phreeqcrm 0.0.5__tar.gz

phreeqcrm-0.0.5/.github/workflows/distro.yml

@@ -0,0 +1,345 @@
+name: ci
+
+on:
+  pull_request:
+    types: [opened, synchronize, reopened, ready_for_review]
+    paths-ignore:
+      - 'CMakePresets.json'
+      - 'build-all-presets.sh'
+      - '.github/workflows/wheels.yml'
+  push:
+    branches:
+      - master
+    paths-ignore:
+      - 'CMakePresets.json'
+      - 'build-all-presets.sh'
+      - '.github/workflows/wheels.yml'
+
+env:
+  NAME: PhreeqcRM
+  BUILD_TYPE: Release
+
+jobs:
+
+  init:
+    if: github.event.pull_request.draft == false
+    runs-on: ubuntu-latest
+    # Map step outputs to job outputs
+    outputs:
+      VER: ${{ steps.vars.outputs.VER }}
+      REL: ${{ steps.vars.outputs.REL }}
+      DATE: ${{ steps.vars.outputs.DATE }}
+      DATE_RFC_3339: ${{ steps.vars.outputs.DATE_RFC_3339 }}
+    steps:
+      - name: Setup vars
+        id: vars
+        run: |
+          echo VER=$(curl -sS https://raw.githubusercontent.com/usgs-coupled/phreeqc-version/main/next_ver.sh | sh) >> $GITHUB_OUTPUT
+          echo REL=$(curl -sS https://raw.githubusercontent.com/usgs-coupled/phreeqc-version/main/rel.py | python3) >> $GITHUB_OUTPUT
+          echo DATE=$(date "+%x")                                                                                   >> $GITHUB_OUTPUT
+          echo DATE_RFC_3339=$(date --rfc-3339=date)                                                                >> $GITHUB_OUTPUT
+
+
+  valgrind:
+    name: valgrind
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v3
+
+    - 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:
+    name: make distcheck
+    needs: init
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v3
+
+    - 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: doxygen
+      run: sudo apt-get -y install doxygen graphviz && cd Doxygen && make
+
+    - name: install yaml-cpp
+      run: sudo apt-get -y install libyaml-cpp-dev
+
+    - name: mkdir
+      run: mkdir ${{github.workspace}}/_build
+
+    - name: configure
+      shell: bash
+      working-directory: ${{github.workspace}}/_build
+      run: ../configure --prefix=$(pwd)/INSTALL
+
+    - name: make
+      shell: bash
+      working-directory: ${{github.workspace}}/_build
+      run: DISTCHECK_CONFIGURE_FLAGS="--enable-fortran-test --with-yaml-cpp" make -j2 distcheck
+
+    - uses: actions/upload-artifact@v3
+      with:
+        name: tarball
+        path: ${{github.workspace}}/_build/*.tar.gz
+
+  autotools:
+    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@v3
+      with:
+        name: tarball
+
+    # - name: Install GNU Fortran (macOS)
+    #   if: ${{ runner.os == 'macOS' }}
+    #   uses: awvwgk/setup-fortran@main
+    #   with:
+    #     compiler: gcc
+    #     version: 12
+
+    # - name: Verify gfortran
+    #   run: |
+    #     which gfortran
+    #     gfortran --version
+
+    - name: Install ninja yaml-cpp valgrind (Linux)
+      if: runner.os == 'Linux'
+      run: sudo apt-get install -y ninja-build valgrind libyaml-cpp-dev
+
+    - name: Install gcc(gfortran) ninja yaml-cpp (macOS)
+      if: runner.os == 'macOS'
+      run: |
+        brew reinstall gcc
+        brew install ninja yaml-cpp
+
+    - name: Verify gfortran
+      run: |
+        which gfortran
+        gfortran --version
+
+    - name: Extract tarball
+      run: tar xvzf phreeqcrm-${{ 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: 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 *
+
+    - uses: actions/checkout@v3
+
+    - 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 CMake 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:
+    #name: cmake
+    name: ${{ matrix.os }} shared=${{ matrix.build_shared_libs }} yaml=${{ matrix.phreeqcrm_with_yaml_cpp }}
+    needs: [init, distcheck]
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [macos-11, 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:
+
+    - uses: actions/download-artifact@v3
+      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 yaml-cpp valgrind (Linux)
+      if: ${{ runner.os == 'Linux' }}
+      #run: sudo apt-get install -y ninja-build valgrind libyaml-cpp-dev python3-numpy
+      run: sudo apt-get install -y ninja-build valgrind libyaml-cpp-dev
+
+    - name: Install ninja yaml-cpp (macOS)
+      if: ${{ runner.os == 'macOS' }}
+      run: brew install ninja yaml-cpp
+
+    - 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@v4
+      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 (Non-Windows)
+      if: ${{ runner.os != 'Windows' && matrix.phreeqcrm_with_yaml_cpp != 'ON' }}
+      run: cmake -G Ninja -B build -S phreeqcrm-${{ 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_FORTRAN_TESTING:BOOL=ON
+
+    - name: Configure with CMake (Non-Windows)
+      if: ${{ runner.os != 'Windows' && matrix.phreeqcrm_with_yaml_cpp == 'ON' }}
+      run: cmake -G Ninja -B build -S phreeqcrm-${{ 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_FORTRAN_TESTING:BOOL=ON -DPHREEQCRM_BUILD_PYTHON:BOOL=ON 
+
+    - name: Configure with CMake (Windows)
+      if: ${{ runner.os == 'Windows' && matrix.phreeqcrm_with_yaml_cpp != 'ON' }}
+      run: cmake -G Ninja -B build -S phreeqcrm-${{ 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_FORTRAN_TESTING:BOOL=ON
+
+    - name: Configure with CMake (Windows)
+      if: ${{ runner.os == 'Windows' && 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_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@v3
+
+    - 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 -DPHREEQCRM_FORTRAN_TESTING: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 -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

