ci.yml

name: ci

on:
  pull_request:
    types: [opened, synchronize, reopened, ready_for_review]
    paths-ignore:
      - '.github/workflows/dist.yml'
      - '.github/workflows/wheels.yml'
      - '.gitignore'
      - 'build-all-presets.sh'
      - 'CMakePresets.json'
  push:
    # branches:
    #   - master
    paths-ignore:
      - '.github/workflows/dist.yml'
      - '.github/workflows/wheels.yml'
      - '.gitignore'
      - 'build-all-presets.sh'
      - 'CMakePresets.json'
  workflow_dispatch:
    inputs:
      # name:
      #   description: 'NAME: File will be called name.lowercase()-VER-REL.tar.gz'
      #   required: true
      #   default: 'PhreeqcRM'

      date:
        description: 'DATE: Leave blank to use todays date'
        required: false
        default: ''

      rel:
        description: 'REL: Leave blank to automatically generate (2021-03-09 = 15700)'
        required: false
        default: ''

      ver:
        description: 'VER: Leave blank to use MAJOR.MINOR.(PATCH+1) (from https://github.com/usgs-coupled/phreeqc-version/blob/main/phreeqc-version.txt)'
        required: false
        default: ''  

env:
  # NAME: PhreeqcRM
  BUILD_TYPE: Release

jobs:

  log-the-inputs:
    runs-on: ubuntu-latest
    steps:
      - run: |
          # echo "Name: $NAME"
          echo "Date: $DATE"
          echo "REL: $REL"
          echo "VER: $VER"
        env:
          # NAME: ${{ inputs.name }}
          DATE: ${{ inputs.date }}
          REL: ${{ inputs.rel }}
          VER: ${{ inputs.ver }}

  init:
    if: github.event.pull_request.draft == false
    runs-on: ubuntu-latest
    env:
      # NAME: ${{ inputs.name }}
      DATE: ${{ inputs.date }}
      REL: ${{ inputs.rel }}
      VER: ${{ inputs.ver }}
    # Map step outputs to job outputs
    outputs:
      # NAME: ${{ steps.vars.outputs.NAME }} 
      # NAME_LOWERCASE: ${{ steps.vars.outputs.NAME_LOWERCASE }} 
      VER: ${{ steps.vars.outputs.VER }}
      REL: ${{ steps.vars.outputs.REL }}
      DATE: ${{ steps.vars.outputs.DATE }}
      DATE_FULL: ${{ steps.vars.outputs.DATE_FULL }}
      DATE_RFC_3339: ${{ steps.vars.outputs.DATE_RFC_3339 }}
    steps:
      - name: Setup vars
        id: vars
        run: |
          # if [ -z "${NAME}" ]; then
          #   echo NAME="PhreeqcRM"                                                                                       >> "${GITHUB_OUTPUT}"
          #   echo NAME_LOWERCASE=$(echo "PhreeqcRM" | tr '[:upper:]' '[:lower:]')                                        >> "${GITHUB_OUTPUT}"
          # else
          #   echo NAME="${NAME}"                                                                                         >> "${GITHUB_OUTPUT}"
          #   echo NAME_LOWERCASE=$(echo "${NAME}" | tr '[:upper:]' '[:lower:]')                                          >> "${GITHUB_OUTPUT}"
          # fi
          
          if [ -z "${VER}" ]; then
            echo VER="$(curl -sS https://raw.githubusercontent.com/usgs-coupled/phreeqc-version/main/next_ver.sh | sh)" >> "${GITHUB_OUTPUT}"
          else
            echo VER="${VER}"                                                                                           >> "${GITHUB_OUTPUT}"
          fi
          
          if [ -z "${REL}" ]; then
            echo REL="$(curl -sS https://raw.githubusercontent.com/usgs-coupled/phreeqc-version/main/rel.py | python3)" >> "${GITHUB_OUTPUT}"
          else
            echo REL="${REL}"                                                                                           >> "${GITHUB_OUTPUT}"
          fi
          
