pyopenms-wheels.yml

# This builds python wheels on manylinux, macOS and Windows and uploads them
# to public pypi for release and for nightlies also to pypi.cs.uni-tuebingen.de

name: pyopenms-wheels-and-packages

# Controls when the action will run. Triggers the workflow on push or pull request
# events but only for the master branch
on:
  workflow_dispatch:
    inputs:
      upload-to-pypi:
        type: boolean
        description: actually upload the release package to pypi.org
        default: false
  push:
    tags:
      - 'Release*'
    branches: [ nightly, py_nightly_test ]

# A workflow run is made up of one or more jobs that can run sequentially or in parallel
jobs:
  build-win:
    runs-on: windows-latest
    steps:
    - uses: actions/checkout@v4
      with:
        path: OpenMS
      
    - name: Setup cmake
      uses: jwlawson/actions-setup-cmake@v2
      with:
        cmake-version: '3.25.x'

    - name: Reduce PATH # This fixes a bug described in https://github.com/facebook/watchman/commit/59bcfbf91d2a24ab580b8a78e384f133cc202383
      run: echo "DISTUTILS_USE_SDK=1"

    - name: Get number of CPU cores
      uses: SimenB/github-actions-cpu-cores@v2
      id: cpu-cores

    - name: Install Qt
      uses: jurplel/install-qt-action@v4
      with:
        version: '6.*'
        host: 'windows' # default: win64_msvc2017_64
        target: 'desktop'
        install-deps: 'true'
        archives: 'qtsvg qtbase'
        cache: 'false'

    - name: Install Miniconda
      shell: bash # uses git bash on windows
      run: |
            MINICONDA_FILENAME=Miniconda3-latest-Windows-x86_64.exe
            curl -o $MINICONDA_FILENAME "https://repo.anaconda.com/miniconda/$MINICONDA_FILENAME"
            ./Miniconda3-latest-Windows-x86_64.exe //InstallationType=JustMe //RegisterPython=0 //S //D=$HOME/miniconda3


    - name: Download contrib build from archive (Windows)
      shell: bash
      env:
        GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
      run: |
          cd OpenMS/contrib
          # Download the file using the URL fetched from GitHub
          gh release download -R OpenMS/contrib --pattern 'contrib_build-Windows.tar.gz'
          # Extract the archive
          7z x -so contrib_build-Windows.tar.gz | 7z x -si -ttar
          rm contrib_build-Windows.tar.gz
          ls -la

    # https://github.com/marketplace/actions/visual-studio-shell
    - name: Set up Visual Studio shell
      uses: egor-tensin/vs-shell@v2
      with:
        arch: x64

    - name: Setup conda paths
      shell: bash
      run: |
        echo "$HOME/miniconda3/bin" >> $GITHUB_PATH
        echo "$HOME/miniconda3/Scripts" >> $GITHUB_PATH

    - name: Build on Windows
      shell: bash
      run: |
        PYTHON_VERSIONS=$(cat OpenMS/.github/workflows/python_versions.json)
        CMAKE_PREFIX_PATH="$(echo $Qt6_Dir)/lib/cmake;${Qt6_Dir}"
        #mkdir bld
        #pushd bld
        # TODO: set generator via variable, then we can share this step
        # cmake --version
        # cmake -G "Visual Studio 17 2022" -A x64 -DOPENMS_CONTRIB_LIBS="$GITHUB_WORKSPACE/OpenMS/contrib" -DCMAKE_PREFIX_PATH="$(echo $Qt6_Dir)/lib/cmake;${Qt6_Dir}" ../OpenMS
        # Note: multiple --targets only supported by CMake 3.15+
        # cmake --build . --config Release --target OpenMS
        
        #ctest --progress --output-on-failure -VV -S $GITHUB_WORKSPACE/OpenMS/tools/ci/cibuild.cmake
        export CXXFLAGS="-D_DISABLE_CONSTEXPR_MUTEX_CONSTRUCTOR $CXXFLAGS"
      
        mkdir pyopenms_whls

        # The growing PATH leads to a failure in the last iteration of the pyopenms build process.
        # We will store the PATH variable in the beginning and reset it with every iteration.
        RESET_PATH=$PATH

        for py in $(echo "${PYTHON_VERSIONS}" | jq -r '.[]'); do

          # clean previous pyopenms libs
          find . -name "_pyopenms*.pyd" -exec rm -rf {} \;
          # reset the path
          PATH=$RESET_PATH

          # create and activate conda environment
          py=$(echo "$py" | tr -d " \r\n")
          pynodot=$(echo "$py" | tr -d ".")
          conda create -n pyoms-bld-"${pynodot}" python="${py}"
          source activate pyoms-bld-"${pynodot}"

