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Home > Programming > Programming Language > Learning Cython Programming (Second Edition)
Learning Cython Programming (Second Edition)
Learning Cython Programming (Second Edition)

Learning Cython Programming (Second Edition): Expand your existing legacy applications in C using Python , Second Edition

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Learning Cython Programming (Second Edition)

Chapter 2. Understanding Cython

As I mentioned previously, there are a number of methods of using Cython. As the basics are very familiar to any Python programmer, it's important to review the linking models before getting into the programming language. This is what drives the design of applications when using Cython.

Next, we will get more familiar with the Cython programming language constructs, namely, the distinction between cdef and cpdef. Then, we will look at getting the most out of Cython by interfacing directly with native C types. Later in this book, we will see that it's possible to use native C++ STL container types. This is where you will gain the optimizations in execution, as no Python runtime is required to work with native types.

Finally, we will see how easy it is to work with callbacks to and from C and Python code. This is an interesting technique whereby you can offload logic from C code to Python.

Therefore, in this chapter, we will be diving into...

Linking models

Linking models are extremely important when considering how we can extend or embed things in native applications. There are two main linking models for Cython:

Fully embedded Python within C/C++ code, which looks like the following screenshot:

Linking models

Using this method of embedding the Python runtime into a native application means you initiate execution of code directly from any point in your C/C++ code, as opposed to the Chapter 1, Cython Won't Bite where we had to run the Python interpreter and call an import to execute native code.

For the sake of completeness, here is the import model of using Cython:

Linking models

This would be a more Pythonic approach to Cython, and will be helpful if your code base is mostly Python. We will review an example of the Python lxml module, which provides a Cython backend, later in this book, and we can compare it to the native Python backend to review the speed and execution of both code bases to perform the same task.

Cython keyword – cdef

The cdef keyword tells the compiler that this statement is a native C type or native function. Remember from Chapter 1, Cython Won't Bite that we used this line to declare the C prototype function:

cdef int AddFunction(int, int)

This is the line that let us wrap the native C function into a Python callable using the Python def keyword. We can use this in many contexts, for example, we can declare normal variables for use within a function to speed up execution:

def square(int x):
    return x ** 2

This is a trivial example, but it will tell the compiler that we will always be squaring an integer. However, for normal Python code, it's a little more complicated as Python has to worry a lot more about losing precision when it comes to handling many different types. But in this case, we know exactly what the type is and how it can be handled.

You might also have noticed that this is a simple def function, but because it will be fed to the Cython compiler, this...

Typedef and function pointers

The typedef in C/C++ code allows the programmer to give a new name or alias to any type. For example, one could typedef an int to myint. Or you can just simply typedef a struct so that you don't have to refer to the struct with the keyword struct every time. For example, consider this C struct and typedef:

struct foobar {
  int x;
  char * y;
};
typedef struct foobar foobar_t;

In Cython, this can be described by the following:

cdef struct foobar:
    int x
    char * y
ctypedef foobar foobar_t

Note we can also typedef pointer types as below:

ctypedef int * int_ptr

We can also typedef function C/C++ pointers, as follows:

typedef void (*cfptr) (int)

In Cython, this will be as follows:

ctypedef void (*cfptr)(int)

Using the function pointer is just as you would expect:

cdef cfptr myfunctionptr = &myfunc

There is some magic going on here with function pointers as it's simply not safe for raw Python code to directly call a Python function or vice versa. Cython...

The public keyword

This is a very powerful keyword in Cython. It allows any cdef declaration with the public modifier to output a respective C/C++ header with the relative declaration accessible from C/C++. For example, we can declare:

cdef public struct CythonStruct:
    size_t number_of_elements;
    char ** elements;

Once the compiler handles this, you will have an output of cython_input.h:

 struct CythonStruct {
    size_t number_of_elements;
    char ** elements;
};

The main caveat, if you're going to call the Python public declarations directly from C, is that, if your link model is fully embedded and linked against libpython.so, you need to use some boilerplate code to initialize Python correctly:

#include <Python.h>

int main(int argc, char **argv) {
    Py_Initialize ();
    // code in here
    Py_Finalize ();
    return 0;
}

And before calling anything with the function, you need to initialize the Python module example if you have a cythonfile.pyx file, and compile it with...

