test.yml

# The starting point of this script are the links provided on the maturing doc:
# * https://github.com/nanoporetech/fast-ctc-decode/blob/b226ea0f2b2f4f474eff47349703d57d2ea4801b/.github/workflows/publish.yml
# * https://github.com/konstin/complex-manylinux-maturin-docker/blob/main/.github/workflows/build.yml

# Description of the usage of virtual env:
# * https://packaging.python.org/guides/installing-using-pip-and-virtual-environments/

name: test-cdshealpix

on: [push, workflow_dispatch]


# Jobs run in parallel, see https://docs.github.com/en/actions/reference/workflow-syntax-for-github-actions#jobs
# Github hosted runner are: see https://docs.github.com/en/actions/using-github-hosted-runners/about-github-hosted-runners
jobs:

  # Linux is specific because of manylinux, we have to use a docker file
  test-linux64-wheels:
    # Containers run in Linux
    runs-on: ubuntu-latest
    # Docker Hub image that 'build-linux-wheels' executes in.
    # See https://github.com/pypa/manylinux for this particular container:
    # * CPython 3.8, 3.9, 3.10, ... installed in /opt/python/<python tag>-<abi tag>
    container: quay.io/pypa/manylinux2014_x86_64
    # We are now in CentOS 7 64 bits
    steps:
     # Checkout the project
     - name: "Checkout branch ${{ github.head_ref }}"
       uses: actions/checkout@v3
       with:
         ref: ${{ github.head_ref }}
     # We need to install rust in the docker image (else, cargo is already available in github action)
     - name: "Install Rust"
       run: |
         curl --proto '=https' --tlsv1.2 -sSf https://sh.rustup.rs | sh -s -- -y
     # Test Rust code
     #- name: Run rust wrapper tests
     #  run: |
     #    source $HOME/.cargo/env
     #    cargo test --verbose -- --nocapture
     # Build and install locally wheels for all pre-installed python version (in /opt/python/, see docker image comment)
     # installing first maturin and using maturin: https://github.com/PyO3/maturin#pypy
     - name: "Build and test wheels"
       run: |
         source $HOME/.cargo/env
         for PYBIN in /opt/python/cp3[8910]*/bin; do
           echo "Loop on PYBIN: $PYBIN"
           # With maturin develop, we have to use virtualenv
           "${PYBIN}/pip" install virtualenv
           "${PYBIN}/virtualenv" cdshealpixenv
           source cdshealpixenv/bin/activate
           # No we are in the virtual env
           pip install --upgrade pip
           echo "INSTALL MATURIN"
           pip install maturin
           maturin -V
           echo "MATURIN BUILD"
           maturin build --release --compatibility manylinux2014
           echo "MATURIN DEVELOP"
           maturin develop --release
           echo "INSTALL DEPENDENCIES"
           pip install -r requirements-dev.txt
           echo "PERFORM TESTS"
           cd python
           python -m pytest -v -s cdshealpix/tests/test_nested_healpix.py
           python -m pytest -v -s cdshealpix/tests/test_ring_healpix.py
           cd ..
           echo "CLEAN"
           pip freeze > requirements-uninstall.txt
           pip uninstall -r requirements-uninstall.txt -y
           deactivate
           rm -r cdshealpixenv/
         done

