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Scheme creation #52

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Scheme creation #52

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ab6bf7f
argparse -> click; bio_hansel -> biohansel; creating base for `biohan…
Jul 13, 2018
1b6471a
add create subcommand; restructure/refactor for different subcommands
Jul 16, 2018
79e29c9
fix packaging and add ability to `python setup.py test` to run tests
Aug 1, 2018
68b5c7e
Update .travis.yml
peterk87 Aug 7, 2018
d6d2270
Update cli.py
peterk87 Aug 9, 2018
7017458
Update utils.py
peterk87 Aug 9, 2018
c2fb9cf
Update cli.py
peterk87 Aug 9, 2018
f1df3ad
Update utils.py
peterk87 Aug 9, 2018
47fa20f
Update utils.py; docs fix, refactoring, renaming
Aug 9, 2018
51dafd0
Update utils.py
Aug 9, 2018
9511966
Better arg names
Aug 9, 2018
cc9e671
doc fix; deconstruct complex condition
Aug 9, 2018
98cd34d
flipped condition in is_overall_coverage_low; added unit test
Aug 9, 2018
aca1769
wip: scheme creation from HC of SNV binary matrix
Sep 7, 2018
ad7ba3c
fix flat clusters table column order; greatest to least distance thre…
peterk87 Dec 4, 2018
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6 changes: 4 additions & 2 deletions MANIFEST.in
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Original file line number Diff line number Diff line change
Expand Up @@ -2,6 +2,8 @@ include LICENSE
include README.rst
include MANIFEST.in
include setup.py
recursive-include *.py *.fasta
recursive-include biohansel/subtype/data *.fasta
exclude ipynbs
exclude venv
exclude venv
exclude .venv
global-exclude *.py[co] __pycache__
3 changes: 1 addition & 2 deletions README.rst
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Expand Up @@ -268,7 +268,7 @@ Get the latest development code using Git from GitHub:
pip install -e .


Run tests with pytest_:
Run tests with `$ python setup.py test` or pytest_:

.. code-block:: bash

Expand All @@ -280,7 +280,6 @@ Run tests with pytest_:
pytest -s tests/test_qc.py



Legal
=====

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275 changes: 0 additions & 275 deletions bio_hansel/main.py
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4 changes: 2 additions & 2 deletions bio_hansel/__init__.py → biohansel/__init__.py
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@@ -1,7 +1,7 @@
# -*- coding: utf-8 -*-

__version__ = '2.0.0'
program_name = 'bio_hansel'
__version__ = '3.0.0'
program_name = 'biohansel'
program_summary = 'Subtype microbial genomes using SNV targeting k-mer subtyping schemes.'
program_desc = program_summary + '''
Includes schemes for Salmonella enterica spp. enterica serovar Heidelberg and Enteritidis subtyping.
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