Interfacing with External C Code

One of the main uses of Cython is wrapping existing libraries of C code. This is achieved by using external declarations to declare the C functions and variables from the library that you want to use.

You can also use public declarations to make C functions and variables defined in a Cython module available to external C code. The need for this is expected to be less frequent, but you might want to do it, for example, if you are embedding Python in another application as a scripting language. Just as a Cython module can be used as a bridge to allow Python code to call C code, it can also be used to allow C code to call Python code.

External declarations

By default, C functions and variables declared at the module level are local to the module (i.e. they have the C static storage class). They can also be declared extern to specify that they are defined elsewhere, for example,:

cdef extern int spam_counter

cdef extern void order_spam(int tons)

Referencing C header files

When you use an extern definition on its own as in the examples above, Cython includes a declaration for it in the generated C file. This can cause problems if the declaration doesn’t exactly match the declaration that will be seen by other C code. If you’re wrapping an existing C library, for example, it’s important that the generated C code is compiled with exactly the same declarations as the rest of the library.

To achieve this, you can tell Cython that the declarations are to be found in a C header file, like this:

cdef extern from "spam.h":

    int spam_counter

    void order_spam(int tons)

The cdef extern from clause does three things:

  1. It directs Cython to place a #include statement for the named header file in the generated C code.

  2. It prevents Cython from generating any C code for the declarations found in the associated block.

  3. It treats all declarations within the block as though they started with cdef extern.

It’s important to understand that Cython does not itself read the C header file, so you still need to provide Cython versions of any declarations from it that you use. However, the Cython declarations don’t always have to exactly match the C ones, and in some cases they shouldn’t or can’t. In particular:

  1. Leave out any platform-specific extensions to C declarations such as __declspec().

  2. If the header file declares a big struct and you only want to use a few members, you only need to declare the members you’re interested in. Leaving the rest out doesn’t do any harm, because the C compiler will use the full definition from the header file.

    In some cases, you might not need any of the struct’s members, in which case you can just put pass in the body of the struct declaration, e.g.:

    cdef extern from "foo.h":
    struct spam:
        pass

    Note

    you can only do this inside a cdef extern from block; struct declarations anywhere else must be non-empty.

  3. If the header file uses typedef names such as word to refer to platform-dependent flavours of numeric types, you will need a corresponding ctypedef statement, but you don’t need to match the type exactly, just use something of the right general kind (int, float, etc). For example,:

    ctypedef int word

    will work okay whatever the actual size of a word is (provided the header file defines it correctly). Conversion to and from Python types, if any, will also be used for this new type.

  4. If the header file uses macros to define constants, translate them into a normal external variable declaration. You can also declare them as an enum if they contain normal int values. Note that Cython considers enum to be equivalent to int, so do not do this for non-int values.

  5. If the header file defines a function using a macro, declare it as though it were an ordinary function, with appropriate argument and result types.

  6. For archaic reasons C uses the keyword void to declare a function taking no parameters. In Cython as in Python, simply declare such functions as foo().

A few more tricks and tips:

  • If you want to include a C header because it’s needed by another header, but don’t want to use any declarations from it, put pass in the extern-from block:

    cdef extern from "spam.h":
    pass

  • If you want to include a system header, put angle brackets inside the quotes:

    cdef extern from "<sysheader.h>":
    ...

  • If you want to include some external declarations, but don’t want to specify a header file (because it’s included by some other header that you’ve already included) you can put * in place of the header file name:

    cdef extern from *:
    ...

  • If a cdef extern from "inc.h" block is not empty and contains only function or variable declarations (and no type declarations of any kind), Cython will put the #include "inc.h" statement after all declarations generated by Cython. This means that the included file has access to the variables, functions, structures, … which are declared by Cython.

Implementing functions in C

When you want to call C code from a Cython module, usually that code will be in some external library that you link your extension against. However, you can also directly compile C (or C++) code as part of your Cython module. In the .pyx file, you can put something like:

cdef extern from "spam.c":
    void order_spam(int tons)

Cython will assume that the function order_spam() is defined in the file spam.c. If you also want to cimport this function from another module, it must be declared (not extern!) in the .pxd file:

cdef void order_spam(int tons)

For this to work, the signature of order_spam() in spam.c must match the signature that Cython uses, in particular the function must be static:

static void order_spam(int tons)
{
    printf("Ordered %i tons of spam!\n", tons);
}

Styles of struct, union and enum declaration

There are two main ways that structs, unions and enums can be declared in C header files: using a tag name, or using a typedef. There are also some variations based on various combinations of these.

