Python interface to libsequence via pybind11
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README.rst

pylibseq: Python bindings for libsequence

This package provides Python bindings for the C++11 library libsequence.

The bindings are implemented using pybind11.

This package serves two roles:

  • It provides a means of using some of the more widely-used bits of libsequence within the Python language
  • The unit tests of this package also serve as unit tests for libsequence.

What this package does not (currently) do:

  • provide an interface for I/O operations. Python I/O and C++ I/O are fundamentally very different. Bridging the gap requires either adding features to pybind11 and/or adding modules to this package that depend on the boost Python interface, which would add an additional C++ dependency to this package.

Build status

Master branch:

Travis CI Build Status (master branch)

Development branch:

Travis CI Build Status (dev branch)

Requirements:

  • libsequence must be installed on your system. Currently, this package requires libsequence >= 1.9.6
  • Python 3
  • An up-to-date C++ compiler that is C++11 compatible via the flag -std=c++11. Roughly, this means GCC >= 4.8 and clang >= 3.5.

Note

If you installing from GitHub, then pybind11 is a dependency.

The recommended method for installing libsequence is bioconda. If you do not use that system, then you should install libsequence from source.

If you want to modify the package, you will need pybind11 installed via your favorite Python package manager.

Currently, only Linux is supported. The reason is that OS X's case-insensitive file system is preventing current versions of libsequence from compiling. This situation will be resolved once all deprecated features are removed from libsequence

Changelog (rough)

  • 0.2.0: The package has been completely refactored. We now use pybind11 to integrate C++ and Python. Previous versions of this project used Cython. The API now corrresponds to libsequence 1.9.2. Python >= 3.4 is required.
  • 0.1.9: Made memory management more robust: more unique_ptr instead of raw pointers. Cleanup __dealloc__ functions in extension types. Package now sets __version__. Class names are now "Pythonic" (and identical to the corresponding type names from libsequence) due to aliasing the C++ names from libsequence. Change from distutils to setuptools. Documentation fixes. Expose haplotype diversity and number of haplotype statistics. First (very alpha) release of pymsstats.
  • 0.1.8: made sure C++ objects/fxns are declared "nogil". Raw pointers replaced with C++'s unique_ptr.
  • 0.1.7: improvements to build system. Add option to build from GitHub.
  • 0.1.6: update to libsequence 1.8.9. Add --use-cython option to setup.py

Installation:

For many users, the best way to install the latest release will be via bioconda,

conda -c bioconda install pylibseq

The latest release of the package is available via PyPi, and can be installed with your favorite Python package manager:

$ pip install --upgrade pylibseq

Or, you may install from GitHub:

Note

The GitHub version does not contain the .cpp files generated by pybind11. You need to generate those!

$ git clone http://github.com/molpopgen/pylibseq
$ cd pylibseq
$ ./configure
$ sudo pip install .

Note

If you are using GCC on OS X (instead of clang), add --install-option=--gcc when installing.

You may also install from GitHub using pip:

$ pip install git+git://github.com/molpopgen/pylibseq

If you have libsequence in a "funny location" (e.g., something other that /usr/local):

$ CPPFLAGS=-I/path/to/libsequence/headers LDFLAGS=-L/path/to/libsequence/library sudo python setup.py install

For example, if libsequence is installed into /opt:

$ CPPFLAGS=-I/opt/include LDFLAGS=-L/opt/lib sudo python setup.py install

Unit testing:

$ ./configure
$ python setup.py build_ext -i
$ python -m unittest discover tests

Note

If using GCC on OS X (instead of clang), add --gcc to the setup.py command

Documentation: