# Contributing¶

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 Github. To check out the repository, use

git clone https://github.com/htseq/htseq.git


## Languages¶

HTSeq is exposed in and mostly written in Python 3.

Several parts of HTSeq are written 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 functions 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.

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.

Note

We are considering moving away from SWIG in order to improve code readability. If you are interested in contributing to this aspect of HTSeq and are proficient in C++ and a cross-language tool (e.g. pybind11), please reach out!

## Build process¶

HTSeq follows the standard python packaging guidelines and relies on a setup.py script that is simultaneously compatible withPython 2 and 3. To build the code, run:

python setup.py build


and to install:

python setup.py install


To test the code, run:

./test.sh


and to test specifically htseq-count and htseq-count-barcodes only:

./test.sh -o


To use anaconda for testing, use the -a option and edit the test script to use your evironment.

If you are not modifying the low-level C/C++/Cython interfaces, you can do without Cython and SWIG. This is how users normally install HTSeq using pip. If you do modify those files, the setup.py has a preprocessing step that calls Cython and/or SWIG if these programs are found. You set the SWIG and CYTHON environment variables to point to your executables if you have special requirements.

HTSeq relies on Continuous Integration (CI), at the moment Github Actions is used.

To build the documentation, Sphinx is used. Just go into the doc folder and call:

make html


to regenerate the documentation. Official docs are stored on readthedocs.

## Distributing¶

To wrap up a package, call:

python setup.py sdist


This makes a directory dists and in there, a tarball with all the source files (Python and C/C++). If you are a maintainer of HTSeq, you can upload this file onto PyPI on the testing server. Then, you should run the Tracis CI tests that try to install HTSeq directly from PyPI (without the source code). If all goes well, you can upload the tar file onto the live PyPI server.

## Files¶

The package contains source files for Python 2 and 3 in separate folders. Within each of those folders, the following files are found:

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, HTSeq/scripts/count_with_barcodes.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, scripts/htseq-count-barcodes and scripts/htseq-qa:
Short stubs to call the scripts from the command line, e.g., htseq-qa.
doc/:
this documentation, in Sphinx reStructuredText format, and a Makefile to drive Sphinx.
test.sh
Performs all the deoctests in the documentation, using the example data in the example_data directory.

Furthermore, there are these files to support development:

setup.py:
A typical setuptools setup.py file.

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.md:
Points the user to the web site.

and these directories

example_files/:
a few example files used for testing purposes.