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diff --git a/docs/src/tutorial/clibraries.rst b/docs/src/tutorial/clibraries.rst index dd91d9ef2..3542dbe8e 100644 --- a/docs/src/tutorial/clibraries.rst +++ b/docs/src/tutorial/clibraries.rst @@ -5,6 +5,9 @@ Using C libraries ****************** +.. include:: + ../two-syntax-variants-used + Apart from writing fast code, one of the main use cases of Cython is to call external C libraries from Python code. As Cython code compiles down to C code itself, it is actually trivial to call C @@ -24,7 +27,7 @@ decide to use its double ended queue implementation. To make the handling easier, however, you decide to wrap it in a Python extension type that can encapsulate all memory management. -.. [CAlg] Simon Howard, C Algorithms library, http://c-algorithms.sourceforge.net/ +.. [CAlg] Simon Howard, C Algorithms library, https://fragglet.github.io/c-algorithms/ Defining external declarations @@ -33,15 +36,17 @@ Defining external declarations You can download CAlg `here <https://codeload.github.com/fragglet/c-algorithms/zip/master>`_. The C API of the queue implementation, which is defined in the header -file ``c-algorithms/src/queue.h``, essentially looks like this: +file :file:`c-algorithms/src/queue.h`, essentially looks like this: .. literalinclude:: ../../examples/tutorial/clibraries/c-algorithms/src/queue.h :language: C + :caption: queue.h To get started, the first step is to redefine the C API in a ``.pxd`` -file, say, ``cqueue.pxd``: +file, say, :file:`cqueue.pxd`: .. literalinclude:: ../../examples/tutorial/clibraries/cqueue.pxd + :caption: cqueue.pxd Note how these declarations are almost identical to the header file declarations, so you can often just copy them over. However, you do @@ -100,20 +105,30 @@ Writing a wrapper class After declaring our C library's API, we can start to design the Queue class that should wrap the C queue. It will live in a file called -``queue.pyx``. [#]_ +:file:`queue.pyx`/:file:`queue.py`. [#]_ -.. [#] Note that the name of the ``.pyx`` file must be different from - the ``cqueue.pxd`` file with declarations from the C library, +.. [#] Note that the name of the ``.pyx``/``.py`` file must be different from + the :file:`cqueue.pxd` file with declarations from the C library, as both do not describe the same code. A ``.pxd`` file next to - a ``.pyx`` file with the same name defines exported - declarations for code in the ``.pyx`` file. As the - ``cqueue.pxd`` file contains declarations of a regular C - library, there must not be a ``.pyx`` file with the same name + a ``.pyx``/``.py`` file with the same name defines exported + declarations for code in the ``.pyx``/``.py`` file. As the + :file:`cqueue.pxd` file contains declarations of a regular C + library, there must not be a ``.pyx``/``.py`` file with the same name that Cython associates with it. Here is a first start for the Queue class: -.. literalinclude:: ../../examples/tutorial/clibraries/queue.pyx +.. tabs:: + + .. group-tab:: Pure Python + + .. literalinclude:: ../../examples/tutorial/clibraries/queue.py + :caption: queue.py + + .. group-tab:: Cython + + .. literalinclude:: ../../examples/tutorial/clibraries/queue.pyx + :caption: queue.pyx Note that it says ``__cinit__`` rather than ``__init__``. While ``__init__`` is available as well, it is not guaranteed to be run (for @@ -122,10 +137,11 @@ ancestor's constructor). Because not initializing C pointers often leads to hard crashes of the Python interpreter, Cython provides ``__cinit__`` which is *always* called immediately on construction, before CPython even considers calling ``__init__``, and which -therefore is the right place to initialise ``cdef`` fields of the new -instance. However, as ``__cinit__`` is called during object -construction, ``self`` is not fully constructed yet, and one must -avoid doing anything with ``self`` but assigning to ``cdef`` fields. +therefore is the right place to initialise static attributes +(``cdef`` fields) of the new instance. However, as ``__cinit__`` is +called during object construction, ``self`` is not fully constructed yet, +and one must avoid doing anything with ``self`` but assigning to static +attributes (``cdef`` fields). Note also that the above method takes no parameters, although subtypes may want to accept some. A no-arguments ``__cinit__()`` method is a @@ -152,7 +168,17 @@ pointer to the new queue. The Python way to get out of this is