          if [ -z "${DATE}" ]; then
            echo DATE="$(TZ='America/Denver' date '+%x')"                                                               >> "${GITHUB_OUTPUT}"
            echo DATE_RFC_3339="$(TZ='America/Denver' date --rfc-3339=date)"                                            >> "${GITHUB_OUTPUT}"
            echo DATE_FULL="$(TZ='America/Denver' date)"                                                                >> "${GITHUB_OUTPUT}"
          else
            echo DATE="${DATE}"                                                                                         >> "${GITHUB_OUTPUT}"
            echo DATE_RFC_3339="$(TZ='America/Denver' date --rfc-3339=date --date=${DATE})"                             >> "${GITHUB_OUTPUT}"
            echo DATE_FULL="$(TZ='America/Denver' date --date=${DATE})"                                                 >> "${GITHUB_OUTPUT}"
          fi

  results:
    name: display results
    needs: init
    runs-on: ubuntu-latest
    steps:
      - name: results
        run: |
          # echo NAME="${{ needs.init.outputs.NAME }}"
          echo VER="${{ needs.init.outputs.VER }}"
          echo REL="${{ needs.init.outputs.REL }}"
          echo DATE="${{ needs.init.outputs.DATE }}"
          echo DATE_RFC_3339="${{ needs.init.outputs.DATE_RFC_3339 }}"
          echo DATE_FULL="${{ needs.init.outputs.DATE_FULL }}"
          # echo TARBALL="${{ needs.init.outputs.NAME_LOWERCASE }}-${{ needs.init.outputs.VER }}-${{ needs.init.outputs.REL }}.tar.gz"
          echo TARBALL="phreeqcrm-${{ needs.init.outputs.VER }}-${{ needs.init.outputs.REL }}.tar.gz"

  valgrind:
    # if: ${{ false }}
    name: valgrind
    runs-on: ubuntu-latest
    steps:
    - uses: actions/checkout@v4

    - name: update apt-get
      run: sudo apt-get -y update

    - name: install yaml-cpp
      run: sudo apt-get -y install libyaml-cpp-dev

    - name: install ninja
      run: sudo apt-get -y install ninja-build

    - name: install libc6-dbg
      run: sudo apt-get -y install libc6-dbg

    - name: install valgrind
      run: sudo snap install valgrind --classic

    - name: ctest -S cmemcheck.cmake
      run: ctest -S cmemcheck.cmake -VV --output-on-failure -j 2

  distcheck:
    # if: ${{ false }}
    name: make distcheck
    needs: init
    runs-on: ubuntu-latest
    # env:
    #   # NAME is consumed by jenkins-dist.sh
    #   NAME: ${{ needs.init.outputs.NAME }}

    steps:
    - uses: actions/checkout@v4

    - name: autoreconf
      run: autoreconf -fvi

    - name: versioning
      run: ./jenkins-dist.sh -v ${{ needs.init.outputs.VER }} -r ${{ needs.init.outputs.REL }} -d ${{ needs.init.outputs.DATE }}

    - name: prepare doxygen
      run: sudo apt-get -y install doxygen graphviz

    - name: update doxygen using micromamba env
      uses: mamba-org/setup-micromamba@v1
      with:
        environment-file: Doxygen/doxygen.environment.yml

    - name: run doxygen
      shell: micromamba-shell {0}
      run: cd Doxygen && make

    - name: install yaml-cpp and dos2unix
      run: sudo apt-get -y install libyaml-cpp-dev dos2unix

    - name: mkdir
      run: mkdir ${{github.workspace}}/_build

    - name: configure
      shell: bash
      working-directory: ${{github.workspace}}/_build
      run: ../configure --prefix=$(pwd)/INSTALL

    - name: make distcheck
      shell: bash
      working-directory: ${{github.workspace}}/_build
      run: DISTCHECK_CONFIGURE_FLAGS="--enable-fortran-test --with-yaml-cpp" make -j2 distcheck

