modify fastANI command line in build action #5
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| name: build-macos | |
| on: | |
| push: | |
| branches: master | |
| # To be able to trigger a manual build | |
| workflow_dispatch: | |
| jobs: | |
| build: | |
| runs-on: macos-latest | |
| strategy: | |
| matrix: | |
| python-version: ["3.9", "3.10", "3.11", "3.12"] | |
| env: | |
| GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | |
| defaults: | |
| run: | |
| shell: bash -l {0} | |
| steps: | |
| - name: Checkout Repo | |
| uses: actions/checkout@v4 | |
| - name: Install Miniconda (Python ${{ matrix.python-version }}) | |
| uses: conda-incubator/setup-miniconda@v3 | |
| with: | |
| auto-update-conda: true | |
| python-version: ${{ matrix.python-version }} | |
| activate-environment: pyani-github | |
| auto-activate-base: false | |
| channels: defaults,bioconda,conda-forge | |
| channel-priority: flexible | |
| - name: Check Miniconda Installation | |
| run: | | |
| conda info | |
| conda list | |
| - name: Install pip | |
| run: python -m pip install --upgrade pip | |
| - name: Install Development Requirements | |
| run: conda install --file requirements-dev.txt -y | |
| - name: Install Requirements | |
| run: conda install --file requirements.txt -y | |
| - name: Install third-party tools | |
| run: conda install --file requirements-thirdparty-macos.txt -y | |
| - name: Install and Check FastANI | |
| run: | | |
| conda install --file requirements-fastani-macos.txt -y | |
| fastani -h | |
| - name: Install PyQT | |
| run: conda install --file requirements-pyqt-conda.txt -y | |
| - name: Install pip requirements | |
| run: pip install -r requirements-pip.txt | |
| - name: Install pyani | |
| run: pip install -e . | |
| - name: Check pytest modules | |
| run: python -m pytest -v --collect-only | |
| - name: Run Tests with pytest | |
| run: python -m pytest -v --cov=pyani --cov-report=xml:.coverage-${{ matrix.python-version }}.xml | |
| - name: Upload coverage Results | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: test-coverage-${{ matrix.python-version }} | |
| path: .coverage-${{ matrix.python-version }}.xml | |
| retention-days: 1 | |
| if: ${{ always() }} |