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# -*- coding: utf-8 -*-
#
# Copyright (c) 2023, 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.
"""Run data tests for cclib."""
import importlib
import logging
import os
import sys
import unittest
from typing import List, Optional, Type, Union
import cclib
__filedir__ = os.path.realpath(os.path.dirname(__file__))
# We need this in Python3 for importing things from the same directory
# within the unit test files.
sys.path.insert(1, os.path.join(__filedir__, 'data'))
parser_names = [
"ADF", "DALTON", "FChk", "GAMESS", "GAMESSDAT", "GAMESSUK", "Gaussian", "Jaguar",
"Molpro", "Molcas", "MOPAC", "NWChem", "ORCA", "Psi4", "QChem",
"Turbomole",
]
all_parsers = {name: getattr(cclib.parser, name) for name in parser_names}
# Not used currently, but keeping in a list to keep track of which parsers
# are in the legacy bin.
legacy_parser_names = ["Psi3"]
module_names = [
"SP", "SPun", "GeoOpt", "Basis", "Core", # Basic calculations.
"MP", "CC", "CI", "TD", "TDun", # Post-SCF calculations.
"BOMD", "NMR", "Polar", "Scan", "vib" # Other property calculations.
]
all_modules = {
tn: importlib.import_module(f".data.test{tn}", package="test")
for tn in module_names
}
def gettestdata():
"""Return a dict of the test file data."""
testdatadir = os.path.dirname(os.path.realpath(__file__))
with open(f"{testdatadir}/testdata") as testdatafile:
lines = testdatafile.readlines()
# Remove blank lines and those starting with '#'.
lines = [line for line in lines if (line.strip() and line[0] != '#')]
# Remove comment at end of lines (everything after a '#').
lines = [line.split('#')[0] for line in lines]
# Transform remaining lines into dictionaries.
cols = [line.split() for line in lines]
labels = ('module', 'parser', 'class', 'subdir', 'files')
testdata = [dict(zip(labels, (c[0], c[1], c[2], c[3], c[4:]))) for c in cols]
return testdata
def get_program_dir(parser_name: str) -> str:
"""Return a directory name given a parser name.
In at least one case (GAMESS-UK) the directory is named differently.
"""
if parser_name == "GAMESSUK":
return "GAMESS-UK"
return parser_name
def getdatafile(parser: Union[str, Type[cclib.parser.logfileparser.Logfile]], subdir, files, stream=None, loglevel: int = logging.ERROR, datatype: Optional[Type[cclib.parser.data.ccData]] = None):
"""Returns a parsed logfile.
Inputs:
parser - a logfile parser class (subclass of LogFile)
subdir - subdirectory containing data files (program version)
files - data filename(s)
stream - where to log to (sys.stdout by default)
loglevel - what level to log at
datatype - ccData or child class
Outputs:
data - the resulting data object
logfile - the parser object used for parsing
"""
# Convert any string into the parser object we will be using.
if isinstance(parser, str):
parser = all_parsers[parser]
datadir = os.path.abspath(os.path.join(os.path.dirname(__file__), "..", "data"))
programdir = os.path.join(get_program_dir(parser.__name__), subdir)
inputs = [os.path.join(datadir, programdir, fn) for fn in files]
# We should be able to pass a list of length one here, but for some reason
# this does not work with some parsers and we get errors.
if len(inputs) == 1:
inputs = inputs[0]
stream = stream or sys.stdout
logfile = parser(inputs, logstream=stream, loglevel=loglevel,
datatype=datatype or cclib.parser.data.ccData)
data = logfile.parse()
return data, logfile
def ccdata_getattribute_with_coverage(self, attr):
"""A bookkeeping version of __getattribute__ for ccData objects."""
if attr != '_attrlist' and attr in self._attrlist:
if not hasattr(self, 'coverage'):
self.coverage = {}
self.coverage[attr] = self.coverage.get(attr, 0) + 1
return object.__getattribute__(self, attr)
class DataSuite:
"""Suite containing data (logfile) tests in cclib.
