Unverified Commit e7fa38b3 authored by Jeroen F.J. Laros's avatar Jeroen F.J. Laros Committed by GitHub
Browse files

Merge pull request #5 from mutalyzer/package

Package
parents f6bf50c6 d60c01b3
from os.path import dirname, abspath
from configparser import ConfigParser
from pkg_resources import get_distribution
from .backtranslate import BackTranslate
config = ConfigParser()
with open('{}/setup.cfg'.format(dirname(abspath(__file__)))) as handle:
config.read_file(handle)
def _get_metadata(name):
pkg = get_distribution(__package__)
for line in pkg.get_metadata_lines(pkg.PKG_INFO):
if line.startswith('{}: '.format(name)):
return line.split(': ')[1]
return ''
_copyright_notice = 'Copyright (c) {} {} <{}>'.format(
config.get('metadata', 'copyright'),
config.get('metadata', 'author'),
config.get('metadata', 'author_email'))
_copyright_notice = 'Copyright (c) {} <{}>'.format(
_get_metadata('Author'), _get_metadata('Author-email'))
usage = [config.get('metadata', 'description'), _copyright_notice]
usage = [_get_metadata('Summary'), _copyright_notice]
def doc_split(func):
......@@ -23,7 +25,5 @@ def doc_split(func):
def version(name):
return '{} version {}\n\n{}\nHomepage: {}'.format(
config.get('metadata', 'name'),
config.get('metadata', 'version'),
_copyright_notice,
config.get('metadata', 'url'))
_get_metadata('Name'), _get_metadata('Version'), _copyright_notice,
_get_metadata('Home-page'))
../setup.cfg
\ No newline at end of file
......@@ -11,7 +11,7 @@ def _three_to_one():
def subst_to_cds(substitutions, offset):
""" Convert a set of substitutions to CDS coordinates.
"""Convert a set of substitutions to CDS coordinates.
:arg dict substitutions: Set of single nucleotide substitutions indexed by
position.
......
[metadata]
name = backtranslate
version = 0.1.1
version = 0.1.2
description = Functions for reverse translation.
long_description = file: README.rst
author = LUMC, Jeroen F.J. Laros
......@@ -9,20 +9,22 @@ url = https://github.com/mutalyzer/backtranslate
keywords = bioinformatics
license = MIT
classifiers =
Intended Audience :: Developers
Intended Audience :: Science/Research
Operating System :: OS Independent
Programming Language :: Python :: 3
Programming Language :: Python :: 3.5
Programming Language :: Python :: 3.6
copyright = 2015-2019
Topic :: Scientific/Engineering
[options]
packages = find:
install_requires =
biopython
configparser
python-Levenshtein
[options.package_data]
backtranslate = setup.cfg
biopython==1.76
python-Levenshtein==0.12.0
tests_require =
fake-open==0.0.1
pytest==4.0.1
[options.entry_points]
console_scripts =
......
"""
Tests for the backtranslate.backtranslate module.
"""
from __future__ import (
absolute_import, division, print_function, unicode_literals)
from future.builtins import str, zip
"""Tests for the backtranslate.backtranslate module."""
from backtranslate.backtranslate import BackTranslate, cmp_subst
class TestParser(object):
"""
Test the backtranslate.backtranslate module.
"""
"""Test the backtranslate.backtranslate module."""
def setup(self):
self.bt = BackTranslate()
......
"""
Tests for the backtranslate CLI.
"""
from __future__ import (
absolute_import, division, print_function, unicode_literals)
from future.builtins import str, zip
"""Tests for the backtranslate CLI."""
import sys
from hashlib import md5
......@@ -16,9 +10,7 @@ from backtranslate import cli
class TestParser(object):
"""
Test the backtranslate.backtranslate module.
"""
"""Test the backtranslate.backtranslate module."""
def setup(self):
self._input = open('data/mhv.fa')
self._output = StringIO()
......
......@@ -2,5 +2,5 @@
envlist = py35, py36
[testenv]
commands = py.test -W error
commands = py.test
whitelist_externals = py.test
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