1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
|
#! /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.
##
##############################################################################
import sys
import os
import argparse
import collections
import unittest
from dendropy.utility import metavar
from dendropy.utility import messaging
sys.path.insert(0, os.path.dirname(__file__))
from dendropy.test.support import dendropytest
def main():
group_names = (
("@all" , ".*"),
("@datamodel" , ".*_datamodel_.*"),
("@dataio" , ".*_dataio_.*"),
("@newick" , ".*_newick_.*"),
("@tree" , ".*_tree_.*"),
)
test_group_patterns = collections.OrderedDict(group_names)
test_group_names = list(test_group_patterns)
parser = argparse.ArgumentParser()
parser.add_argument("test_names",
metavar="TEST",
nargs="*",
help= "Name of test(s) to run. These can be (dot-)qualified module, test"
"case, or test name (e.g., 'test_module', 'test_module.TestCase1',"
"'test_module.TestCase1.test1') or special pre-defined groups of"
"tests (e.g., '@datamodel', '@dataio'). Type '--help-testgroups' for"
"a list of available groups.")
parser.add_argument("--help-testgroups",
action="store_true",
default=False,
help="Show list of available test groups and exit.")
parser.add_argument("--list-only",
action="store_true",
default=False,
help="Do not actually run tests: just print list of test module names and exit.")
parser.add_argument("-v", "--verbosity",
default=3,
type=int,
help="Messaging noisiness (default: %(default)s)")
parser.add_argument("--logging-level",
default=os.environ.get(metavar.LOGGING_LEVEL_ENVAR, "NOTSET"),
choices=["NOTSET", "DEBUG", "INFO", "WARNING", "ERROR", "CRITICAL"],
help="Test logging level (default: '%(default)s')")
parser.add_argument("-f", "--fail-fast",
action="store_true",
default=False,
help="Stop the test run on the first error or failure.")
parser.add_argument("-I", "--fail-incomplete",
action="store_true",
default=False,
help="Fail incomplete or partially-complete test stubs.")
args = parser.parse_args()
if args.help_testgroups:
out = sys.stdout
out.write("Available special test groups:\n")
for name in test_group_names:
out.write(" - {}\n".format(name))
sys.exit(0)
# Set logging level:
os.environ[metavar.LOGGING_LEVEL_ENVAR] = args.logging_level
_LOG = messaging.get_logger("dendropy")
# Set test specifications
if args.fail_incomplete:
os.environ[metavar.FAIL_INCOMPLETE_TESTS_ENVAR] = "1"
# get test modules
test_names = []
filter_patterns = []
for name in args.test_names:
if name is None:
continue
if name.startswith("@"):
try:
filter_patterns.append(test_group_patterns[name])
except KeyError:
sys.exit("Unrecognized test group name '{}'. Accepted names: {}".format(name, test_group_names))
else:
name = name.replace(os.sep, ".")
if name.endswith(".py"):
name = name[:-3]
if not name.startswith("dendropy.test."):
if name.startswith("test."):
name = "dendropy." + name
else:
name = "dendropy.test." + name
test_names.append(name)
if not test_names and not filter_patterns:
test_names = dendropytest.discover_test_module_paths() # get all
if filter_patterns:
test_names.extend(dendropytest.discover_test_module_paths(filter_patterns))
test_names = sorted(set(test_names))
# 0: nothing
# 1: errors and mishaps only + 0
# 2: warnings + 1
# 3: general messages + 2
if args.verbosity >= 3 or args.list_only:
if args.list_only:
out = sys.stdout
else:
out = sys.stderr
out.write("DendroPy tests to be run:\n")
for mp in test_names:
out.write(" + {}\n".format(mp))
if args.list_only:
sys.exit(0)
tests = unittest.defaultTestLoader.loadTestsFromNames(test_names)
test_suite = unittest.TestSuite(tests)
test_runner = unittest.TextTestRunner(verbosity=args.verbosity, failfast=args.fail_fast)
test_runner.run(test_suite)
if __name__ == '__main__':
main()
|
