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Merge pull request #18 from cropsinsilico/conda_recipe
Conda recipe
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‎.github/workflows/conda_recipe.yml‎

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name: Test of conda recipe build
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'on':
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push:
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branches-ignore:
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- gh-pages
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tags:
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- '*'
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schedule:
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- cron: 0 10 * * 1
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jobs:
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build_conda_recipe:
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runs-on: ${{ matrix.os }}
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defaults:
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run:
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shell: bash -el {0}
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strategy:
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matrix:
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sundials-version: [latest]
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os: [ubuntu-latest, macos-latest, windows-latest]
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fail-fast: false
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steps:
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- name: Check out repository code
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uses: actions/checkout@v4
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with:
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submodules: true
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###################################
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# CONDA SETUP
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###################################
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- name: Set up MSVC Compiler on windows
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uses: ilammy/msvc-dev-cmd@v1
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if: matrix.os == 'windows-latest'
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- name: Set up miniconda test environment (W/O MPI)
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uses: conda-incubator/setup-miniconda@v3
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with:
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activate-environment: ""
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auto-activate-base: true
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auto-update-conda: true
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channels: conda-forge
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channel-priority: strict
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miniforge-variant: Miniforge3
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miniforge-version: latest
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conda-remove-defaults: true
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- name: Install conda-build
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run: |
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conda info
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conda list
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conda install conda-build py-lief=0.14 cmake numpy -y
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- name: Check conda installation
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run: |
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conda info
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conda list
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- name: Build conda recipe
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run: |
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conda-build --use-local --no-anaconda-upload --output-folder ./local_channel/ recipe/
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- name: Install from local conda recipe
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run: |
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conda install -c ./local_channel ePhotosynthesis
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conda list
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###################################
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# Test
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###################################
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- name: Test ePhoto executable install by conda
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run: |
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ePhoto -d 4 --evn tests/data/InputEvn.txt --grn tests/data/InputGRNC.txt --enzyme tests/data/InputEnzyme.txt --atpcost tests/data/InputATPCost.txt --output output_conda.data
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- name: Check output from ePhoto executable install by conda
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run: |
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python scripts/devtasks.py compare-files output_conda.data --driver 4
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- name: Build example against the installed library using CMake/Make (Unix)
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if: matrix.os != 'windows-latest'
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run: |
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conda list
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cd tests/external
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mkdir build
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cd build
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cmake .. -DCMAKE_VERBOSE_MAKEFILE:BOOL=ON
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cmake --build .
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- name: Build example against the installed library using CMake/Ninja (Windows)
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if: matrix.os == 'windows-latest'
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run: |
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conda list
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cd tests/external
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mkdir build
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cd build
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cmake -GNinja -D CMAKE_BUILD_TYPE=Release -D CMAKE_VERBOSE_MAKEFILE:BOOL=ON ..
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cmake --build .
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- name: Test built example executable (Unix)
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if: matrix.os != 'windows-latest'
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run: |
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cd tests
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./external/build/example
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- name: Test built example executable (Windows)
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if: matrix.os == 'windows-latest'
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run: |
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cd tests
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ls
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ls ./external/build/
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# ./external/build/Release/example
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./external/build/example
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- name: Check built example executable output
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run: |
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python scripts/devtasks.py compare-files tests/example_output.data --driver 4