          # set current python executable
          CURRENT_PYTHON_EXECUTABLE=$(which python)

          ${CURRENT_PYTHON_EXECUTABLE} -m pip install --upgrade pip
          # pip install all the stuff
          ${CURRENT_PYTHON_EXECUTABLE} -m pip install -r $GITHUB_WORKSPACE/OpenMS/src/pyOpenMS/requirements_bld.txt
          
          # Get the Python root directory
          export Python_ROOT_DIR=$(conda info --json | jq -r '.sys.prefix')
          echo "Python root directory: $Python_ROOT_DIR"

          export BUILD_NAME="pyopenms-wheels-${{ runner.arch }}-class-pyopenms-$py-${{ github.run_number }}" #TODO make this more expressive

          # build pyopenms distribution
          ctest --output-on-failure -VV -S $GITHUB_WORKSPACE/OpenMS/tools/ci/cibuild.cmake --config Release

          echo "Current dir is `pwd`"
          echo "wheels are in `find . | grep whl`"
          echo "current ls is `ls -la`"
          # copy to directory
          cp OpenMS/bld/pyOpenMS/dist/*.whl pyopenms_whls/
          # clean up
          #conda deactivate
          #conda remove --name "pyoms-bld-${pynodot}" --all
        done

      env: 
          SOURCE_DIRECTORY: "${{ github.workspace }}/OpenMS"
          CMAKE_GENERATOR: "Visual Studio 17 2022"
          CMAKE_GENERATOR_PLATFORM: "x64"
          OPENMS_CONTRIB_LIBS: "${{ github.workspace }}/OpenMS/contrib"
          #CMAKE_PREFIX_PATH: "$(echo $Qt6_Dir)/lib/cmake;${Qt6_Dir}" #TODO move this to env
          BUILD_TYPE: "Release"
          CI_PROVIDER: "GitHub-Actions"
          CMAKE_CCACHE_EXE: "ccache"
          CCACHE_BASEDIR: ${{ github.workspace }}
          CCACHE_DIR: ${{ github.workspace }}/.ccache
          CCACHE_COMPRESS: true
          CCACHE_COMPRESSLEVEL: 12
          CCACHE_MAXSIZE: 400M
          PYOPENMS: "ON"
          PY_NUM_THREADS: ${{ steps.cpu-cores.outputs.count }}
          ENABLE_TUTORIALS: "OFF"
          ENABLE_DOCS: "OFF"
          ENABLE_PIPELINE_TESTING: "OFF"
          ENABLE_STYLE_TESTING: "OFF"
          ENABLE_TOPP_TESTING: "OFF"
          ENABLE_CLASS_TESTING: "OFF"


    - name: Run Unit Tests
      shell: bash
      run: |
           ctest --output-on-failure -V -S $GITHUB_WORKSPACE/OpenMS/tools/ci/citest.cmake -C Release
      env:
          SOURCE_DIRECTORY: "${{ github.workspace }}/OpenMS"
          CI_PROVIDER: "GitHub-Actions"
          BUILD_NAME: "${{ runner.arch }}-class-pyopenms-${{ github.run_number }}"
          BUILD_TYPE: "Release"
          # The rest of the vars should be saved in the CMakeCache

    - uses: actions/upload-artifact@v4
      name: Upload artifacts
      with:
        name: ${{ runner.os }}-${{ runner.arch }}-wheels
        path: pyopenms_whls
        
  build-macos-arm:
    runs-on: macos-latest
    env:
      SYSTEM_VERSION_COMPAT: 0 # workaround for mac see https://github.com/actions/setup-python/issues/469 for details.
    steps:
    - uses: actions/checkout@v4
      with:
        path: OpenMS

    - name: Get number of CPU cores
      uses: SimenB/github-actions-cpu-cores@v2
      id: cpu-cores

    - name: Setup cmake
      uses: jwlawson/actions-setup-cmake@v2
      with:
        cmake-version: '3.25.x'

    - name: Install Miniconda
      shell: bash
      run: |
            MINICONDA_FILENAME=Miniconda3-latest-MacOSX-arm64.sh
            curl -o $MINICONDA_FILENAME "https://repo.anaconda.com/miniconda/$MINICONDA_FILENAME"
            bash ${MINICONDA_FILENAME} -b -f -p $HOME/miniconda3

    - name: Setup conda paths
      shell: bash
      run: |
        echo "$HOME/miniconda3/bin" >> $GITHUB_PATH
        echo "$HOME/miniconda3/Scripts" >> $GITHUB_PATH