Keyword cpdef

So far, we have seen two different function declarations in Cython, def and cdef, to define functions. There is one more declaration—cpdef. The def is a Python-only function, so it is only callable from Python or Cython code blocks; calling from C does not work. The cdef is the opposite; this means that it's callable from C and not from Python. For example, if we create a function such as:

cpdef public test (int x):
   …
  return 1

It will generate the following function prototype:

__PYX_EXTERN_C DL_IMPORT(PyObject) *test(int, int __pyx_skip_dispatch);

The public keyword will make sure we generate the needed header so that we can call it from C. Calling from pure Python, we can work with this as if it was just any other Python function. The drawback of using cpdef is that the native return type is PyObject *, which requires you to know exactly what the return type is and consult the Python API documentation to access the data. I prefer keeping bindings between...

Linking models

Linking models are extremely important when considering how we can extend or embed things in native applications. There are two main linking models for Cython:

Fully embedded Python within C/C++ code, which looks like the following screenshot:

Using this method of embedding the Python runtime into a native application means you initiate execution of code directly from any point in your C/C++ code, as opposed to the Chapter 1, Cython Won't Bite where we had to run the Python interpreter and call an import to execute native code.

For the sake of completeness, here is the import model of using Cython:

This would be a more Pythonic approach to Cython, and will be helpful if your code base is mostly Python. We will review an example of the Python lxml module, which provides a Cython backend, later in this book, and we can compare it to the native Python backend to review the speed and execution of both code bases to perform the same task.

Cython keyword – cdef

The cdef keyword tells the compiler that this statement is a native C type or native function. Remember from Chapter 1, Cython Won't Bite that we used this line to declare the C prototype function:

cdef int AddFunction(int, int)

This is the line that let us wrap the native C function into a Python callable using the Python def keyword. We can use this in many contexts, for example, we can declare normal variables for use within a function to speed up execution:

def square(int x):
    return x ** 2

This is a trivial example, but it will tell the compiler that we will always be squaring an integer. However, for normal Python code, it's a little more complicated as Python has to worry a lot more about losing precision when it comes to handling many different types. But in this case, we know exactly what the type is and how it can be handled.

You might also have noticed that this is a simple def function, but because it will be fed to the Cython compiler, this will work just...

Typedef and function pointers

The typedef in C/C++ code allows the programmer to give a new name or alias to any type. For example, one could typedef an int to myint. Or you can just simply typedef a struct so that you don't have to refer to the struct with the keyword struct every time. For example, consider this C struct and typedef:

struct foobar {
  int x;
  char * y;
};
typedef struct foobar foobar_t;

In Cython, this can be described by the following:

cdef struct foobar:
    int x
    char * y
ctypedef foobar foobar_t

Note we can also typedef pointer types as below:

ctypedef int * int_ptr

We can also typedef function C/C++ pointers, as follows:

typedef void (*cfptr) (int)

In Cython, this will be as follows:

ctypedef void (*cfptr)(int)

Using the function pointer is just as you would expect:

cdef cfptr myfunctionptr = &myfunc

There is some magic going on here with function pointers as it's simply not safe for raw Python code to directly call a Python function or vice versa. Cython understands...

The public keyword

This is a very powerful keyword in Cython. It allows any cdef declaration with the public modifier to output a respective C/C++ header with the relative declaration accessible from C/C++. For example, we can declare:

cdef public struct CythonStruct:
    size_t number_of_elements;
    char ** elements;

Once the compiler handles this, you will have an output of cython_input.h:

 struct CythonStruct {
    size_t number_of_elements;
    char ** elements;
};

The main caveat, if you're going to call the Python public declarations directly from C, is that, if your link model is fully embedded and linked against libpython.so, you need to use some boilerplate code to initialize Python correctly:

#include <Python.h>

int main(int argc, char **argv) {
    Py_Initialize ();
    // code in here
    Py_Finalize ();
    return 0;
}

And before calling anything with the function, you need to initialize the Python module example if you have a cythonfile.pyx file, and compile it with the...