    - uses: actions/upload-artifact@v4
      with:
        name: tarball
        path: ${{github.workspace}}/_build/*.tar.gz

    - name: PhreeqcRM_ReadMe.txt
      shell: bash
      run: cp doc/README.TXT PhreeqcRM_ReadMe.txt

    - uses: actions/upload-artifact@v4
      with:
        name: readme
        path: ${{github.workspace}}/PhreeqcRM_ReadMe.txt

    - name: unix2dos
      shell: bash
      run: git ls-files --eol | grep -v '^i/-text' | grep -v '^i/ ' | grep -v 'Makefile.am' | grep -v 'configure.ac' | awk -F $'\t' '{print $2}' | xargs unix2dos

    - name: make dist-zip
      shell: bash
      working-directory: ${{github.workspace}}/_build
      run: make dist-zip

    - uses: actions/upload-artifact@v4
      with:
        name: zip
        path: ${{github.workspace}}/_build/*.zip

  autotools:
    # if: ${{ false }}
    name: autotools
    needs: [init, distcheck]
    strategy:
      fail-fast: false
      matrix:
        os: [macos-latest, ubuntu-latest]

    runs-on: ${{ matrix.os }}

    env:
      VER_STRING: ${{ needs.init.outputs.VER }}-${{ needs.init.outputs.REL }}

    steps:

    - uses: actions/download-artifact@v4
      with:
        name: tarball

    # - name: Install GNU Fortran (macOS)
    #   if: ${{ runner.os == 'macOS' }}
    #   uses: awvwgk/setup-fortran@main
    #   with:
    #     compiler: gcc
    #     version: 12

    # - name: Verify gfortran
    #   run: |
    #     which gfortran
    #     gfortran --version

    - name: Install ninja yaml-cpp valgrind (Linux)
      if: runner.os == 'Linux'
      run: |
        sudo apt-get -y update
        sudo apt-get install -y ninja-build valgrind libyaml-cpp-dev

    - name: Install gcc(gfortran) ninja yaml-cpp (macOS)
      if: runner.os == 'macOS'
      run: |
        brew reinstall gcc
        brew install ninja yaml-cpp
        # ls -alR /usr/local/Cellar/

    - name: Verify gfortran
      run: |
        which gfortran
        gfortran --version

    - name: Extract tarball
      run: tar xvzf phreeqcrm-${{ env.VER_STRING }}.tar.gz

    - name: mkdir build
      run: mkdir ${{ github.workspace }}/build

    - name: Configure with autotools
      working-directory: ${{ github.workspace }}/build
      run: ../phreeqcrm-${{ env.VER_STRING }}/configure --enable-fortran-test --with-yaml-cpp

    - name: Print phreeqcrm.pc
      working-directory: ${{ github.workspace }}/build
      run:  cat phreeqcrm.pc

    - name: Build with autotools
      working-directory: ${{ github.workspace }}/build
      run: make -j4

    - name: Make check
      working-directory: ${{ github.workspace }}/build
      run: make check -j4

    - name: cat Tests/test-suite.log
      if: ${{ always() }}
      working-directory: ${{ github.workspace }}/build
      run: cat Tests/test-suite.log

    - name: Install with autotools
      working-directory: ${{ github.workspace }}/build
      run: sudo make install

    - name: Run ldconfig (Linux)
      if: runner.os == 'Linux'
      working-directory: ${{ github.workspace }}/build
      run: sudo ldconfig

    - name: Cleanup
      run: rm -rf *

    - name: Check phreeqcrm.pc
      run:  ls -al /usr/local/share/pkgconfig

    - name: Set PKG_CONFIG_PATH (macOS)
      if: runner.os == 'macOS'
      run: echo "PKG_CONFIG_PATH=/usr/local/share/pkgconfig" >> $GITHUB_ENV