‎.github/workflows/test-suite.yml‎

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auto-update-conda: true
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channels: conda-forge
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channel-priority: strict
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miniforge-variant: Miniforge3
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miniforge-version: latest
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use-mamba: true
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mamba-version: "1.5.10"
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conda-remove-defaults: true
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- name: Set up miniconda test environment (W/ MPI)
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if: matrix.with-mpi == true
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auto-update-conda: true
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channels: conda-forge
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channel-priority: strict
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miniforge-variant: Miniforge3
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miniforge-version: latest
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use-mamba: true
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mamba-version: "1.5.10"
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conda-remove-defaults: true
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- name: Set USERPROFILE
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if: matrix.os == 'windows-latest'
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- name: Install specific version of Sundials via conda
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if: matrix.sundials-version != 'latest' && matrix.with-mpi == false
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run: |
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mamba install sundials==${{ matrix.sundials-version }} -y
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- name: Check mamba installation
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conda install sundials==${{ matrix.sundials-version }} -y
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- name: Check conda installation
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run: |
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mamba info
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mamba list
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conda info
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conda list
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- name: Install doxgen on unix systems
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if: matrix.os != 'windows-latest'
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run: |
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mamba install doxygen>=1.9.2 graphviz -y
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conda install doxygen>=1.9.2 graphviz -y
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- name: Install compilers using conda on Linux/Mac
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if: matrix.os != 'windows-latest' && matrix.with-valgrind != true
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run: |
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mamba install c-compiler cxx-compiler
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conda install c-compiler cxx-compiler
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- name: Install valgrind on unix systems (and required debug symbols)
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if: matrix.os != 'windows-latest' && matrix.with-valgrind == true
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run: |
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sudo apt-get update
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sudo apt-get install libc6-dbg
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mamba install valgrind
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conda install valgrind
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###################################
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# INSTALL SUNDIALS W/ MPI
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- name: Test C++
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if: matrix.with-coverage != true
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run: |
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mamba list
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conda list
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echo "PATH=$PATH"
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cd build
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which ctest
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ctest ${{ env.TEST_FLAGS }}
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- name: Test C++ (COVERAGE)
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if: matrix.with-coverage && matrix.os != 'windows-latest'
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run: |
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mamba list
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conda list
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echo "PATH=$PATH"
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cd build
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make coverage

‎CMakeLists.txt‎

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@@ -35,7 +35,7 @@ set(PACKAGE_STRING "ePhotosynthesis 1.0.0")
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set(PACKAGE_VERSION_MAJOR "1")
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set(PACKAGE_VERSION_MINOR "0")
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set(PACKAGE_VERSION_PATCH "0")
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set(PACKAGE_VERSION_PATCH "1")
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set(PACKAGE_VERSION_LABEL "")
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if(PACKAGE_VERSION_LABEL)
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LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR}
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ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR}
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RUNTIME DESTINATION ${CMAKE_INSTALL_BINDIR}
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PUBLIC_HEADER DESTINATION EPHOTOSYNTHESIS_INSTALL_INCLUDEDIR
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PUBLIC_HEADER DESTINATION ${EPHOTOSYNTHESIS_INSTALL_INCLUDEDIR}
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COMPONENT CXX
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)
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install(
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DESTINATION ${CMAKE_INSTALL_LIBDIR}/cmake/ePhotosynthesis
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COMPONENT CXX
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)
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install(
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FILES cmake/FindSUNDIALS.cmake
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DESTINATION ${CMAKE_INSTALL_LIBDIR}/cmake/ePhotosynthesis
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COMPONENT CXX
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)
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install(
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FILES ${CMAKE_CURRENT_BINARY_DIR}/ePhotosynthesis_export.h
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DESTINATION ${EPHOTOSYNTHESIS_INSTALL_INCLUDEDIR}
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COMPONENT CXX
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)
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install(
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DIRECTORY include/
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DESTINATION ${EPHOTOSYNTHESIS_INSTALL_INCLUDEDIR}
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COMPONENT CXX
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)
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# install(
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# DIRECTORY param
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# DESTINATION ${EPHOTOSYNTHESIS_INSTALL_INCLUDEDIR}
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set(TEST_LIST "")
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foreach(TEST_PATH ${TEST_SOURCES})
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list(APPEND TEST_LIST ${TEST_PATH})
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if(NOT TEST_PATH MATCHES ".*external.*")
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message(STATUS "TEST_PATH = ${TEST_PATH}")
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list(APPEND TEST_LIST ${TEST_PATH})
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endif()
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endforeach()
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add_executable(testRunner ${TEST_LIST})
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target_link_libraries(testRunner EPhotosynthesis)

‎README.md‎

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# ePhotosynthesis
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3-
This is a C++ port of the ePhotosynthesis Matlab model code. The code is built with
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This is a C++ port of the ePhotosynthesis Matlab model code. ePhotosynthesis is a dynamic mechanistic model of photosynthesis. The code is built with
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*CMake*.
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The Matlab origin code is tagged [C++ conversion](https://github.com/cropsinsilico/ePhotosynthesis/releases/tag/1.0.0). The scripts
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--debugDelta Debug deltas
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--debugInternal Debug internals
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```
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```
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### Citation
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Zhu XG, Wang Y, Ort DR, Long SP. e-Photosynthesis: a comprehensive dynamic mechanistic model of C3 photosynthesis: from light capture to sucrose synthesis. Plant Cell Environ. 2013 Sep;36(9):1711-27. doi: 10.1111/pce.12025. Epub 2012 Nov 19. PMID: 23072293.