to raise a ``MemoryError`` [#]_. We can thus change the init function as follows: -.. literalinclude:: ../../examples/tutorial/clibraries/queue2.pyx +.. tabs:: + + .. group-tab:: Pure Python + + .. literalinclude:: ../../examples/tutorial/clibraries/queue2.py + :caption: queue.py + + .. group-tab:: Cython + + .. literalinclude:: ../../examples/tutorial/clibraries/queue2.pyx + :caption: queue.pyx .. [#] In the specific case of a ``MemoryError``, creating a new exception instance in order to raise it may actually fail because @@ -169,31 +195,60 @@ longer used (i.e. all references to it have been deleted). To this end, CPython provides a callback that Cython makes available as a special method ``__dealloc__()``. In our case, all we have to do is to free the C Queue, but only if we succeeded in initialising it in -the init method:: +the init method: + +.. tabs:: + + .. group-tab:: Pure Python + + .. code-block:: python + + def __dealloc__(self): + if self._c_queue is not cython.NULL: + cqueue.queue_free(self._c_queue) - def __dealloc__(self): - if self._c_queue is not NULL: - cqueue.queue_free(self._c_queue) + .. group-tab:: Cython + .. code-block:: cython + + def __dealloc__(self): + if self._c_queue is not NULL: + cqueue.queue_free(self._c_queue) Compiling and linking ===================== At this point, we have a working Cython module that we can test. To -compile it, we need to configure a ``setup.py`` script for distutils. -Here is the most basic script for compiling a Cython module:: +compile it, we need to configure a ``setup.py`` script for setuptools. +Here is the most basic script for compiling a Cython module + +.. tabs:: + + .. group-tab:: Pure Python + + .. code-block:: python + + from setuptools import Extension, setup + from Cython.Build import cythonize + + setup( + ext_modules = cythonize([Extension("queue", ["queue.py"])]) + ) + + .. group-tab:: Cython - from distutils.core import setup - from distutils.extension import Extension - from Cython.Build import cythonize + .. code-block:: cython - setup( - ext_modules = cythonize([Extension("queue", ["queue.pyx"])]) - ) + from setuptools import Extension, setup + from Cython.Build import cythonize + + setup( + ext_modules = cythonize([Extension("queue", ["queue.pyx"])]) + ) To build against the external C library, we need to make sure Cython finds the necessary libraries. -There are two ways to archive this. First we can tell distutils where to find +There are two ways to archive this. First we can tell setuptools where to find the c-source to compile the :file:`queue.c` implementation automatically. Alternatively, we can build and install C-Alg as system library and dynamically link it. The latter is useful if other applications also use C-Alg. @@ -202,33 +257,69 @@ if other applications also use C-Alg. Static Linking --------------- -To build the c-code automatically we need to include compiler directives in `queue.pyx`:: +To build the c-code automatically we need to include compiler directives in :file:`queue.pyx`/:file:`queue.py` + +.. tabs:: + + .. group-tab:: Pure Python + + .. code-block:: python + + # distutils: sources = c-algorithms/src/queue.c + # distutils: include_dirs = c-algorithms/src/ + + import cython + from cython.cimports import cqueue - # distutils: sources = c-algorithms/src/queue.c - # distutils: include_dirs = c-algorithms/src/ + @cython.cclass + class Queue: + _c_queue = cython.declare(cython.pointer(cqueue.Queue)) - cimport cqueue + def __cinit__(self): + self._c_queue = cqueue.queue_new() + if self._c_queue is cython.NULL: + raise MemoryError() - cdef class Queue: - cdef cqueue.Queue* _c_queue - def __cinit__(self): - self._c_queue = cqueue.queue_new() - if self._c_queue is NULL: - raise MemoryError() + def __dealloc__(self): + if self._c_queue is not cython.NULL: + cqueue.queue_free(self._c_queue) - def __dealloc__(self): - if self._c_queue is not NULL: - cqueue.queue_free(self._c_queue) + .. group-tab:: Cython + + .. code-block:: cython + + # distutils: sources = c-algorithms/src/queue.c + # distutils: include_dirs = c-algorithms/src/ + + + cimport cqueue + + + cdef class Queue: + cdef cqueue.Queue* _c_queue + + def __cinit__(self): + self._c_queue = cqueue.queue_new() + if self._c_queue is NULL: + raise MemoryError() + + def __dealloc__(self): + if self._c_queue is not NULL: + cqueue.queue_free(self._c_queue) The ``sources`` compiler directive gives the path of the C -files that