    - name: Force update all brew python
      run: |
        brew update
        # GHA messes with links https://github.com/actions/setup-python/issues/577 so we just force replace their installs' with brew's
        for pkg in $(brew list --formula | grep -E '^python(@[0-9]+\.[0-9]+)?$'); do
            brew upgrade --force --overwrite "$pkg"
        done
        brew cleanup

    - name: Install build tools
      run: brew install --force --overwrite autoconf automake libtool

    - name: Install contrib packages from brew
      run: |
        ## Needed for Qt. Install before to overwrite the default softlinks on the GH runners
        brew install --force --overwrite --quiet ccache autoconf automake libtool ninja && brew link --overwrite ccache
        brew install --force --overwrite libsvm xerces-c boost eigen sqlite coinutils cbc cgl clp qt@6 libomp
        brew link --force libomp 
        echo "cmake_prefix=$(brew --prefix qt@6)/lib/cmake;$(brew --prefix libomp)" >> $GITHUB_OUTPUT
        echo "Qt6_DIR=$(brew --prefix qt@6)/lib/cmake/Qt6" >> $GITHUB_ENV
        if [[ "${{ steps.set-vars.outputs.pkg_type }}" != "none" ]]; then
          brew install --force --overwrite --quiet doxygen ghostscript graphviz
        fi

    - name: Build on macos arm
      run: |
        PYTHON_VERSIONS=$(cat OpenMS/.github/workflows/python_versions.json)
        # export CC=clang
        # export CXX=clang++
        # export MACOSX_DEPLOYMENT_TARGET=12
        # Unfortunately, on macOS due to the inofficial way of enabling OpenMP on AppleClang, passing the following
        # options to setup.py extra_compile_args does not work. See also https://gist.github.com/andyfaff/084005bee32aee83d6b59e843278ab3e
        export CFLAGS="-Xpreprocessor -fopenmp $CFLAGS"
        export CXXFLAGS="-Xpreprocessor -fopenmp $CXXFLAGS"

        # mkdir bld
        # pushd bld
        # Use -DCMAKE_FIND_DEBUG_MODE=ON for debug

        # export OpenMP_ROOT="$(brew --prefix libomp)"
        export CMAKE_PREFIX_PATH="$(brew --prefix libomp);$(echo $Qt6_DIR)/lib/cmake;${Qt6_DIR}"

        #ctest --output-on-failure -V -S $GITHUB_WORKSPACE/OpenMS/tools/ci/cibuild.cmake

        #cmake -DCMAKE_BUILD_TYPE="Release" -DCMAKE_PREFIX_PATH="$(brew --prefix libomp);$(echo $Qt6_Dir)/lib/cmake;${Qt6_Dir}" -DCMAKE_OSX_DEPLOYMENT_TARGET=12 -DBOOST_USE_STATIC=OFF ../OpenMS
        #make -j${{ steps.cpu-cores.outputs.count }} OpenMS

        mkdir pyopenms_whls

        for py in $(echo "${PYTHON_VERSIONS}" | jq -r '.[]'); do

          # clean previous pyopenms libs
          # do at the top of the python version loop so that we leave the final libraries for testing
          find . -name "_pyopenms*.so" -exec rm -rf {} \;

          py=$(echo "$py" | tr -d " \n")
          pynodot=$(echo "$py" | tr -d ".")
          conda create -n pyoms-bld-"${pynodot}" python="${py}"
          source activate pyoms-bld-"${pynodot}"

          # set current python executable
          CURRENT_PYTHON_EXECUTABLE=$(which python)
          
          ${CURRENT_PYTHON_EXECUTABLE} -m pip install --upgrade pip
          # pip install all the stuff
          ${CURRENT_PYTHON_EXECUTABLE} -m pip install -r $GITHUB_WORKSPACE/OpenMS/src/pyOpenMS/requirements_bld.txt

          # Get the Python root directory
          export Python_ROOT_DIR=$(conda info --json | jq -r '.sys.prefix')
          echo "Python root directory: $Python_ROOT_DIR"

          export BUILD_NAME="pyopenms-wheels-${{ runner.arch }}-class-pyopenms-$py-${{ github.run_number }}" #TODO make this more expressive

          # build pyopenms distribution (macOS)
          ctest --output-on-failure -VV -S $GITHUB_WORKSPACE/OpenMS/tools/ci/cibuild.cmake
          # TODO REMOVE DEBUGGING
          echo "Current dir is `pwd`"
          echo "wheels are in `find . | grep whl`"
          echo "current ls is `ls -la`"

          # cmake -DPYTHON_EXECUTABLE:FILEPATH=$CURRENT_PYTHON_EXECUTABLE -DPYOPENMS=ON -DPY_NUM_THREADS=${{ steps.cpu-cores.outputs.count }} .
          # make -j${{ steps.cpu-cores.outputs.count }} pyopenms