    - name: Check phreeqcrm.pc cflags
      run:  pkg-config --cflags phreeqcrm

    - name: Check phreeqcrm.pc libs
      run:  pkg-config --libs phreeqcrm

    - uses: actions/checkout@v4

    - name: Test autotools install
      working-directory: ${{ github.workspace }}/Tests
      run: env CC='cc' CXX='c++ -std=c++11' make -f autotools.mk autotools_test && ./autotools_test

    - name: Clean autotools test
      working-directory: ${{ github.workspace }}/Tests
      run: make -f autotools.mk clean

    - name: Test autotools pkg-config
      working-directory: ${{ github.workspace }}/Tests
      run: env CC='cc' CXX='c++ -std=c++11' make -f pkgconfig.mk pkgconfig_test && ./pkgconfig_test

  cmake:
    # if: ${{ false }}
    name: ${{ matrix.os }} shared=${{ matrix.build_shared_libs }} yaml=${{ matrix.phreeqcrm_with_yaml_cpp }} type=${{ matrix.BUILD_TYPE }}
    needs: [init, distcheck]
    strategy:
      fail-fast: false
      matrix:
        os: [macos-12, ubuntu-20.04, ubuntu-22.04, windows-2019, windows-2022]
        build_shared_libs: [OFF, ON]
        phreeqcrm_with_yaml_cpp: [OFF, ON]
        BUILD_TYPE: [Debug, Release]

    runs-on: ${{ matrix.os }}

    env:
      VER_STRING: ${{ needs.init.outputs.VER }}-${{ needs.init.outputs.REL }}

    steps:

    # Note: This allows ${{ env.VCPKG_INSTALLATION_ROOT }} to be used in the remaining steps
    # Although its already set in the environment it can't be accessed using the env context
    # until it is stored in the $GITHUB_ENV file
    - name: init VCPKG_INSTALLATION_ROOT
      shell: bash
      run: echo "VCPKG_INSTALLATION_ROOT=$VCPKG_INSTALLATION_ROOT" >> $GITHUB_ENV

    - uses: actions/download-artifact@v4
      with:
        name: tarball

    - name: Install GNU Fortran (macOS)
      if: ${{ runner.os == 'macOS' }}
      uses: fortran-lang/setup-fortran@v1
      with:
        compiler: gcc
        version: 12
  
    - name: Install oneAPI Fortran (Windows)
      if: ${{ runner.os == 'Windows' }}
      uses: fortran-lang/setup-fortran@v1
      with:
        compiler: intel-classic
        version: '2021.10'

    - name: Unset CC/CXX (Windows)
      if: runner.os == 'Windows'
      shell: bash
      run: |
        echo "CC=" >> $GITHUB_ENV
        echo "CXX=" >> $GITHUB_ENV   

    - name: Install ninja valgrind (Linux)
      if: ${{ runner.os == 'Linux' }}
      #run: sudo apt-get install -y ninja-build valgrind libyaml-cpp-dev python3-numpy
      run: |
        sudo apt-get -y update
        sudo apt-get install -y ninja-build valgrind

    - name: Install ninja (macOS)
      if: ${{ runner.os == 'macOS' }}
      run: |
        brew install ninja
        ls -alR /usr/local/Cellar/

    - name: Install yaml-cpp (Linux)
      if: ${{ runner.os == 'Linux' && matrix.phreeqcrm_with_yaml_cpp == 'ON' }}
      run: vcpkg install yaml-cpp:x64-linux

    - name: Install yaml-cpp (macOS)
      if: ${{ runner.os == 'macOS' && matrix.phreeqcrm_with_yaml_cpp == 'ON' }}
      run: vcpkg install yaml-cpp:x64-osx

    - name: Install yaml-cpp (Windows)
      if: ${{ runner.os == 'Windows' && matrix.phreeqcrm_with_yaml_cpp == 'ON' }}
      run: vcpkg install yaml-cpp:x64-windows