Keyword cpdef

So far, we have seen two different function declarations in Cython, def and cdef, to define functions. There is one more declaration—cpdef. The def is a Python-only function, so it is only callable from Python or Cython code blocks; calling from C does not work. The cdef is the opposite; this means that it's callable from C and not from Python. For example, if we create a function such as:

cpdef public test (int x):
   …
  return 1

It will generate the following function prototype:

__PYX_EXTERN_C DL_IMPORT(PyObject) *test(int, int __pyx_skip_dispatch);

The public keyword will make sure we generate the needed header so that we can call it from C. Calling from pure Python, we can work with this as if it was just any other Python function. The drawback of using cpdef is that the native return type is PyObject *, which requires you to know exactly what the return type is and consult the Python API documentation to access the data. I prefer keeping bindings between the languages simpler...

Logging from C/C++ into Python

An example of everything brought together is reusing the Python logging module directly from C. We want a few macros, such as info, error, and debug that can all handle a variable number of arguments and works as if we are calling a simple printf method.

To achieve this, we must make a Python logging backend for our C/C++ code. We need an initialization function to tell Python about our output logfile, and some wrappers for each info, error, and debug. We can simply write the public cdef wrappers as:

import logging

cdef public void initLoggingWithLogFile(const char * logfile):
    logging.basicConfig(filename = logfile,
                        level = logging.DEBUG,
                        format = '%(levelname)s %(asctime)s: %(message)s',
                        datefmt = '%m/%d/%Y %I:%M:%S')

cdef public void python_info(char * message):
    logging.info(message)

cdef public void python_debug(char * message):
    logging.debug(message)

cdef public void...
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Key benefits

  • *Learn how to extend C applications with pure Python code
  • *Get more from Python – you’ll not only learn Cython, you’ll also unlock a greater understanding of how to harness Python
  • *Packed with tips and tricks that make Cython look easy, dive into this accessible programming guide and find out what happens when you bring C and Python together!

Description

Cython is a hybrid programming language used to write C extensions for Python language. Combining the practicality of Python and speed and ease of the C language it’s an exciting language worth learning if you want to build fast applications with ease. This new edition of Learning Cython Programming shows you how to get started, taking you through the fundamentals so you can begin to experience its unique powers. You’ll find out how to get set up, before exploring the relationship between Python and Cython. You’ll also look at debugging Cython, before moving on to C++ constructs, Caveat on C++ usage, Python threading and GIL in Cython. Finally, you’ll learn object initialization and compile time, and gain a deeper insight into Python 3, which will help you not only become a confident Cython developer, but a much more fluent Python developer too.

Who is this book for?

This book is for developers who are familiar with the basics of C and Python programming and wish to learn Cython programming to extend their applications.

What you will learn

  • *Reuse Python logging in C
  • *Make an IRC bot out of your C application
  • *Extend an application so you have a web server for rest calls
  • *Practice Cython against your C++ code
  • *Discover tricks to work with Python ConfigParser in C
  • *Create Python bindings for native libraries
  • *Find out about threading and concurrency related to GIL
  • *Expand Terminal Multiplexer Tmux with Cython
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Publication date : Feb 22, 2016
Length: 110 pages
Edition : 2nd
Language : English
ISBN-13 : 9781783551675
Category :
Programming
Languages :
Cython
Concepts :
Programming Language
Tools :
Xcode

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Product Details

Publication date : Feb 22, 2016
Length: 110 pages
Edition : 2nd
Language : English
ISBN-13 : 9781783551675
Category :
Programming
Languages :
Cython
Concepts :
Programming Language
Tools :
Xcode

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Learning Cython Programming (Second Edition)
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Table of Contents

