add GitHub action and restyle/lint some source files #1
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| name: build-on-push-to-master | ||
| on: | ||
| push: | ||
| branches: master | ||
| # To be able to trigger a manual build | ||
| workflow_dispatch | ||
| jobs: | ||
| build: | ||
| runs-on: macos-latest | ||
| env: | ||
| GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | ||
| steps: | ||
| - name: Checkout Repo | ||
| uses: actions/checkout@v4 | ||
| - name: Install Python | ||
| uses: actions/setup-python@v5 | ||
| with: | ||
| python-version: "3.11" | ||
| - name: Install Miniconda | ||
| uses: actions/setup-miniconda@v3 | ||
| with: | ||
| auto-update-conda: true | ||
| python-version: "3.11" | ||
| activate-environment: pyani-github | ||
| channels: defaults,bioconda,conda-forge | ||
| channel-priority: strict | ||
| environment-file: etc/pyani-environment.yml | ||
| use-only-tar-bz2: true | ||
| - name: Install pip | ||
| run: python -m pip install --upgrade pip | ||
| - name: Install Development Requirements | ||
| run: conda install --file requirements-dev.txt -y | ||
| - name: Install Requirements | ||
| run: conda install --file requirements.txt -y | ||
| - name: Install third-party tools | ||
| run: conda install --file requirements-thirdparty.txt -y | ||
| - name: Install FastANI | ||
| run: conda install --file requirements-fastani.txt -y | ||
| - name: Install PyQT | ||
| run: conda install --file requirements-pyqt-conda.txt -y | ||
| - name: Install pip requirements | ||
| run: pip install -r requirements-pip.txt | ||
| - name: Install pyani | ||
| run: pip install -e . | ||
| - name: Run Fast Tests with pytest | ||
| run: python -m pytest -v -m "not slow" --cov=pyani --cov-report xml:.coverage_fast.xml | ||
| - name: Upload pytest Results | ||
| uses: actions/upload-artifact@v4 | ||
| with: | ||
| name: pytest-results-3.11 | ||
| path: /pyani/test-results-3.11.xml | ||
| retention-days: 1 | ||
| if: ${{ always() }} | ||