‎bin/ePhotosynthesis.cpp‎

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#include <vector>
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#include "cxxopts.hpp"
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#include "globals.hpp"
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#include "modules/trDynaPS.hpp"
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#include "modules/CM.hpp"
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#include "modules/EPS.hpp"
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#include "modules/PR.hpp"
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#include "modules/BF.hpp"
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#include "modules/FI.hpp"
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#include "drivers/drivers.hpp"
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#include "Variables.hpp"
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#include "ePhotosynthesis.hpp"
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using namespace ePhotosynthesis;

‎cmake/ePhotosynthesisConfig.cmake.in‎

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include(CMakeFindDependencyMacro)
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list(APPEND CMAKE_MODULE_PATH ${CMAKE_CURRENT_LIST_DIR})
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find_dependency(Boost REQUIRED COMPONENTS regex)
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find_dependency(Sundials REQUIRED)
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find_dependency(SUNDIALS REQUIRED COMPONENTS kinsol cvode)
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include(${CMAKE_CURRENT_LIST_DIR}/ePhotosynthesisTargets.cmake)
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set(CMAKE_MODULE_PATH ${CMAKE_MODULE_PATH} CACHE INTERNAL "CMAKE_MODULE_PATH")

‎include/ePhotosynthesis.hpp‎

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/**********************************************************************************************************************************************
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* Copyright Xin-Guang Zhu, Yu Wang, Donald R. ORT and Stephen P. LONG
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*
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* CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, CAS, Shanghai,200031
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* China Institute of Genomic Biology and Department of Plant Biology, Shanghai Institutes for Biological Sciences, CAS, Shanghai,200031
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* University of Illinois at Urbana Champaign
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* Global Change and Photosynthesis Research Unit, USDA/ARS, 1406 Institute of Genomic Biology, Urbana, IL 61801, USA.
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*
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* Converted from Matlab to C++ by Douglas N. Friedel, National Center for Supercomputing Applications (2020)
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*
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* This file is part of e-photosynthesis.
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*
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* e-photosynthesis is free software; you can redistribute it and/or modify
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* it under the terms of the GNU General Public License as published by
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* the Free Software Foundation;
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*
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* e-photosynthesis is distributed in the hope that it will be useful,
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* but WITHOUT ANY WARRANTY; without even the implied warranty of
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* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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* GNU General Public License for more details.
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*
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* You should have received a copy of the GNU General Public License (GPL)
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* along with this program. If not, see <http://www.gnu.org/licenses/>.
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*
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**********************************************************************************************************************************************/
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#include "globals.hpp"
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#include "modules/trDynaPS.hpp"
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#include "modules/CM.hpp"
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#include "modules/EPS.hpp"
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#include "modules/PR.hpp"
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#include "modules/BF.hpp"
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#include "modules/FI.hpp"
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#include "drivers/drivers.hpp"
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#include "Variables.hpp"

‎recipe/bld.bat‎

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@setlocal
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set CONFIGURATION=Release
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mkdir conda_build
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cd conda_build
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:: Call cmake
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cmake -GNinja ^
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-D CMAKE_BUILD_TYPE=%CONFIGURATION% ^
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-D CMAKE_INSTALL_PREFIX=%LIBRARY_PREFIX% ^
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-D CMAKE_VERBOSE_MAKEFILE=ON ..
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if errorlevel 1 exit 1
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:: Using ninja
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ninja all
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ninja install
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:: Run tests
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if errorlevel 1 exit 1
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ctest -C "%Configuration%" -V
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if errorlevel 1 exit 1
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@endlocal

‎recipe/build.sh‎

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#!/bin/sh
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set -euo pipefail
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# Using cmake
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mkdir conda_build
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cd conda_build
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cmake -D CMAKE_BUILD_TYPE=Release -D CMAKE_INSTALL_PREFIX=$PREFIX ..
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# Make all, run tests, then install
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make all VERBOSE=1
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ctest -V
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make install

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