def parse_qchem_matrix(data):
ret_val = [[]]
def parse_line(cols, m):
row = int(m.group(1)) - 1
data = [float(f) for f in m.group(2).strip().split()]
while len(ret_val) < row + 1:
ret_val.append([])
while len(ret_val[row]) < cols[-1] + 1:
ret_val[row].append(None)
if len(cols) != len(data):
raise OutputParsingError("ragged matrix in output:\n{}".format(indented(data)))
for d, col in zip(data, cols):
ret_val[row][col] = d
def parse_group_of_lines(m):
columns = [int(s.strip()) - 1 for s in m.group(1).split()]
re.sub(r"(\d)((?:\s+-?\d+\.\d+)+)", partial(parse_line, columns), m.group(2))
re.sub(r"((?:\d+[ \t]*)+\n)[ \t]+((?:\d+(?:\s+-?\d+\.\d+)+\s+)+)", parse_group_of_lines, data)
if None in flattened(ret_val):
raise OutputParsingError("output matrix missing value:\n{}".format(indented(data)))
return Matrix(ret_val)
return decorate_it
#--------------------------------------------------------------------------------#
# construct suites
# get the list of tests
grendel_suite_all = unittest.defaultTestLoader.discover(
os.path.dirname(__file__))
profile_suite = unittest.TestSuite()
profile_subsuites = defaultdict(lambda: unittest.TestSuite())
standard_suite = unittest.TestSuite()
long_only_suite = unittest.TestSuite()
subsuites = defaultdict(lambda: unittest.TestSuite())
# Now iterate over all of the tests
for test in flattened(grendel_suite_all):
test_func = getattr(test, test.id().split('.')[-1], None)
if test_func is not None:
#----------------------------------------#
profile_subsuite = getattr(test_func, '__profile__', None)
if profile_subsuite is not None:
profile_suite.addTest(test)
if isinstance(profile_subsuite, tuple):
for subsuite in profile_subsuite:
profile_subsuites[subsuite].addTest(test)
#----------------------------------------#
long_test_attr = getattr(test_func, '__is_long_test__', None)
if long_test_attr:
long_only_suite.addTest(test)
if hide_skipped_tests:
# Change the __name__ attribute so that it doesn't get discovered
f.__subsuites__ = []
for arg in args:
f.__subsuites__.append(arg)
return f
return decorate_it
#--------------------------------------------------------------------------------#
# construct suites
# get the list of tests
grendel_suite_all = unittest.defaultTestLoader.discover(os.path.dirname(__file__))
profile_suite = unittest.TestSuite()
profile_subsuites = defaultdict(lambda: unittest.TestSuite())
standard_suite = unittest.TestSuite()
long_only_suite = unittest.TestSuite()
subsuites = defaultdict(lambda: unittest.TestSuite())
# Now iterate over all of the tests
for test in flattened(grendel_suite_all):
test_func = getattr(test, test.id().split('.')[-1], None)
if test_func is not None:
#----------------------------------------#
profile_subsuite = getattr(test_func, '__profile__', None)
if profile_subsuite is not None:
profile_suite.addTest(test)
if isinstance(profile_subsuite, tuple):
for subsuite in profile_subsuite:
profile_subsuites[subsuite].addTest(test)
#----------------------------------------#
long_test_attr = getattr(test_func, '__is_long_test__', None)
if long_test_attr:
long_only_suite.addTest(test)
if hide_skipped_tests:
# Change the __name__ attribute so that it doesn't get discovered
def variables(self):
return [f for f in flattened(
[[self.molecule.cartesian_representation[3*i + d] for d in [0,1,2]] for i in self.atom_indices]
)]