It’s important to make the Cython declarations match the style used in the header file, so that Cython can emit the right sort of references to the type in the code it generates. To make this possible, Cython provides two different syntaxes for declaring a struct, union or enum type. The style introduced above corresponds to the use of a tag name. To get the other style, you prefix the declaration with ctypedef, as illustrated below.

The following table shows the various possible styles that can be found in a header file, and the corresponding Cython declaration that you should put in the cdef extern from block. Struct declarations are used as an example; the same applies equally to union and enum declarations.

C code

Possibilities for corresponding Cython Code

Comments

 
struct Foo {
  ...
};

cdef struct Foo:
  ...

Cython will refer to the as struct Foo in the generated C code.

 
typedef struct {
  ...
} Foo;

ctypedef struct Foo:
  ...

Cython will refer to the type simply as Foo in the generated C code.

 
typedef struct foo {
  ...
} Foo;

cdef struct foo:
  ...
ctypedef foo Foo #optional

or:

ctypedef struct Foo:
  ...

If the C header uses both a tag and a typedef with different names, you can use either form of declaration in Cython (although if you need to forward reference the type, you’ll have to use the first form).

 
typedef struct Foo {
  ...
} Foo;

cdef struct Foo:
  ...

If the header uses the same name for the tag and typedef, you won’t be able to include a ctypedef for it – but then, it’s not necessary.

See also use of External extension types. Note that in all the cases below, you refer to the type in Cython code simply as Foo, not struct Foo.

Accessing Python/C API routines

One particular use of the cdef extern from statement is for gaining access to routines in the Python/C API. For example,:

cdef extern from "Python.h":

    object PyString_FromStringAndSize(char *s, Py_ssize_t len)

will allow you to create Python strings containing null bytes.

Special Types

Cython predefines the name Py_ssize_t for use with Python/C API routines. To make your extensions compatible with 64-bit systems, you should always use this type where it is specified in the documentation of Python/C API routines.

Windows Calling Conventions

The __stdcall and __cdecl calling convention specifiers can be used in Cython, with the same syntax as used by C compilers on Windows, for example,:

cdef extern int __stdcall FrobnicateWindow(long handle)

cdef void (__stdcall *callback)(void *)

If __stdcall is used, the function is only considered compatible with other __stdcall functions of the same signature.

Resolving naming conflicts - C name specifications

Each Cython module has a single module-level namespace for both Python and C names. This can be inconvenient if you want to wrap some external C functions and provide the Python user with Python functions of the same names.

Cython provides a couple of different ways of solving this problem. The best way, especially if you have many C functions to wrap, is to put the extern C function declarations into a .pxd file and thus a different namespace, using the facilities described in sharing declarations between Cython modules. Writing them into a .pxd file allows their reuse across modules, avoids naming collisions in the normal Python way and even makes it easy to rename them on cimport. For example, if your decl.pxd file declared a C function eject_tomato:

cdef extern from "myheader.h":
    void eject_tomato(float speed)

then you can cimport and wrap it in a .pyx file as follows:

from decl cimport eject_tomato as c_eject_tomato

def eject_tomato(speed):
    c_eject_tomato(speed)

or simply cimport the .pxd file and use it as prefix:

cimport decl

def eject_tomato(speed):
    decl.eject_tomato(speed)

Note that this has no runtime lookup overhead, as it would in Python. Cython resolves the names in the .pxd file at compile time.

For special cases where namespacing or renaming on import is not enough, e.g. when a name in C conflicts with a Python keyword, you can use a C name specification to give different Cython and C names to the C function at declaration time. Suppose, for example, that you want to wrap an external C function called yield(). If you declare it as:

cdef extern from "myheader.h":
    void c_yield "yield" (float speed)

then its Cython visible name will be c_yield, whereas its name in C will be yield. You can then wrap it with:

def call_yield(speed):
    c_yield(speed)

As for functions, C names can be specified for variables, structs, unions, enums, struct and union members, and enum values. For example:

cdef extern int one "eins", two "zwei"
cdef extern float three "drei"

cdef struct spam "SPAM":
    int i "eye"

cdef enum surprise "inquisition":
    first "alpha"
    second "beta" = 3

Note that Cython will not do any validation or name mangling on the string you provide. It will inject the bare text into the C code unmodified, so you are entirely on your own with this feature. If you want to declare a name xyz and have Cython inject the text “make the C compiler fail here” into the C file for it, you can do this using a C name declaration. Consider this an advanced feature, only for the rare cases where everything else fails.