7 Chapters
1. Cython Won't Bite Chevron down icon Chevron up icon
1. Cython Won't Bite
Installing Cython
Getting started – Hello World
Summary
2. Understanding Cython Chevron down icon Chevron up icon
2. Understanding Cython
Linking models
Cython keyword – cdef
Typedef and function pointers
The public keyword
Keyword cpdef
Logging from C/C++ into Python
Using Python ConfigParser from C/C++
Callbacks from Python to C/C++
Cython PXD
Integration with build systems
Summary
3. Extending Applications Chevron down icon Chevron up icon
3. Extending Applications
Cython pure Python code
Compiling pure Python code
Python garbage collector
Extending Tmux
Embedding Python
Cythonizing struct cmd_entry
Implementing a Tmux command
Hooking everything together
Summary
4. Debugging Cython Chevron down icon Chevron up icon
4. Debugging Cython
Using GDB with Cython
Cython caveats
Summary
5. Advanced Cython Chevron down icon Chevron up icon
5. Advanced Cython
Cython and C++
C++ new and del keyword
Overloading
Templates
Static class member attribute
Calling C++ functions – Caveat
Python distutils
Python threading and GIL
Cython keywords
Messaging server
Caveat on GIL
Unit testing the native code
Preventing subclassing
Parsing large amounts of data
Summary
6. Further Reading Chevron down icon Chevron up icon
6. Further Reading
Overview
OpenMP support
Compile time preprocessor
Python 3
PyPy
AutoPXD
Pyrex and Cython
SWIG and Cython
Cython and NumPy
Numba versus Cython
Parakeet and Numba
Relevant Links
Summary
Index Chevron down icon Chevron up icon
Index

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(1 Ratings)
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Todd Leonhardt Dec 25, 2016
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For the vast majority of people looking to learn Cython, this book is absolutely horrible. It is poorly written and does a truly bad job of covering the basics of Python. If you want to learn Cython, there are vastly better resources: the online docs at cython.org are excellent, as is the book "Cython" by Kurt Smith. There is also a good 3.5 hour training video on Youtube from SciPy 2015.However, this book does have a few hidden gems for someone who is already a seasoned C, Python, and Cython developer. It does have a couple excellent examples of how to get C applications to easily call into Python code by using Cython.The book really should have a different title. As a "Learning Cython Programming" book, it deserves 1 star. But as a "Learning how to easily call Python code from a C application by using Cython" book, it would deserve 3 or 4 stars. But I would estimate that less than 5% of the people interested in learning Cython fish to learn it for this purpose - probably about 80% want to learn it to optimize existing Python code and maybe 15 to 20% want to learn it to wrap existing C/C++ code so it can be called from Python.
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About the author

Profile icon Philip Herron
Philip Herron
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Philip Herron is a developer who focuses his passion toward compilers and virtual machine implementations. When he was first accepted to Google Summer of Code 2010, he used inspiration from Paul Biggar's PhD on the optimization of dynamic languages to develop a proof of the concept GCC frontend to compile Python. This project sparked his deep interest in how Python works. After completing a consecutive year on the same project in 2011, Philip applied to Cython under the Python foundation to gain a deeper appreciation of the standard Python implementation. Through this he started leveraging the advantages of Python to control the logic in systems or even add more high-level interfaces, such as embedding Flask web servers in a REST API to a system-level piece of software, without writing any C code. Philip currently works as a software consultant for Instil Software based in Northern Ireland. He develops mobile applications with embedded native code for video streaming. Instil has given him a lot of support in becoming a better engineer. He has written several tutorials for the UK-based Linux Format magazine on Python and loves to share his passion for the Python programming language.
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FAQs

What is the digital copy I get with my Print order? Chevron down icon Chevron up icon

When you buy any Print edition of our Books, you can redeem (for free) the eBook edition of the Print Book you’ve purchased. This gives you instant access to your book when you make an order via PDF, EPUB or our online Reader experience.