This is supposed to represent a single run of the entire data test suite in cclib or
a subset of it. The main functions are to load data, run test cases in the data/
subdirectory, and do some basic bookkeeping.
"""
def __init__(self, parsers, modules, terse: bool = False, silent: bool = False, loglevel: int = logging.ERROR, stream=sys.stdout) -> None:
self.parsers = parsers
self.modules = modules
self.terse = terse or silent
self.silent = silent
self.loglevel = loglevel
self.stream = stream
# Load the test data and filter with parsers and modules.
self.testdata = gettestdata()
self.testdata = [td for td in self.testdata if td['parser'] in self.parsers]
self.testdata = [td for td in self.testdata if td['module'] in self.modules]
# We want to gather the unit tests and results in several lists/dicts,
# in order to easily generate summaries at the end.
self.errors = []
self.failures = []
self.alltests = []
self.perpackage = {p: [0, 0, 0, 0] for p in self.parsers}
def testall(self) -> List[str]:
"""Run all unittests in all modules.
Run unit tests for all or a subset of parsers and modules. Arguments:
stream - stream used for all output
"""
stream_test = self.stream
if self.terse:
devnull = open(os.devnull, 'w')
stream_test = devnull
for td in self.testdata:
module = self.modules[td['module']]
parser = self.parsers[td['parser']]
test = getattr(module, td['class'])
description = ''
if not self.silent:
print("", file=stream_test)
description = f"{td['subdir']}/{','.join(td['files'])}: {test.__doc__}"
print(f"*** {description} ***", file=self.stream)
test.data, test.logfile = getdatafile(
parser, td['subdir'], td['files'], stream=self.stream, loglevel=self.loglevel,
datatype=test.datatype if hasattr(test, 'datatype') else None
)
# By overriding __getattribute__ temporarily with a custom method, we collect
# coverage information for data attributes while the tests are run. This slightly
# hacky approach is very convenient since it is self-contained and we don't
# need to worry about it when writing the actual test cases.
test.data.__class__.__getattribute__ = ccdata_getattribute_with_coverage
# Here we actually run the tests for this line in testdata.
myunittest = unittest.makeSuite(test)
results = unittest.TextTestRunner(stream=stream_test, verbosity=2).run(myunittest)
# We don't want to collect coverage stats beyond this point, so set __getattribute__
# back to its original value. Note that we are setting the class method.
test.data.__class__.__getattribute__ = object.__getattribute__
self.perpackage[td['parser']][0] += results.testsRun
self.perpackage[td['parser']][1] += len(results.errors)
self.perpackage[td['parser']][2] += len(results.failures)
self.perpackage[td['parser']][3] += len(getattr(results, 'skipped', []))
self.alltests.append(test)
self.errors.extend(
[f"{description}\n{''.join(map(str, e))}" for e in results.errors]
)
self.failures.extend(
[f"{description}\n{''.join(map(str, f))}" for f in results.failures]
)
if self.terse:
devnull.close()
return self.errors or self.failures
def summary(self) -> None:
"""Prints a summary of the suite after it has been run."""
if self.errors:
print("\n********* SUMMARY OF ERRORS *********\n", file=self.stream)
print("\n".join(self.errors), file=self.stream)
if self.failures:
print("\n********* SUMMARY OF FAILURES *********\n", file=self.stream)
print("\n".join(self.failures), file=self.stream)
print("\n********* SUMMARY PER PACKAGE ****************", file=self.stream)
names = sorted(self.perpackage.keys())
total = [0, 0, 0, 0]
print(" "*14, "\t".join(["Total", "Passed", "Failed", "Errors", "Skipped"]), file=self.stream)
fmt = "%3d\t%3d\t%3d\t%3d\t%3d"
for name in names:
l = self.perpackage[name]
args = (l[0], l[0]-l[1]-l[2]-l[3], l[2], l[1], l[3])
print(name.ljust(15), fmt % args, file=self.stream)
for i in range(4):
total[i] += l[i]
print("\n********* SUMMARY OF EVERYTHING **************", file=self.stream)
print(
f"TOTAL: {int(total[0])}\tPASSED: {int(total[0] - (total[1] + total[2] + total[3]))}\tFAILED: {int(total[2])}\tERRORS: {int(total[1])}\tSKIPPED: {int(total[3])}",
file=self.stream,
)
def visualtests(self, stream=sys.stdout) -> None:
"""These are not formal tests -- but they should be eyeballed."""