phreeqcrm-0.0.5/.github/workflows/wheels.yml

@@ -0,0 +1,114 @@
+name: cd
+
+on:
+  pull_request:
+    branches:
+      - master
+  push:
+    branches:
+      - master
+  workflow_dispatch:
+  release:
+    types:
+      - published
+
+env:
+  FORCE_COLOR: 3
+  YAML_CPP_REF: b8882652fcbeba4c00dec019a39da91e702e474e
+  USE_LIB_CMAKE_YAML_CPP: ${{ true }}
+
+jobs:
+  build:
+    name: ${{ matrix.os }} (python ${{ matrix.python-version }})
+
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [macos-11, macos-12, ubuntu-20.04, ubuntu-22.04, windows-2019, windows-2022]
+        python-version: ["3.8", "3.9", "3.10", "3.11"]
+
+    runs-on: ${{ matrix.os }}
+
+    steps:
+      - uses: actions/checkout@v3
+        with:
+          path: phreeqcrm-source
+
+      - uses: actions/checkout@v3
+        with:
+            repository: jbeder/yaml-cpp
+            ref: ${{ env.YAML_CPP_REF }}
+            path: yaml-cpp-source
+
+      - name: Install ninja (Linux)
+        if: ${{ runner.os == 'Linux' }}
+        run: sudo apt-get -y install ninja-build
+
+      - name: Install ninja (macOS)
+        if: ${{ runner.os == 'macOS' }}
+        run: brew install ninja
+
+      - name: Set up Visual Studio shell (Windows)
+        if: runner.os == 'Windows'
+        uses: egor-tensin/vs-shell@v2
+        with:
+          arch: x64
+
+      - name: Cache yaml-cpp
+        id: cache-yaml-cpp
+        uses: actions/cache@v3
+        with:
+          path: ${{ github.workspace }}/yaml-cpp-install
+          key: ${{ matrix.os }}-yaml-cpp-${{ env.YAML_CPP_REF }}
+
+      - name: Configure yaml-cpp
+        if: steps.cache-yaml-cpp.outputs.cache-hit != 'true'
+        run: cmake -G "Ninja Multi-Config" -B yaml-cpp-build -S yaml-cpp-source -DYAML_CPP_BUILD_TOOLS:BOOL=OFF -DCMAKE_INSTALL_PREFIX:PATH=$(pwd)/yaml-cpp-install -DCMAKE_POSITION_INDEPENDENT_CODE=ON
+
+      - name: Build yaml-cpp
+        if: steps.cache-yaml-cpp.outputs.cache-hit != 'true'
+        run: cmake --build yaml-cpp-build --config Release
+
+      - name: Test yaml-cpp
+        if: steps.cache-yaml-cpp.outputs.cache-hit != 'true'
+        run: ctest --test-dir yaml-cpp-build
+
+      - name: Install yaml-cpp
+        if: steps.cache-yaml-cpp.outputs.cache-hit != 'true'
+        run: cmake --install yaml-cpp-build
+
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v4