          # copy to directory
          cp OpenMS/bld/pyOpenMS/dist/*.whl pyopenms_whls/

          # clean up
          # conda deactivate
          # conda remove --name pyoms-bld-"${pynodot}" --all

        done

      env:
          CC: "clang"
          CXX: "clang++"
          BOOST_USE_STATIC: "OFF" #TODO check if necessary?
          MACOSX_DEPLOYMENT_TARGET: "12"
          SOURCE_DIRECTORY: "${{ github.workspace }}/OpenMS"
          CMAKE_GENERATOR: "Ninja"
          OPENMS_CONTRIB_LIBS: "$GITHUB_WORKSPACE/OpenMS/contrib"
          BUILD_TYPE: "Release"
          BUILD_NAME: "${{ runner.arch }}-class-pyopenms-${{ github.run_number }}" #TODO make this more expressive
          BUILD_FLAGS: "-j${{ steps.cpu-cores.outputs.count }}"
          CI_PROVIDER: "GitHub-Actions"
          CMAKE_CCACHE_EXE: "ccache"
          CCACHE_BASEDIR: ${{ github.workspace }}
          CCACHE_DIR: ${{ github.workspace }}/.ccache
          CCACHE_COMPRESS: true
          CCACHE_COMPRESSLEVEL: 12
          CCACHE_MAXSIZE: 400M
          # MT_ENABLE_OPENMP: "ON"
          PYOPENMS: "ON"
          PY_NUM_THREADS: ${{ steps.cpu-cores.outputs.count }}
          ENABLE_TUTORIALS: "OFF"
          ENABLE_DOCS: "OFF"
          ENABLE_PIPELINE_TESTING: "OFF"
          ENABLE_STYLE_TESTING: "OFF"
          ENABLE_TOPP_TESTING: "OFF"
          ENABLE_CLASS_TESTING: "OFF"

    - name: Run Unit Tests
      shell: bash
      run: |
            ctest --output-on-failure -V -S $GITHUB_WORKSPACE/OpenMS/tools/ci/citest.cmake
      env:
          SOURCE_DIRECTORY: "${{ github.workspace }}/OpenMS"
          CI_PROVIDER: "GitHub-Actions"
          BUILD_NAME: "${{ runner.arch }}-class-pyopenms-${{ github.run_number }}"
          # The rest of the vars should be saved in the CMakeCache

    - uses: actions/upload-artifact@v4
      name: Upload artifacts
      if: always()
      with:
        name: ${{ runner.os }}-buildfiles
        path: |
          CMakeCache.txt
          pyOpenMS/env.py
        
    - uses: actions/upload-artifact@v4
      name: Upload wheels
      with:
        name: ${{ runner.os }}-${{ runner.arch }}-wheels
        path: pyopenms_whls
        
  build-macos:
    runs-on: macos-13
    env:
      SYSTEM_VERSION_COMPAT: 0 # workaround for mac see https://github.com/actions/setup-python/issues/469 for details.
    steps:
    - uses: actions/checkout@v4
      with:
        path: OpenMS

    - name: Get number of CPU cores
      uses: SimenB/github-actions-cpu-cores@v2
      id: cpu-cores

    - name: Setup cmake
      uses: jwlawson/actions-setup-cmake@v2
      with:
        cmake-version: '3.25.x'

    - name: Install Miniconda
      shell: bash
      run: |
            MINICONDA_FILENAME=Miniconda3-latest-MacOSX-x86_64.sh
            curl -o $MINICONDA_FILENAME "https://repo.anaconda.com/miniconda/$MINICONDA_FILENAME"
            bash ${MINICONDA_FILENAME} -b -f -p $HOME/miniconda3

    - name: Setup conda paths
      shell: bash
      run: |
        echo "$HOME/miniconda3/bin" >> $GITHUB_PATH
        echo "$HOME/miniconda3/Scripts" >> $GITHUB_PATH
      
    - name: Force update all brew python
      run: |
        brew update
        # GHA messes with links https://github.com/actions/setup-python/issues/577 so we just force replace their installs' with brew's
        for pkg in $(brew list --formula | grep -E '^python(@[0-9]+\.[0-9]+)?$'); do
            brew upgrade --force --overwrite "$pkg"
        done
        brew cleanup

    - name: Install build tools
      run: brew install --force --overwrite autoconf automake libtool

