Build and run the tests of the Pandora python library. #141
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| name: Build and test Pandora | |
| run-name: Build and run the tests of the Pandora python library. | |
| on: [push] | |
| jobs: | |
| Run-Pandora-Tests: | |
| runs-on: ${{ matrix.os }} | |
| timeout-minutes: 60 | |
| strategy: | |
| matrix: | |
| os: [ubuntu-latest, macos-latest] | |
| python-version: ["3.8", "3.11"] | |
| steps: | |
| - name: Check out repository code | |
| uses: actions/checkout@v3 | |
| - name: Setup Python | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Setup Conda | |
| uses: mamba-org/setup-micromamba@v1 | |
| with: | |
| environment-file: etc/environment.yml | |
| cache-environment: true | |
| create-args: | |
| python=${{ matrix.python-version }} | |
| - name: Install Pandora and setup requirements | |
| run: | | |
| rm tests/test_config.py | |
| echo "SMARTPCA = 'smartpca'" > tests/test_config.py | |
| echo "CONVERTF = 'convertf'" >> tests/test_config.py | |
| cat tests/test_config.py | |
| # - name: Setup tmate session | |
| # uses: mxschmitt/action-tmate@v3 | |
| - name: Run Pandora tests | |
| run: | | |
| PYTHONPATH=. pytest -svx --color=yes -k 'mds and test_bootstrap_and_embed_multiple_numpy' | |
| shell: micromamba-shell {0} | |
| Install-using-pip: | |
| runs-on: ${{ matrix.os }} | |
| timeout-minutes: 60 | |
| strategy: | |
| matrix: | |
| os: [ ubuntu-latest, macos-latest ] | |
| steps: | |
| - name: Check out repository code | |
| uses: actions/checkout@v3 | |
| - name: Setup Python | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: '3.11' | |
| - name: Setup smartpca | |
| uses: mamba-org/setup-micromamba@v1 | |
| with: | |
| environment-name: eigensoft | |
| create-args: >- | |
| python=3.11 | |
| eigensoft | |
| -c bioconda | |
| - name: Install Pythia using pip | |
| run: | | |
| pip install . | |
| shell: micromamba-shell {0} | |
| - name: Test Pandora installation by running the CLI (Bootstrap) | |
| uses: ./.github/actions/test-pandora-cli | |
| with: | |
| config-file: config_example.yaml | |
| - name: Test Pandora installation by running the CLI (sliding-window) | |
| uses: ./.github/actions/test-pandora-cli | |
| with: | |
| config-file: config_example_sliding_window.yaml |