test_and_build.yml

name: CI
on:
    push:
      paths-ignore:
        - "README.md"
        - "**/docs/**"
        - ".github/workflows/docs.yml"

    pull_request:
      branches:
        - master
        - dev
        
    schedule:
        - cron: "0 11 * * *"

jobs:
    skip_duplicate:
        runs-on: ubuntu-latest
        outputs:
            should_skip: ${{ steps.skip_check.outputs.should_skip }}
        steps:
            - id: skip_check
              uses: fkirc/skip-duplicate-actions@master
              with:
                  github_token: ${{ github.token }}
                  concurrent_skipping: never
                  skip_after_successful_duplicate: true
                  paths_ignore: '["**/README.md", "**/docs/**"]'
                  do_not_skip: '["pull_request",  "schedule"]'

    test-pip:
        name: Test with Pip install
        needs: skip_duplicate
        if: ${{ needs.skip_duplicate.outputs.should_skip == 'false' }}
        strategy:
            fail-fast: false
            matrix:
                python-version: ["3.9", "3.10", "3.11"]
                os: ["ubuntu-latest", "macos-latest", "macos-12"]
        runs-on: ${{ matrix.os }}
        steps:
            - name: Checkout
              uses: actions/checkout@v4
            - name: Set up Python ${{ matrix.python-version }}
              uses: actions/setup-python@v5
              with:
                  python-version: ${{ matrix.python-version }}
            - name: Install dependencies
              run: |
                  python -m pip install --upgrade pip wheel
                  pip install --upgrade flake8 coverage pytest-cov cython
                  
                  if [[ ${{matrix.os}} == macos-latest ]];
                  then
                    brew update
                    brew install hdf5
                  fi

                  pip install -e .
            - name: Lint with flake8
              run: |
                  # stop the build if there are Python syntax errors or undefined names
                  flake8

            - name: Test pip on ${{ matrix.python-version }}
              run: |
                  python -m pytest -vv --cov=astromodels/ --cov-report=xml --junitxml=junit/test-results.xml
              env:
                  OMP_NUM_THREADS: 1
                  MKL_NUM_THREADS: 1
                  NUMEXPR_NUM_THREADS: 1
                  MPLBACKEND: "Agg"

            - name: Publish Unit Test Results Ubuntu
              uses: EnricoMi/publish-unit-test-result-action@v2
              if: runner.os == 'Linux'
              with:
                files: junit/test-*.xml
                comment_mode: off

            - name: Publish Unit Test Results MacOS
              uses: EnricoMi/publish-unit-test-result-action/composite@v2
              if: runner.os == 'macOS'
              with:
                files: junit/test-*.xml
                comment_mode: off

            - name: Upload coverage to Codecov
              uses: codecov/codecov-action@v4
              with:
                  file: ./coverage.xml
                  files: ./coverage1.xml,./coverage2.xml
                  directory: ./coverage/reports/

    test-conda:
        name: Test Conda version
        needs: skip_duplicate
        if: ${{ needs.skip_duplicate.outputs.should_skip == 'false' }}
        strategy:
            fail-fast: false
            matrix:
                os: ["ubuntu-latest", "macos-latest", "macos-12"]
                python-version: [3.9]
        runs-on: ${{ matrix.os }}
        steps:
            - name: Checkout
              uses: actions/checkout@v4
            # - name: Cache conda
            #   uses: actions/cache@v4
            #   env:
            #     # Increase this value to reset cache if etc/example-environment.yml has not changed
            #     CACHE_NUMBER: 0
            #   with:
            #       path: ~/conda_pkgs_dir
            #       key: conda-${{ matrix.os }}-python-${{ matrix.python-version }}-${{ hashFiles('ci/environment.yml') }}
            - name: Add conda ${{ matrix.python-version }} to system path
              uses: conda-incubator/setup-miniconda@v3
              with:
                  activate-environment: "test_env"
                  auto-activate-base: false
                  architecture: "x64"
                  #mamba-version: "*"
                  miniforge-version: latest
                  python-version: ${{ matrix.python-version }}
                  auto-update-conda: true
                  environment-file: ci/environment.yml
                  use-only-tar-bz2: true
                  channel-priority: strict
                  channels: conda-forge, xspecmodels
              

            - name: Init Env
              shell: bash -l {0}
              run: |
                  # Make sure we fail in case of error
                  if [[ ${{matrix.os}} == ubuntu-latest ]];
                  then
                  miniconda_os=Linux
                  compilers="gcc_linux-64 gxx_linux-64 gfortran_linux-64"
                  else  # osx
                  miniconda_os=MacOSX
                  compilers="clang_osx-64 clangxx_osx-64 gfortran_osx-64"

                  # On macOS we also need the conda libx11 libraries used to build xspec
                  # We also need to pin down ncurses, for now only on macos.
                  xorg="xorg-libx11"
                  fi


                  export PKG_VERSION=$(python -c "import versioneer;print(versioneer.get_version())")

                  mamba install ${PKG} codecov pytest-cov git flake8

            - name: Conda list
              shell: bash -l {0}
              run: |
                  conda list
            - name: install it
              shell: bash -l {0}
              run: |
                  pip install -e .
            - name: Lint with flake8
              shell: bash -l {0}
              run: |
                  # stop the build if there are Python syntax errors or undefined names
                  flake8

            - name: Test conda install
              shell: bash -l {0}
              run: |
              
                  echo "======>  importing XSPEC..."
                  python -c "import astromodels.xspec"
                  python -m pytest -vv --cov=astromodels --cov-report=xml

              env:
                  OMP_NUM_THREADS: 1
                  MKL_NUM_THREADS: 1
                  NUMEXPR_NUM_THREADS: 1
                  MPLBACKEND: "Agg"

            - name: Upload coverage to Codecov
              uses: codecov/codecov-action@v4
              with:
                  file: ./coverage.xml
                  files: ./coverage1.xml,./coverage2.xml
                  directory: ./coverage/reports/