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Install Python ${{ matrix.python-version }} dependencies
+        run: |
+          python --version
+          python -m pip install --upgrade pip
+          pip install pipx
+
+      - name: Build package (using share/cmake/yaml-cpp)
+        if: ${{ !env.USE_LIB_CMAKE_YAML_CPP }}
+        env:
+          yaml-cpp_DIR: ${{ github.workspace }}/yaml-cpp-install/share/cmake/yaml-cpp
+        working-directory: phreeqcrm-source
+        run: pipx run build
+
+      - name: Build package (using lib/cmake/yaml-cpp)
+        if: ${{ env.USE_LIB_CMAKE_YAML_CPP }}
+        env:
+          yaml-cpp_DIR: ${{ github.workspace }}/yaml-cpp-install/lib/cmake/yaml-cpp
+        working-directory: phreeqcrm-source
+        run: pipx run build
+
+      - uses: actions/upload-artifact@v3
+        with:
+          name: wheels
+          path: phreeqcrm-source/dist/*.whl
+
+      - uses: actions/upload-artifact@v3
+        if: ${{ matrix.python-version == '3.10' && matrix.os == 'ubuntu-22.04' }}
+        with:
+          name: source
+          path: phreeqcrm-source/dist/*.tar.gz

phreeqcrm-0.0.5/.gitignore

@@ -0,0 +1,70 @@
+
+# /
+
+# Doxygen/
+Doxygen/html
+
+# Tests/
+Tests/Makefile.in
+
+# Tests/vs2012/
+Tests/vs2012/FortranAdvect.u2d
+Tests/vs2012/Tests.opensdf
+Tests/vs2012/Tests.sdf
+Tests/vs2012/Tests.v11.suo
+Tests/vs2012/mpi
+Tests/vs2012/mpi_debug
+Tests/vs2012/openmp
+Tests/vs2012/openmp_debug
+Tests/vs2012/vc110.pdb
+Tests/vs2012/x64
+
+# backup files
+*~
+.vshistory/
+
+# autotools
+aclocal.m4
+configure
+Makefile.in
+autom4te.cache/
+config/
+m4/libtool.m4
+m4/ltoptions.m4
+m4/ltsugar.m4
+m4/ltversion.m4
+m4/lt~obsolete.m4
+
+
+# ignore directories beginning with '_'
+_*/
+
+# dist files
+configure.ac.dist
+Makefile.am.dist
+doc/NOTICE.TXT.dist
+doc/README.TXT.dist
+src/PhreeqcRM.h.dist
+src/IPhreeqcPhast/IPhreeqc/IPhreeqc.h.dist
+src/IPhreeqcPhast/IPhreeqc/Version.h.dist
+CMakeLists.txt.dist
+
+# mod files (vscode extension?)
+src/phreeqcrm.mod
+
+# re-encoded files
+src/IPhreeqcPhast/IPhreeqc/phreeqcpp/print.utf-8.cpp
+src/IPhreeqcPhast/IPhreeqc/phreeqcpp/print.windows-1252.cpp
+
+# Doxygen/make
+src/RM_interface.F90.save
+src/YAML_interface.F90.save
+
+# wheels
+dist/
+
+# ex11-advect
+swig/python/ex11-advect/ex11-advect.yaml
+swig/python/ex11-advect/ex11-advect.chem.txt
+swig/python/ex11-advect/ex11-advect.log.txt
+swig/python/ex11-advect/.ipynb_checkpoints/