    - name: Install contrib packages from brew
      run: |
        ## Update the package lists for Brew
        ## Needed for Qt. Install before to overwrite the default softlinks on the GH runners
        brew install --force --overwrite --quiet ccache autoconf automake libtool ninja && brew link --overwrite ccache
        brew install --force --overwrite libsvm xerces-c boost eigen sqlite coinutils cbc cgl clp qt@6 libomp
        echo "cmake_prefix=$(brew --prefix qt@6)/lib/cmake;$(brew --prefix qt@6);$(brew --prefix libomp)" >> $GITHUB_OUTPUT
        echo "Qt6_DIR=$(brew --prefix qt@6)/lib/cmake/Qt6" >> $GITHUB_ENV
        if [[ "${{ steps.set-vars.outputs.pkg_type }}" != "none" ]]; then
          brew install --force --overwrite --quiet doxygen ghostscript graphviz
        fi

    - name: Build on macos intel
      run: |
        PYTHON_VERSIONS=$(cat OpenMS/.github/workflows/python_versions.json)
        export CC=clang
        export CXX=clang++
        export MACOSX_DEPLOYMENT_TARGET=12
        # Unfortunately, on macOS due to the inofficial way of enabling OpenMP on AppleClang, passing the following
        # options to setup.py extra_compile_args does not work. See also https://gist.github.com/andyfaff/084005bee32aee83d6b59e843278ab3e
        export CFLAGS="-Xpreprocessor -fopenmp $CFLAGS"
        export CXXFLAGS="-Xpreprocessor -fopenmp $CXXFLAGS"
        # export OpenMP_ROOT="$(brew --prefix libomp)"
        export CMAKE_PREFIX_PATH="$(brew --prefix libomp);$(echo $Qt6_Dir)/lib/cmake;${Qt6_Dir}"

        #mkdir bld
        #pushd bld
        # Use -DCMAKE_FIND_DEBUG_MODE=ON for debug
        #cmake -DCMAKE_BUILD_TYPE="Release" -DCMAKE_PREFIX_PATH="$(brew --prefix libomp);$(echo $Qt6_Dir)/lib/cmake;${Qt6_Dir}" -DCMAKE_OSX_DEPLOYMENT_TARGET=12 -DBOOST_USE_STATIC=OFF ../OpenMS
        #make -j${{ steps.cpu-cores.outputs.count }} OpenMS

        mkdir pyopenms_whls

        for py in $(echo "${PYTHON_VERSIONS}" | jq -r '.[]'); do

          # clean previous pyopenms libs
          # do at the top of the python version loop so that we leave the final libraries for testing
          find . -name "_pyopenms*.so" -exec rm -rf {} \;

          py=$(echo "$py" | tr -d " \n")
          pynodot=$(echo "$py" | tr -d ".")
          conda create -n pyoms-bld-"${pynodot}" python="${py}"
          source activate pyoms-bld-"${pynodot}"

          # set current python executable
          CURRENT_PYTHON_EXECUTABLE=$(which python)

          ${CURRENT_PYTHON_EXECUTABLE} -m pip install --upgrade pip
          # pip install all the stuff
          ${CURRENT_PYTHON_EXECUTABLE} -m pip install -r $GITHUB_WORKSPACE/OpenMS/src/pyOpenMS/requirements_bld.txt

          # Get the Python root directory
          export Python_ROOT_DIR=$(conda info --json | jq -r '.sys.prefix')
          echo "Python root directory: $Python_ROOT_DIR"

          export BUILD_NAME="pyopenms-wheels-${{ runner.arch }}-class-pyopenms-$py-${{ github.run_number }}" #TODO make this more expressive

          # build pyopenms distribution (macOS)
          ctest --output-on-failure -VV -S $GITHUB_WORKSPACE/OpenMS/tools/ci/cibuild.cmake
          # TODO REMOVE DEBUGGING
          echo "Current dir is `pwd`"
          echo "wheels are in `find . | grep whl`"
          echo "current ls is `ls -la`"
          # cmake -DPYTHON_EXECUTABLE:FILEPATH=$CURRENT_PYTHON_EXECUTABLE -DPYOPENMS=ON -DPY_NUM_THREADS=${{ steps.cpu-cores.outputs.count }} .
          # make -j${{ steps.cpu-cores.outputs.count }} pyopenms

