doc/source/dev/contributor/cython.rst
.. _adding-cython:
As written on the Cython website_:
Cython is an optimising static compiler for both the Python programming language and the extended Cython programming language (based on Pyrex). It makes writing C extensions for Python as easy as Python itself.
If your code currently performs a lot of loops in Python, it might
benefit from compilation with Cython. This document is intended to be a
very brief introduction: just enough to see how to use Cython with
SciPy. Once you have your code compiling, you can learn more about how
to optimize it by reviewing the Cython documentation_.
There are only two things you need to do in order for SciPy compile your code with Cython:
#. Include your code in a file with a .pyx
extension rather than a .py extension. All files with a .pyx
extension are automatically converted by Cython to .c or .cpp
files when SciPy is built.
#. Add the new .pyx file to the meson.build build configuration
of the subpackage in which your code lives. Typically, there are already
other .pyx patterns present (if not, look in another submodule) so
there's an example to follow for what exact content to add to
meson.build.
|linprog-rs|_ contains the implementation of the
revised simplex method for scipy.optimize.linprog. The revised
simplex method performs many elementary row operations on matrices, and
so it was a natural candidate to be Cythonized.
Note that scipy/optimize/_linprog_rs.py imports the BGLU and
LU classes from ._bglu_dense exactly as if they were regular
Python classes. But they’re not. BGLU and LU are Cython classes
defined in |bglu-dense|_. There is nothing
about the way they are imported or used that suggests that they are
written in Cython; the only way so far that we can tell they are Cython
classes is that they are defined in a file with a .pyx extension.
Even in /scipy/optimize/_bglu_dense.pyx, most of the code resembles
Python. The most notable differences are the presence of cimport,
cdef, and Cython decorators_. None of these are strictly
necessary. Without them, the pure Python code can still be compiled by
Cython. The Cython language extensions are *just* tweaks to improve
performance. This .pyx file is automatically converted to a .c
file by Cython when SciPy is built.
The only thing left is to add the build configuration, which will look something like:
.. code:: meson
_bglu_dense_c = opt_gen.process('_bglu_dense.pyx')
py3.extension_module('_bglu_dense',
_bglu_dense_c,
c_args: cython_c_args,
dependencies: np_dep,
link_args: version_link_args,
install: true,
subdir: 'scipy/optimize'
)
When SciPy is built, _bglu_dense.pyx will be transpiled by cython
to C code, and then that generated C file is treated by Meson like any other C
code in SciPy - producing an extension modules that we will be able to import
and use the LU and BGLU classes from.
See a video run-through of this exercise: \ Cythonizing SciPy Code_ \
#. Update Cython and create a new branch
(e.g., git checkout -b cython_test) in which to make some
experimental changes to SciPy
#. Add some simple Python code in a .py file in the
/scipy/optimize directory, say /scipy/optimize/mypython.py.
For example:
::
def myfun():
i = 1
while i < 10000000:
i += 1
return i
#. Let’s see how long this pure-Python loop takes so we can compare the performance of Cython. For example, in an IPython console in Spyder:
::
from scipy.optimize.mypython import myfun
%timeit myfun()
I get something like:
::
715 ms ± 10.7 ms per loop
#. Save your .py file to a .pyx file, e.g. \ mycython.pyx.
#. Add the .pyx to scipy/optimize/meson.build, in the way described in
the previous section.
#. Rebuild SciPy. Note that an extension module (a .so or .pyd file)
has been added to the build/scipy/optimize/ directory.
#. Time it, e.g. by dropping into IPython with spin ipython and then:
::
from scipy.optimize.mycython import myfun
%timeit myfun()
I get something like:
::
359 ms ± 6.98 ms per loop
Cython sped up the pure Python code by a factor of ~2.
#. That’s not much of an improvement in the scheme of things. To see
why, it helps to have Cython create an “annotated” version of our
code to show bottlenecks. In a terminal window, call Cython on your
.pyx file with the -a flag:
::
cython -a scipy/optimize/mycython.pyx
Note that this creates a new ``.html`` file in the
``/scipy/optimize`` directory. Open the ``.html`` file in any
browser.
#. The yellow-highlighted lines in the file indicate potential
interaction between the compiled code and Python, which slows things
down considerably. The intensity of the highlighting indicates the
estimated severity of the interaction. In this case, much of the
interaction can be avoided if we define the variable i as an
integer so that Cython doesn’t have to consider the possibility of
it being a general Python object:
::
def myfun():
cdef int i = 1 # our first line of Cython code
while i < 10000000:
i += 1
return i
Recreating the annotated ``.html`` file shows that most of the
Python interaction has disappeared.
#. Rebuild SciPy, open an fresh IPython console, and %timeit:
::
from scipy.optimize.mycython import myfun %timeit myfun()
I get something like: 68.6 ns ± 1.95 ns per loop. The Cython code ran
about 10 million times faster than the original Python code.
In this case, the compiler probably optimized away the loop, simply returning the final result. This sort of speedup is not typical for real code, but this exercise certainly illustrates the power of Cython when the alternative is many low-level operations in Python.
.. _Cython website: https://cython.org/ .. _Cython documentation: http://docs.cython.org/en/latest/
.. _Cython decorators: https://cython.readthedocs.io/en/latest/src/userguide/numpy_tutorial.html
.. |linprog-rs| replace:: scipy.optimize._linprog_rs.py
.. _linprog-rs: https://github.com/scipy/scipy/blob/main/scipy/optimize/_linprog_rs.py
.. |bglu-dense| replace:: /scipy/optimize/_bglu_dense.pyx
.. _bglu-dense: https://github.com/scipy/scipy/blob/main/scipy/optimize/_bglu_dense.pyx
.. _Cythonizing SciPy Code: https://youtu.be/K9bF7cjUJ7c