tests.yml

# 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
          
      - 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'