What is the delivery time and cost of print book? Chevron down icon Chevron up icon

Shipping Details

USA:

'

Economy: Delivery to most addresses in the US within 10-15 business days

Premium: Trackable Delivery to most addresses in the US within 3-8 business days

UK:

Economy: Delivery to most addresses in the U.K. within 7-9 business days.
Shipments are not trackable

Premium: Trackable delivery to most addresses in the U.K. within 3-4 business days!
Add one extra business day for deliveries to Northern Ireland and Scottish Highlands and islands

EU:

Premium: Trackable delivery to most EU destinations within 4-9 business days.

Australia:

Economy: Can deliver to P. O. Boxes and private residences.
Trackable service with delivery to addresses in Australia only.
Delivery time ranges from 7-9 business days for VIC and 8-10 business days for Interstate metro
Delivery time is up to 15 business days for remote areas of WA, NT & QLD.

Premium: Delivery to addresses in Australia only
Trackable delivery to most P. O. Boxes and private residences in Australia within 4-5 days based on the distance to a destination following dispatch.

India:

Premium: Delivery to most Indian addresses within 5-6 business days

Rest of the World:

Premium: Countries in the American continent: Trackable delivery to most countries within 4-7 business days

Asia:

Premium: Delivery to most Asian addresses within 5-9 business days

Disclaimer:
All orders received before 5 PM U.K time would start printing from the next business day. So the estimated delivery times start from the next day as well. Orders received after 5 PM U.K time (in our internal systems) on a business day or anytime on the weekend will begin printing the second to next business day. For example, an order placed at 11 AM today will begin printing tomorrow, whereas an order placed at 9 PM tonight will begin printing the day after tomorrow.


Unfortunately, due to several restrictions, we are unable to ship to the following countries:

  1. Afghanistan
  2. American Samoa
  3. Belarus
  4. Brunei Darussalam
  5. Central African Republic
  6. The Democratic Republic of Congo
  7. Eritrea
  8. Guinea-bissau
  9. Iran
  10. Lebanon
  11. Libiya Arab Jamahriya
  12. Somalia
  13. Sudan
  14. Russian Federation
  15. Syrian Arab Republic
  16. Ukraine
  17. Venezuela
What is custom duty/charge? Chevron down icon Chevron up icon

Customs duty are charges levied on goods when they cross international borders. It is a tax that is imposed on imported goods. These duties are charged by special authorities and bodies created by local governments and are meant to protect local industries, economies, and businesses.

Do I have to pay customs charges for the print book order? Chevron down icon Chevron up icon

The orders shipped to the countries that are listed under EU27 will not bear custom charges. They are paid by Packt as part of the order.

List of EU27 countries: www.gov.uk/eu-eea:

A custom duty or localized taxes may be applicable on the shipment and would be charged by the recipient country outside of the EU27 which should be paid by the customer and these duties are not included in the shipping charges been charged on the order.

How do I know my custom duty charges? Chevron down icon Chevron up icon

The amount of duty payable varies greatly depending on the imported goods, the country of origin and several other factors like the total invoice amount or dimensions like weight, and other such criteria applicable in your country.

For example:

  • If you live in Mexico, and the declared value of your ordered items is over $ 50, for you to receive a package, you will have to pay additional import tax of 19% which will be $ 9.50 to the courier service.
  • Whereas if you live in Turkey, and the declared value of your ordered items is over € 22, for you to receive a package, you will have to pay additional import tax of 18% which will be € 3.96 to the courier service.
How can I cancel my order? Chevron down icon Chevron up icon

Cancellation Policy for Published Printed Books:

You can cancel any order within 1 hour of placing the order. Simply contact customercare@packt.com with your order details or payment transaction id. If your order has already started the shipment process, we will do our best to stop it. However, if it is already on the way to you then when you receive it, you can contact us at customercare@packt.com using the returns and refund process.

Please understand that Packt Publishing cannot provide refunds or cancel any order except for the cases described in our Return Policy (i.e. Packt Publishing agrees to replace your printed book because it arrives damaged or material defect in book), Packt Publishing will not accept returns.