    # - name: Set up Python ${{ matrix.python-version }}
    - name: Set up Python 3.8
      uses: actions/setup-python@v5
      with:
        # python-version: ${{ matrix.python-version }}
        python-version: 3.8

    - name: Install dependencies
      run: |
        python -m pip install --upgrade pip
        python -m pip install numpy
        python -m pip install PyYAML
        python -m pip install pytest
        # @todo if [ -f requirements.txt ]; then pip install -r requirements.txt; fi

    - name: Set up Visual Studio shell (Windows)
      if: runner.os == 'Windows'
      uses: egor-tensin/vs-shell@v2
      with:
        arch: x64

    - name: Extract tarball
      run: tar xvzf phreeqcrm-${{ env.VER_STRING }}.tar.gz

    - name: Configure with CMake
      if: ${{ matrix.phreeqcrm_with_yaml_cpp != 'ON' }}
      run: cmake -L -G Ninja -B build -S phreeqcrm-${{ env.VER_STRING }} -DCMAKE_BUILD_TYPE=${{ env.BUILD_TYPE }} -DBUILD_SHARED_LIBS:BOOL=${{ matrix.build_shared_libs }} -DPHREEQCRM_WITH_YAML_CPP=${{ matrix.phreeqcrm_with_yaml_cpp }} -DPHREEQCRM_FORTRAN_TESTING:BOOL=ON

    - name: Configure with CMake (using vcpkg toolchain)
      if: ${{ matrix.phreeqcrm_with_yaml_cpp == 'ON' }}
      run: cmake -L -G Ninja --toolchain ${{ env.VCPKG_INSTALLATION_ROOT }}/scripts/buildsystems/vcpkg.cmake -B build -S phreeqcrm-${{ env.VER_STRING }} -DCMAKE_BUILD_TYPE=${{ env.BUILD_TYPE }} -DBUILD_SHARED_LIBS:BOOL=${{ matrix.build_shared_libs }} -DPHREEQCRM_WITH_YAML_CPP=${{ matrix.phreeqcrm_with_yaml_cpp }} -DPHREEQCRM_FORTRAN_TESTING:BOOL=ON -DPHREEQCRM_BUILD_PYTHON:BOOL=ON

    - name: Print phreeqcrm.pc
      working-directory: ${{ github.workspace }}/build
      run:  cat phreeqcrm.pc

    - name: Build with CMake
      run: cmake --build ${{ github.workspace }}/build --config ${{ env.BUILD_TYPE }}

    - name: Test with CMake
      working-directory: ${{ github.workspace }}/build
      run: ctest -C ${{ env.BUILD_TYPE }} --output-on-failure

    - name: Install (Non-Windows)
      if: runner.os != 'Windows'
      run: sudo cmake --install build

    - name: Install (Windows)
      if: runner.os == 'Windows'
      run: cmake --install build

    - name: Run ldconfig (Linux)
      if: ${{ runner.os == 'Linux' && matrix.build_shared_libs == 'ON' }}
      run: sudo ldconfig

    - name: Cleanup (Non-Windows)
      if: runner.os != 'Windows'
      run: sudo rm -rf *

    - name: Cleanup (Windows)
      if: runner.os == 'Windows'
      run: Remove-Item -Recurse -Force *

    - uses: actions/checkout@v4

    - name: Test install (configure) (Non-Windows)
      if: ${{ matrix.phreeqcrm_with_yaml_cpp != 'ON' }}
      working-directory: ${{ github.workspace }}/Tests
      run: cmake -L -G Ninja -B build -S . -DCMAKE_BUILD_TYPE=${{ env.BUILD_TYPE }} -D_PHREEQCRM_TEST_INSTALL:BOOL=ON -DPHREEQCRM_FORTRAN_TESTING:BOOL=ON

    - name: Test install (configure) (using vcpkg toolchain)
      if: ${{ matrix.phreeqcrm_with_yaml_cpp == 'ON' }}
      working-directory: ${{ github.workspace }}/Tests
      run: cmake -L -G Ninja --toolchain ${{ env.VCPKG_INSTALLATION_ROOT }}/scripts/buildsystems/vcpkg.cmake -B build -S . -DCMAKE_BUILD_TYPE=${{ env.BUILD_TYPE }} -D_PHREEQCRM_TEST_INSTALL:BOOL=ON -DPHREEQCRM_FORTRAN_TESTING:BOOL=ON

    - name: Test install (build)
      working-directory: ${{ github.workspace }}/Tests
      run: cmake --build build --config ${{ env.BUILD_TYPE }}

    - name: Test install (ctest) (Non-Windows)
      if: runner.os != 'Windows'
      working-directory: ${{ github.workspace }}/Tests/build
      run: ctest -C ${{ env.BUILD_TYPE }} --output-on-failure

    - name: Test install (ctest) (Windows)
      if: runner.os == 'Windows'
      working-directory: ${{ github.workspace }}/Tests/build
      run: |
        $env:PATH="${{ env.VCPKG_INSTALLATION_ROOT }}\packages\yaml-cpp_x64-windows\bin;C:\Program Files (x86)\PhreeqcRM\bin;$env:PATH"
        ctest -C ${{ env.BUILD_TYPE }} --output-on-failure

  cmake-mpi:
    if: ${{ false }}
    name: ${{ matrix.os }} mpi=${{ matrix.mpi }} shared=${{ matrix.build_shared_libs }} yaml=${{ matrix.phreeqcrm_with_yaml_cpp }}
    needs: [init, distcheck]
    strategy:
      fail-fast: false
      matrix:
        os: [macos-12, ubuntu-20.04, ubuntu-22.04, windows-2019, windows-2022]
        build_shared_libs: [ON]
        phreeqcrm_with_yaml_cpp: [ON]
        mpi: ['mpich', 'ompi', 'impi', 'msmpi']  # see https://github.com/mpi4py/setup-mpi/blob/master/setup-mpi.sh
        # BUILD_TYPE: [Debug, Release]
        exclude:
          - os: macos-12
            mpi: 'impi'
          - os: macos-12
            mpi: 'msmpi'
          - os: ubuntu-20.04
            mpi: 'msmpi'
          - os: ubuntu-22.04
            mpi: 'msmpi'
          - os: windows-2019
            mpi: 'mpich'
          - os: windows-2019
            mpi: 'ompi'
          - os: windows-2022
            mpi: 'mpich'
          - os: windows-2022
            mpi: 'ompi'
    timeout-minutes: 20

    runs-on: ${{ matrix.os }}

    env:
      VER_STRING: ${{ needs.init.outputs.VER }}-${{ needs.init.outputs.REL }}

    steps:

    # Note: This allows ${{ env.VCPKG_INSTALLATION_ROOT }} to be used in the remaining steps
    # Although its already set in the environment it can't be accessed using the env context
    # until it is stored in the $GITHUB_ENV file
    - name: init VCPKG_INSTALLATION_ROOT
      shell: bash
      run: echo "VCPKG_INSTALLATION_ROOT=$VCPKG_INSTALLATION_ROOT" >> $GITHUB_ENV

    - uses: actions/download-artifact@v4
      with:
        name: tarball

    - name: Install GNU Fortran (macOS)
      if: ${{ runner.os == 'macOS' }}
      uses: awvwgk/setup-fortran@main
      with:
        compiler: gcc
        version: 12

    # - name: Install oneAPI Fortran (Windows)
    #   if: ${{ runner.os == 'Windows' }}
    #   uses: i-RIC/install-intelfortran-action@v1
    #   with:
    #     cache: true

    - name: Install ninja (Linux)
      if: ${{ runner.os == 'Linux' }}
      #run: sudo apt-get install -y ninja-build valgrind libyaml-cpp-dev python3-numpy
      run: |
        sudo apt-get -y update
        sudo apt-get install -y ninja-build

