Metadata-Version: 2.1
Name: uta-align
Version: 0.2.0a3
Summary: C-based sequence alignment for Python
Home-page: https://github.com/biocommons/uta-align/
Author: Kevin Jacobs, Reece Hart
Author-email: reecehart+biocommons@gmail.com
Maintainer: Reece Hart
Maintainer-email: reecehart+biocommons@gmail.com
License: Apache License 2.0
Description: ``uta-align`` provides C-based (Cython) Needleman-Wunsch and
        Smith-Waterman alignment algorithms
        
        |build_status| |pypi_badge|
        
        Original author: Kevin Jacobs
        
        
        .. important:: Python 3.6+ only
        
        
        Installation
        @@@@@@@@@@@@
        
        From source::
        
          $ python setup.py install
        
        
        
        For Development
        ###############
        
        * Install developer environment::
        
            $ make devready
        
        * Activate the environment::
        
            $ source venv/3.7/bin/activate
        
          (or other python version as appropriate for your system)
        
        
        * During development, you'll need to recompile any code changes to the
          .pyx files, like this::
        
            $ pip install -e .
        
        
        * Test it (in current Python environment)::
        
            $ make test
            ======================================== test session starts ========================================
            platform linux -- Python 3.7.5, pytest-5.3.5, py-1.8.1, pluggy-0.13.1
            rootdir: /home/reece/projects/biocommons/uta-align, inifile: setup.cfg, testpaths: tests
            collected 5 items                                                                                   
            tests/test_align_algorithms.py .                                                              [ 20%]
            tests/test_align_gap_open.py ..                                                               [ 60%]
            tests/test_cigar_utils.py .                                                                   [ 80%]
            tests/test_nw.py .                                                                            [100%]
            ========================================= 5 passed in 0.12s =========================================
        
        
        * Tox test it (in multiple environments::
          
            $ make tox
            
            GLOB sdist-make: /home/reece/projects/biocommons/uta-align/setup.py
            py37 inst-nodeps: /home/reece/projects/biocommons/uta-align/.tox/.tmp/package/1/uta-align-1.1.13a2.dev7+g98b7cc9.d20200303.zip
            ...
            py37: commands succeeded
            congratulations :)
        
        
        
        
        .. |pypi_badge| image:: https://badge.fury.io/py/uta-align.png
          :target: https://pypi.python.org/pypi?name=uta-align
          :align: middle
        
        .. |build_status| image:: https://travis-ci.org/biocommons/uta-align.svg?branch=master
           :target: https://travis-ci.org/biocommons/uta-align
           :align: middle
        
Platform: UNKNOWN
Description-Content-Type: text/x-rst; charset=UTF-8
Provides-Extra: dev
