Removed Python 2 support.

backtranslate/__init__.py

@@ -1,31 +1,29 @@
-"""
-backtranslate: Functions for reverse translation.
+from os.path import dirname, abspath
 
+from configparser import ConfigParser
 
-Copyright (c) 2015 Leiden University Medical Center <[email protected]>
-Copyright (c) 2015 Jeroen F.J. Laros <[email protected]>
+from .backtranslate import BackTranslate
 
-Licensed under the MIT license, see the LICENSE file.
-"""
-from __future__ import (
-    absolute_import, division, print_function, unicode_literals)
-from future.builtins import str, zip
 
+config = ConfigParser()
+with open('{}/setup.cfg'.format(dirname(abspath(__file__)))) as handle:
+    config.read_file(handle)
 
-__version_info__ = ('0', '1', '0')
+_copyright_notice = 'Copyright (c) {} {} <{}>'.format(
+    config.get('metadata', 'copyright'),
+    config.get('metadata', 'author'),
+    config.get('metadata', 'author_email'))
 
-__version__ = '.'.join(__version_info__)
-__author__ = 'LUMC, Jeroen F.J. Laros'
-__contact__ = '[email protected]'
-__homepage__ = 'https://github.com/mutalyzer/backtranslate'
-
-usage = __doc__.split("\n\n\n")
+usage = [config.get('metadata', 'description'), _copyright_notice]
 
 
 def doc_split(func):
-    return func.__doc__.split("\n\n")[0]
+    return func.__doc__.split('\n\n')[0]
 
 
 def version(name):
-    return "%s version %s\n\nAuthor   : %s <%s>\nHomepage : %s" % (name,
-        __version__, __author__, __contact__, __homepage__)
+    return '{} version {}\n\n{}\nHomepage: {}'.format(
+        config.get('metadata', 'name'),
+        config.get('metadata', 'version'),
+        _copyright_notice,
+        config.get('metadata', 'url'))

backtranslate/backtranslate.py

@@ -1,16 +1,11 @@
-from __future__ import (
-    absolute_import, division, print_function, unicode_literals)
-from future.builtins import str, zip
-
 from collections import defaultdict
 
 from Bio.Data import CodonTable
 from Levenshtein import hamming
 
 
 def cmp_subst(subst_1, subst_2):
-    """
-    Compare two substitution sets.
+    """Compare two substitution sets.
 
     :arg dict subst_1: Substitution set.
     :arg dict subst_2: Substitution set.
@@ -28,8 +23,7 @@ def cmp_subst(subst_1, subst_2):
 
 
 def reverse_translation_table(table_id=1):
-    """
-    Calculate a reverse translation table.
+    """Calculate a reverse translation table.
 
     :arg int table_id: Translation table id.
 
@@ -47,20 +41,16 @@ def reverse_translation_table(table_id=1):
 
 
 class BackTranslate(object):
-    """
-    Back translation.
-    """
+    """Back translation."""
     def __init__(self, table_id=1):
-        """
-        Initialise the class.
+        """Initialise the class.
 
         :arg int table_id: Translation table id.
         """
         self._back_table = reverse_translation_table(table_id)
 
     def _one_subst(self, substitutions, reference_codon, amino_acid):
-        """
-        Find single nucleotide substitutions that given a reference codon
+        """Find single nucleotide substitutions that given a reference codon
         explains an observed amino acid.
 
         :arg defaultdict(set) substitutions: Set of single nucleotide
@@ -76,8 +66,7 @@ def _one_subst(self, substitutions, reference_codon, amino_acid):
                             (reference_codon[position], codon[position]))
 
     def with_dna(self, reference_codon, amino_acid):
-        """
-        Find single nucleotide substitutions that given a reference codon
+        """Find single nucleotide substitutions that given a reference codon
         explains an observed amino acid.
 
         :arg str reference_codon: Original codon.
@@ -93,9 +82,8 @@ def with_dna(self, reference_codon, amino_acid):
         return dict(substitutions)
 
     def without_dna(self, reference_amino_acid, amino_acid):
-        """
-        Find single nucleotide substitutions that given a reference amino acid
-        explains an observed amino acid.
+        """Find single nucleotide substitutions that given a reference amino
+        acid explains an observed amino acid.
 
         :arg str reference_amino_acid: Original amino acid.
         :arg str amino_acid: Observed amino acid.
@@ -111,9 +99,8 @@ def without_dna(self, reference_amino_acid, amino_acid):
         return dict(substitutions)
 
     def improvable(self):
-        """
-        Calculate all pairs of amino acid substututions that can be improved by
-        looking at the underlying codon.
+        """Calculate all pairs of amino acid substututions that can be improved
+        by looking at the underlying codon.
 