    - name: Install ninja (macOS)
      if: ${{ runner.os == 'macOS' }}
      run: |
        brew install ninja
        ls -alR /usr/local/Cellar/

    - name: Install yaml-cpp (Linux)
      if: ${{ runner.os == 'Linux' && matrix.phreeqcrm_with_yaml_cpp == 'ON' }}
      run: vcpkg install yaml-cpp:x64-linux

    - name: Install yaml-cpp (macOS)
      if: ${{ runner.os == 'macOS' && matrix.phreeqcrm_with_yaml_cpp == 'ON' }}
      run: vcpkg install yaml-cpp:x64-osx

    - name: Install yaml-cpp (Windows)
      if: ${{ runner.os == 'Windows' && matrix.phreeqcrm_with_yaml_cpp == 'ON' }}
      run: vcpkg install yaml-cpp:x64-windows

    # # - name: Set up Python ${{ matrix.python-version }}
    # - name: Set up Python 3.8
    #   uses: actions/setup-python@v5
    #   with:
    #     # python-version: ${{ matrix.python-version }}
    #     python-version: 3.8

    # - name: Install dependencies
    #   run: |
    #     python -m pip install --upgrade pip
    #     python -m pip install numpy
    #     python -m pip install PyYAML
    #     python -m pip install pytest
    #     # @todo if [ -f requirements.txt ]; then pip install -r requirements.txt; fi

    # Note: this makes the entire environment available using ${{ env.VARIABLE }} syntax
    # see above
    - name: Set up Visual Studio shell (Windows)
      if: runner.os == 'Windows'
      uses: egor-tensin/vs-shell@v2
      with:
        arch: x64

    - name: Setup mpi
      uses: mpi4py/setup-mpi@v1
      with:
        mpi: ${{ matrix.mpi }}

    - name: CMake version
      run: cmake --version

    - name: Locate CMake
      if: runner.os == 'Windows'
      shell: cmd
      run: |
        where cmake

    - name: Extract tarball
      run: tar xvzf phreeqcrm-${{ env.VER_STRING }}.tar.gz

    - name: Configure with CMake
      if: ${{ matrix.phreeqcrm_with_yaml_cpp != 'ON' }}
      run: cmake -G Ninja -B build -S phreeqcrm-${{ env.VER_STRING }} -DCMAKE_BUILD_TYPE=${{ env.BUILD_TYPE }} -DBUILD_SHARED_LIBS:BOOL=${{ matrix.build_shared_libs }} -DPHREEQCRM_WITH_YAML_CPP=${{ matrix.phreeqcrm_with_yaml_cpp }} -DPHREEQCRM_BUILD_MPI:BOOL=ON

    - name: Configure with CMake (using vcpkg toolchain)
      if: ${{ matrix.phreeqcrm_with_yaml_cpp == 'ON' }}
      run: cmake -G Ninja --toolchain ${{ env.VCPKG_INSTALLATION_ROOT }}/scripts/buildsystems/vcpkg.cmake -B build -S phreeqcrm-${{ env.VER_STRING }} -DCMAKE_BUILD_TYPE=${{ env.BUILD_TYPE }} -DBUILD_SHARED_LIBS:BOOL=${{ matrix.build_shared_libs }} -DPHREEQCRM_WITH_YAML_CPP=${{ matrix.phreeqcrm_with_yaml_cpp }} -DPHREEQCRM_BUILD_MPI:BOOL=ON

    - name: Print phreeqcrm.pc
      working-directory: ${{ github.workspace }}/build
      run:  cat phreeqcrm.pc

    - name: Build with CMake
      run: cmake --build ${{ github.workspace }}/build --config ${{ env.BUILD_TYPE }}

    - name: Test with CMake
      working-directory: ${{ github.workspace }}/build
      run: ctest -C ${{ env.BUILD_TYPE }} --output-on-failure

