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Merge pull request #121 from cindytsai/codecov
Upload code coverage
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‎.github/workflows/example-test-run.yml‎

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make LIBYT_PATH="${{ steps.strings.outputs.install }}"
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OMPI_MCA_osc=sm,pt2pt mpirun -np 3 ./example DataIOTest.py
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example-parallel-codecov:
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name: parallel
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runs-on: ${{ matrix.os }}
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strategy:
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fail-fast: false
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matrix:
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os: ['ubuntu-latest']
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mpi_compiler: ['openmpi']
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python_version: ['3.10']
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install_dep_command: ['sudo apt-get install -y libreadline-dev uuid-dev lcov']
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build_pybind11_option: ['-DUSE_PYBIND11=ON', '-DUSE_PYBIND11=OFF']
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steps:
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- uses: actions/checkout@v4
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- name: Setup MPI ${{ matrix.mpi_compiler }} environment
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uses: mpi4py/setup-mpi@v1
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with:
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mpi: ${{ matrix.mpi_compiler }}
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- name: Setup Python ${{ matrix.python_version }} environment
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uses: actions/setup-python@v5
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with:
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python-version: ${{ matrix.python_version }}
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cache: 'pip'
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- run: |
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python -m pip install --upgrade pip
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pip install numpy mpi4py yt yt-libyt pandas
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- name: Install other dependencies
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run: |
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${{ matrix.install_dep_command }}
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- name: Configure and Build
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run: |
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cd ${{ github.workspace }}
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rm -rf build
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cmake -B build -S . -DINTERACTIVE_MODE=ON -DJUPYTER_KERNEL=ON -DCODE_COVERAGE=ON \
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${{ matrix.build_pybind11_option }}
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cmake --build build
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- name: End-to-End Test - AMR Example - MPI Size 3
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working-directory: ${{ github.workspace }}/build/example/amr-example
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run: |
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OMPI_MCA_osc=sm,pt2pt mpirun -np 3 ./example
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- name: Generate code coverage report
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working-directory: ${{ github.workspace }}/build/src/CMakeFiles/yt.dir
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run: |
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lcov --directory . --capture --ignore-errors mismatch --output-file coverage.info
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lcov --extract coverage.info "*/libyt/src/*" "*/libyt/include/*" -o coverage-project-only.info
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- name: Upload code coverage report to Codecov
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uses: codecov/codecov-action@v5
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with:
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token: ${{ secrets.CODECOV_TOKEN }}
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files: ${{ github.workspace }}/build/src/CMakeFiles/yt.dir/coverage-project-only.info
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verbose: true
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example-serial-test-run:
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name: serial
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runs-on: ${{ matrix.os }}
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make clean
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make OPTIONS=-DSERIAL_MODE LIBYT_PATH="${{ steps.strings.outputs.install }}"
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./example DataIOTest.py
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example-serial-codecov:
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name: serial
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runs-on: ${{ matrix.os }}
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strategy:
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fail-fast: false
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matrix:
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os: ['ubuntu-latest']
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python_version: ['3.10']
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install_dep_command: ['sudo apt-get install -y libreadline-dev uuid-dev lcov']
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build_pybind11_option: ['-DUSE_PYBIND11=ON', '-DUSE_PYBIND11=OFF']
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steps:
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- uses: actions/checkout@v4
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- name: Setup Python ${{ matrix.python_version }} environment
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uses: actions/setup-python@v5
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with:
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python-version: ${{ matrix.python_version }}
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cache: 'pip'
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- run: |
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python -m pip install --upgrade pip
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pip install numpy yt yt-libyt pandas
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- name: Install other dependencies
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run: |
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${{ matrix.install_dep_command }}
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- name: Configure and Build
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run: |
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cd ${{ github.workspace }}
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rm -rf build
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cmake -B build -S . -DINTERACTIVE_MODE=ON -DJUPYTER_KERNEL=ON -DSERIAL_MODE=ON -DCODE_COVERAGE=ON \
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${{ matrix.build_pybind11_option }}
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cmake --build build
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- name: End-to-End Test - AMR Example - Serial
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working-directory: ${{ github.workspace }}/build/example/amr-example
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run: |
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./example
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- name: Generate code coverage report
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working-directory: ${{ github.workspace }}/build/src/CMakeFiles/yt.dir
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run: |
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lcov --directory . --capture --ignore-errors mismatch --output-file coverage.info
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lcov --extract coverage.info "*/libyt/src/*" "*/libyt/include/*" -o coverage-project-only.info
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- name: Upload code coverage report to Codecov
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uses: codecov/codecov-action@v5
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with:
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token: ${{ secrets.CODECOV_TOKEN }}
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files: ${{ github.workspace }}/build/src/CMakeFiles/yt.dir/coverage-project-only.info
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verbose: true

