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#! /usr/bin/env python
##############################################################################
## DendroPy Phylogenetic Computing Library.
##
## Copyright 2010-2015 Jeet Sukumaran and Mark T. Holder.
## All rights reserved.
##
## See "LICENSE.rst" for terms and conditions of usage.
##
## If you use this work or any portion thereof in published work,
## please cite it as:
##
## Sukumaran, J. and M. T. Holder. 2010. DendroPy: a Python library
## for phylogenetic computing. Bioinformatics 26: 1569-1571.
##
##############################################################################
"""
Extension to the basic unittest TestCase.
"""
import collections
import sys
import re
import os
import unittest
from distutils.util import strtobool
from dendropy.utility import metavar
from dendropy.utility import messaging
# Defining this here means that unittest will exclude all lines from this
# module in the traceback report when an assertion fails, allowing
# for the starting point of the traceback to be the point where the assertion
# was made, rather than the point where an exception was raised because
# the assertion was false.
__unittest = True
def discover_test_module_paths(filter_patterns=None):
"""
Discovers test modules. If ``filter_patterns`` is |None|, then
all files in *immediate* directory that begin with 'test' will
be added to the set returned. If ``filter_patterns`` is not |None|, then it
should be a list of regular expression patterns, and only files that match
at least one of the patterns will be returned.
"""
test_module_pattern = re.compile("^test.*\.py$", re.IGNORECASE)
if filter_patterns:
filter_pattern = re.compile("(" + r"\|".join(filter_patterns) + ")")
else:
filter_pattern = None
path = os.path.dirname(os.path.dirname(__file__))
filenames = os.listdir(path)
test_modules = []
for filename in filenames:
if test_module_pattern.match(filename):
if filter_pattern is None or filter_pattern.match(filename):
# test_modules.append("" + os.path.splitext(filename)[0])
test_modules.append("dendropy.test." + os.path.splitext(filename)[0])
return test_modules
def get_test_suite(test_names=None):
"""
If ``test_names`` is not |None|, creates a test suite out of those
modules. Otherwise, creates a test suite from all of the modules in
``dendropy.test`` using the discovery.
"""
if test_names is None:
test_names = discover_test_module_paths()
tests = unittest.defaultTestLoader.loadTestsFromNames(test_names)
return unittest.TestSuite(tests)
class ExtendedTestCase(unittest.TestCase):
"""
Extends unittest.TestCase with various new assertion tests.
"""
def _get_logger(self):
if not hasattr(self, "_logger") or self._logger is None:
self._logger = messaging.get_logger(self.__class__.__name__)
return self._logger
def _set_logger(self, logger):
self._logger = logger
logger = property(_get_logger, _set_logger)
def assertCountEqual(self, *args, **kwargs):
if sys.hexversion >= 0x03020000:
super(ExtendedTestCase, self).assertCountEqual(*args, **kwargs)
else:
self.assertEqual(collections.Counter(args[0]), collections.Counter(args[1]))
def fail_incomplete_tests(self):
return bool(strtobool(os.environ.get(metavar.FAIL_INCOMPLETE_TESTS_ENVAR, "0")))
def assertEqualUnorderedSequences(self, x1, x2):
c1 = collections.Counter(x1)
c2 = collections.Counter(x2)
return self.assertEqual(c1, c2)
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