def testMissingTplKey(self):
# make sure it gracefully fails when a template key is missing
test_input = ["-c", MISSING_TPL_KEY_INI]
if logger.isEnabledFor(logging.DEBUG):
main(test_input)
with capture_stderr(main, test_input) as output:
self.assertTrue('required for template file' in output)
def testDefInpWithBadBuffer(self):
bad_buffer = 'xyz'
with capture_stderr(main,
["-f", DEF_INPUT, "-b", bad_buffer]) as output:
self.assertTrue(
'WARNING: Problems reading data: Input for buffer ({}) could not be converted to '
'a float.'.format(bad_buffer) in output)
def testArrayWrongDelimiter(self):
test_input = ["-f", VEC_INPUT]
main(test_input)
if logger.isEnabledFor(logging.DEBUG):
main(test_input)
with capture_stderr(main, test_input) as output:
self.assertTrue("delimiter" in output)
def testMissingFilledTplName(self):
# new file name not specified by either config file or command line
test_input = ["-c", PAR_NO_NEW_FILE_NAME_INI]
if logger.isEnabledFor(logging.DEBUG):
main(test_input)
with capture_stderr(main, test_input) as output:
self.assertTrue(FILLED_TPL_FNAME in output)
def testTplKeyInMain(self):
# aim for a helpful message if the template key is in main
test_input = ["-c", TPL_KEY_IN_MAIN_INI]
if logger.isEnabledFor(logging.DEBUG):
main(test_input)
with capture_stderr(main, test_input) as output:
self.assertTrue('Unexpected key' in output)
def testValBeforeSection(self):
# make sure it gracefully fails when a template key is missing
test_input = ["-c", VAL_BEFORE_SECTION_INI]
if logger.isEnabledFor(logging.DEBUG):
main(test_input)
with capture_stderr(main, test_input) as output:
self.assertTrue('must start with' in output)
def testMissingMain(self):
# make sure it gracefully fails when a template key is missing
test_input = ["-c", MISSING_MAIN_INI]
if logger.isEnabledFor(logging.DEBUG):
main(test_input)
with capture_stderr(main, test_input) as output:
self.assertTrue("missing the required 'main' section" in output)
def testExtraSection(self):
# catch an error if the program finds an unexpected section
test_input = ["-c", EXTRA_SEC_INI]
if logger.isEnabledFor(logging.DEBUG):
main(test_input)
with capture_stderr(main, test_input) as output:
self.assertTrue('not one of the valid section names' in output)
def testHelp(self):
test_input = ['-h']
if logger.isEnabledFor(logging.DEBUG):
main(test_input)
with capture_stderr(main, test_input) as output:
self.assertFalse(output)
with capture_stdout(main, test_input) as output:
self.assertTrue("optional arguments" in output)
def testNoArgs(self):
test_input = []
if logger.isEnabledFor(logging.DEBUG):
main(test_input)
with capture_stdout(main, test_input) as output:
self.assertTrue("arguments:" in output)
with capture_stderr(main, test_input) as output:
self.assertTrue("required" in output)
def testIncDimen(self):
# Test what happens when the lines do not all have the same number of dimensions
test_input = ["-f", BAD_INPUT2, "-d", ' ']
if logger.isEnabledFor(logging.DEBUG):
main(test_input)
with capture_stderr(main, test_input) as output:
self.assertTrue("Problems reading data" in output)
self.assertTrue("3 values " in output)
self.assertTrue("2 values" in output)
def testAddNothing(self):
# this first test does not really doing anything, and warns the user
try:
with capture_stderr(main, [INPUT_PATH]) as output:
self.assertTrue(
"Return file will be the same as the input" in output)
self.assertFalse(diff_lines(INPUT_PATH, DEF_OUT_PATH))
finally:
silent_remove(DEF_OUT_PATH, DISABLE_REMOVE)
def testCheckWaterOrder(self):
test_input = ["-c", CHECK_WATER_ORDER_INI]
if logger.isEnabledFor(logging.DEBUG):
main(test_input)
try:
with capture_stderr(main, test_input) as output:
for message in WATER_OUT_OF_ORDER_MESSAGES:
self.assertTrue(message in output)
self.assertLess(len(output), 650)
finally:
silent_remove(DEF_OUT, disable=DISABLE_REMOVE)
def testMixedInput(self):
"""
This input file has tuples and lists that cannot be handled by np.loadtxt
"""
test_input = ["-f", MIXED_INPUT, "-n", "-d", ","]
try:
with capture_stderr(main, test_input) as output:
self.assertTrue("could not be converted to a float" in output)
self.assertFalse(diff_lines(MIXED_OUT, GOOD_MIXED_OUT))
finally:
silent_remove(MIXED_OUT, disable=DISABLE_REMOVE)
def testAllNanInput(self):
"""
This input file has only tuples and lists
"""
try:
with capture_stderr(
main, ["-f", ALL_NAN_INPUT, "-n", "-d", ","]) as output:
self.assertTrue("could not be converted to a float" in output)
self.assertFalse(diff_lines(ALL_NAN_OUT, GOOD_ALL_NAN_OUT))
finally:
