Notes for Contributers

If you intend to contribute to the development of HTSeq, these notes will help you to get started.

Source code

The source code is on an Subversion repository, hosted on SourceForge.

To check out the repository, use

svn co https://htseq.svn.sourceforge.net/svnroot/htseq/trunk htseq

To browse the repository, see here.

Languages

A good part of HTSeq is actually not written in Python but in Cython. In case you don’t know it yet: Cython, a fork from Pyrex, is a kind of Python compiler. You annotate Python code with additional type informations (the lines starting with cdef in the source code). Cython will then transform the Cython source file (with extension pyx) into a C file, which calls the appropriate funnctions of Python’s C API. Without type annotation, this looks and feels the same as normal Python and is not really faster, either. With type annotation, significant performance gains are possible, especially in inner loops.

A small part, namely the StepVector class, is written in C++ and exported with SWIG. (SWIG, the “Simple Wrapper and Interface Generator” is a very useful tool to generate C/C++ code to wrap an existing C/C++ library such that it becomes accessible as a native library within a number of scripting languages.) I am not so happy with this any more (the abstraction panelty of the object-oriented SWIG wrapping turned out to be a bit high) and ultimatively want to rewrite this part.

Build process

I do not want to burden the user with having to install SWIG or Cython. Both these tools work by generating C/C++ code which then can be compiled without the need of any files from SWIG or Cython. Hence, I’ve divided the build process into two steps:

• Step 1: Generate the C/C++ files from the SWIG and Cython source files. This is done by the calling make in the src directory. Note that the Makefile there contains only calls to cython and swig but not to the C compiler. (Note: I am using Cython 0.11. Compiling with Cython 0.12 does not work at the moment, but I will update at some point.)
• Step 2: The C files are compiled and copied together with the Python source files into a build directory. This is done by calling python setup.py build in the root directory. It creates (as usual for a setup.py script) a new directory build and in it a subdirectory for the machine architecture, which then contains the package directory.

To test during development, set the PYTHONPATH to point to the maschine-specific directory in the build directory, so that Python can find the HTSeq directory that setup.py build puts there. Whenever you make a change, call the shell script build_it, which contains just two lines: the first calls make in src, the second calls setup.py build.

Distributing

To wrap up a package, call build_it (or at least make in src) and then setup.py sdist. This makes a directory dists and in there, a tarball with all the source files (Python and C/C++) and all kinds of other stuff (unfortunately including the example_files directory, that I hence always delete manually before running setup.py sdist to keep the package lean). The tarball contains, when unpacked the setup.py script, which allows installing with setup.py install.

I am using setuptools (and not distutils) so that I can make Python eggs with setup.py bdist_egg. For Windows binaries, I use setup.py bdist_wininst --compiler=mingw32 on my virtual Windows box.

Files

The package contains the following source files:

HTSeq/__init__.py:

The outer face of HTSeq. This file defines the name space of HTSeq and contains the definition of all classes without performance-critical methods. The file imports _HTSeq in its own namespace, so that, for the user, it does not matter whether an object is defined here or in _HTSeq.pyx.

src/HTSeq/_HTSeq.pyx:

The core of HTSeq. All classes with perfomance-critical methods are defined here. For most of it, this file looks as a normal Python file. Only where performance is critical, type annotation has been added. See the Cython manual for details.

src/HTSeq/_HTSeq.pxd:

The “header file” for _HTSeq.pyx. It contains the type annotation for all the fields of the classes defined in _HTSeq.pyx. If a user would want to write her own Cython code, she could use Cython’s cimport directive to import this header file and so make Cython aware of the typed definitions of fields and methods in _HTSeq.pyx, which may improve performance because it allows Cython to kick out all unnecessary type checking.

HTSeq/_HTSeq_internal.py:

There are a few limitation to the standard Python code allowed in Cython files; most importantly, the yield statement is not yet supported. Hence, _HTSeq.pyx imports this file, and whenever a method in _HTSeq.pyx needs a yield, it calls a function which is put in here.

src/step_vector.h:

The C++ step_vector class template. As this is a pure template, there is no step_vector.cc file with definitions. If you want to use a step_vector in a C++ project, this is all you need.

src/StepVector.i:

An input file to SWIG, which produces the Python wrapper around step_vector.h, i.e., the StepVector module containing the StepVector class. Note that this file contains not only SWIG directives but also Python and come C++ code.

src/AutoPyObjPtr.i:

A very small SWIG library that allows SWIG-wrapped C++ container classes to store Python objects in a way that Python’s garbage collector is happy with.

HTSeq/scripts/count.py and HTSeq/scripts/qa.py:

The source code for the stand-alone scripts htseq-count and htseq-qa. They reside in the sub-package HTSeq.scripts, allowing to call the scripts with, e.g., python -m HTSeq.scripts.qa.

scripts/htseq-count and scripts/htseq-qa:

Short stubs to call the scripts from the command line simply as, e.g., htseq-qa.

Furthermore, there are these files to support development:

src/Makefile:

Generates C/C++ files from SWIG and Cython source files but does no C/C++ compiling.

setup.py:

A typical setuptools setup.py file.

build_it:

A three-line shell script that * generates a file HTSeq/_version.py from the file VERSION. * calls make in src to process src/Makefile * runs setup.py build (see above)

clean:

Another two-line shell script to first call make clean in src and then delete whatever setup.py may have written.

test.py

Performs all the deoctests in the documentation, using the example data in the example_data directory.

Finally, there are these files

VERSION:

a one-line text-fil with the version number. It is read by setup.py, used by build_it to generate the one-line Python file HTSeq/_version.py and also used when building the documentation.

MANIFEST.in:

Brings some files to the attention of setup.py sdist which would otherwise not be included

LICENCE:

The GPL, v3

README:

Points the user to the web site.

and these directories

doc/:

this documentation, in Sphinx reStructuredText format, and a Makefile to drive Sphinx.

example_files/:

a few example files to be use by the doctests in the documentation.