ci.yml

# This workflow will install Python dependencies, run tests and lint with a variety of Python versions
# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions

name: Continuous Integration

on:
  workflow_dispatch:
  push:
    branches: [ main ]
  pull_request:
    branches: [ main ]
  schedule:
    # run this every week at 12 noon on Monday
    - cron: '0 12 * * 1'
  

jobs:
  build-and-test:
    runs-on: ${{ matrix.os }}
    strategy:
      fail-fast: false
      matrix:
        python-version: [3.7, 3.8, 3.9, "3.10", 3.11, 3.12]
        # macos13 runs on until and macos14 now runs on arm64
        os: [ubuntu-20.04, macos-latest, macos-13]
        exclude:
          # Python 3.7 is not available on M1 Mac homebrew
          - os: macos-latest
            python-version: 3.7
        include:
          - os: ubuntu-20.04
            INSTALL_DEPS: sudo apt-get update && sudo apt-get -y install gfortran-7 swig libopenmpi-dev openmpi-bin libopenblas-dev && sudo ln -s `which gfortran-7` /usr/local/bin/gfortran
          - os: macos-latest
            # Different versions of homebrew put the gfortran in different
            INSTALL_DEPS: >
              brew update-reset 
              && HOMEBREW_NO_AUTO_UPDATE=1  HOMEBREW_NO_INSTALLED_DEPENDENTS_CHECK=1 brew install gcc swig libomp open-mpi openblas 
              && COSMOSIS_GCC_VER=$(brew list --versions gcc | awk '{print $2}' | cut -d. -f1)
              && GFORTRAN_PATH1=/usr/local/bin/gfortran
              && GFORTRAN_PATH2=/usr/local/bin/gfortran-${COSMOSIS_GCC_VER}
              && GFORTRAN_PATH3=/opt/homebrew/bin/gfortran
              && GFORTRAN_PATH4=/opt/homebrew/bin/gfortran-${COSMOSIS_GCC_VER}
              && if ! which -s gfortran
              ; then if [ -f $GFORTRAN_PATH2 ]; then ln -s $GFORTRAN_PATH2 $GFORTRAN_PATH1; echo Linking gfortran from /usr/local
              ;      elif [ -f $GFORTRAN_PATH4 ]; then ln -s $GFORTRAN_PATH4 $GFORTRAN_PATH3; echo Linking gfortran from /opt/homebrew
              ;      else echo "gfortran not found" && exit 1
              ;      fi
              ; fi
              && echo "gfortran now at $(which -a gfortran)"
          - os: macos-13
            # Different versions of homebrew put the gfortran in different
            INSTALL_DEPS: >
              brew update-reset 
              && HOMEBREW_NO_AUTO_UPDATE=1  HOMEBREW_NO_INSTALLED_DEPENDENTS_CHECK=1 brew install gcc swig libomp open-mpi openblas 
              && COSMOSIS_GCC_VER=$(brew list --versions gcc | awk '{print $2}' | cut -d. -f1)
              && GFORTRAN_PATH1=/usr/local/bin/gfortran
              && GFORTRAN_PATH2=/usr/local/bin/gfortran-${COSMOSIS_GCC_VER}
              && GFORTRAN_PATH3=/opt/homebrew/bin/gfortran
              && GFORTRAN_PATH4=/opt/homebrew/bin/gfortran-${COSMOSIS_GCC_VER}
              && if ! which -s gfortran
              ; then if [ -f $GFORTRAN_PATH2 ]; then ln -s $GFORTRAN_PATH2 $GFORTRAN_PATH1; echo Linking gfortran from /usr/local
              ;      elif [ -f $GFORTRAN_PATH4 ]; then ln -s $GFORTRAN_PATH4 $GFORTRAN_PATH3; echo Linking gfortran from /opt/homebrew
              ;      else echo "gfortran not found" && exit 1
              ;      fi
              ; fi
              && echo "gfortran now at $(which -a gfortran)"
    steps:
    - name: Checkout repository
      uses: actions/checkout@v3
      with:
        submodules: true

    - name: Set up Python ${{ matrix.python-version }}
      uses: actions/setup-python@v5
      with:
        python-version: ${{ matrix.python-version }}
        cache: 'pip' # caching pip dependencies
        cache-dependency-path: 'setup.py'

    - name: Install dependencies
      run: ${{ matrix.INSTALL_DEPS }}


    - name: Install python dependencies
      run: |
        python -m pip install --upgrade pip
        if [[ "${{ matrix.os }}" == "macos-13" || "${{ matrix.python-version }}" == '3.7' || "${{ matrix.python-version}}" == '3.8' ]]; then
          pip install "numpy<2"
        else
          pip install "numpy>=2"
        fi
        pip install -vv .
        pip install --no-binary=mpi4py mpi4py astropy pytest pytest-cov getdist derivative numdifftools

    - name: Install PocoMC
      if: matrix.python-version != '3.7'
      run: |
        pip install pocomc==1.2.6

    - name: Test nautilus alone
      if: (matrix.python-version == '3.12' || matrix.python-version == '3.11' || matrix.python-version =='3.10') && (matrix.os == 'macos-13')
      run: |
        # On some systems it seems like nautilus runs out of
        # memory when run with the full test suite.
        python cosmosis/test/test_samplers.py test_nautilus

    - name: Test with pytest
      run: |
        cosmosis --version
        if [[ "${{ matrix.os }}" == 'macos-13' && ("${{ matrix.python-version }}" == '3.10' || "${{ matrix.python-version }}" == '3.11' || "${{ matrix.python-version }}" == '3.12' ) ]]; then
          export SKIP_NAUTILUS=1
        fi
        mkdir tmp && cd tmp && pytest --pyargs cosmosis --cov cosmosis --cov-report=xml

    - name: Upload coverage reports to Codecov
      uses: codecov/codecov-action@v3
      if: matrix.python-version == '3.9' && matrix.os == 'ubuntu-20.04'
      env:
        CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}