          # copy to directory
          cp OpenMS/bld/pyOpenMS/dist/*.whl pyopenms_whls/

          # clean up
          #conda deactivate
          #conda remove --name pyoms-bld-"${pynodot}" --all

          # clean previous pyopenms libs
          #find . -name "_pyopenms*.so" -exec rm -rf {} \;

        done

      env:
        CC: "clang"
        CXX: "clang++"
        MACOSX_DEPLOYMENT_TARGET: "12"
        SOURCE_DIRECTORY: "${{ github.workspace }}/OpenMS"
        CMAKE_GENERATOR: "Ninja"
        OPENMS_CONTRIB_LIBS: "$GITHUB_WORKSPACE/OpenMS/contrib"
        BOOST_USE_STATIC: "OFF"
        BUILD_TYPE: "Release"
        BUILD_NAME: "${{ runner.arch }}-class-pyopenms-${{ github.run_number }}" #TODO make this more expressive
        BUILD_FLAGS: "-j${{ steps.cpu-cores.outputs.count }}"
        CI_PROVIDER: "GitHub-Actions"
        CMAKE_CCACHE_EXE: "ccache"
        CCACHE_BASEDIR: ${{ github.workspace }}
        CCACHE_DIR: ${{ github.workspace }}/.ccache
        CCACHE_COMPRESS: true
        CCACHE_COMPRESSLEVEL: 12
        CCACHE_MAXSIZE: 400M
        #MT_ENABLE_OPENMP: "ON"
        PYOPENMS: "ON"
        PY_NUM_THREADS: ${{ steps.cpu-cores.outputs.count }}
        ENABLE_TUTORIALS: "OFF"
        ENABLE_DOCS: "OFF"
        ENABLE_STYLE_TESTING: "OFF"
        ENABLE_PIPELINE_TESTING: "OFF"
        ENABLE_TOPP_TESTING: "OFF"
        ENABLE_CLASS_TESTING: "OFF"

    - name: Test
      shell: bash
      run: |
            ctest --output-on-failure -V -S $GITHUB_WORKSPACE/OpenMS/tools/ci/citest.cmake
      env:
          SOURCE_DIRECTORY: "${{ github.workspace }}/OpenMS"
          CI_PROVIDER: "GitHub-Actions"
          BUILD_NAME: "${{ runner.arch }}-class-pyopenms-${{ github.run_number }}"
          # The rest of the vars should be saved in the CMakeCache
        
    - uses: actions/upload-artifact@v4
      name: Upload wheels
      with:
        name: ${{ runner.os }}-${{ runner.arch }}-wheels
        path: pyopenms_whls

  build-lnx:
    runs-on: [ubuntu-latest]
    container: ghcr.io/openms/contrib_manylinux_2_34:latest

    steps:
    # Cancels older builds if still running
    - uses: rokroskar/workflow-run-cleanup-action@master
      env:
        GITHUB_TOKEN: "${{ secrets.GITHUB_TOKEN }}"
      # Disable warning for this line
      if: "!startsWith(github.ref, 'refs/tags/') && github.ref != 'refs/heads/master' && github.ref != 'refs/heads/develop'" # noqa

    - uses: actions/checkout@v4
      name: Checkout sources
      with:
        path: OpenMS

    - name: Get number of CPU cores
      uses: SimenB/github-actions-cpu-cores@v2
      id: cpu-cores

    - name: Setup cmake
      uses: jwlawson/actions-setup-cmake@v2
      with:
        cmake-version: '3.25.x'

    - name: Build on manylinux for broad compatibility
      shell: bash
      run: |
        PYTHON_VERSIONS=$(cat OpenMS/.github/workflows/python_versions.json)
        yum install -y jq
        yum install -y ninja-build # Install Ninja for build files
        cmake --version

        mkdir -p $GITHUB_WORKSPACE/data/wheelhouse/
        mkdir -p $GITHUB_WORKSPACE/data/wheelhouse/before_fix/

        LD_OLD_LIBRARY_PATH=$LD_LIBRARY_PATH

        # compile and configure OpenMS
        for py in $(echo "${PYTHON_VERSIONS}" | jq -r '.[]'); do

          # Check if there is already and existing build,
          # if so: clean previous pyopenms libs,
          # do at the top of the python version loop so that we leave the final libraries for testing

          if [ -d "OpenMS/bld/pyOpenMS/pyopenms" ]; then
            rm OpenMS/bld/pyOpenMS/pyopenms/_pyopenms*.so
          fi
        
          py=$(echo "$py" | tr -d " \n")
          pynodot=$(echo "$py" | tr -d ".")
          PYBIN=$(echo /opt/python/cp*${pynodot})
          
          # Create a venv for this python version
          "$PYBIN/bin/python" -m venv $pynodot
          source $pynodot/bin/activate
          
          "$PYBIN/bin/pip" install --upgrade pip
          # pip install all the stuff
          "$PYBIN/bin/pip" install -r $GITHUB_WORKSPACE/OpenMS/src/pyOpenMS/requirements_bld.txt

