The WhatsHap source code is on Bitbucket. WhatsHap is developed in Python 3, Cython and C++.
For development, make sure that you install Cython and tox. We also recommend using a virtualenv. This sequence of commands should work:
git clone https://bitbucket.org/whatshap/whatshap cd whatshap python3 -m venv venv source venv/bin/activate pip install -e .[dev]
The last command installs also all the development dependencies, such as Cython. Use only
pip install -e . to omit those.
Next, you can run WhatsHap like this:
Development installation when using Conda¶
If you are using Bioconda, it is convenient to develop WhatsHap in a separate environment:
conda create -n whatshap-dev python=3.6 pysam PyVCF pyfaidx xopen Cython pytest sphinx-issues source activate whatshap-dev git clone https://bitbucket.org/whatshap/whatshap cd whatshap pip install -e .
The last command installs WhatsHap into your Conda environment named
whatshap-dev. So when
whatshap you will run the latest version you just cloned.
While in the virtual environment, you can run the tests for the current Python version like this:
Whenever you change any Cython code (
.pyx files), you need to re-run the
pip install -e . step in order to compile it.
Optionally, to run tests for all supported Python versions, you can run
tox. It creates separate virtual environments for each Python
version, installs WhatsHap into it and then runs the tests. It also tests documentation generation
sphinx. Run it like this:
tox is installed on the system, you do not need to be inside a virtual environment for this.
However, you need to have all tested Python versions installed on the system! See the instructions
below for how to do this on Ubuntu.
Installing other Python versions in Ubuntu¶
Ubuntu comes with one default Python 3 version, and in order to test WhatsHap with older or newer Python versions, follow the instructions for enabling the “deadsnakes” repository. After you have done so, ensure you have the following packages:
sudo apt install build-essential python-software-properties
Then get and install the desired Python versions. Make sure you install the
For example, for Python 3.4:
sudo apt update sudo apt install python3.4-dev
Here is one way to get a backtrace from gdb (assuming the bug occurs while running the tests):
$ gdb python3 (gdb) run -m pytest
After you get a SIGSEGV, let gdb print a backtrace:
Wrapping C++ classes¶
The WhatsHap phasing algorithm is written in C++, as are many of the core data structures such as the “Read” class. To make the C++ classes usable from Python, we use Cython to wrap the classes. All these definitions are spread across multiple files. To add new attributes or methods to an existing class or to add a new class, changes need to be made in different places.
Let us look at the “Read” class. The following places in the code may need to be changed if the Read class is changed or extended:
src/read.cpp: Implementation of the class (C++).
src/read.h: Header with the class declaration (also normal C++).
whatshap/cpp.pxd: Cython declarations of the class. This repeats – using the Cython syntax this time – a subset of the information from the
src/read.hfile. This duplication is required because Cython cannot read
.hfiles (it would need a full C++ parser for that).
Note that the
cpp.pxdfile contains definitions for all the
.hheaders. (It would be cleaner to have them in separate
.pxdfiles, but this leads to problems when linking the compiled files.)
whatshap/core.pxd: This contains declarations of all Cython classes wrapping C++ classes. Note that the class
Readin this file has the same name as the C++ class, but that it is not the same as the C++ one! The distinction is made by prefixing the C++ class with
cpp., which is the name of the module in which it is declared in (that is, the C++ class
Readis declared in
cpp.pxd). The wrapping (Cython) class
Readstores the C++ class in an attribute named
thisptr. If you add a new class, it needs to be added to this file. If you only modify an existing one, you probably do not need to change this file.
whatshap/core.pyx: The Cython implementation of the wrapper classes. Again, the name
Readby itself is the Python wrapper class and
cpp.Readis the name for the C++ class.
Before adding yet more C++ code, which then requires extra code for wrapping it,
consider writing an implementation in Cython instead. See
for example, which started out as a Python module and was then transferred to
Cython to make it faster. Here, the Cython code is not merely a wrapper, but
contains the implementation itself.
Documentation is hosted on Read the Docs.
In theory, it is built automatically whenever a commit is made. The documentation in the
master branch should be visible at https://whatshap.readthedocs.io/en/latest/
and documentation for the most recent released version should be visible at https://whatshap.readthedocs.io/en/stable/.
However, the connection between Bitbucket and Read the Docs has never worked
well in this particular project, so builds actually need to be triggered manually
until we have solved this problem.
To generate documentation locally, ensure that you installed sphinx and add-ons
necessary to build documantation (running
pip install -e .[dev] will take
care of this). Then go into the
doc/ directory and run
make. You can
doc/_build/html/index.html in your browser. The theme that is
used is a bit different from the one the Read the Docs uses.
Making a release¶
If this is the first time you attempt to upload a distribution to PyPI, create a
configuration file named
.pypirc in your home directory with the following
[distutils] index-servers = pypi [pypi] username=my-user-name password=my-password
See also this blog post about getting started with
PyPI. In particular,
note that a
% in your password needs to be doubled and that the password
must not be put between quotation marks even if it contains spaces.
Set the correct version number in the changelog. Ensure that the list of changes is up-to-date.
Ensure you have no uncommitted changes in the working copy.
tox, ensuring all tests pass.
Tag the current commit with the version number (there must be a
git tag v0.1
Create a distribution (
.tar.gzfile), ensuring that the auto-generated version number in the tarball is as you expect it:
python3 setup.py sdist
Upload the distribution to PyPI (the tarball must be regenerated since
uploadrequires a preceding
twine upload dist/whatshap-x.yz.tar.gz
You may need to install the
twinetool to run this command.
Push the tag:
git push --tags
Update the bioconda recipe. It is probly easiest to edit the recipe via the web interface and send in a pull request. Ensure that the list of dependencies (the
requirements:section in the recipe) is in sync with the
Since this is just a version bump, the pull request does not need a review by other bioconda developers. As soon as the tests pass and if you have the proper permissions, it can be merged directly.
If something went wrong, fix the problem and follow the above instructions again, but with an incremented revision in the version number. That is, go from version x.y to x.y.1. Do not change a version that has already been uploaded.
Adding a new subcommand¶
Follow the instructions in