Fix dependencies and require numpy>=1.21 #535
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| name: tests | |
| on: | |
| push: | |
| pull_request: | |
| types: [opened, reopened] | |
| env: | |
| # Increase this value to reset cache if environment.yml has not changed. | |
| PY_CACHE_NUMBER: 2 | |
| PY_ENV: ccc_gene_expr | |
| jobs: | |
| ccc_pytest: | |
| name: Python tests for CCC | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| max-parallel: 4 | |
| fail-fast: false | |
| matrix: | |
| python-version: ["3.9", "3.10"] | |
| os: [ubuntu-latest, macOS-latest, windows-latest] | |
| steps: | |
| - name: Checkout git repo | |
| uses: actions/checkout@v3 | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v3 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Install dependencies | |
| run: | | |
| python -m pip install --upgrade pip | |
| pip install pytest numpy scipy numba pandas==1.4.* scikit-learn==1.1.* | |
| - name: Test CCC with pytest | |
| env: | |
| PYTHONPATH: libs/ | |
| run: | | |
| pytest tests/test_coef.py tests/test_pytorch_core.py tests/test_scipy_stats.py tests/test_sklearn_metrics.py | |
| pytest: | |
| name: Python tests for analyses | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| max-parallel: 4 | |
| fail-fast: false | |
| matrix: | |
| python-version: ["3.9"] | |
| os: [ubuntu-latest, macOS-latest, windows-latest] | |
| steps: | |
| - name: Checkout git repo | |
| uses: actions/checkout@v3 | |
| - name: Cache conda | |
| id: cache | |
| uses: actions/cache@v3 | |
| with: | |
| path: "${{ env.PY_ENV }}.tar.gz" | |
| key: ${{ runner.os }}-${{ env.PY_CACHE_NUMBER }}-${{ hashFiles('environment/environment.yml', 'environment/scripts/install_r_packages.r', 'environment/scripts/install_other_packages.sh') }} | |
| - name: Setup Miniconda | |
| if: steps.cache.outputs.cache-hit != 'true' | |
| uses: conda-incubator/setup-miniconda@v2 | |
| with: | |
| activate-environment: ${{ env.PY_ENV }} | |
| environment-file: environment/environment.yml | |
| auto-activate-base: false | |
| miniforge-variant: Mambaforge | |
| miniforge-version: 'latest' | |
| use-mamba: true | |
| - name: Install other packages and Conda-Pack environment | |
| if: steps.cache.outputs.cache-hit != 'true' | |
| shell: bash -l {0} | |
| run: | | |
| # other packages (R packages mainly) | |
| bash environment/scripts/install_other_packages.sh | |
| # install conda-pack, and pack environment | |
| conda install --yes -c conda-forge conda-pack coverage | |
| conda pack -f -n ${{ env.PY_ENV }} -o "${{ env.PY_ENV }}.tar.gz" | |
| - name: Unpack environment | |
| shell: bash -l {0} | |
| run: | | |
| mkdir -p "${{ env.PY_ENV }}" | |
| tar -xzf "${{ env.PY_ENV }}.tar.gz" -C "${{ env.PY_ENV }}" | |
| - name: Setup data and run pytest (Windows systems) | |
| if: runner.os == 'Windows' | |
| env: | |
| PYTHONPATH: libs/ | |
| shell: cmd | |
| run: | | |
| echo on | |
| cd ${{ env.PY_ENV }} | |
| call .\Scripts\activate.bat | |
| .\Scripts\conda-unpack.exe | |
| cd .. | |
| set R_HOME=%CONDA_PREFIX%\Lib\R | |
| python environment\scripts\setup_data.py --mode testing | |
| pytest -v -rs tests | |
| - name: Setup data and run pytest (non-Windows systems) | |
| if: runner.os != 'Windows' | |
| shell: bash | |
| env: | |
| PYTHONPATH: libs/ | |
| run: | | |
| source ${{ env.PY_ENV }}/bin/activate | |
| conda-unpack | |
| python environment/scripts/setup_data.py --mode testing | |
| if [ "$RUNNER_OS" == "Linux" ]; then | |
| # for linux/ubuntu, run the tests once: with numba jit activated | |
| # (which is the expected implementation) and with the jit | |
| # deactivated (otherwise coverage does not work). | |
| # numba jit activated | |
| pytest -v -rs tests | |
| # numba jit deactivated + code coverage | |
| export NUMBA_DISABLE_JIT=1 | |
| coverage run --source=libs/ -m pytest -v -rs tests | |
| coverage xml -o coverage.xml | |
| else | |
| pytest -v -rs tests | |
| fi | |
| - name: Codecov upload | |
| if: runner.os == 'Linux' | |
| uses: codecov/codecov-action@v2 | |
| with: | |
| files: ./coverage.xml | |
| name: codecov-${{ matrix.os }}-python${{ matrix.python-version }} | |
| fail_ci_if_error: true | |
| verbose: true |