Merge commit 'e5c4d819de6ffc5246306e4ed4301c69d9754efa' #309
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| name: CMake | |
| on: | |
| push: | |
| pull_request: | |
| branches: | |
| - master | |
| schedule: | |
| - cron: '15 14 4,11,18,25 * *' | |
| workflow_dispatch: | |
| env: | |
| # Customize the CMake build type here (Release, Debug, RelWithDebInfo, etc.) | |
| BUILD_TYPE: Release | |
| NAME: IPhreeqc | |
| jobs: | |
| init: | |
| 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 | |
| test: | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| os: [macos-latest, ubuntu-latest, windows-latest] | |
| runs-on: ${{ matrix.os }} | |
| env: | |
| BUILD_DIR: _ctest # set in ctest.cmake | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Install ninja valgrind (Linux) | |
| if: runner.os == 'Linux' | |
| run: sudo apt-get update && sudo apt-get install -y ninja-build valgrind | |
| - 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: CTest | |
| run: ctest -S ctest.cmake -V --output-on-failure --timeout 900 | |
| - name: Upload results | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: ${{ matrix.os }}-${{ github.job }}-results | |
| path: ${{ github.workspace }}/${{ env.BUILD_DIR }}/Testing/ | |
| test-shared: | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| os: [macos-latest, ubuntu-latest, windows-latest] | |
| runs-on: ${{ matrix.os }} | |
| env: | |
| BUILD_DIR: _ctest_shared # set in ctest-shared.cmake | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Install ninja valgrind (Linux) | |
| if: runner.os == 'Linux' | |
| run: sudo apt-get update && sudo apt-get install -y ninja-build valgrind | |
| - 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: CTest | |
| run: ctest -S ctest-shared.cmake -V --output-on-failure --timeout 900 | |
| - name: Upload results | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: ${{ matrix.os }}-${{ github.job }}-results | |
| path: ${{ github.workspace }}/${{ env.BUILD_DIR }}/Testing/ | |
| test-clang: | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| os: [macos-latest, ubuntu-latest, windows-latest] | |
| shared_libs: [OFF, ON] | |
| enable_module: [OFF, ON] | |
| runs-on: ${{ matrix.os }} | |
| env: | |
| BUILD_DIR: _build | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Install ninja valgrind (Linux) | |
| if: runner.os == 'Linux' | |
| run: sudo apt-get update && sudo apt-get install -y ninja-build clang valgrind | |
| - 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: CMake configure | |
| if: runner.os == 'Linux' | |
| run: CC=clang CXX=clang++ cmake -B ${{ env.BUILD_DIR }} -DBUILD_SHARED_LIBS=${{ matrix.shared_libs }} -DIPHREEQC_ENABLE_MODULE=${{ matrix.enable_module }} -DCMAKE_CXX_STANDARD=20 -DCMAKE_CXX_STANDARD_REQUIRED=ON | |
| - name: CMake configure | |
| if: runner.os == 'macOS' | |
| run: CC=$(brew --prefix llvm@15)/bin/clang CXX=$(brew --prefix llvm@15)/bin/clang++ cmake -B ${{ env.BUILD_DIR }} -DBUILD_SHARED_LIBS=${{ matrix.shared_libs }} -DIPHREEQC_ENABLE_MODULE=${{ matrix.enable_module }} -DCMAKE_CXX_STANDARD=20 -DCMAKE_CXX_STANDARD_REQUIRED=ON | |