          # configure (don't copy deps since we use auditwheel)

          export Python_ROOT_DIR=$PYBIN
          export BUILD_NAME="pyopenms-wheels-${{ runner.arch }}-class-pyopenms-$py-${{ github.run_number }}" #TODO make this more expressive

          ctest --output-on-failure -V -S $GITHUB_WORKSPACE/OpenMS/tools/ci/cibuild.cmake
          
          # ensure auditwheel can find the libraries
          export LD_LIBRARY_PATH=$LD_OLD_LIBRARY_PATH:`pwd`/OpenMS/bld/lib

          # strip the libraries before repairing
          strip --strip-all OpenMS/bld/lib/libOpenMS.so
          strip --strip-all OpenMS/bld/lib/libOpenSwathAlgo.so

          pushd OpenMS/bld/pyOpenMS
            # Bundle stripped plus external shared libraries into the wheels
            for whl in dist/pyopenms*.whl; do
              auditwheel repair "$whl" -w wheelhouse/
            done

            mv wheelhouse/* $GITHUB_WORKSPACE/data/wheelhouse/
          popd
          export LD_LIBRARY_PATH=$LD_OLD_LIBRARY_PATH
          
          # deactivate the venv
          deactivate
        done
      env: 
          SOURCE_DIRECTORY: "${{ github.workspace }}/OpenMS"
          CMAKE_GENERATOR: "Ninja"
          OPENMS_CONTRIB_LIBS: "/contrib-build/"
          BUILD_TYPE: "Release"
          BUILD_FLAGS: "-j${{ steps.cpu-cores.outputs.count }}"
          NO_DEPENDENCIES: "ON"
          Python_FIND_STRATEGY: "LOCATION"
          PYOPENMS: "ON"
          PY_NUM_THREADS: ${{ steps.cpu-cores.outputs.count }}
          CI_PROVIDER: "GitHub-Actions"
          CMAKE_CXX_COMPILER: "g++"
          CMAKE_PREFIX_PATH: "/contrib-build/"
          ENABLE_TUTORIALS: "OFF"
          ENABLE_DOCS: "OFF"
          ENABLE_STYLE_TESTING: "OFF"
          ENABLE_PIPELINE_TESTING: "OFF"
          ENABLE_TOPP_TESTING: "OFF"
          ENABLE_CLASS_TESTING: "OFF"

    - name: Test
      shell: bash
      run: |
            ctest --output-on-failure -V -S $GITHUB_WORKSPACE/OpenMS/tools/ci/citest.cmake
      env:
          SOURCE_DIRECTORY: "${{ github.workspace }}/OpenMS"
          CI_PROVIDER: "GitHub-Actions"
          BUILD_NAME: "${{ runner.arch }}-class-pyopenms-${{ github.run_number }}"
          # The rest of the vars should be saved in the CMakeCache

    - uses: actions/upload-artifact@v4
      name: Upload artifacts
      with:
        name: ${{ runner.os }}-${{ runner.arch }}-wheels
        path: data/wheelhouse/

# Tests the build workflows
  test:
    needs: [build-win, build-macos, build-lnx, build-macos-arm]
    runs-on: ${{ matrix.os }}
    env:
      SYSTEM_VERSION_COMPAT: 0 #courtesy of https://github.com/actions/setup-python/issues/469 in lieu of an actual solution.
    strategy:
      matrix:
        os: [ubuntu-latest, macos-13, windows-latest, macos-latest]
    steps:
    - uses: actions/checkout@v4
      name: Checkout sources
      with:
        path: OpenMS

    - name: Install Miniconda
      shell: bash
      run: |
          if [[ "${{ runner.os }}" == "Linux" ]]; then
            MINICONDA_FILENAME=Miniconda3-latest-Linux-x86_64.sh
            curl -o $MINICONDA_FILENAME "https://repo.anaconda.com/miniconda/$MINICONDA_FILENAME"
            bash ${MINICONDA_FILENAME} -b -f -p $HOME/miniconda3
          elif [[ "${{ runner.os }}" == "macOS" && "${{ runner.arch }}" == "X64" ]]; then
            MINICONDA_FILENAME=Miniconda3-latest-MacOSX-x86_64.sh
            curl -o $MINICONDA_FILENAME "https://repo.anaconda.com/miniconda/$MINICONDA_FILENAME"
            bash ${MINICONDA_FILENAME} -b -f -p $HOME/miniconda3
          elif [[ "${{ runner.os }}" == "macOS" && "${{ runner.arch }}" == "ARM64"  ]]; then
            MINICONDA_FILENAME=Miniconda3-latest-MacOSX-arm64.sh
            curl -o $MINICONDA_FILENAME "https://repo.anaconda.com/miniconda/$MINICONDA_FILENAME"
            bash ${MINICONDA_FILENAME} -b -f -p $HOME/miniconda3
          elif [[ "${{ runner.os }}" == "Windows" ]]; then
            MINICONDA_FILENAME=Miniconda3-latest-Windows-x86_64.exe
            curl -o $MINICONDA_FILENAME "https://repo.anaconda.com/miniconda/$MINICONDA_FILENAME"
            ./Miniconda3-latest-Windows-x86_64.exe //InstallationType=JustMe //RegisterPython=0 //S
          fi

