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Merge pull request #17 from cropsinsilico/cvode_7.1.1
Sundials 7.1.1
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‎.github/workflows/test-suite.yml‎

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name: Test of package installation & execution
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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_cxx:
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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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with-coverage: [false, true]
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with-asan: [false, true]
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with-elf: [false]
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with-valgrind: [false, true]
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with-mpi: [false]
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with-python: [false]
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include:
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- sundials-version: "5.7.0"
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os: ubuntu-latest
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with-coverage: false
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with-asan: false
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with-elf: false
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with-valgrind: false
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with-mpi: false
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with-python: false
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- sundials-version: "6.7.0"
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os: ubuntu-latest
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with-coverage: false
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with-asan: false
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with-elf: false
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with-valgrind: false
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with-mpi: false
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with-python: false
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- sundials-version: "7.1.1"
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os: ubuntu-latest
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with-coverage: false
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with-asan: false
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with-elf: false
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with-valgrind: false
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with-mpi: false
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with-python: false
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- sundials-version: latest
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os: ubuntu-latest
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with-coverage: false
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with-asan: false
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with-elf: false
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with-valgrind: false
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with-mpi: true
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with-python: false
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- sundials-version: "6.7.0"
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os: ubuntu-latest
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with-coverage: false
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with-asan: false
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with-elf: false
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with-valgrind: false
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with-mpi: true
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with-python: false
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- sundials-version: "7.1.1"
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os: ubuntu-latest
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with-coverage: false
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with-asan: false
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with-elf: false
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with-valgrind: false
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with-mpi: true
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with-python: false
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- sundials-version: latest
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os: ubuntu-latest
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with-coverage: false
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with-asan: false
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with-elf: false
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with-valgrind: false
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with-mpi: false
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with-python: true
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exclude:
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- os: windows-latest
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with-asan: true
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- os: ubuntu-latest
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with-asan: true
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- os: windows-latest
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with-valgrind: true
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- os: windows-latest
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with-elf: true
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- os: macos-latest
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with-valgrind: true
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- os: macos-latest
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with-elf: true
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- with-valgrind: true
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with-elf: true
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- with-valgrind: true
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with-asan: true
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- with-coverage: true
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with-valgrind: true
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- with-coverage: true
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with-asan: true
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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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if: matrix.with-mpi == false
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uses: conda-incubator/setup-miniconda@v3
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with:
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activate-environment: ephoto
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environment-file: environment.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-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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uses: conda-incubator/setup-miniconda@v3
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with:
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activate-environment: ephoto
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environment-file: environment_mpi.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-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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run: |
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echo "USERPROFILE=${{ github.workspace }}" >> "$GITHUB_ENV"
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- name: Install specific version of Sundials via conda
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if: matrix.sundials-version != 'latest' && matrix.with-mpi == false
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run: |
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mamba install sundials==${{ matrix.sundials-version }} -y
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- name: Check mamba installation
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run: |
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mamba info
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mamba 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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- 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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- 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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###################################
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# INSTALL SUNDIALS W/ MPI
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###################################
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- name: CMake flags for building Sundials W/ MPI
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shell: bash -l {0}
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if: matrix.with-mpi == true
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run: |
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CMAKE_BUILD_TYPE_TEST="RelWithDebInfo"
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echo "CMAKE_BUILD_TYPE_TEST=RelWithDebInfo" >> "$GITHUB_ENV"
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echo "CMAKE_ARGS=-DCMAKE_VERBOSE_MAKEFILE:BOOL=ON -DENABLE_MPI:BOOL=ON -DEXAMPLES_ENABLE_C:BOOL=OFF -DEXAMPLES_ENABLE_CXX:BOOL=OFF" >> "$GITHUB_ENV"
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- name: Clone Sundials for build W/ MPI
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if: matrix.with-mpi == true
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run: |
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git clone https://github.com/LLNL/sundials.git
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- name: Check out specific version of Sundials for build W/ MPI
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if: matrix.sundials-version != 'latest' && matrix.with-mpi == true
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run: |
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cd sundials
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git checkout tags/v${{ matrix.sundials-version }} -b tagged
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- name: Configure Sundials W/ MPI
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if: matrix.with-mpi == true
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run: |
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cd sundials
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mkdir build
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cd build
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cmake .. ${{ env.CMAKE_ARGS }}
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- name: Build Sundials W/ MPI in parallel (CONDA, UNIX)
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if: matrix.with-mpi == true && matrix.os != 'windows-latest'
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run: |
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cd sundials/build
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cmake --build . --config ${{ env.CMAKE_BUILD_TYPE_TEST }} -- -j 4
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- name: Build Sundials W/ MPI in serial (CONDA, WINDOWS)
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if: matrix.with-mpi == true && matrix.os == 'windows-latest'
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run: |
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cd sundials/build
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cmake --build . --config ${{ env.CMAKE_BUILD_TYPE_TEST }}
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- name: Install Sundials W/ MPI
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if: matrix.with-mpi == true