  # # Linux is specific because of manylinux, we have to use a docker file
  # test-linux32-wheels:
  #   # Containers run in Linux
  #   runs-on: ubuntu-latest
  #   # Docker Hub image that 'build-linux-wheels' executes in.
  #   # See https://github.com/pypa/manylinux for this particular container:
  #   # * CPython 3.8, 3.9, 3.10 ... installed in /opt/python/<python tag>-<abi tag>
  #   container: quay.io/pypa/manylinux2014_i686
  #   # We are now in CentOS 7 32 bits
  #   steps:
  #    # Checkout the project
  #    - name: "Checkout branch ${{ github.head_ref }}"
  #      uses: actions/checkout@v3
  #    # We need to install rust in the docker image (else, cargo is already available in github action)
  #    - name: "Install Rust"
  #      run: |
  #        curl --proto '=https' --tlsv1.2 -sSf https://sh.rustup.rs | sh -s -- --default-host i686-unknown-linux-gnu -y
  #    # Test Rust code
  #    #- name: Run rust wrapper tests
  #    #  run: |
  #    #    source $HOME/.cargo/env
  #    #    cargo test --verbose -- --nocapture
  #    # Build wheels for all pre-installed python version (in /opt/python/, see docker image comment)
  #    # installing first maturin and using maturin: https://github.com/PyO3/maturin#pypy
  #    - name: "Build and test wheels"
  #      run: |
  #        source $HOME/.cargo/env
  #        for PYBIN in /opt/python/cp3[8910]*/bin; do
  #          echo "Loop on PYBIN: $PYBIN"
  #          # With maturin develop, we have to use virtualenv
  #          "${PYBIN}/pip" install virtualenv
  #          "${PYBIN}/virtualenv" cdshealpixenv
  #          source cdshealpixenv/bin/activate
  #          pip install --upgrade pip
  #          # No we are in the virtual env
  #          echo "INSTALL MATURIN"
  #          pip install maturin
  #          maturin -V
  #          echo "MATURIN DEVELOP"
  #          maturin build --release --compatibility manylinux2014 --target i686-unknown-linux-gnu
  #          echo "MATURIN DEVELOP"
  #          maturin develop --release --target i686-unknown-linux-gnu
  #          echo "INSTALL DEPENDENCIES"
  #          pip install -r requirements-dev.txt
  #          echo "PERFORM TESTS"
  #          python -m pytest -v -s cdshealpix/tests/test_nested_healpix.py
  #          python -m pytest -v -s cdshealpix/tests/test_ring_healpix.py
  #          echo "CLEAN"
  #          pip freeze > requirements-uninstall.txt
  #          pip uninstall -r requirements-uninstall.txt -y
  #          deactivate
  #          rm -r cdshealpixenv/
  #        done

  test-linux32-wheels:
    runs-on: ubuntu-latest
    env:
      img: quay.io/pypa/manylinux2014_i686
    steps:
      - name: Checkout
        uses: actions/checkout@v3
      - name: "Set up QEMU"
        id: qemu
        uses: docker/setup-qemu-action@v1
      - name: Install dependencies
        run: |
          docker run --rm -v ${{ github.workspace }}:/ws:rw --workdir=/ws \
          ${{ env.img }} \
          bash -exc 'curl --proto "=https" --tlsv1.2 -sSf https://sh.rustup.rs | sh -s -- -y && \
            source $HOME/.cargo/env && \
            for PYBIN in /opt/python/cp3[78910]*/bin; do
              echo "Loop on PYBIN: $PYBIN"
              "${PYBIN}/pip" install virtualenv
              "${PYBIN}/virtualenv" cdshealpixenv
              source cdshealpixenv/bin/activate
              pip install --upgrade pip
              pip install maturin
              maturin build --release --compatibility manylinux2014
              maturin develop --release
              pip install -r requirements-dev.txt
              cd python
              python -m pytest -v -s cdshealpix/tests/test_nested_healpix.py
              python -m pytest -v -s cdshealpix/tests/test_ring_healpix.py
              cd ..
              pip freeze > requirements-uninstall.txt
              pip uninstall -r requirements-uninstall.txt -y
              deactivate
              rm -r cdshealpixenv/
            done'


  ## So far desactivated because too long to build astropy wheels
  #test-aarch64-wheels:
  #  runs-on: ubuntu-latest
  #  env:
  #    img: quay.io/pypa/manylinux2014_aarch64
  #  steps:
  #    - name: Checkout
  #      uses: actions/checkout@v3
  #    - name: "Set up QEMU"
  #      id: qemu
  #      uses: docker/setup-qemu-action@v1
  #    - name: Install dependencies
  #      run: |
  #        docker run --rm -v ${{ github.workspace }}:/ws:rw --workdir=/ws \
  #        ${{ env.img }} \
  #        bash -exc 'curl --proto "=https" --tlsv1.2 -sSf https://sh.rustup.rs | sh -s -- --default-host aarch64-unknown-linux-gnu -y && \
  #          source $HOME/.cargo/env && \
  #          for PYBIN in /opt/python/cp3[78910]*/bin; do
  #            echo "Loop on PYBIN: $PYBIN"
  #            "${PYBIN}/pip" install virtualenv
  #            "${PYBIN}/virtualenv" cdshealpixenv
  #            source cdshealpixenv/bin/activate
  #            pip install --upgrade pip
  #            pip install maturin
  #            cargo build --release --config "net.git-fetch-with-cli = true"
  #            maturin build --release --compatibility manylinux2014 --target aarch64-unknown-linux-gnu --config "net.git-fetch-with-cli = true"
  #            maturin develop --release --target aarch64-unknown-linux-gnu --config "net.git-fetch-with-cli = true"
  #            pip install -r requirements-dev.txt
  #            cd python
  #            python -m pytest -v -s cdshealpix/tests/test_nested_healpix.py
  #            python -m pytest -v -s cdshealpix/tests/test_ring_healpix.py
  #            cd ..
  #            pip freeze > requirements-uninstall.txt
  #            pip uninstall -r requirements-uninstall.txt -y
  #            deactivate
  #            rm -r cdshealpixenv/
  #          done'