What is your returns and refunds policy? Chevron down icon Chevron up icon

Return Policy:

We want you to be happy with your purchase from Packtpub.com. We will not hassle you with returning print books to us. If the print book you receive from us is incorrect, damaged, doesn't work or is unacceptably late, please contact Customer Relations Team on customercare@packt.com with the order number and issue details as explained below:

  1. If you ordered (eBook, Video or Print Book) incorrectly or accidentally, please contact Customer Relations Team on customercare@packt.com within one hour of placing the order and we will replace/refund you the item cost.
  2. Sadly, if your eBook or Video file is faulty or a fault occurs during the eBook or Video being made available to you, i.e. during download then you should contact Customer Relations Team within 14 days of purchase on customercare@packt.com who will be able to resolve this issue for you.
  3. You will have a choice of replacement or refund of the problem items.(damaged, defective or incorrect)
  4. Once Customer Care Team confirms that you will be refunded, you should receive the refund within 10 to 12 working days.
  5. If you are only requesting a refund of one book from a multiple order, then we will refund you the appropriate single item.
  6. Where the items were shipped under a free shipping offer, there will be no shipping costs to refund.

On the off chance your printed book arrives damaged, with book material defect, contact our Customer Relation Team on customercare@packt.com within 14 days of receipt of the book with appropriate evidence of damage and we will work with you to secure a replacement copy, if necessary. Please note that each printed book you order from us is individually made by Packt's professional book-printing partner which is on a print-on-demand basis.

What tax is charged? Chevron down icon Chevron up icon

Currently, no tax is charged on the purchase of any print book (subject to change based on the laws and regulations). A localized VAT fee is charged only to our European and UK customers on eBooks, Video and subscriptions that they buy. GST is charged to Indian customers for eBooks and video purchases.

What payment methods can I use? Chevron down icon Chevron up icon

You can pay with the following card types:

  1. Visa Debit
  2. Visa Credit
  3. MasterCard
  4. PayPal
What is the delivery time and cost of print books? Chevron down icon Chevron up icon

Shipping Details

USA:

'

Economy: Delivery to most addresses in the US within 10-15 business days

Premium: Trackable Delivery to most addresses in the US within 3-8 business days

UK:

Economy: Delivery to most addresses in the U.K. within 7-9 business days.
Shipments are not trackable

Premium: Trackable delivery to most addresses in the U.K. within 3-4 business days!
Add one extra business day for deliveries to Northern Ireland and Scottish Highlands and islands

EU:

Premium: Trackable delivery to most EU destinations within 4-9 business days.

Australia:

Economy: Can deliver to P. O. Boxes and private residences.
Trackable service with delivery to addresses in Australia only.
Delivery time ranges from 7-9 business days for VIC and 8-10 business days for Interstate metro
Delivery time is up to 15 business days for remote areas of WA, NT & QLD.

Premium: Delivery to addresses in Australia only
Trackable delivery to most P. O. Boxes and private residences in Australia within 4-5 days based on the distance to a destination following dispatch.

India:

Premium: Delivery to most Indian addresses within 5-6 business days

Rest of the World:

Premium: Countries in the American continent: Trackable delivery to most countries within 4-7 business days

Asia:

Premium: Delivery to most Asian addresses within 5-9 business days

Disclaimer:
All orders received before 5 PM U.K time would start printing from the next business day. So the estimated delivery times start from the next day as well. Orders received after 5 PM U.K time (in our internal systems) on a business day or anytime on the weekend will begin printing the second to next business day. For example, an order placed at 11 AM today will begin printing tomorrow, whereas an order placed at 9 PM tonight will begin printing the day after tomorrow.


Unfortunately, due to several restrictions, we are unable to ship to the following countries:

  1. Afghanistan
  2. American Samoa
  3. Belarus
  4. Brunei Darussalam
  5. Central African Republic
  6. The Democratic Republic of Congo
  7. Eritrea
  8. Guinea-bissau
  9. Iran
  10. Lebanon
  11. Libiya Arab Jamahriya
  12. Somalia
  13. Sudan
  14. Russian Federation
  15. Syrian Arab Republic
  16. Ukraine
  17. Venezuela
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