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run: |
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cd sundials/build
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cmake --install . --prefix /home/runner/miniconda3/envs/ephoto
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###################################
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# PIP INSTALL THINGS
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###################################
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- name: Install packages not current on conda-forge (gcovr)
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if: matrix.with-coverage == true
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run: |
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pip install gcovr
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###################################
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# SET CONFIG FLAGS
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###################################
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- name: Global config flags
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run: |
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CMAKE_BUILD_TYPE_TEST="Debug"
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echo "CMAKE_BUILD_TYPE_TEST=Debug" >> "$GITHUB_ENV"
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echo "CMAKE_ARGS=-DCMAKE_VERBOSE_MAKEFILE:BOOL=ON" >> "$GITHUB_ENV"
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echo "CMAKE_ARGS_TEST=-DBUILD_TESTS=ON" >> "$GITHUB_ENV"
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echo "TEST_FLAGS=-C ${CMAKE_BUILD_TYPE_TEST} --output-on-failure -VV" >> "$GITHUB_ENV"
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echo "BUILD_ARGS=--config ${CMAKE_BUILD_TYPE_TEST}" >> "$GITHUB_ENV"
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- name: Set flags to build in parallel (UNIX)
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if: matrix.os != 'windows-latest'
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run: |
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echo "BUILD_ARGS=${{ env.BUILD_ARGS }} -- -j 4" >> "$GITHUB_ENV"
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- name: Coverage config flags
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if: matrix.with-coverage == true && matrix.os != 'windows-latest'
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run: |
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echo "CMAKE_ARGS_TEST=${{ env.CMAKE_ARGS_TEST }} -DTEST_COVERAGE=ON" >> "$GITHUB_ENV"
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- name: ASAN config flags
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if: matrix.with-asan == true
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run: |
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echo "CMAKE_ARGS=${{ env.CMAKE_ARGS }} -DWITH_ASAN=ON" >> "$GITHUB_ENV"
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echo "ASAN_OPTIONS=detect_odr_violation=0:detect_container_overflow=0" >> $GITHUB_ENV
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echo "TEST_FLAGS=${{ env.TEST_FLAGS }} -E valgrind*" >> "$GITHUB_ENV"
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- name: ASAN dynamic library
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if: matrix.with-asan == true && matrix.os == 'macos-latest'
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run: |
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echo "DYLD_INSERT_LIBRARIES=$(clang -print-file-name=libclang_rt.asan_osx_dynamic.dylib)" >> "$GITHUB_ENV"
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- name: ELF config flags
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if: matrix.with-elf == true
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run: |
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echo "CMAKE_ARGS_TEST=${{ env.CMAKE_ARGS_TEST }} -DTEST_ELF=ON" >> "$GITHUB_ENV"
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- name: Valgrind off config flags
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if: matrix.with-valgrind == true
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run: |
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echo "CMAKE_ARGS_TEST=${{ env.CMAKE_ARGS_TEST }} -DTEST_VALGRIND=ON" >> "$GITHUB_ENV"
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###################################
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# Add paths for Windows dlls
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###################################
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- name: Conda library paths on Windows
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if: matrix.os == 'windows-latest'
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run: |
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# This isn't necessary, but it speeds up the build
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LIB_DIRECTORY="${CONDA_PREFIX}/Library/lib"
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ls ${LIB_DIRECTORY}
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echo "${LIB_DIRECTORY}" >> $GITHUB_PATH
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DLL_DIRECTORY="${CONDA_PREFIX}/Library/bin"
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ls ${DLL_DIRECTORY}
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echo "${DLL_DIRECTORY}" >> $GITHUB_PATH
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###################################
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# Configure
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###################################
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- name: Configure (CONDA)
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run: |
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mkdir build
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cd build
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which cmake
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cmake .. ${{ env.CMAKE_ARGS }} ${{ env.CMAKE_ARGS_TEST }}
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###################################
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# Build CXX
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###################################
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- name: Build C++ & C
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run: |
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cd build
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cmake --build . ${{ env.BUILD_ARGS }}
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###################################
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# Test CXX
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###################################
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- name: Test C++
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if: matrix.with-coverage != true
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run: |
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mamba list
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echo "PATH=$PATH"
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cd build
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which ctest
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ctest ${{ env.TEST_FLAGS }}
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- name: Test C++ (COVERAGE)
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if: matrix.with-coverage && matrix.os != 'windows-latest'
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run: |
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mamba list
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echo "PATH=$PATH"
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cd build
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make coverage
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- name: Preserve coverage information
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if: matrix.with-coverage && matrix.os != 'windows-latest'
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run: |
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cp -r build/coverage coverage
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###################################
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# Build Python
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###################################
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- name: Configure Python
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if: matrix.with-python == true
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run: |
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cd build
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cmake .. -DBUILD_PYTHON=ON ${{ env.CMAKE_ARGS }}
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- name: Build & install Python
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if: matrix.with-python == true
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run: |
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cd build
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cmake --build . --target pyPhotosynthesis ${{ env.BUILD_ARGS }}
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cmake --install . --prefix /home/runner/miniconda3/envs/ephoto --component Python
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###################################
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# Test Python
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###################################
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- name: Test Python Interfaces
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if: matrix.with-python == true
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run: |
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pytest -sv tests/python
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###################################
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# Docs tests
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###################################
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- name: Build docs
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if: matrix.os != 'windows-latest'
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run: |
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python scripts/devtasks.py docs --rebuild
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###################################
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# Coverage
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###################################
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- name: Upload coverage report
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if: matrix.with-coverage == true && matrix.os != 'windows-latest'
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uses: codecov/codecov-action@v4
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with:
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name: ${{ matrix.os }}-${{ matrix.sundials-version }}-${{ matrix.with-coverage }}-${{ matrix.with-asan }}-${{ matrix.with-elf }}-${{ matrix.with-valgrind }}-${{ matrix.with-mpi }}-${{ matrix.with-python }}
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token: ${{ secrets.CODECOV_TOKEN }}
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file: coverage/coverage.info
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functionalities: gcov

‎.gitignore‎

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doc/html
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doc/latex
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*~
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__pycache__

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