    - name: Setup conda paths
      shell: bash
      run: |
        echo "$HOME/miniconda3/bin" >> $GITHUB_PATH
        echo "$HOME/miniconda3/Scripts" >> $GITHUB_PATH

    - name: Download artifacts
      uses: actions/download-artifact@v4
      with:
          name: ${{ runner.os }}-${{ runner.arch }}-wheels

    - name: Test
      shell: bash 
      run: |
        PYTHON_VERSIONS=$(cat OpenMS/.github/workflows/python_versions.json)
        echo $PYTHON_VERSIONS

        for py in $(echo "${PYTHON_VERSIONS}" | jq -r '.[]'); do
          py=$(echo "$py" | tr -d " \r\n")
          pynodot=$(echo "$py" | tr -d ".")
          conda create -n pyoms-bld-$pynodot python=$py
          source activate pyoms-bld-$pynodot

          # Find .whl for current python version
          CURRENT_VERSION=$(echo $py | sed "s/\.//g") # remove "." for find
          echo "Testing python version $CURRENT_VERSION"
          CURRENT_WHL=$(find $GITHUB_WORKSPACE -name "*cp$CURRENT_VERSION*.whl") # Probably $GITHUB_WORKSPACE
          if [[ "$CURRENT_WHL" == '' ]]; then

            continue

          fi
          echo "Found wheel $CURRENT_WHL : Testing.."

          # pip install all the stuff
          python -m pip install --upgrade pip
          python -m pip install $CURRENT_WHL

          # check if package was installed
          python -c "import importlib.util; p_name = 'pyopenms'; package = importlib.util.find_spec(p_name); print(p_name + ' was sucessfully installed! Nice one!') if package is not None else print('Something seems to be wrong!')"
          # run test
          python -c "exec(\"import pyopenms\nprint(pyopenms.EmpiricalFormula(\'C6H12O6\').getMonoWeight())\")"

          conda deactivate

          # clean up
          conda remove --name pyoms-bld-$pynodot --all

        done

  # Upload the wheels (the action only runs on ubuntu slaves)
  publish:
    needs: [test] # doesn't really NEED it but we want the tests to pass first
    runs-on: ubuntu-latest
    steps:
    # haha github is just ridiculous.. not getting their actions to do basic stuff for years
    - name: Download artifacts
      uses: actions/download-artifact@v4
      with:
          name: Linux-X64-wheels
          path: /home/runner/work/OpenMS/OpenMS/Linux-X64-wheels
    - name: Download artifacts
      uses: actions/download-artifact@v4
      with:
          name: Windows-X64-wheels
          path: /home/runner/work/OpenMS/OpenMS/Windows-X64-wheels
    - name: Download artifacts
      uses: actions/download-artifact@v4
      with:
          name: macOS-X64-wheels
          path: /home/runner/work/OpenMS/OpenMS/macOS-X64-wheels
    - name: Download artifacts
      uses: actions/download-artifact@v4
      with:
          name: macOS-ARM64-wheels
          path: /home/runner/work/OpenMS/OpenMS/macOS-ARM64-wheels

    - name: Merge all artifacts
      run: |
            mkdir wheels
            cp -lr *-wheels/* wheels/
            pwd
            ls -la wheels/

    - name: Publish package to nightly PyPI
        # Upload the wheels to our pypi server for develop, nightly and release branches (unless it's explictly stated to upload it to pypi.org)
      if: contains(github.ref, 'develop') || contains(github.ref, 'nightly') || (contains(github.ref, 'Release') && inputs.upload-to-pypi == 'false')
      uses: pypa/gh-action-pypi-publish@release/v1
      with:
        repository-url: https://pypi.cs.uni-tuebingen.de/
        user: openms
        password: ${{ secrets.abiservices_pypi_pw }}
        packages-dir: ${{ github.workspace }}/wheels

    - name: Publish package to PyPI
      if: contains(github.ref, 'Release') && inputs.upload-to-pypi
      uses: pypa/gh-action-pypi-publish@release/v1
      with:
        user: __token__
        repository-url: https://pypi.org/
        password: ${{ secrets.pypi_api_token_release }}
        packages-dir: ${{ github.workspace }}/wheels