Including verbatim C code

For advanced use cases, Cython allows you to directly write C code as “docstring” of a cdef extern from block:

cdef extern from *:
    """
    /* This is C code which will be put
     * in the .c file output by Cython */
    static long square(long x) {return x * x;}
    #define assign(x, y) ((x) = (y))
    """
    long square(long x)
    void assign(long& x, long y)

The above is essentially equivalent to having the C code in a file header.h and writing

cdef extern from "header.h":
    long square(long x)
    void assign(long& x, long y)

It is also possible to combine a header file and verbatim C code:

cdef extern from "badheader.h":
    """
    /* This macro breaks stuff */
    #undef int
    """
    # Stuff from badheader.h

In this case, the C code #undef int is put right after #include "badheader.h" in the C code generated by Cython.

Note that the string is parsed like any other docstring in Python. If you require character escapes to be passed into the C code file, use a raw docstring, i.e. r""" ... """.

Using Cython Declarations from C

Cython provides two methods for making C declarations from a Cython module available for use by external C code—public declarations and C API declarations.

Note

You do not need to use either of these to make declarations from one Cython module available to another Cython module – you should use the cimport statement for that. Sharing Declarations Between Cython Modules.

Public Declarations

You can make C types, variables and functions defined in a Cython module accessible to C code that is linked together with the Cython-generated C file, by declaring them with the public keyword:

cdef public struct Bunny: # public type declaration
    int vorpalness

cdef public int spam # public variable declaration

cdef public void grail(Bunny *) # public function declaration

If there are any public declarations in a Cython module, a header file called modulename.h file is generated containing equivalent C declarations for inclusion in other C code.

A typical use case for this is building an extension module from multiple C sources, one of them being Cython generated (i.e. with something like Extension("grail", sources=["grail.pyx", "grail_helper.c"]) in setup.py. In this case, the file grail_helper.c just needs to add #include "grail.h" in order to access the public Cython variables.

A more advanced use case is embedding Python in C using Cython. In this case, make sure to call Py_Initialize() and Py_Finalize(). For example, in the following snippet that includes grail.h:

#include <Python.h>
#include "grail.h"

int main() {
    Py_Initialize();
    initgrail();  /* Python 2.x only ! */
    Bunny b;
    grail(b);
    Py_Finalize();
}

This C code can then be built together with the Cython-generated C code in a single program (or library).

In Python 3.x, calling the module init function directly should be avoided. Instead, use the inittab mechanism to link Cython modules into a single shared library or program.

err = PyImport_AppendInittab("grail", PyInit_grail);
Py_Initialize();
grail_module = PyImport_ImportModule("grail");

If the Cython module resides within a package, then the name of the .h file consists of the full dotted name of the module, e.g. a module called foo.spam would have a header file called foo.spam.h.

Note

On some operating systems like Linux, it is also possible to first build the Cython extension in the usual way and then link against the resulting .so file like a dynamic library. Beware that this is not portable, so it should be avoided.

C API Declarations

The other way of making declarations available to C code is to declare them with the api keyword. You can use this keyword with C functions and extension types. A header file called modulename_api.h is produced containing declarations of the functions and extension types, and a function called import_modulename().

C code wanting to use these functions or extension types needs to include the header and call the import_modulename() function. The other functions can then be called and the extension types used as usual.

If the C code wanting to use these functions is part of more than one shared library or executable, then import_modulename() function needs to be called in each of the shared libraries which use these functions. If you crash with a segmentation fault (SIGSEGV on linux) when calling into one of these api calls, this is likely an indication that the shared library which contains the api call which is generating the segmentation fault does not call the import_modulename() function before the api call which crashes.