| - name: CMake configure | |
| if: runner.os == 'Windows' | |
| run: cmake -B ${{ env.BUILD_DIR }} -A x64 -T "ClangCL" -DBUILD_SHARED_LIBS=${{ matrix.shared_libs }} -DIPHREEQC_ENABLE_MODULE=${{ matrix.enable_module }} -DCMAKE_CXX_STANDARD=20 -DCMAKE_CXX_STANDARD_REQUIRED=ON | |
| - name: CMake build | |
| run: cmake --build ${{ env.BUILD_DIR }} | |
| - name: CTest | |
| run: ctest --test-dir ${{ env.BUILD_DIR }} | |
| - name: Upload results | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: ${{ matrix.os }}-${{ github.job }}-SHARED=${{ matrix.shared_libs }}-MODULE=${{ matrix.enable_module }}-results | |
| path: ${{ github.workspace }}/${{ env.BUILD_DIR }}/Testing/ | |
| chm: | |
| runs-on: windows-latest | |
| steps: | |
| - name: Checkout phreeqc3-HTMLversion | |
| uses: actions/checkout@v4 | |
| with: | |
| repository: usgs-coupled-subtrees/phreeqc3-HTMLversion | |
| ref: master | |
| - name: cache htmlhelp | |
| id: cache-htmlhelp | |
| uses: actions/cache@v4 | |
| with: | |
| path: "C:/Program Files (x86)/HTML Help Workshop" | |
| key: ${{ runner.os }}-htmlhelp | |
| - name: install htmlhelp | |
| if: steps.cache-htmlhelp.outputs.cache-hit != 'true' | |
| timeout-minutes: 5 | |
| run: | | |
| curl -L -O --max-time 120 http://web.archive.org/web/20160201063255/http://download.microsoft.com/download/0/A/9/0A939EF6-E31C-430F-A3DF-DFAE7960D564/htmlhelp.exe | |
| cmd /c start /wait .\htmlhelp.exe /q /c /t:$(Get-Location)\tmp | |
| $file = "$(Get-Location)\tmp\htmlhelp.inf" | |
| (Get-Content $file) | Foreach-Object { $_ ` | |
| -replace '^BeginPrompt', ';;BeginPrompt' ` | |
| -replace '^EndPrompt', ';;EndPrompt' ` | |
| -replace '^49000=CustomLDID49000, 1', '49000=CustomLDID49000, 5' ` | |
| -replace '^"hhupd.exe', ';;hhupd.exe' ` | |
| -replace '^DefaultInstallDir="C:\\Program Files\\HTML Help Workshop"', 'DefaultInstallDir="%ProgramFiles%\\HTML Help Workshop"' | |
| } | Set-Content $file | |
| cmd /c start /wait .\tmp\setup.exe | |
| Remove-Item -Recurse -Force .\tmp | |
| Remove-Item -Recurse -Force .\htmlhelp.exe | |
| # the next line doesn't seem to work (supposed to set the path) | |
| # echo 'C:\Program Files (x86)\HTML Help Workshop' >> $GITHUB_PATH | |
| - name: compile chm | |
| shell: bash | |
| run: | | |
| pushd HTML | |
| bash fixup_html.bash | |
| popd | |
| # hhc returns 1 on success | |
| set +e | |
| 'C:\Program Files (x86)\HTML Help Workshop\hhc' phreeqc3.hhp | tee hhc.out | |
| status=${PIPESTATUS[0]} | |
| set -e | |
| if [ "$status" -eq 1 ]; then | |
| echo "[OK]" | |
| exit 0 | |
| else | |
| echo "[FAILED]" | |
| exit 1 | |
| fi | |
| - uses: actions/upload-artifact@v4 | |
| with: | |
| name: chm | |
| path: ${{github.workspace}}/phreeqc3.chm | |
| R-CMD-check: | |
| needs: [init] | |
| runs-on: ${{ matrix.config.os }} | |
| name: ${{ matrix.config.os }} (${{ matrix.config.r }}) | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| config: | |
