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CONTRIBUTING.md

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notes for PyPartMC developers

Implementation outline

  • PyPartMC is written in C++, Fortran and uses pybind11 and CMake.
  • JSON support is handled with nlohmann::json and pybind11_json
  • PartMC and selected parts of SUNDIALS are statically linked (and compiled in during pip install or python -m build)
  • C (SUNDIALS, netCDF), C++ (pybind11, ...) and Fortran (PartMC, CAMP, netCDF-fortran) dependencies are linked through git submodules
  • MOSAIC dependency is optionally linked through setting the environmental variable MOSAIC_HOME
  • a drop-in replacement of the PartMC spec file routines is used for i/o from/to JSON

Implementation architecture

flowchart TD
    subgraph J ["Julia"]
        julia_user_code["Julia user code"] --> PyCall.jl
    end
    subgraph M ["Matlab"]
        matlab_user_code["Matlab user code"] --> matlab_python["Matlab built-in\nPython interface"]
    end
    subgraph P ["Python"]
        python_user_code -.-> NumPy
        python_user_code["Python user code"] ---> PyPartMC["pubind11-generated\nPyPartMC module"]
        matlab_python --> PyPartMC
        PyCall.jl --> PyPartMC
    end
    subgraph Cpp ["C++"]
        cpp_user_code["C++ user code"] ----> ppmc_cpp
        PyPartMC --> ppmc_cpp["PyPartMC-C++"]
        ppmc_cpp --> pybind11_json
        pybind11_json ---> nlohmann::JSON
        spec_file_pypartmc_cpp --> nlohmann::JSON
    end
    subgraph C ["C"]
        spec_file_pypartmc_c --> spec_file_pypartmc_cpp["SpecFile-C++"]
        ppmc_cpp --> ppmc_c["PyPartMC-C"]
        netCDF-C
        SUNDIALS
        camp_c["CAMP C code"]
    end
    subgraph Fortran ["Fortran"]
        PartMC -....-> MOSAIC
        ppmc_c --> ppmc_f["PyPartMC-F"]
        ppmc_f ---> PartMC
        PartMC --> netCDF-F
        netCDF-F --> netCDF-C
        PartMC --> SUNDIALS
        PartMC ---> camp_f
        camp_f["CAMP"] --> camp_c
        PartMC ----> spec_file_pypartmc_f[SpecFile-F]
        spec_file_pypartmc_f --> spec_file_pypartmc_c["SpecFile-C"]
    end

    style PartMC fill:#7ae7ff,stroke-width:2px,color:#2B2B2B
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How to debug

git clone --recursive git+https://github.com/open-atmos/PyPartMC.git
cd PyPartMC
DEBUG=1 VERBOSE=1 pip --verbose install -e .
gdb python 
(gdb) run -m pytest -s -vv -We -p no:unraisableexception tests

Pre-commit hooks

PyPartMC codebase benefits from Pylint, Black and isort code analysis (which are all part of the CI workflows where we also use pre-commit hooks. The pre-commit hooks can be run locally, and then the resultant changes need to be staged before committing. To set up the hooks locally, install pre-commit via pip install pre-commit and set up the git hooks via pre-commit install (this needs to be done every time you clone the project). To run all pre-commit hooks, run pre-commit run --all-files. The .pre-commit-config.yaml file can be modified in case new hooks are to be added or existing ones need to be altered.