Change tests #744
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| # This is a basic workflow to help you get started with Actions | |
| name: build | |
| # Controls when the action will run. Triggers the workflow on push or pull request | |
| # events but only for the master branch | |
| on: | |
| push: | |
| pull_request: | |
| jobs: | |
| build: | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| os: [ubuntu-20.04, windows-2019, macos-latest] | |
| python-version: ["3.8", "3.10", "3.11"] | |
| include: | |
| - os: windows-2019 | |
| triplet: x64-windows | |
| env: | |
| CONDA_ENV_NAME: gadma_env | |
| steps: | |
| - name: Cancel previous runs. | |
| uses: styfle/[email protected] | |
| with: | |
| access_token: ${{ github.token }} | |
| - name: Checkout. | |
| uses: actions/checkout@v2 | |
| - name: Set up Python 3. | |
| uses: actions/setup-python@v2 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Set up Conda environment. | |
| uses: conda-incubator/setup-miniconda@v3 | |
| with: | |
| auto-update-conda: true | |
| python-version: ${{ matrix.python-version }} | |
| channels: conda-forge,bioconda | |
| activate-environment: ${{ env.CONDA_ENV_NAME }} | |
| solver: classic | |
| - name: Install dadi and scikit-allel using conda. | |
| run: | | |
| conda install dadi | |
| conda install scikit-allel | |
| - name: Install GADMA and its dependencies. | |
| run: | | |
| bash install | |
| # pip3 install Cython==0.29.18 # otherwise ConfigsSpace cause error for macOS | |
| # TypeError: Expected float, got numpy.float64 when using Float | |
| pip3 install -r requirements/bayes_opt.txt | |
| pip3 install -r requirements/bayes_opt_addit.txt | |
| pip3 install . | |
| - name: Install msprime and momi2 (MacOS). | |
| run: | | |
| brew install gsl homebrew/core/hdf5 | |
| conda install msprime | |
| pip3 install numpy | |
| brew install libomp llvm | |
| export LDFLAGS="-L/usr/local/opt/llvm/lib" | |
| export CPPFLAGS="-I/usr/local/opt/llvm/include" | |
| python3 -m pip install wheel==0.38.4 | |
| CC=$(brew --prefix llvm)/bin/clang pip install momi | |
| python3 -m pip install --upgrade wheel | |
| if: matrix.os == 'macos-latest' && matrix.python-version == '3.8' | |
| # For some reason the last version of wheel cause an error for momi and dadi installation | |
| # The error is the following: ModuleNotFoundError: No module named 'numpy' | |
| - name: Install momi2 (Linux) | |
| run: | | |
| python3 -m pip install wheel==0.38.4 | |
| # Install non-Python-package dependencies, e.g. with conda | |
| conda install hdf5 gsl | |
| # Install momi and Python dependencies with pip | |
| pip install numpy | |
| pip install momi | |
| python3 -m pip install --upgrade wheel | |
| if: matrix.os != 'macos-latest' && matrix.python-version == '3.8' | |
| - name: Uninstall SMAC (Windows). | |
| if: runner.os == 'Windows' | |
| shell: bash -l {0} | |
| run: | | |
| pip3 uninstall -y smac | |
| - name: Uninstall SMAC (MacOS py3.6) | |
| if: runner.os == 'MacOS' && matrix.python-version == '3.6' | |
| run: pip3 uninstall -y smac | |
| - name: Check installations of packages. | |
| run: | | |
| python3 -c "import numpy" | |
| python3 -c "import scipy" | |
| python3 -c "import dadi" | |
| python3 -c "import moments" | |
| python3 -c "import gadma" | |
| - name: Show versions of all installed packages. | |
| run: python3 -m pip freeze | |
| - name: Show available engines and optimizations in gadma. | |
| run: | | |
| python3 -c "import gadma;print(gadma.engines.engine._registered_engines.keys())" | |
| python3 -c "import gadma;print(gadma.optimizers.global_optimizer._registered_global_optimizers.keys())" | |
| - name: Install dependencies for tests. | |
| run: | | |
| pip3 install -r requirements/tests.txt | |
| - name: Run tests and codecov. | |
| run: | | |
| pytest --timeout=600 --cov=gadma --cov-report=xml -v tests --disable-warnings | |
| - name: Upload coverage to Codecov | |
| uses: codecov/codecov-action@v1 | |
| with: | |
| token: ${{ secrets.CODECOV_TOKEN }} | |
| file: ./coverage.xml | |
| flags: unittests | |
| if: runner.os == 'Linux' && matrix.python-version == '3.6' | |