         :returns list: List of improvable substitutions.
         """

backtranslate/setup.cfg

@@ -0,0 +1 @@
+../setup.cfg

backtranslate/util.py

@@ -1,13 +1,8 @@
-from __future__ import (
-    absolute_import, division, print_function, unicode_literals)
-from future.builtins import str, zip
-
 from Bio.Data import IUPACData
 
 
 def _three_to_one():
-    """
-    The three letter to one letter table for amino acids including stop.
+    """The three letter to one letter table for amino acids including stop.
 
     :returns dict: Three letter to one letter amino acids table.
     """
@@ -16,8 +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.

setup.cfg

@@ -0,0 +1,29 @@
+[metadata]
+name = backtranslate
+version = 0.1.1
+description = Functions for reverse translation.
+long_description = file: README.rst
+author = LUMC, Jeroen F.J. Laros
+author_email = [email protected]
+url = https://github.com/mutalyzer/backtranslate
+keywords = bioinformatics
+license = MIT
+classifiers =
+    Programming Language :: Python :: 3
+    Programming Language :: Python :: 3.5
+    Programming Language :: Python :: 3.6
+copyright = 2015-2019
+
+[options]
+packages = find:
+install_requires =
+    biopython
+    configparser
+    python-Levenshtein
+
+[options.package_data]
+backtranslate = setup.cfg
+
+[options.entry_points]
+console_scripts =
+    backtranslate = backtranslate.cli:main

setup.py

@@ -1,81 +1,4 @@
-import os
-import sys
-
 from setuptools import setup
 
 
-package = 'backtranslate'
-package_name = 'BackTranslate'
-description = '{}: Functions for reverse translation.'.format(package_name)
-documentation = 'README.md'
-license = 'MIT License'
-keywords = ['bioinformatics']
-
-dependencies = ['biopython', 'future', 'python-Levenshtein']
-develop_dependencies = ['fake-open', 'pytest', 'tox']
-supported = [(2, 7), (3, 3), (3, 4)]
-classifiers = [
-    'Development Status :: 3 - Alpha',
-    'Intended Audience :: Science/Research',
-    'Intended Audience :: Developers',
-    'Topic :: Scientific/Engineering :: Bio-Informatics',
-]
-
-
-if sys.version_info < supported[0]:
-    raise Exception('{} requires Python {}.{} or higher.'.format(
-        package, *supported[0]))
-
-if sys.version_info[:2] == supported[0]:
-    dependencies.extend(['argparse', 'importlib'])
-
-# This is quite the hack, but we don't want to import our package from here
-# since that's recipe for disaster (it might have some uninstalled
-# dependencies, or we might import another already installed version).
-distmeta = {}
-for line in open(os.path.join(package, '__init__.py')):
-    try:
-        field, value = (x.strip() for x in line.split('='))
-    except ValueError:
-        continue
-    if field == '__version_info__':
-        value = value.strip('[]()')
-        value = '.'.join(x.strip(' \'"') for x in value.split(','))
-    else:
-        value = value.strip('\'"')
-    distmeta[field] = value
-
-try:
-    with open(documentation) as readme:
-        long_description = readme.read()
-except IOError:
-    long_description = 'See ' + distmeta['__homepage__']
-
-language_string = 'Programming Language :: Python'
-classifiers += [
-    'License :: OSI Approved :: {}'.format(license),
-    'Operating System :: OS Independent',
-    language_string,
-    '{} :: {}'.format(language_string, supported[0][0]),
-    '{} :: {}'.format(language_string, supported[-1][0])] + \
-    ['{} :: {}.{}'.format(language_string, *version) for version in supported]
-
-setup(
-    name=package_name,
-    version=distmeta['__version_info__'],
-    description=description,
-    long_description=long_description,
-    author=distmeta['__author__'],
-    author_email=distmeta['__contact__'],
-    url=distmeta['__homepage__'],
-    license=license,
-    platforms=['any'],
-    packages=[package],
-    install_requires=dependencies,
-    tests_require=develop_dependencies,
-    entry_points={
-        'console_scripts': ['{0} = {0}.cli:main'.format(package)]
-    },
-    classifiers=classifiers,
-    keywords=' '.join(keywords)
-)
+setup()

tox.ini

@@ -1,6 +1,6 @@
 [tox]
-envlist = py27,py34
+envlist = py35, py36
 
 [testenv]
-commands = py.test
+commands = py.test -W error
 whitelist_externals = py.test