Merge pull request #399 from prophyle/pyup-scheduled-update-2024-04-01 #279
Workflow file for this run
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| name: CodeCov | |
| on: [push, pull_request] | |
| jobs: | |
| coverage: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@master | |
| #- name: Setup Python | |
| #uses: actions/setup-python@master | |
| #with: | |
| # python-version: 3.7 | |
| - name: Setup ProPhyle environment | |
| run: | | |
| export PATH="/usr/share/miniconda/bin:$PATH" | |
| conda install -c conda-forge -q mamba | |
| mamba create -c conda-forge -c bioconda --name prophyle -y "python>=3.8" ete3 bitarray parallel psutil scipy sphinx coverage pysam samtools | |
| - name: Generate coverage report | |
| run: | | |
| export PATH="/usr/share/miniconda/bin:$PATH" | |
| source activate prophyle | |
| #pip install coverage | |
| make coverage | |
| coverage combine | |
| coverage xml | |
| - name: Upload coverage to Codecov | |
| uses: codecov/codecov-action@v2 | |
| with: | |
| #flags: unittests # optional | |
| #name: codecov-umbrella # optional | |
| #fail_ci_if_error: true # optional (default = false) | |
| verbose: true # optional (default = false) |