Change tests #742
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| # 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 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 }} | |
| - name: Set up Python 3. | |
| uses: actions/setup-python@v2 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| # - name: Install minimal requirements before everything else | |
| # run: | | |
| # pip3 install -r requirements/minimal.txt | |
| - name: Install msprime and momi2 (MacOS). | |
| run: | | |
| brew install gsl homebrew/core/hdf5 | |
| conda install msprime | |
| pip3 install numpy | |
| brew install libomp llvm | |
| export LDFLAGS="-L/usr/local/opt/llvm/lib" | |
| export CPPFLAGS="-I/usr/local/opt/llvm/include" | |
| python3 -m pip install wheel==0.38.4 | |
| CC=$(brew --prefix llvm)/bin/clang pip install momi | |
| python3 -m pip install --upgrade wheel | |
| if: matrix.os == 'macos-latest' | |
| # 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' | |
| - 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: 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' | |