phreeqcrm-0.0.5/.gitlab-ci.yml

@@ -0,0 +1,119 @@
+#
+# https://code.chs.usgs.gov/coupled/phreeqcrm
+# SRC 2020-01-28T10:03:39-07:00
+# SRC 2021-10-31T11:57:41-06:00  -- changed pull to squash -- HEAD:b74733e436f6b7a67f5e84ad0554ffe79a1c2e82
+#
+image: ${CI_REGISTRY}/coupled/containers/buildpack-deps:bionic-scm
+
+stages:
+  - sync
+  - trigger
+
+before_script:
+  - eval $(ssh-agent -s)
+  - echo "${SSH_PRIVATE_KEY_ENC}" | base64 --decode | tr -d '\r' | ssh-add -
+  - mkdir -p ~/.ssh
+  - chmod 700 ~/.ssh
+  - ssh-keyscan ${CI_SERVER_HOST} >> ~/.ssh/known_hosts
+  - chmod 644 ~/.ssh/known_hosts
+  - git config --global user.email "darth@empire.com"
+  - git config --global user.name "Darth Vader"
+
+subtree-sync:
+  stage: sync
+
+  ##
+  ## Only run if on the master branch and the variable GROUP is set
+  ##
+  ## change this to
+  ## only:
+  ##  - master@$GROUP/phreeqcrm
+  ## and set GROUP to coupled before merge
+  only:
+    refs:
+      - master
+    variables:
+      - $GROUP
+
+  script:
+    ##
+    ## Must re-clone in order for the subtree merge to work
+    ## tried re-setting the url for the origin but didn't work
+    ##
+    - cd ..
+    - rm -rf ${CI_PROJECT_NAME}
+    - git clone git@${CI_SERVER_HOST}:${CI_PROJECT_PATH}.git
+    - cd ${CI_PROJECT_NAME}
+
+    ##
+    ## Sync subtrees
+    ##
+    - |
+      #!/bin/bash -ex
+      #
+      # PhreeqcRM/           git@${CI_SERVER_HOST}:${GROUP}/phreeqcrm.git
+      # ├─database/          ├─git@${CI_SERVER_HOST}:${GROUP}/subtrees/phreeqc3-database.git            database
+      # └─src/               └─git@${CI_SERVER_HOST}:${GROUP}/subtrees/PhreeqcRM-src.git                src
+      #   └─IPhreeqcPhast/     └─IPhreeqcPhast
+      #     └─IPhreeqc/          └─git@${CI_SERVER_HOST}:${GROUP}/subtrees/IPhreeqc-src.git             src/IPhreeqcPhast/IPhreeqc
+      #       └─phreeqcpp/         └─git@${CI_SERVER_HOST}:${GROUP}/subtrees/phreeqc3-src.git           src/IPhreeqcPhast/IPhreeqc/phreeqcpp
+      #         └─common/            └─git@${CI_SERVER_HOST}:${GROUP}/subtrees/phreeqc3-src-common.git  src/IPhreeqcPhast/IPhreeqc/phreeqcpp/common
+
+      git_subtree() {
+        git subtree "${1}" --prefix="${2}" "${4}" master 2>&1 | grep -v "^[[:digit:]].*/[[:digit:]].*"
+      }
+
+      declare -A urls=( \
+        ["phreeqc3-database.git"]="git@${CI_SERVER_HOST}:${GROUP}/subtrees/phreeqc3-database.git" \
+        ["PhreeqcRM-src.git"]="git@${CI_SERVER_HOST}:${GROUP}/subtrees/PhreeqcRM-src.git" \
+      )
+
+      declare -A prefixes=( \
+        ["phreeqc3-database.git"]="database" \
+        ["PhreeqcRM-src.git"]="src" \
+      )
+
+      export GIT_EDITOR=true
+
+      for remote in "${!urls[@]}"; do
+        #git_subtree "pull" "${prefixes[$remote]}" "$remote" "${urls[$remote]}"
+        git subtree pull --prefix "${prefixes[$remote]}" --squash "${urls[$remote]}" master
+      done
+
+      for remote in "${!urls[@]}"; do
+        git_subtree "push" "${prefixes[$remote]}" "$remote" "${urls[$remote]}"
+      done
+
+      git status
+      git push origin master
+
+trigger-downstream:
+  stage: trigger
+  ##
+  ## Only run if on the master branch and the variable GROUP is set
+  ##
+  ## change this to
+  ## only:
+  ##  - master@$GROUP/phreeqcrm
+  ## and set GROUP to coupled before merge
+  only:
+    refs:
+      - master
+    variables:
+      - $GROUP
+
+  ## Downstream Projects
+  ## triggers and ids are stored at the group level
+  ## phast3     https://code.chs.usgs.gov/coupled/phast3
+  ## vs2drt-src https://code.chs.usgs.gov/coupled/subtrees/vs2drt-src
+  script:
+    - echo triggering phast3
+    - curl -X POST -F token=${PHAST3_TRIGGER} -F ref=master https://code.chs.usgs.gov/api/v4/projects/${PHAST3_ID}/trigger/pipeline
+    - sleep 360
+    - echo triggering vs2drt-src
+    - curl -X POST -F token=${VS2DRT_SRC_TRIGGER} -F ref=master https://code.chs.usgs.gov/api/v4/projects/${VS2DRT_SRC_ID}/trigger/pipeline
+    - sleep 120
+
+  ## Upstream Projects
+  ## phreeqcrm-src     https://code.chs.usgs.gov/coupled/subtrees/phreeqcrm-src
+  ## phreeqc3-database https://code.chs.usgs.gov/coupled/subtrees/phreeqc3-database