  test-macos-wheels:
    runs-on: macos-latest
    strategy:
      matrix:
        python-version: ['3.8', '3.9', '3.10', '3.11', '3.12']
    steps:
     # Checkout the project
     - name: "Checkout branch ${{ github.head_ref }}"
       uses: actions/checkout@v3
       with:
         ref: ${{ github.head_ref }}
     # Test Rust code
     #- name: Run rust wrapper tests
     #  run: cargo test --verbose -- --nocapture
     # Set up python, see https://docs.github.com/en/actions/guides/building-and-testing-python
     - name: "Set up Python ${{ matrix.python-version }} on MacOS"
       uses: actions/setup-python@v2
       with:
         python-version: ${{ matrix.python-version }}
     # Test python code
     - name: "Build and test wheel for Python ${{ matrix.python-version }} on MacOS"
       run: |
         # Install, create and activate a python virtualenv
         rustup target add aarch64-apple-darwin
         pip install virtualenv
         virtualenv cdshealpixenv
         source cdshealpixenv/bin/activate
         # Install and use maturin
         pip install --upgrade pip
         pip install maturin
         maturin -V
         maturin build --release --target universal2-apple-darwin
         maturin develop --release
         # Install dependencies
         pip install -r requirements-dev.txt
         # Run tests
         cd python
         python -m pytest -v -s cdshealpix/tests/test_nested_healpix.py
         python -m pytest -v -s cdshealpix/tests/test_ring_healpix.py
         cd ..
         # Clean
         #pip freeze > requirements-uninstall.txt
         #pip uninstall -r requirements-uninstall.txt -y
         deactivate
         #rm -r cdshealpixenv/

  test-windows-wheels:
    runs-on: windows-latest
    strategy:
      matrix:
        python-version: ['3.8', '3.9', '3.10', '3.11', '3.12']
    steps:
      # Checkout the project
      - name: "Checkout branch ${{ github.head_ref }}"
        uses: actions/checkout@v3
        with:
          ref: ${{ github.head_ref }}
      # Test Rust code
      #- name: Run rust wrapper tests
      #  run: cargo test --verbose -- --nocapture
      # Set up python, see https://docs.github.com/en/actions/guides/building-and-testing-python
      - name: "Set up Python ${{ matrix.python-version }} on Windows"
        uses: actions/setup-python@v2
        with:
          python-version: ${{ matrix.python-version }}
      # Test python code
      - name: "Build and test wheel for Python ${{ matrix.python-version }} on Windows"
        run: |
          # Install, create and activate a python virtualenv
          # See: https://mothergeo-py.readthedocs.io/en/latest/development/how-to/venv-win.html
          pip install virtualenv
          virtualenv cdshealpixenv
          .\cdshealpixenv\Scripts\activate
          pip install --upgrade pip
          # Install and use maturin
          pip install maturin
          maturin -V
          maturin develop --release
          # Install dependencies
          pip install -r requirements-dev.txt
          # Run tests
          cd python
          python -m pytest -v "cdshealpix\tests\test_nested_healpix.py"
          python -m pytest -v "cdshealpix\tests\test_ring_healpix.py"
          cd ..
          deactivate

  # Build the doc and run the tests in the doc (only for python 3.9 on ubuntu)
  test-doc:
    runs-on: ubuntu-latest
    steps:
      - name: "Checkout branch ${{ github.head_ref }}"
        uses: actions/checkout@v3
        with:
          ref: ${{ github.head_ref }}
      - name: "Set up Python 3.9 on Ubuntu"
        uses: actions/setup-python@v4
        with:
          python-version: '3.9'
      - name: "Build and test doc"
        run: |
          # Install virtualenv
          pip install virtualenv
          # Create and activate a new virtualenv
          virtualenv cdshealpixenv
          source cdshealpixenv/bin/activate
          # Install maturin
          pip install --upgrade pip
          pip install maturin
          maturin -V
          # Build and install cdshealpix
          maturin develop --release
          # Install dependencies needed to build the docs
          pip install -r requirements-doc.txt
          # Compile the docs and run the test examples
          cd ./docs
          # * Generate the HTML files
          make html
          # * Run the API test examples
          make doctest
          cd ..
          # Switch of the virtualenv
          deactivate