    - name: Install (Non-Windows)
      if: runner.os != 'Windows'
      run: sudo cmake --install build

    - name: Install (Windows)
      if: runner.os == 'Windows'
      run: cmake --install build

    # - name: Run ldconfig (Linux)
    #   if: ${{ runner.os == 'Linux' && matrix.build_shared_libs == 'ON' }}
    #   run: sudo ldconfig

    # - name: Cleanup (Non-Windows)
    #   if: runner.os != 'Windows'
    #   run: sudo rm -rf *

    # - name: Cleanup (Windows)
    #   if: runner.os == 'Windows'
    #   run: Remove-Item -Recurse -Force *

    # - uses: actions/checkout@v4

    # - name: Test install (configure) (Non-Windows)
    #   if: runner.os != 'Windows'
    #   working-directory: ${{ github.workspace }}/Tests
    #   run: cmake -G Ninja -B build -S . -DCMAKE_BUILD_TYPE=${{ env.BUILD_TYPE }} -D_PHREEQCRM_TEST_INSTALL:BOOL=ON

    # - name: Test install (configure) (Windows)
    #   if: runner.os == 'Windows'
    #   working-directory: ${{ github.workspace }}/Tests
    #   run: cmake -G Ninja --toolchain ${{ env.VCPKG_INSTALLATION_ROOT }}/scripts/buildsystems/vcpkg.cmake -B build -S . -DCMAKE_BUILD_TYPE=${{ env.BUILD_TYPE }} -D_PHREEQCRM_TEST_INSTALL:BOOL=ON

    # - name: Test install (build)
    #   working-directory: ${{ github.workspace }}/Tests
    #   run: cmake --build build --config ${{ env.BUILD_TYPE }}

    # - name: Test install (ctest) (Non-Windows)
    #   if: runner.os != 'Windows'
    #   working-directory: ${{ github.workspace }}/Tests/build
    #   run: ctest -C ${{ env.BUILD_TYPE }} --output-on-failure

    # - name: Test install (ctest) (Windows)
    #   if: runner.os == 'Windows'
    #   working-directory: ${{ github.workspace }}/Tests/build
    #   run: |
    #     $env:PATH="${{ env.VCPKG_INSTALLATION_ROOT }}\packages\yaml-cpp_x64-windows\bin;C:\Program Files (x86)\PhreeqcRM\bin;$env:PATH"
    #     ctest -C ${{ env.BUILD_TYPE }} --output-on-failure

  deploy_pages:
    # todo update github.ref below
    if: github.repository == 'usgs-coupled/phreeqcrm' && github.ref == 'refs/heads/master' && github.event_name == 'push'

    needs: [init, distcheck]

    runs-on: ubuntu-latest

    # Grant GITHUB_TOKEN the permissions required to make a Pages deployment
    permissions:
      actions: read     # req'd by actions/deploy-pages@v4
      pages: write      # to deploy to Pages
      id-token: write   # to verify the deployment originates from an appropriate source

    # Deploy to the github-pages environment
    environment:
      name: github-pages
      url: ${{ steps.deployment.outputs.page_url }}

    env:
      VER_STRING: ${{ needs.init.outputs.VER }}-${{ needs.init.outputs.REL }}

    steps:
      - uses: actions/download-artifact@v4
        with:
          name: tarball

      - run: tar xvzf phreeqcrm-${{ env.VER_STRING }}.tar.gz

      - name: Fix permissions
        run: |
          chmod -c -R +rX "phreeqcrm-${{ env.VER_STRING }}/Doxygen/html" | while read line; do
            echo "::warning title=Invalid file permissions automatically fixed::$line"
          done

      - name: Upload artifact
        uses: actions/upload-pages-artifact@v3
        with:
          path: phreeqcrm-${{ env.VER_STRING }}/Doxygen/html

      - name: Deploy to GitHub Pages
        id: deployment
        uses: actions/deploy-pages@v4