‎.github/workflows/unit-test.yml‎

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# Since some of the classes is still coupled to MPI, we need to run the unit tests with/without MPI.
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# Also upload the code coverage report to codecov
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name: unit test
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os: ['ubuntu-latest']
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mpi_compiler: ['openmpi', 'mpich']
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python_version: ['3.10']
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lcov_cmd: ['--ignore-errors mismatch']
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build_options:
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- "-DINTERACTIVE_MODE=ON -DLIBYT_RUN_TEST=ON -DUSE_PYBIND11=ON"
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- "-DINTERACTIVE_MODE=ON -DLIBYT_RUN_TEST=ON -DUSE_PYBIND11=OFF"
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- "-DINTERACTIVE_MODE=ON -DLIBYT_RUN_TEST=ON -DCODE_COVERAGE=ON -DUSE_PYBIND11=ON"
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- "-DINTERACTIVE_MODE=ON -DLIBYT_RUN_TEST=ON -DCODE_COVERAGE=ON -DUSE_PYBIND11=OFF"
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steps:
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- uses: actions/checkout@v4
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- name: Install other dependencies
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run: |
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sudo apt-get install -y libreadline-dev
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sudo apt-get install -y libreadline-dev lcov
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- name: Set reusable strings
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id: strings
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run: |
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OMPI_MCA_osc=sm,pt2pt mpirun -np 3 ./TestDataStructureAmrWithCommMpi
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- name: Generate code coverage report
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working-directory: ${{ steps.strings.outputs.build-output-dir }}/src/CMakeFiles/yt.dir
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run: |
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lcov --directory . --capture ${{ matrix.lcov_cmd }} --output-file coverage.info
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lcov --extract coverage.info "*/libyt/src/*" "*/libyt/include/*" -o coverage-project-only.info
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- name: Upload code coverage report to Codecov
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uses: codecov/codecov-action@v5
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with:
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token: ${{ secrets.CODECOV_TOKEN }}
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files: ${{ steps.strings.outputs.build-output-dir }}/src/CMakeFiles/yt.dir/coverage-project-only.info
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verbose: true
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unit-test:
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name: serial
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runs-on: ${{ matrix.os }}
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matrix:
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os: ['ubuntu-latest']
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python_version: ['3.8', '3.9', '3.10', '3.11', '3.12', '3.13', '3.14']
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lcov_cmd: ['--ignore-errors mismatch']
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build_options:
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- "-DSERIAL_MODE=ON -DINTERACTIVE_MODE=ON -DLIBYT_RUN_TEST=ON -DUSE_PYBIND11=ON"
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- "-DSERIAL_MODE=ON -DINTERACTIVE_MODE=ON -DLIBYT_RUN_TEST=ON -DUSE_PYBIND11=OFF"
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- "-DSERIAL_MODE=ON -DINTERACTIVE_MODE=ON -DLIBYT_RUN_TEST=ON -DCODE_COVERAGE=ON -DUSE_PYBIND11=ON"
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- "-DSERIAL_MODE=ON -DINTERACTIVE_MODE=ON -DLIBYT_RUN_TEST=ON -DCODE_COVERAGE=ON -DUSE_PYBIND11=OFF"
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include:
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- os: ubuntu-22.04
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python_version: '3.7'
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build_options: "-DSERIAL_MODE=ON -DINTERACTIVE_MODE=ON -DLIBYT_RUN_TEST=ON -DUSE_PYBIND11=ON"
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build_options: "-DSERIAL_MODE=ON -DINTERACTIVE_MODE=ON -DLIBYT_RUN_TEST=ON -DCODE_COVERAGE=ON -DUSE_PYBIND11=ON"
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- os: ubuntu-22.04
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python_version: '3.7'
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build_options: "-DSERIAL_MODE=ON -DINTERACTIVE_MODE=ON -DLIBYT_RUN_TEST=ON -DUSE_PYBIND11=OFF"
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build_options: "-DSERIAL_MODE=ON -DINTERACTIVE_MODE=ON -DLIBYT_RUN_TEST=ON -DCODE_COVERAGE=ON -DUSE_PYBIND11=OFF"
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steps:
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- uses: actions/checkout@v4
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- name: Install other dependencies
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run: |
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sudo apt-get install -y libreadline-dev
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sudo apt-get install -y libreadline-dev lcov
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- name: Set reusable strings
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id: strings
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working-directory: ${{ steps.strings.outputs.build-output-dir }}/test/unit_test
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run: |
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./TestDataStructureAmr
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- name: Generate code coverage report
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working-directory: ${{ steps.strings.outputs.build-output-dir }}/src/CMakeFiles/yt.dir
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run: |
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lcov --directory . --capture ${{ matrix.lcov_cmd }} --output-file coverage.info
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lcov --extract coverage.info "*/libyt/src/*" "*/libyt/include/*" -o coverage-project-only.info
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- name: Upload code coverage report to Codecov
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uses: codecov/codecov-action@v5
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with:
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token: ${{ secrets.CODECOV_TOKEN }}
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files: ${{ steps.strings.outputs.build-output-dir }}/src/CMakeFiles/yt.dir/coverage-project-only.info
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verbose: true