distutils is going to compile and +files that setuptools is going to compile and link (statically) into the resulting extension module. In general all relevant header files should be found in ``include_dirs``. -Now we can build the project using:: +Now we can build the project using: + +.. code-block:: bash $ python setup.py build_ext -i -And test whether our build was successful:: +And test whether our build was successful: + +.. code-block:: bash $ python -c 'import queue; Q = queue.Queue()' @@ -240,14 +331,18 @@ Dynamic linking is useful, if the library we are going to wrap is already installed on the system. To perform dynamic linking we first need to build and install c-alg. -To build c-algorithms on your system:: +To build c-algorithms on your system: + +.. code-block:: bash $ cd c-algorithms $ sh autogen.sh $ ./configure $ make -to install CAlg run:: +to install CAlg run: + +.. code-block:: bash $ make install @@ -262,26 +357,53 @@ Afterwards the file :file:`/usr/local/lib/libcalg.so` should exist. In this approach we need to tell the setup script to link with an external library. To do so we need to extend the setup script to install change the extension setup from -:: +.. tabs:: + + .. group-tab:: Pure Python - ext_modules = cythonize([Extension("queue", ["queue.pyx"])]) + .. code-block:: python + + ext_modules = cythonize([Extension("queue", ["queue.py"])]) + + .. group-tab:: Cython + + .. code-block:: cython + + ext_modules = cythonize([Extension("queue", ["queue.pyx"])]) to -:: +.. tabs:: + + .. group-tab:: Pure Python + + .. code-block:: python - ext_modules = cythonize([ - Extension("queue", ["queue.pyx"], - libraries=["calg"]) - ]) + ext_modules = cythonize([ + Extension("queue", ["queue.py"], + libraries=["calg"]) + ]) -Now we should be able to build the project using:: + .. group-tab:: Cython + + .. code-block:: cython + + ext_modules = cythonize([ + Extension("queue", ["queue.pyx"], + libraries=["calg"]) + ]) + +Now we should be able to build the project using: + +.. code-block:: bash $ python setup.py build_ext -i If the `libcalg` is not installed in a 'normal' location, users can provide the required parameters externally by passing appropriate C compiler -flags, such as:: +flags, such as: + +.. code-block:: bash CFLAGS="-I/usr/local/otherdir/calg/include" \ LDFLAGS="-L/usr/local/otherdir/calg/lib" \ @@ -290,12 +412,16 @@ flags, such as:: Before we run the module, we also need to make sure that `libcalg` is in -the `LD_LIBRARY_PATH` environment variable, e.g. by setting:: +the `LD_LIBRARY_PATH` environment variable, e.g. by setting: + +.. code-block:: bash $ export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/local/lib Once we have compiled the module for the first time, we can now import -it and instantiate a new Queue:: +it and instantiate a new Queue: + +.. code-block:: bash $ export PYTHONPATH=. $ python -c 'import queue; Q = queue.Queue()' @@ -313,7 +439,7 @@ practice to look at what interfaces Python offers, e.g. in its queue, it's enough to provide the methods ``append()``, ``peek()`` and ``pop()``, and additionally an ``extend()`` method to add multiple values at once. Also, since we already know that all values will be -coming from C, it's best to provide only ``cdef`` methods for now, and +coming from C, it's best to provide only ``cdef``/``@cfunc`` methods for now, and to give them a straight C interface. In C, it is common for data structures to store data as a ``void*`` to @@ -323,28 +449,76 @@ additional memory allocations through a trick: we cast our ``int`` values to ``void*`` and vice versa, and store the value directly as the pointer value. -Here is a simple implementation for the ``append()`` method:: +Here is a simple implementation for the ``append()`` method: + +.. tabs:: + + .. group-tab:: Pure Python + + .. code-block:: python + + @cython.cfunc + def append(self, value: cython.int): + cqueue.queue_push_tail(self._c_queue, cython.cast(cython.p_void, value)) + + .. group-tab:: Cython + + .. code-block:: cython - cdef append(self, int value): - cqueue.queue_push_tail(self._c_queue, <void*>value) + cdef append(self, int value): + cqueue.queue_push_tail(self._c_queue, <void*>value) Again, the same error handling considerations as for the ``__cinit__()`` method apply, so that we end up with this -implementation instead:: +implementation instead: + +.. tabs:: + + .. group-tab:: Pure Python + + .. code-block:: python + + @cython.cfunc + def append(self, value: cython.int): + if not cqueue.queue_push_tail(self._c_queue, + cython.cast(cython.p_void, value)): + raise MemoryError() + + .. group-tab:: Cython + + .. code-block:: cython - cdef append(self, int value): - if not cqueue.queue_push_tail(self._c_queue, - <void*>value): - raise MemoryError() + cdef append(self, int value): + if not cqueue.queue_push_tail(self._c_queue, + <void*>value): + raise MemoryError() -Adding an ``extend()`` method should now be straight forward:: +Adding an ``extend()`` method should now be straight forward: - cdef extend(self, int* values, size_t count): - """Append all ints to the queue. - """ - cdef int value - for value in values[:count]: # Slicing pointer to limit the iteration boundaries. - self.append(value) +.. tabs:: + + .. group-tab:: Pure Python + + .. code-block:: python + + @cython.cfunc + def extend(self, values: cython.p_int, count: cython.size_t): + """Append all ints to the queue. + """ + value: cython.int + for value in values[:count]: # Slicing pointer to limit the iteration boundaries. + self.append(value) + + .. group-tab:: Cython + + .. code-block:: cython + + cdef extend(self, int* values, size_t count): + """Append all ints to the queue. + """ + cdef int value + for value in values[:count]: # Slicing pointer to limit the iteration boundaries. + self.append(value) This becomes handy when reading values from a C array, for example. @@ -353,13 +527,31 @@ the two methods to get the first element: ``peek()`` and ``pop()``, which provide read-only and destructive read access respectively. To avoid compiler warnings when casting ``void*`` to ``int`` directly, we use an intermediate data type that is big enough to hold a ``void*``. -Here, ``Py_ssize_t``:: +Here, ``Py_ssize_t``: + +.. tabs:: + + .. group-tab:: Pure Python + + .. code-block:: python + + @cython.cfunc + def peek(self) -> cython.int: + return cython.cast(cython.Py_ssize_t, cqueue.queue_peek_head(self._c_queue)) + + @cython.cfunc + def pop(self) -> cython.int: + return cython.cast(cython.Py_ssize_t, cqueue.queue_pop_head(self._c_queue)) + + .. group-tab:: Cython - cdef int peek(self): - return <Py_ssize_t>cqueue.queue_peek_head(self._c_queue) + .. code-block:: cython - cdef int pop(self): - return <Py_ssize_t>cqueue.queue_pop_head(self._c_queue) + cdef int peek(self): + return <Py_ssize_t>cqueue.queue_peek_head(self._c_queue) + + cdef int pop(self): + return <Py_ssize_t>cqueue.queue_pop_head(self._c_queue) Normally, in C, we risk losing data when we convert a larger integer type to a smaller integer type without checking the boundaries, and ``Py_ssize_t`` @@ -380,62 +572,88 @@ from ints, we cannot distinguish anymore if the return value was the queue was ``0``. In Cython code, we want the first case to raise an exception, whereas the second case should simply return ``0``. To deal with this, we need to special case this value, -and check if the queue really is empty or not:: +and check if the queue really is empty or not: + +.. tabs:: + + .. group-tab:: Pure Python + + .. code-block:: python + + @cython.cfunc + def peek(self) -> cython.int: + value: cython.int = cython.cast(cython.Py_ssize_t, cqueue.queue_peek_head(self._c_queue)) + if value == 0: + # this may mean that the queue is empty, or + # that it happens to contain a 0 value + if cqueue.queue_is_empty(self._c_queue): + raise IndexError("Queue is empty") + return value + + .. group-tab:: Cython + + .. code-block:: cython - cdef int peek(self) except? -1: - cdef int value = <Py_ssize_t>cqueue.queue_peek_head(self._c_queue) - if value == 0: - # this may mean that the queue is empty, or - # that it happens to contain a 0 value - if cqueue.queue_is_empty(self._c_queue): - raise IndexError("Queue is empty") - return value + cdef int peek(self): + cdef int value = <Py_ssize_t>cqueue.queue_peek_head(self._c_queue) + if value == 0: + # this may mean that the queue is empty, or + # that it happens to contain a 0 value + if cqueue.queue_is_empty(self._c_queue): + raise IndexError("Queue is empty") + return value Note how we have effectively created a fast path through the method in the hopefully common cases that the return value is not ``0``. Only that specific case needs an additional check if the queue is empty. -The ``except? -1`` declaration in the method signature falls into the -same category. If the function was a Python function returning a +If the ``peek`` function was a Python