phreeqcrm-0.0.5/.gitmodules

@@ -0,0 +1,4 @@
+[submodule "pybind/pybind11"]
+	path = pybind/pybind11
+	url = https://github.com/pybind/pybind11.git
+	branch = stable

phreeqcrm-0.0.5/.pre-commit-config.yaml

@@ -0,0 +1,12 @@
+repos:
+-   repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: c8bad492e1b1d65d9126dba3fe3bd49a5a52b9d6 # v2.1.0
+    hooks:
+    -   id: end-of-file-fixer
+        files: CMakeLists.txt|configure.ac|Makefile.am|\.xml$|\.yml$
+        exclude: src/IPhreeqcPhast/IPhreeqc/phreeqcpp/test.xml$|Doxygen/DoxygenLayout.xml$
+    -   id: trailing-whitespace
+        files: CMakeLists.txt|configure.ac|Makefile.am|\.xml$|\.yml$
+        exclude: src/IPhreeqcPhast/IPhreeqc/phreeqcpp/test.xml$|Doxygen/DoxygenLayout.xml$
+    -   id: no-commit-to-branch
+        args: [--branch, main, --branch, master, --branch, develop]

phreeqcrm-0.0.5/.vscode/c_cpp_properties.json

@@ -0,0 +1,10 @@
+{
+    "configurations": [
+        {
+            "name": "CMake",
+            "compileCommands": "${config:cmake.buildDirectory}/compile_commands.json",
+            "configurationProvider": "ms-vscode.cmake-tools"
+        }
+    ],
+    "version": 4
+}