‎CMakeLists.txt‎

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option(LIBYT_RUN_TEST "Run unit test" OFF)
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option(LIBYT_RUN_MEMORY_PROFILE "Run memory profile" OFF)
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option(CODE_COVERAGE "Enable coverage reporting" OFF)
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## set path for dependencies ##
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set(Python_ROOT_DIR ${PYTHON_PATH})

‎README.md‎

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[![unit test](https://github.com/yt-project/libyt/actions/workflows/unit-test.yml/badge.svg?branch=main)](https://github.com/yt-project/libyt/actions/workflows/unit-test.yml)
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[![memory profile](https://github.com/yt-project/libyt/actions/workflows/memory-profile.yml/badge.svg?branch=main)](https://github.com/yt-project/libyt/actions/workflows/memory-profile.yml)
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[![Documentation Status](https://readthedocs.org/projects/libyt/badge/?version=latest)](https://libyt.readthedocs.io/en/latest/?badge=latest)
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[![codecov](https://codecov.io/gh/yt-project/libyt/graph/badge.svg?token=NRYLAipewN)](https://codecov.io/gh/yt-project/libyt)
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`libyt` is an open source C library for simulation, that allows researchers to analyze and visualize data using [`yt`](https://yt-project.org/) or other Python packages in parallel during simulation runtime.
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‎src/CMakeLists.txt‎

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yt_set_UserParameter.cpp
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)
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# set code coverage and add yt as target
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add_library(coverage_config INTERFACE)
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if (CODE_COVERAGE AND CMAKE_CXX_COMPILER_ID MATCHES "GNU|Clang")
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# Add required flags (GCC & LLVM/Clang)
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target_compile_options(
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coverage_config
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INTERFACE
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-O0 # no optimization
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-g # generate debug info
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--coverage # sets all required flags
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)
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target_link_options(coverage_config INTERFACE --coverage)
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endif (CODE_COVERAGE AND CMAKE_CXX_COMPILER_ID MATCHES "GNU|Clang")
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target_link_libraries(yt PUBLIC coverage_config)
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# set and print options and apply compile definition -D
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function (set_option option_name)
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if (${option_name})

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