| - {os: macos-latest, r: 'release'} | |
| - {os: windows-latest, r: 'release'} | |
| - {os: ubuntu-latest, r: 'devel', http-user-agent: 'release'} | |
| - {os: ubuntu-latest, r: 'release'} | |
| - {os: ubuntu-latest, r: 'oldrel-1'} | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: versioning | |
| run: ./jenkins-dist.sh -v ${{ needs.init.outputs.VER }} -r ${{ needs.init.outputs.REL }} -d ${{ needs.init.outputs.DATE }} | |
| - name: Setup R | |
| uses: r-lib/actions/setup-r@v2 | |
| with: | |
| r-version: ${{ matrix.config.r }} | |
| http-user-agent: ${{ matrix.config.http-user-agent }} | |
| use-public-rspm: true | |
| - name: create source | |
| working-directory: R | |
| run: make VERSION=${{ needs.init.outputs.VER }} RELEASE_DATE=${{ needs.init.outputs.DATE_RFC_3339 }} source | |
| - name: Install dependencies | |
| uses: r-lib/actions/setup-r-dependencies@v2 | |
| with: | |
| extra-packages: any::roxygen2, any::pkgbuild, any::rcmdcheck | |
| needs: roxygen2, pkgbuild, check | |
| working-directory: R/phreeqc | |
| - name: Display sessionInfo() | |
| run: sessionInfo() | |
| working-directory: R/phreeqc | |
| shell: Rscript {0} | |
| - name: roxygen2::roxygenise() | |
| run: roxygen2::roxygenise() | |
| working-directory: R/phreeqc | |
| shell: Rscript {0} | |
| - name: Check | |
| uses: r-lib/actions/check-r-package@v2 | |
| with: | |
| working-directory: R/phreeqc | |
| - name: List files | |
| if: matrix.config.os == 'ubuntu-latest' && matrix.config.r == 'release' | |
| run: | | |
| pwd | |
| ls -lR | |
| find -name "*.tar.gz" | |
| - uses: actions/upload-artifact@v4 | |
| if: matrix.config.os == 'ubuntu-latest' && matrix.config.r == 'release' | |
| with: | |
| name: cran | |
| path: ${{ github.workspace }}/R/phreeqc/check/phreeqc_*.tar.gz | |
| # r-build: | |
| # needs: [init] | |
| # runs-on: ubuntu-latest | |
| # steps: | |
| # - uses: actions/checkout@v4 | |
| # - uses: r-lib/actions/setup-r@v2 | |
| # with: | |
| # use-public-rspm: true | |
| # - name: install devtools | |
| # run: Rscript -e 'install.packages("devtools")' | |
| # - name: install curl | |
| # run: Rscript -e 'install.packages("curl")' | |
| # - name: versioning | |
| # run: ./jenkins-dist.sh -v ${{ needs.init.outputs.VER }} -r ${{ needs.init.outputs.REL }} -d ${{ needs.init.outputs.DATE }} | |
| # - name: setup clang | |
| # run: | | |
| # mkdir -p ~/.R | |
| # echo CC=clang -Qunused-arguments > ~/.R/Makevars | |
| # echo CXX=clang++ -Qunused-arguments >> ~/.R/Makevars | |
| # - name: check | |
| # run: cd R && make VERSION=${{ needs.init.outputs.VER }} check_built | |
| # - uses: actions/upload-artifact@v4 | |
| # with: | |
| # name: cran | |
| # path: ${{github.workspace}}/R/phreeqc_*.tar.gz | |
| # r-valgrind: | |
| # needs: [r-build] | |
| # runs-on: ubuntu-latest | |
| # steps: | |
| # - uses: actions/checkout@v4 | |
| # - uses: actions/download-artifact@v4 | |
| # with: | |
| # name: cran | |
| # path: R | |
