Calling C functions — Anaconda Enterprise 4.4 documentation

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# Calling C functions

This tutorial describes shortly what you need to know in order to call C library functions from Cython code. For a longer and more comprehensive tutorial about using external C libraries, wrapping them and handling errors, see Using C libraries.

For simplicity, let’s start with a function from the standard C library. This does not add any dependencies to your code, and it has the additional advantage that Cython already defines many such functions for you. So you can just cimport and use them.

For example, let’s say you need a low-level way to parse a number from a `char*` value. You could use the `atoi()` function, as defined by the `stdlib.h` header file. This can be done as follows:

    from libc.stdlib cimport atoi

    cdef parse_charptr_to_py_int(char* s):
        assert s is not NULL, "byte string value is NULL"
        return atoi(s)   # note: atoi() has no error detection!

You can find a complete list of these standard cimport files in Cython’s source package Cython/Includes/. They are stored in `.pxd` files, the standard way to provide reusable Cython declarations that can be shared across modules (see Sharing Declarations Between Cython Modules).

Cython also has a complete set of declarations for CPython’s C-API. For example, to test at C compilation time which CPython version your code is being compiled with, you can do this:

    from cpython.version cimport PY_VERSION_HEX

    # Python version >= 3.2 final ?
    print PY_VERSION_HEX >= 0x030200F0

Cython also provides declarations for the C math library:

    from libc.math cimport sin

    cdef double f(double x):
        return sin(x*x)

## Dynamic linking

The libc math library is special in that it is not linked by default on some Unix-like systems, such as Linux. In addition to cimporting the declarations, you must configure your build system to link against the shared library `m`. For distutils, it is enough to add it to the `libraries` parameter of the `Extension()` setup:

    from distutils.core import setup
    from distutils.extension import Extension
    from Cython.Build import cythonize

    ext_modules=[
        Extension("demo",
                  sources=["demo.pyx"],
                  libraries=["m"] # Unix-like specific
        )
    ]

    setup(
      name = "Demos",
      ext_modules = cythonize(ext_modules)
    )

## External declarations

If you want to access C code for which Cython does not provide a ready to use declaration, you must declare them yourself. For example, the above `sin()` function is defined as follows:

    cdef extern from "math.h":
        double sin(double x)

This declares the `sin()` function in a way that makes it available to Cython code and instructs Cython to generate C code that includes the `math.h` header file. The C compiler will see the original declaration in `math.h` at compile time, but Cython does not parse “math.h” and requires a separate definition.

Just like the `sin()` function from the math library, it is possible to declare and call into any C library as long as the module that Cython generates is properly linked against the shared or static library.

Note that you can easily export an external C function from your Cython module by declaring it as `cpdef`. This generates a Python wrapper for it and adds it to the module dict. Here is a Cython module that provides direct access to the C `sin()` function for Python code:

    """
    >>> sin(0)
    0.0
    """

    cdef extern from "math.h":
        cpdef double sin(double x)

You get the same result when this declaration appears in the `.pxd` file that belongs to the Cython module (i.e. that has the same name, see Sharing Declarations Between Cython Modules). This allows the C declaration to be reused in other Cython modules, while still providing an automatically generated Python wrapper in this specific module.

## Naming parameters

Both C and Cython support signature declarations without parameter names like this:

    cdef extern from "string.h":
        char* strstr(const char*, const char*)

However, this prevents Cython code from calling it with keyword arguments (supported since Cython 0.19). It is therefore preferable to write the declaration like this instead:

    cdef extern from "string.h":
        char* strstr(const char *haystack, const char *needle)

You can now make it clear which of the two arguments does what in your call, thus avoiding any ambiguities and often making your code more readable:

    cdef char* data = "hfvcakdfagbcffvschvxcdfgccbcfhvgcsnfxjh"

    pos = strstr(needle='akd', haystack=data)
    print pos != NULL

Note that changing existing parameter names later is a backwards incompatible API modification, just as for Python code. Thus, if you provide your own declarations for external C or C++ functions, it is usually worth the additional bit of effort to choose the names of their arguments well.