I have this kind c/cython project :

project/
├── src/
│   └── modules/
│       ├── cython1.pyx
│       ├── cython1.pxd
│       ├── cython2.pyx
│       ├── cython2.pxd
│       ├── includes/
│       │   ├── c1.h
│       │   ├── c1.c
│       │   ├── d2.h
│       │   ├── c2.c
│       └── ...
└── setup.py

with this setup.py:

filenames = ['module1', 'module2']
extensions = [Extension(name=f"modules.{name}", 
                        sources=[f"modules/{name}.pyx"],
                        include_dirs=["modules/includes", ]) for name in filenames]

setup(
    ext_modules=cythonize(extensions),
    packages=['project'],
    include_package_data=True,
    package_data = {
        'module': ['*.pxd', '*.so'],
    },
    ]
)

I have several issues.

in pxd files, I use definitions from c files as follows : cdef extern from "includes/c1.c" and the project compiles and runs without any issue.
When I try to cimport module1 in another context, I have a fatal error: ‘c1.c’ file not found.

When I setup cdef extern from "includes/c1.h" in the pxd files, the project compiles but its execution gives errors (functions from c files are not in namespace).

I tried to add corresponding c files to the source list for each module (sources=[f"modules/{name}.pyx", "c1.c"]), then I get a message saying that c functions are declared multiple times. The fact is that I use c functions in the different cython modules. Moreover, the different c/h files interact with each other (for instance there can be an #include “c1.h” in “c2.c”).

In the end, I just can’t manage it, and can’t figure out how to structure the project so that it runs properly and can also be cimported. I understand from the forums that one solution might be to precompile c file as a shared library, but I can’t get this procedure to work directly in setup.py.

What’s the best way to structure the project and to write the setup.py?