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
|
# -*- coding: utf-8 -*-
#
# Copyright (c) 2019, the cclib development team
#
# This file is part of cclib (http://cclib.github.io) and is distributed under
# the terms of the BSD 3-Clause License.
"""Unit tests for the logfileparser module."""
import io
import os
import sys
import tempfile
import unittest
from six import add_move, MovedModule
add_move(MovedModule('mock', 'mock', 'unittest.mock'))
from six.moves import mock
from six.moves.urllib.request import urlopen
import numpy
import cclib
__filedir__ = os.path.dirname(__file__)
__filepath__ = os.path.realpath(__filedir__)
__datadir__ = os.path.join(__filepath__, "..", "..")
class FileWrapperTest(unittest.TestCase):
def test_file_seek(self):
"""Can we seek anywhere in a file object?"""
fpath = os.path.join(__datadir__,"data/ADF/basicADF2007.01/dvb_gopt.adfout")
with open(fpath, 'r') as fobject:
wrapper = cclib.parser.logfileparser.FileWrapper(fobject)
wrapper.seek(0, 0)
self.assertEqual(wrapper.pos, 0)
wrapper.seek(10, 0)
self.assertEqual(wrapper.pos, 10)
wrapper.seek(0, 2)
self.assertEqual(wrapper.pos, wrapper.size)
@unittest.skipIf(os.environ.get('CCLIB_SKIP_NETWORK_TESTS', False),
"Skipping network tests")
def test_url_seek(self):
"""Can we seek only to the end of an url stream?"""
url = "https://raw.githubusercontent.com/cclib/cclib/master/data/ADF/basicADF2007.01/dvb_gopt.adfout"
stream = urlopen(url)
wrapper = cclib.parser.logfileparser.FileWrapper(stream)
# Unfortunately, the behavior of this wrapper differs between Python 2 and 3,
# so we need to diverge the assertions. We should try to keep the code as
# consistent as possible, but the Errors raised are actually different.
wrapper.seek(0, 2)
self.assertEqual(wrapper.pos, wrapper.size)
if sys.version_info[0] == 2:
self.assertRaises(AttributeError, wrapper.seek, 0, 0)
self.assertRaises(AttributeError, wrapper.seek, 0, 1)
else:
self.assertRaises(io.UnsupportedOperation, wrapper.seek, 0, 0)
self.assertRaises(io.UnsupportedOperation, wrapper.seek, 0, 1)
@unittest.skip("Broken test")
def test_stdin_seek(self):
"""We shouldn't be able to seek anywhere in standard input."""
wrapper = cclib.parser.logfileparser.FileWrapper(sys.stdin)
self.assertRaises(IOError, wrapper.seek, 0, 0)
self.assertRaises(IOError, wrapper.seek, 0, 1)
@unittest.skip("Broken test")
def test_data_stdin(self):
"""Check that the same attributes are parsed when a file is piped through standard input."""
logfiles = [
"data/ADF/basicADF2007.01/dvb_gopt.adfout",
"data/GAMESS/basicGAMESS-US2017/C_bigbasis.out",
]
get_attributes = lambda data: [a for a in data._attrlist if hasattr(data, a)]
for lf in logfiles:
path = "%s/%s" % (__datadir__, lf)
expected_attributes = get_attributes(cclib.io.ccread(path))
with open(path) as handle:
contents = handle.read()
# This is fix strings not being unicode in Python2.
try:
stdin = io.StringIO(contents)
except TypeError:
stdin = io.StringIO(unicode(contents))
stdin.seek = sys.stdin.seek
data = cclib.io.ccread(stdin)
self.assertEqual(get_attributes(data), expected_attributes)
class LogfileTest(unittest.TestCase):
"""Unit tests for the Logfile class."""
def test_float_basic(self):
"""Are floats converted from strings correctly?"""
float = cclib.parser.logfileparser.Logfile('').float
self.assertEqual(float("0.0"), 0.0)
self.assertEqual(float("1.0"), 1.0)
self.assertEqual(float("-1.0"), -1.0)
def test_float_numeric_format(self):
"""Does numeric formatting get converted correctly?"""
float = cclib.parser.logfileparser.Logfile('').float
self.assertEqual(float("1.2345E+02"), 123.45)
self.assertEqual(float("1.2345D+02"), 123.45)
def test_float_stars(self):
"""Does the function return nan for stars?"""
float = cclib.parser.logfileparser.Logfile('').float
self.assertTrue(numpy.isnan(float("*")))
self.assertTrue(numpy.isnan(float("*****")))
def test_normalisesym_base_class_error(self):
"""Does this method raise an error in the base class?"""
normalisesym = cclib.parser.logfileparser.Logfile('').normalisesym
self.assertRaises(NotImplementedError, normalisesym, 'Ag')
def test_parse_check_values(self):
"""Are custom checks performed after parsing finishes?
The purpose of this test is not to comprehensively cover all the checks,
but rather to make sure the call and logging works. The unit tests
for the data class should have comprehensive coverage.
"""
_, path = tempfile.mkstemp()
parser = cclib.parser.logfileparser.Logfile(path)
parser.extract = lambda self, inputfile, line: None
parser.logger = mock.Mock()
parser.etenergies = [1, -1]
parser.parse()
parser.logger.error.assert_called_once()
if __name__ == "__main__":
unittest.main()
|