Any public C type or extension type declarations in the Cython module are also made available when you include modulename_api.h.:

# delorean.pyx

cdef public struct Vehicle:
    int speed
    float power

cdef api void activate(Vehicle *v):
    if v.speed >= 88 and v.power >= 1.21:
        print("Time travel achieved")

# marty.c
#include "delorean_api.h"

Vehicle car;

int main(int argc, char *argv[]) {
	Py_Initialize();
	import_delorean();
	car.speed = atoi(argv[1]);
	car.power = atof(argv[2]);
	activate(&car);
	Py_Finalize();
}

Note

Any types defined in the Cython module that are used as argument or return types of the exported functions will need to be declared public, otherwise they won’t be included in the generated header file, and you will get errors when you try to compile a C file that uses the header.

Using the api method does not require the C code using the declarations to be linked with the extension module in any way, as the Python import machinery is used to make the connection dynamically. However, only functions can be accessed this way, not variables. Note also that for the module import mechanism to be set up correctly, the user must call Py_Initialize() and Py_Finalize(); if you experience a segmentation fault in the call to import_modulename(), it is likely that this wasn’t done.

You can use both public and api on the same function to make it available by both methods, e.g.:

cdef public api void belt_and_braces():
    ...

However, note that you should include either modulename.h or modulename_api.h in a given C file, not both, otherwise you may get conflicting dual definitions.

If the Cython module resides within a package, then:

  • The name of the header file contains of the full dotted name of the module.

  • The name of the importing function contains the full name with dots replaced by double underscores.

E.g. a module called foo.spam would have an API header file called foo.spam_api.h and an importing function called import_foo__spam().

Multiple public and API declarations

You can declare a whole group of items as public and/or api all at once by enclosing them in a cdef block, for example,:

cdef public api:
    void order_spam(int tons)
    char *get_lunch(float tomato_size)

This can be a useful thing to do in a .pxd file (see Sharing Declarations Between Cython Modules) to make the module’s public interface available by all three methods.

Acquiring and Releasing the GIL

Cython provides facilities for acquiring and releasing the Global Interpreter Lock (GIL). This may be useful when calling from multi-threaded code into (external C) code that may block, or when wanting to use Python from a (native) C thread callback. Releasing the GIL should obviously only be done for thread-safe code or for code that uses other means of protection against race conditions and concurrency issues.

Note that acquiring the GIL is a blocking thread-synchronising operation, and therefore potentially costly. It might not be worth releasing the GIL for minor calculations. Usually, I/O operations and substantial computations in parallel code will benefit from it.

Releasing the GIL

You can release the GIL around a section of code using the with nogil statement:

with nogil:
    <code to be executed with the GIL released>

Code in the body of the with-statement must not raise exceptions or manipulate Python objects in any way, and must not call anything that manipulates Python objects without first re-acquiring the GIL. Cython validates these operations at compile time, but cannot look into external C functions, for example. They must be correctly declared as requiring or not requiring the GIL (see below) in order to make Cython’s checks effective.

Acquiring the GIL

A C function that is to be used as a callback from C code that is executed without the GIL needs to acquire the GIL before it can manipulate Python objects. This can be done by specifying with gil in the function header:

cdef void my_callback(void *data) with gil:
    ...

If the callback may be called from another non-Python thread, care must be taken to initialize the GIL first, through a call to PyEval_InitThreads(). If you’re already using cython.parallel in your module, this will already have been taken care of.

The GIL may also be acquired through the with gil statement:

with gil:
    <execute this block with the GIL acquired>

Declaring a function as callable without the GIL

You can specify nogil in a C function header or function type to declare that it is safe to call without the GIL.:

cdef void my_gil_free_func(int spam) nogil:
    ...

When you implement such a function in Cython, it cannot have any Python arguments or Python object return type. Furthermore, any operation that involves Python objects (including calling Python functions) must explicitly acquire the GIL first, e.g. by using a with gil block or by calling a function that has been defined with gil. These restrictions are checked by Cython and you will get a compile error if it finds any Python interaction inside of a nogil code section.

Note

The nogil function annotation declares that it is safe to call the function without the GIL. It is perfectly allowed to execute it while holding the GIL. The function does not in itself release the GIL if it is held by the caller.

Declaring a function with gil (i.e. as acquiring the GIL on entry) also implicitly makes its signature nogil.