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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.
##
##############################################################################
"""
Support for coverage analysis.
"""
import unittest
import shutil
import sys
from optparse import OptionParser
from dendropy.utility import messaging
_LOG = messaging.get_logger(__name__)
DENDROPY_COVERAGE_ANALYSIS_AVAILABLE = False
try:
from setuptools import Command
except ImportError:
_LOG.warn("setuptools.Command could not be imported: setuptools extensions not available")
else:
try:
import coverage
except ImportError:
_LOG.warn("coverage could not be imported: test coverage analysis not available")
else:
_LOG.info("coverage imported successfully: test coverage analysis available")
DENDROPY_COVERAGE_ANALYSIS_AVAILABLE = True
from dendropy.test.support.dendropytest import get_test_suite
from dendropy.test.support import pathmap
class CoverageAnalysis(Command):
"""
Code coverage analysis command.
"""
description = "run test coverage analysis"
user_options = [
('erase', None, "remove all existing coverage results"),
('branch', 'b', 'measure branch coverage in addition to statement coverage'),
('test-module=', 't', "explicitly specify a module to test (e.g. 'dendropy.test.test_containers')"),
('no-annotate', None, "do not create annotated source code files"),
('no-html', None, "do not create HTML report files"),
]
def initialize_options(self):
"""
Initialize options to default values.
"""
self.test_module = None
self.branch = False
self.erase = False
self.no_annotate = False
self.no_html = False
self.omit_prefixes = ['dendropy/test']
def finalize_options(self):
pass
def run(self):
"""
Main command implementation.
"""
if self.erase:
_LOG.warn("removing coverage results directory: '%s'" % pathmap.TESTS_COVERAGE_DIR)
try:
shutil.rmtree(pathmap.TESTS_COVERAGE_DIR)
except:
pass
else:
_LOG.info("running coverage analysis ...")
if self.test_module is None:
test_suite = get_test_suite()
else:
test_suite = get_test_suite([self.test_module])
runner = unittest.TextTestRunner()
cov = coverage.coverage(branch=self.branch)
cov.start()
runner.run(test_suite)
cov.stop()
if not self.no_annotate:
cov.annotate(omit_prefixes=self.omit_prefixes,
directory=pathmap.TESTS_COVERAGE_SOURCE_DIR)
if not self.no_html:
cov.html_report(omit_prefixes=self.omit_prefixes,
directory=pathmap.TESTS_COVERAGE_REPORT_DIR)
cov.report(omit_prefixes=self.omit_prefixes)
#if __name__ == "__main__":
# if DENDROPY_COVERAGE_ANALYSIS_AVAILABLE:
# parser = OptionParser(add_help_option=True)
# parser.add_option('--erase', dest='erase', action="store_true", default=False, help="remove all existing coverage results")
# parser.add_option('--branch', '-b', dest='branch', action="store_true", default=False, help='measure branch coverage in addition to statement coverage')
# parser.add_option('--test-file', '-t', dest='test_module', default=None, help="explicitly specify a module to test (e.g. 'dendropy.test.test_containers')")
# parser.add_option('--no-annotate', dest='no_annotate', action="store_true", default=False, help="do not create annotated source code files"),
# parser.add_option('--no-html', dest='no_html', action="store_true", default=False, help="do not create HTML report files"),
# (opts, args) = parser.parse_args()
# cov = CoverageAnalysis()
# cov.erase = opts.erase
# cov.branch = opts.branch
# cov.test_module = opts.test_module
# cov.no_annotate = opts.no_annotate
# cov.no_html = opt.no_html
# cov.run()
# else:
# sys.stderr.write("Coverage command extension not available: either setuptools or coverage or both could not be imported.\n")
# sys.exit(1)
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