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Project description
pylibseq: Python bindings for libsequence
***************************************************************
This package provides Python_ bindings for the C++11 library libsequence_.
The bindings are implemented using Cython_.
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 Cython and/or adding modules to this package that depend on the boost_ Python interface, which would add an additional C++ dependency to this package.
Requirements:
===================================
* libsequence_ must be installed on your system. **Currently, this package requires the dev branch of libsequence**
* Python 2 or Python 3
* An up-to-date C++ compiler that is C++11 compatible via the flag -std=c++11. Roughty, this means GCC >= 4.8 and clang >= 3.5.
You should install libsequence_ from source.
If you want to modify the package, you will need Cython_ installed via your favorite Python package manager.
The supported platforms are Linux and OS X.
Changelog (rough)
==============================
* 0.1.6: update to libsequence 1.8.9. Add --use-cython option to setup.py
Installation:
=======================
The latest release of the package is available via PyPi_, and can be installed with your favorite Python package manager:
.. code-block:: bash
$ pip install --upgrade pylibseq
Or, you may install from GitHub:
.. code_block:: bash
$ git clone http://github.com/molpopgen/pylibseq
$ cd pylibseq
.. code-block:: bash
$ ./configure
$ sudo python setup.py install
If you have libsequence in a "funny location" (*e.g.*, something other that /usr/local):
.. code-block:: bash
$ 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:
.. code-block:: bash
$ CPPFLAGS=-I/opt/include LDFLAGS=-L/opt/lib sudo python setup.py install
Unit testing:
=======================
.. code-block:: bash
$ ./configure
$ python setup.py build_ext -i
$ python -m unittest discover unit_test
Modifying the package
=======================
.. code-block:: bash
$ python setup.py build_ext -i --use-cython
Documentation:
======================
* Project homepage_
* Manual_
.. _libsequence: http://molpopgen.github.io/libsequence/
.. _boost: http://www.boost.org/
.. _Cython: http://www.cython.org/
.. _Python: http://www.cython.org/
.. _Manual: http://molpopgen.github.io/pylibseq/_build/html/index.html
.. _homepage: http://molpopgen.github.io/pylibseq/
.. _PyPi: https://pypi.python.org
***************************************************************
This package provides Python_ bindings for the C++11 library libsequence_.
The bindings are implemented using Cython_.
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 Cython and/or adding modules to this package that depend on the boost_ Python interface, which would add an additional C++ dependency to this package.
Requirements:
===================================
* libsequence_ must be installed on your system. **Currently, this package requires the dev branch of libsequence**
* Python 2 or Python 3
* An up-to-date C++ compiler that is C++11 compatible via the flag -std=c++11. Roughty, this means GCC >= 4.8 and clang >= 3.5.
You should install libsequence_ from source.
If you want to modify the package, you will need Cython_ installed via your favorite Python package manager.
The supported platforms are Linux and OS X.
Changelog (rough)
==============================
* 0.1.6: update to libsequence 1.8.9. Add --use-cython option to setup.py
Installation:
=======================
The latest release of the package is available via PyPi_, and can be installed with your favorite Python package manager:
.. code-block:: bash
$ pip install --upgrade pylibseq
Or, you may install from GitHub:
.. code_block:: bash
$ git clone http://github.com/molpopgen/pylibseq
$ cd pylibseq
.. code-block:: bash
$ ./configure
$ sudo python setup.py install
If you have libsequence in a "funny location" (*e.g.*, something other that /usr/local):
.. code-block:: bash
$ 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:
.. code-block:: bash
$ CPPFLAGS=-I/opt/include LDFLAGS=-L/opt/lib sudo python setup.py install
Unit testing:
=======================
.. code-block:: bash
$ ./configure
$ python setup.py build_ext -i
$ python -m unittest discover unit_test
Modifying the package
=======================
.. code-block:: bash
$ python setup.py build_ext -i --use-cython
Documentation:
======================
* Project homepage_
* Manual_
.. _libsequence: http://molpopgen.github.io/libsequence/
.. _boost: http://www.boost.org/
.. _Cython: http://www.cython.org/
.. _Python: http://www.cython.org/
.. _Manual: http://molpopgen.github.io/pylibseq/_build/html/index.html
.. _homepage: http://molpopgen.github.io/pylibseq/
.. _PyPi: https://pypi.python.org
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