silent_remove(ALL_NAN_OUT, logger.isEnabledFor(logging.DEBUG))
def testAddElemReadDictNoOverwrite(self):
# Make sure preserves the element from the original pdb even though not in the read dict
test_input = ["-c", READ_ELEM_DICT_KEEP_ELEM_INI]
try:
silent_remove(DEF_OUT)
if logger.isEnabledFor(logging.DEBUG):
main(test_input)
else:
with capture_stderr(main, ["-c", READ_ELEM_DICT_KEEP_ELEM_INI]) as output:
self.assertTrue("Please add atom type" in output)
self.assertFalse(diff_lines(DEF_OUT, GOOD_ADD_ELEMENT_OUT))
finally:
silent_remove(DEF_OUT, disable=DISABLE_REMOVE)
def testAddElemReadDict(self):
# There will be a missing element because of a missing key in the specified dictionary
test_input = ["-c", READ_ELEM_DICT_INI]
try:
silent_remove(ADD_ELEMENT_OUT)
if logger.isEnabledFor(logging.DEBUG):
main(test_input)
silent_remove(ADD_ELEMENT_OUT)
with capture_stderr(main, test_input) as output:
self.assertTrue("Please add atom type" in output)
self.assertFalse(diff_lines(ADD_ELEMENT_OUT, GOOD_READ_ELEM_OUT))
finally:
silent_remove(ADD_ELEMENT_OUT, disable=DISABLE_REMOVE)
def testAddElementsMissingType(self):
test_input = ["-c", ADD_ELEMENT_MISSING_TYPE_INI]
try:
if logger.isEnabledFor(logging.DEBUG):
main(test_input)
else:
with capture_stderr(main, test_input) as output:
# testing that only get the warning once, so check output length. May change wording a bit,
# so checked than less than length + a buffer (which is less than if multiple warnings are printed)
self.assertLess(len(output), 200)
self.assertTrue("Please add atom type" in output)
self.assertFalse(diff_lines(ADD_ELEMENT_MISSING_OUT, ADD_ELEMENT_MISSING_ORIG))
finally:
silent_remove(ADD_ELEMENT_MISSING_OUT, disable=DISABLE_REMOVE)
def testBadInput(self):
# Test what happens when cannot convert a value to float
# Note: within Intellij, some values were not nan that were nan outside the environment
# thus, I'm not checking the output for exactly no line differences
try:
test_input = ["-f", BAD_INPUT, '-d', ' ']
if logger.isEnabledFor(logging.DEBUG):
main(test_input)
with capture_stderr(main, test_input) as output:
self.assertTrue("could not be converted to a float" in output)
self.assertLess(
len(diff_lines(BAD_INPUT_OUT, GOOD_BAD_INPUT_OUT)), 7)
finally:
silent_remove(BAD_INPUT_OUT, disable=DISABLE_REMOVE)
def testMakeParEqMissingParam(self):
test_input = ["-c", PAR_EQ_MISS_PARAM_INI]
if logger.isEnabledFor(logging.DEBUG):
main(test_input)
with capture_stderr(main, test_input) as output:
self.assertTrue('Missing parameter value' in output)
def testMakeParEqWrongOrder(self):
test_input = ["-c", PAR_EQ_WRONG_ORDER_INI]
if logger.isEnabledFor(logging.DEBUG):
main(test_input)
with capture_stderr(main, test_input) as output:
self.assertTrue('Check order' in output)
def testMakeParMissingKeyFileName(self):
test_input = ["-c", PAR_NO_NEW_FILE_NAME_INI, "-f", '{ghost}.par']
if logger.isEnabledFor(logging.DEBUG):
main(test_input)
with capture_stderr(main, test_input) as output:
self.assertTrue('required for filled template file name' in output)
def testUnexpectedKey(self):
# main(["-c", UNEXPECTED_KEY_INI])
with capture_stderr(main, ["-c", UNEXPECTED_KEY_INI]) as output:
self.assertTrue("Unexpected key" in output)
def testRepeatKeyNumDict(self):
# main(["-c", ATOM_DICT_REPEAT_INI])
with capture_stderr(main, ["-c", ATOM_DICT_REPEAT_INI]) as output:
self.assertTrue("non-unique" in output)
def testReadBadAtomNumDict(self):
# main(["-c", ATOM_DICT_BAD_INI])
with capture_stderr(main, ["-c", ATOM_DICT_BAD_INI]) as output:
self.assertTrue("xx" in output)
self.assertTrue("Problems with input" in output)
def testMissingTpl(self):
test_input = ["-c", MISSING_TPL_INI]
if logger.isEnabledFor(logging.DEBUG):
main(test_input)
with capture_stderr(main, test_input) as output:
self.assertTrue("template file specified" in output)
def testMissingWord(self):
test_input = ["-d", USER_DICT]
if logger.isEnabledFor(logging.DEBUG):
main(test_input)
with capture_stderr(main, test_input) as output:
self.assertTrue("new_word" in output)
def testVectorNotArray(self):
test_input = ["-f", VEC_INPUT, "-d", ' ']
if logger.isEnabledFor(logging.DEBUG):
main(test_input)
with capture_stderr(main, test_input) as output:
self.assertTrue("File contains a vector" in output)
def testNoArgs(self):
with capture_stderr(main, []) as output:
self.assertTrue("Problems reading file" in output)
def testNoSuchOption(self):
with capture_stderr(main, ["-@", DEF_INPUT]) as output:
self.assertTrue("unrecognized argument" in output)
self.assertTrue(DEF_INPUT in output)
