Fix imports that were not valid for GPy #837
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/[email protected] | |
| 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 | |
| - name: Install momi2 (Linux). | |
| run: | | |
| pip install momi | |
| if: runner.os == 'Linux' | |
| - name: Install dependencies for installation of moments and ignore numpy version in pyproject.toml for MacOS (python3.8). | |
| run: | | |
| pip install Cython | |
| pip install "setuptools_scm>=8" | |
| pip install --no-build-isolation moments-popgen | |
| if: runner.os == 'MacOS' && matrix.python-version == '3.8' | |
| - name: Install GADMA and its dependencies. | |
| run: | | |
| pip install . | |
| - name: Use old matplotlib for tests to enable moments pictures. | |
| run: | | |
| conda install "matplotlib<3.5" | |
| - name: Check installations of packages. | |
| run: | | |
| python -c "import numpy" | |
| python -c "import scipy" | |
| python -c "import dadi" | |
| python -c "import moments" | |
| python -c "import gadma" | |
| - name: Show versions of all installed packages. | |
| run: | | |
| conda list | |
| - name: Show available engines and optimizations in gadma. | |
| run: | | |
| python -c "import gadma;print(gadma.engines.engine._registered_engines.keys())" | |
| python -c "import gadma;print(gadma.optimizers.global_optimizer._registered_global_optimizers.keys())" | |
| - name: Install dependencies for tests. | |
| run: | | |
| pip 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' | |