Change tests #754
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"] | |
| include: | |
| - os: windows-2019 | |
| triplet: x64-windows | |
| env: | |
| CONDA_ENV_NAME: gadma_env | |
| defaults: | |
| run: | |
| shell: bash -el {0} | |
| steps: | |
| - name: Cancel previous runs. | |
| uses: styfle/cancel-workflow-action@0.6.0 | |
| with: | |
| access_token: ${{ github.token }} | |
| - name: Checkout. | |
| uses: actions/checkout@v2 | |
| - name: Set up Conda environment. | |
| uses: conda-incubator/setup-miniconda@v3 | |
| continue-on-error: true | |
| with: | |
| auto-update-conda: true | |
| python-version: ${{ matrix.python-version }} | |
| channels: conda-forge,bioconda | |
| activate-environment: ${{ env.CONDA_ENV_NAME }} | |
| - name: Install dadi and scikit-allel using conda. | |
| run: | | |
| conda install dadi scikit-allel | |
| pip install --upgrade Cython | |
| - name: Install GADMA and its dependencies. | |
| run: | | |
| # pip3 install Cython==0.29.18 # otherwise ConfigsSpace cause error for macOS | |
| # TypeError: Expected float, got numpy.float64 when using Float | |
| pip3 install . | |
| python3 -c "import numpy" | |
| - name: Install SMAC (Linux and MacOS). | |
| if: runner.os != 'Windows' | |
| run: | | |
| conda install --upgrade swig | |
| pip3 install -r requirements/bayes_opt.txt | |
| - name: Install GPy and GPyOpt | |
| run: pip3 install -r requirements/bayes_opt_addit.txt | |
| - 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 == '3.8' | |