-on: ubuntu-latest | |
| strategy: | |
| max-parallel: 5 | |
| matrix: | |
| python: [3.8, 3.9, '3.10'] | |
| fail-fast: false | |
| steps: | |
| - name: checkout git repo | |
| uses: actions/checkout@v2 | |
| - name: conda/mamba | |
| uses: mamba-org/provision-with-micromamba@main | |
| with: | |
| cache-downloads: true | |
| environment-file: false | |
| environment-name: installation | |
| channels: | |
| conda-forge,bioconda,defaults | |
| extra-specs: | | |
| python=${{ matrix.python }} | |
| kraken2 | |
| shustring | |
| samtools | |
| snpeff | |
| bwa | |
| shustring | |
| cd-hit | |
| - name: install package itself | |
| shell: bash -l {0} | |
| run: | | |
| pip install .[testing] | |
| pip install kaleido # required by plotly but sowehow not installed | |
| - name: testing | |
| shell: bash -l {0} | |
| run: | | |
| pytest --cov-report term-missing --cov=sequana | |
| - name: coveralls | |
| shell: bash -l {0} | |
| run: | | |
| pip install coveralls | |
| coveralls --service=github | |
| env: | |
| GITHUB_TOKEN: ${{ github.token }} |