parsers_to_test = {
'ADF2013.01' : getdatafile('ADF', "basicADF2013.01", ["dvb_gopt.adfout"])[0],
'DALTON2015' : getdatafile('DALTON', "basicDALTON-2015", ["dvb_gopt_ks.out"])[0],
'Firefly8.0' : getdatafile('GAMESS', "basicFirefly8.0", ["dvb_gopt_a.out"])[0],
'Gaussian16' : getdatafile('Gaussian', "basicGaussian16", ["dvb_gopt.out"])[0],
'GAMESS-US2018' : getdatafile('GAMESS', "basicGAMESS-US2018", ["dvb_gopt_a.out"])[0],
'Jaguar8.0' : getdatafile('Jaguar', "basicJaguar8.3", ["dvb_gopt_ks.out"])[0],
'Molpro2012' : getdatafile('Molpro', "basicMolpro2012", ["dvb_gopt.out", "dvb_gopt.log"])[0],
# Note that it doesn't make sense to put MOPAC here, as it
# is a semiempirical-only program.
'NWChem6.5' : getdatafile('NWChem', "basicNWChem6.5", ["dvb_gopt_ks.out"])[0],
'ORCA4.2' : getdatafile('ORCA', "basicORCA4.2", ["dvb_gopt.out"])[0],
'Psi4-1.3.1' : getdatafile('Psi4', "basicPsi4-1.3.1", ["dvb_gopt_rks.out"])[0],
'QChem5.4' : getdatafile('QChem', "basicQChem5.4", ["dvb_gopt.out"])[0],
}
parser_names = sorted(parsers_to_test.keys())
output = [parsers_to_test[pn] for pn in parser_names]
print("\n*** Visual tests ***", file=self.stream)
print("MO energies of optimised dvb", file=self.stream)
print(
" ", "".join([f"{pn:12s}" for pn in parser_names]), file=self.stream
)
print(
"HOMO",
" ".join([f"{out.moenergies[0][out.homos[0]]:+9.4f}" for out in output]),
file=self.stream,
)
print(
"LUMO",
" ".join(
[f"{out.moenergies[0][out.homos[0] + 1]:+9.4f}" for out in output]
),
file=self.stream,
)
print(
"H-L ",
" ".join(
[
f"{out.moenergies[0][out.homos[0] + 1] - out.moenergies[0][out.homos[0]]:9.4f}"
for out in output
]
),
file=self.stream,
)
def test_all(parsers, modules, terse: bool, silent: bool, loglevel: int, summary: bool, visual_tests: bool) -> None:
parsers = parsers or all_parsers
modules = modules or all_modules
data_suite = DataSuite(parsers, modules, terse=terse, silent=silent, loglevel=loglevel)
errors_or_failures = data_suite.testall()
if summary and not silent:
data_suite.summary()
if visual_tests and not silent:
data_suite.visualtests()
if errors_or_failures:
sys.exit(1)
if __name__ == "__main__":
import argparse
parser = argparse.ArgumentParser()
parser.add_argument("--debug", action="store_true")
parser.add_argument("--terse", action="store_true")
parser.add_argument("--silent", action="store_true")
parser.add_argument(
"parser_or_module",
nargs="*",
help="Limit the test to the packages/parsers passed as arguments. "
"No arguments implies all parsers."
)
args = parser.parse_args()
loglevel = logging.DEBUG if args.debug else logging.ERROR
# No matching parsers/modules implies all of them.
parsers = {p: all_parsers[p] for p in parser_names
if p in args.parser_or_module} or None
modules = {m: all_modules[m] for m in module_names
if m in args.parser_or_module} or None
test_all(parsers, modules, terse=args.terse, silent=args.silent, loglevel=loglevel, summary=True, visual_tests=True)
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