function returning a Python object value, CPython would simply return ``NULL`` internally instead of a Python object to indicate an exception, which would immediately be propagated by the surrounding code. The problem is that the return type is ``int`` and any ``int`` value is a valid queue item value, so there is no way to explicitly signal an error to the -calling code. In fact, without such a declaration, there is no -obvious way for Cython to know what to return on exceptions and for -calling code to even know that this method *may* exit with an -exception. +calling code. The only way calling code can deal with this situation is to call ``PyErr_Occurred()`` when returning from a function to check if an exception was raised, and if so, propagate the exception. This -obviously has a performance penalty. Cython therefore allows you to -declare which value it should implicitly return in the case of an +obviously has a performance penalty. Cython therefore uses a dedicated value +that it implicitly returns in the case of an exception, so that the surrounding code only needs to check for an exception when receiving this exact value. -We chose to use ``-1`` as the exception return value as we expect it -to be an unlikely value to be put into the queue. The question mark -in the ``except? -1`` declaration indicates that the return value is -ambiguous (there *may* be a ``-1`` value in the queue, after all) and -that an additional exception check using ``PyErr_Occurred()`` is -needed in calling code. Without it, Cython code that calls this -method and receives the exception return value would silently (and -sometimes incorrectly) assume that an exception has been raised. In -any case, all other return values will be passed through almost +By default, the value ``-1`` is used as the exception return value. +All other return values will be passed through almost without a penalty, thus again creating a fast path for 'normal' -values. +values. See :ref:`error_return_values` for more details. + Now that the ``peek()`` method is implemented, the ``pop()`` method also needs adaptation. Since it removes a value from the queue, however, it is not enough to test if the queue is empty *after* the -removal. Instead, we must test it on entry:: +removal. Instead, we must test it on entry: + +.. tabs:: + + .. group-tab:: Pure Python + + .. code-block:: python + + @cython.cfunc + def pop(self) -> cython.int: + if cqueue.queue_is_empty(self._c_queue): + raise IndexError("Queue is empty") + return cython.cast(cython.Py_ssize_t, cqueue.queue_pop_head(self._c_queue)) + + .. group-tab:: Cython - cdef int pop(self) except? -1: - if cqueue.queue_is_empty(self._c_queue): - raise IndexError("Queue is empty") - return <Py_ssize_t>cqueue.queue_pop_head(self._c_queue) + .. code-block:: cython + + cdef int pop(self): + if cqueue.queue_is_empty(self._c_queue): + raise IndexError("Queue is empty") + return <Py_ssize_t>cqueue.queue_pop_head(self._c_queue) The return value for exception propagation is declared exactly as for ``peek()``. @@ -450,7 +668,7 @@ code can use either name):: Note that this method returns either ``True`` or ``False`` as we declared the return type of the ``queue_is_empty()`` function as -``bint`` in ``cqueue.pxd``. +``bint`` in :file:`cqueue.pxd`. Testing the result @@ -464,14 +682,14 @@ you can call. C methods are not visible from Python code, and thus not callable from doctests. A quick way to provide a Python API for the class is to change the -methods from ``cdef`` to ``cpdef``. This will let Cython generate two -entry points, one that is callable from normal Python code using the -Python call semantics and Python objects as arguments, and one that is -callable from C code with fast C semantics and without requiring -intermediate argument conversion from or to Python types. Note that ``cpdef`` -methods ensure that they can be appropriately overridden by Python -methods even when they are called from Cython. This adds a tiny overhead -compared to ``cdef`` methods. +methods from ``cdef``/``@cfunc`` to ``cpdef``/``@ccall``. This will +let Cython generate two entry points, one that is callable from normal +Python code using the Python call semantics and Python objects as arguments, +and one that is callable from C code with fast C semantics and without requiring +intermediate argument conversion from or to Python types. Note that +``cpdef``/``@ccall`` methods ensure that they can