feat: Save sequence.fasta file in output_dir #24
Workflow file for this run
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| name: ci | |
| on: | |
| push: | |
| branches: | |
| - main | |
| pull_request: | |
| branches: | |
| - main | |
| jobs: | |
| linux: | |
| runs-on: ubuntu-latest | |
| permissions: | |
| contents: read | |
| pull-requests: write | |
| strategy: | |
| matrix: | |
| python-version: ['3.10'] | |
| defaults: | |
| run: | |
| shell: bash -l {0} | |
| name: Linux py ${{ matrix.python-version }} tests | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - uses: actions/setup-dotnet@v4 | |
| with: | |
| dotnet-version: '8.x' | |
| - name: Set environment | |
| run: | | |
| set -e | |
| wget -O "${HOME}/mambaforge.sh" "https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-$(uname)-$(uname -m).sh" | |
| bash "${HOME}/mambaforge.sh" -b -p "${HOME}/conda" | |
| source "${HOME}/conda/etc/profile.d/conda.sh" | |
| conda env create --file environment.yml --name bioemu | |
| conda activate bioemu | |
| uv pip install -e ".[dev,md]" | |
| - name: Check style | |
| run: | | |
| set -e | |
| source "${HOME}/conda/etc/profile.d/conda.sh" | |
| conda activate bioemu | |
| pre-commit run --all-files | |
| - name: Run tests | |
| run: | | |
| set -e | |
| source "${HOME}/conda/etc/profile.d/conda.sh" | |
| conda activate bioemu | |
| coverage run --source=bioemu -m pytest tests | |
| coverage xml # produces coverage.xml file | |
| coverage html # produces htmlcov directory | |
| - name: Upload code coverage report | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: code-coverage-html | |
| path: htmlcov | |
| - name: Create code coverage markdown report | |
| run: | | |
| dotnet tool install -g dotnet-reportgenerator-globaltool | |
| reportgenerator -reports:coverage.xml -targetdir:coveragereport -reporttypes:'MarkdownSummaryGithub' | |
| - name: Write to job summary | |
| run: cat coveragereport/SummaryGithub.md >> $GITHUB_STEP_SUMMARY | |
| - name: Add comment to PR # Only applicable if 'MarkdownSummaryGithub' or one of the other Markdown report types is generated | |
| if: github.event_name == 'pull_request' | |
| run: gh pr comment $PR_NUMBER --body-file coveragereport/SummaryGithub.md | |
| env: | |
| GH_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| PR_NUMBER: ${{ github.event.number }} |