| # - name: Display structure of downloaded files | |
| # working-directory: R | |
| # run: ls -lR | |
| # - uses: r-lib/actions/setup-r@v2 | |
| # with: | |
| # use-public-rspm: true | |
| # - name: install devtools | |
| # run: Rscript -e 'install.packages("devtools")' | |
| # - name: install curl | |
| # run: Rscript -e 'install.packages("curl")' | |
| # - name: install valgrind | |
| # run: sudo apt-get install -y valgrind | |
| # - name: setup clang | |
| # run: | | |
| # mkdir -p ~/.R | |
| # echo CC=clang -Qunused-arguments > ~/.R/Makevars | |
| # echo CXX=clang++ -Qunused-arguments >> ~/.R/Makevars | |
| # - name: install | |
| # run: cd R && R CMD INSTALL --build phreeqc_*.tar.gz | |
| # - name: run | |
| # run: cd R && R -d "valgrind --tool=memcheck --leak-check=full" --vanilla < valgrind.R 2>&1 | tee valgrind.full.out | |
| # - uses: actions/upload-artifact@v4 | |
| # with: | |
| # name: valgrind | |
| # path: ${{github.workspace}}/R/valgrind.full.out | |
| distcheck: | |
| needs: [init, chm] | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: actions/download-artifact@v4 | |
| with: | |
| name: chm | |
| - name: mv chm | |
| run: mv phreeqc3.chm doc/. | |
| - 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 install -y doxygen && cd doc && doxygen | |
| - name: autoreconf | |
| run: autoreconf -fvi | |
| - name: mkdir | |
| run: mkdir _build | |
| - name: configure | |
| working-directory: ${{github.workspace}}/_build | |
| run: ../configure --prefix=$(pwd)/INSTALL | |
| - name: make | |
| working-directory: ${{github.workspace}}/_build | |
| run: make -j2 distcheck | |
| - name: convert | |
| run: | | |
| sudo apt install -y dos2unix | |
| native=" | |
| doc/Makefile \ | |
| doc/examples/AccumulateLine.c \ | |
| doc/examples/CreateIPhreeqc.c \ | |
| doc/examples/F90ClearAccumulatedLines.f90 \ | |
| doc/examples/F90CreateIPhreeqc.f90 \ | |
| doc/examples/F90DestroyIPhreeqc.f90 \ | |
| doc/examples/F90GetComponent.f90 \ | |
| doc/examples/F90GetDumpStringLine.f90 \ | |
| doc/examples/F90GetSelectedOutputValue.f90 \ | |
| doc/examples/F90GetVersionString.f90 \ | |
| doc/examples/GetComponent.c \ | |
| doc/examples/GetDumpString.c \ | |
| doc/examples/GetSelectedOutputValue.c \ | |
| doc/examples/GetVersionString.c \ | |
| doc/examples/IPhreeqc.cpp \ | |
| doc/examples/Makefile \ | |
| doc/examples/phreeqc.dat \ | |
| src/CSelectedOutput.cpp \ | |
| src/CSelectedOutput.hxx \ | |
| src/CVar.hxx \ | |
| src/Debug.h \ | |
| src/ErrorReporter.hxx \ | |
| src/IPhreeqc.cpp \ | |
| src/IPhreeqc.f.inc \ | |
| src/IPhreeqc.f90.inc \ | |
| src/IPhreeqc.h \ | |
| src/IPhreeqc.hpp \ | |
| src/IPhreeqcCallbacks.h \ | |
| src/IPhreeqcF.f \ | |
| src/IPhreeqcLib.cpp \ | |
| src/IPhreeqc_interface.F90 \ | |
| src/IPhreeqc_interface_F.cpp \ | |
| src/IPhreeqc_interface_F.h \ | |
| src/Var.c \ | |
| src/Var.h \ | |
| src/Version.h \ | |
| src/fimpl.h \ | |
| src/fwrap.cpp \ | |
| src/fwrap.h \ | |
| src/fwrap1.cpp \ | |
| src/fwrap2.cpp \ | |
| src/fwrap3.cpp \ | |