be appropriately overridden +by Python methods even when they are called from Cython. This adds a tiny overhead +compared to ``cdef``/``@cfunc`` methods. Now that we have both a C-interface and a Python interface for our class, we should make sure that both interfaces are consistent. @@ -482,14 +700,24 @@ C arrays and C memory. Both signatures are incompatible. We will solve this issue by considering that in C, the API could also want to support other input types, e.g. arrays of ``long`` or ``char``, which is usually supported with differently named C API functions such as -``extend_ints()``, ``extend_longs()``, extend_chars()``, etc. This allows +``extend_ints()``, ``extend_longs()``, ``extend_chars()``, etc. This allows us to free the method name ``extend()`` for the duck typed Python method, which can accept arbitrary iterables. The following listing shows the complete implementation that uses -``cpdef`` methods where possible: +``cpdef``/``@ccall`` methods where possible: + +.. tabs:: + + .. group-tab:: Pure Python -.. literalinclude:: ../../examples/tutorial/clibraries/queue3.pyx + .. literalinclude:: ../../examples/tutorial/clibraries/queue3.py + :caption: queue.py + + .. group-tab:: Cython + + .. literalinclude:: ../../examples/tutorial/clibraries/queue3.pyx + :caption: queue.pyx Now we can test our Queue implementation using a python script, for example here :file:`test_queue.py`: @@ -540,29 +768,73 @@ C-API into the callback function. We will use this to pass our Python predicate function. First, we have to define a callback function with the expected -signature that we can pass into the C-API function:: - - cdef int evaluate_predicate(void* context, cqueue.QueueValue value): - "Callback function that can be passed as predicate_func" - try: - # recover Python function object from void* argument - func = <object>context - # call function, convert result into 0/1 for True/False - return bool(func(<int>value)) - except: - # catch any Python errors and return error indicator - return -1 +signature that we can pass into the C-API function: + +.. tabs:: + + .. group-tab:: Pure Python + + .. code-block:: python + + @cython.cfunc + @cython.exceptval(check=False) + def evaluate_predicate(context: cython.p_void, value: cqueue.QueueValue) -> cython.int: + "Callback function that can be passed as predicate_func" + try: + # recover Python function object from void* argument + func = cython.cast(object, context) + # call function, convert result into 0/1 for True/False + return bool(func(cython.cast(int, value))) + except: + # catch any Python errors and return error indicator + return -1 + + .. note:: ``@cfunc`` functions in pure python are defined as ``@exceptval(-1, check=True)`` + by default. Since ``evaluate_predicate()`` should be passed to function as parameter, + we need to turn off exception checking entirely. + + .. group-tab:: Cython + + .. code-block:: cython + + cdef int evaluate_predicate(void* context, cqueue.QueueValue value): + "Callback function that can be passed as predicate_func" + try: + # recover Python function object from void* argument + func = <object>context + # call function, convert result into 0/1 for True/False + return bool(func(<int>value)) + except: + # catch any Python errors and return error indicator + return -1 The main idea is to pass a pointer (a.k.a. borrowed reference) to the function object as the user context argument. We will call the C-API -function as follows:: - - def pop_until(self, python_predicate_function): - result = cqueue.queue_pop_head_until( - self._c_queue, evaluate_predicate, - <void*>python_predicate_function) - if result == -1: - raise RuntimeError("an error occurred") +function as follows: + +.. tabs:: + + .. group-tab:: Pure Python + + .. code-block:: python + + def pop_until(self, python_predicate_function): + result = cqueue.queue_pop_head_until( + self._c_queue, evaluate_predicate, + cython.cast(cython.p_void, python_predicate_function)) + if result == -1: + raise RuntimeError("an error occurred") + + .. group-tab:: Cython + + .. code-block:: cython + + def pop_until(self, python_predicate_function): + result = cqueue.queue_pop_head_until( + self._c_queue, evaluate_predicate, + <void*>python_predicate_function) + if result == -1: + raise RuntimeError("an error occurred") The usual pattern is to first cast the Python object reference into a :c:type:`void*` to pass it into the C-API function, and then cast |