Fix readthedocs file #724
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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: [3.6, 3.8] | |
| include: | |
| - os: windows-2019 | |
| triplet: x64-windows | |
| env: | |
| CONDA_ENV_NAME: gadma_env | |
| 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 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 conda (Windows) | |
| # if: runner.os == 'Windows' && matrix.python-version == '3.8' | |
| # uses: conda-incubator/setup-miniconda@v2 | |
| # with: | |
| # python-version: ${{ matrix.python }} | |
| # channels: conda-forge, r, bioconda | |
| # #channel-priority: strict | |
| # auto-update-conda: true | |
| # use-only-tar-bz2: true | |
| # | |
| # # For future, to check msprime versions: conda search msprime --info | |
| # - name: Install msprime via conda (Windows python3.8) | |
| # if: runner.os == 'Windows' && matrix.python-version == '3.8' | |
| # shell: bash -l {0} #We need a login shell to get conda | |
| # run: | | |
| # # We install msprime from conda to avoid GSL-related build issues | |
| # # when pip installing without binary wheels (on Windows). | |
| # # We install a special version of msprime 0.7.4=py36 | |
| # #conda activate ${{ env.CONDA_ENV_NAME }} | |
| # conda create -n ${{ env.CONDA_ENV_NAME }} msprime python=${{ matrix.python-version }} | |
| - name: Install hdf5, msprime and momi2 (MacOS). | |
| run: | | |
| brew install gsl homebrew/core/hdf5 | |
| pip3 install msprime | |
| brew install libomp llvm | |
| export LDFLAGS="-L/usr/local/opt/llvm/lib" | |
| export CPPFLAGS="-I/usr/local/opt/llvm/include" | |
| CC=$(brew --prefix llvm)/bin/clang pip install momi | |
| if: matrix.os == 'macos-10.15' | |
| # - name: Install GADMA and its dependencies (Windows python3.8). | |
| # if: runner.os == 'Windows' && matrix.python-version == '3.8' | |
| # shell: bash -l {0} | |
| # run: | | |
| # conda activate ${{ env.CONDA_ENV_NAME }} | |
| # bash install | |
| # pip3 install -r requirements/bayes_opt.txt | |
| - 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 | |
| - 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: Install momentsLD engine. | |
| run: | | |
| pip3 uninstall -y moments | |
| pip3 install Cython==0.29.18 # the last version cause erros on Windows and MacOS | |
| pip3 install setuptools==58.2.0 # to install with setup.py | |
| git clone --depth 1 --branch moments-1.1.11 https://bitbucket.org/simongravel/moments.git | |
| cd moments | |
| pip install -r requirements.txt | |
| python3 setup.py build_ext --inplace | |
| pip3 install . | |
| cd .. | |
| # 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: Use specific version of wheel for momi and dadi installation (Linux) | |
| if: matrix.python-version == '3.8' | |
| run: | | |
| python3 -m pip install wheel==0.38.4 | |
| - name: Install dadi==2.2.0 for Python3.8 | |
| if: matrix.python-version == '3.8' | |
| run: | | |
| pip3 install dadi==2.2.0 | |
| - name: Install momi engine (Linux). | |
| if: runner.os == 'Linux' | |
| run: | | |
| python3 -m pip install momi | |
| - 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' | |