| src/fwrap4.cpp \ | |
| src/fwrap5.cpp \ | |
| src/fwrap6.cpp \ | |
| src/fwrap7.cpp \ | |
| src/fwrap8.cpp \ | |
| src/pp_sys.cpp \ | |
| src/thread.h \ | |
| test/llnl.dat \ | |
| test/phreeqc.dat \ | |
| test2/Makefile \ | |
| test2/wateq4f.dat \ | |
| test5/Makefile \ | |
| test5/phreeqc.dat \ | |
| test5/test5.c \ | |
| tests/main_fortran.cxx \ | |
| tests/test_c.c \ | |
| tests/test_cxx.cxx \ | |
| tests/test_f90.F90 \ | |
| unit/TestCVar.cpp \ | |
| unit/TestCVar.h \ | |
| unit/TestInterface.cpp \ | |
| unit/TestInterface.h \ | |
| unit/TestSelectedOutput.cpp \ | |
| unit/TestSelectedOutput.h \ | |
| unit/TestVar.cpp \ | |
| unit/TestVar.h \ | |
| unit/llnl.dat.old \ | |
| unit/missing_e.dat \ | |
| unit/phreeqc.dat.old \ | |
| unit/unit.cpp" | |
| for f in ${native}; do | |
| unix2dos "${f}" | |
| done | |
| - name: dist-zip | |
| working-directory: ${{github.workspace}}/_build | |
| run: make dist-zip | |
| - name: copy | |
| run: cp doc/README IPhreeqc_ReadMe.txt | |
| - uses: actions/upload-artifact@v4 | |
| with: | |
| name: readme | |
| path: ${{github.workspace}}/IPhreeqc_ReadMe.txt | |
| - uses: actions/upload-artifact@v4 | |
| with: | |
| name: tarball | |
| path: ${{github.workspace}}/_build/*.tar.gz | |
| - uses: actions/upload-artifact@v4 | |
| with: | |
| name: zipball | |
| path: ${{github.workspace}}/_build/*.zip | |
| # build: | |
| # needs: [init] | |
| # # The CMake configure and build commands are platform agnostic and should work equally | |
| # # well on Windows or Mac. You can convert this to a matrix build if you need | |
| # # cross-platform coverage. | |
| # # See: https://docs.github.com/en/free-pro-team@latest/actions/learn-github-actions/managing-complex-workflows#using-a-build-matrix | |
| # runs-on: windows-2019 | |
| # # Check all combinations of BUILD_SHARED_LIBS and BUILD_CLR_LIBS | |
| # strategy: | |
| # matrix: | |
| # BUILD_SHARED_LIBS: [ON, OFF] | |
| # BUILD_CLR_LIBS: [ON, OFF] | |
| # exclude: | |
| # - BUILD_SHARED_LIBS: OFF | |
| # BUILD_CLR_LIBS: ON | |
| # steps: | |
| # - uses: actions/checkout@v4 | |
| # - name: Configure CMake | |
| # # Configure CMake in a 'build' subdirectory. `CMAKE_BUILD_TYPE` is only required if you are using a single-configuration generator such as make. | |
| # # See https://cmake.org/cmake/help/latest/variable/CMAKE_BUILD_TYPE.html?highlight=cmake_build_type | |
| # run: cmake -B ${{github.workspace}}/build -DCMAKE_BUILD_TYPE=${{env.BUILD_TYPE}} -DBUILD_SHARED_LIBS=${{matrix.BUILD_SHARED_LIBS}} -DBUILD_CLR_LIBS=${{matrix.BUILD_CLR_LIBS}} | |
| # - name: Build | |
| # # Build your program with the given configuration | |
| # run: cmake --build ${{github.workspace}}/build --config ${{env.BUILD_TYPE}} | |
| # - name: Test | |
| # working-directory: ${{github.workspace}}/build | |
| # # Execute tests defined by the CMake configuration. | |
| # # See https://cmake.org/cmake/help/latest/manual/ctest.1.html for more detail | |
| # run: ctest -C ${{env.BUILD_TYPE}} |