def compare_directories(directory, ref_directory, ignore=()):
extra_files = []
missing_files = []
for root, dirs, files in os.walk(directory):
for single_file in [f for f in files if f not in ignore]:
path = os.path.join(root, single_file)
rel_path = os.path.relpath(path, directory)
ref_path = os.path.join(ref_directory, rel_path)
if os.path.exists(ref_path):
if os.path.splitext(ref_path)[-1] == '.gro':
utils.assert_gro_equal(path, ref_path)
compare(path, ref_path)
else:
extra_files.append(rel_path)
for root, dirs, files in os.walk(ref_directory):
for single_file in [f for f in files if f not in ignore]:
path = os.path.join(root, single_file)
rel_path = os.path.relpath(path, ref_directory)
ref_path = os.path.join(directory, rel_path)
if not os.path.exists(ref_path):
missing_files.append(rel_path)
assert not bool(extra_files), ("The following files are unexpected: {}"
.format(extra_files))
assert not bool(missing_files), ("The following files are missing: {}"
.format(missing_files))
def run_and_compare(arguments, input_dir,
ref_gro, ref_top,
ref_stdout, ref_stderr, runner=_run_external):
"""
Run insane and compare its output against a reference
"""
# Create the command as a list for subprocess.Popen.
# The arguments can be pass to the current function as a string or as a
# list of arguments. If they are passed as a string, they need to be
# converted to a list.
arguments = _arguments_as_list(arguments)
# The name of the output gro file must be provided to insane for insane to
# work. Since we also need that file name, let's get it from insane's
# arguments.
gro_output = _output_from_arguments(arguments, option='-o')
if ref_top is not None:
top_output = _output_from_arguments(arguments, option='-p')
# We want insane to run in a temporary directory. This allows to keep the
# file system clean, and it avoids mixing output of different tests.
with utils.tempdir():
out, err, returncode = run_insane(arguments, input_dir, runner=runner)
assert not returncode
assert os.path.exists(gro_output)
if os.path.splitext(gro_output)[-1] == '.gro':
utils.assert_gro_equal(gro_output, ref_gro)
else:
compare(gro_output, ref_gro)
compare(utils.ContextStringIO(out), ref_stdout)
compare(utils.ContextStringIO(err), ref_stderr)
if ref_top is not None:
compare(top_output, ref_top)
def compare_directories(directory, ref_directory, ignore=()):
extra_files = []
missing_files = []
for root, dirs, files in os.walk(directory):
for single_file in [f for f in files if f not in ignore]:
path = os.path.join(root, single_file)
rel_path = os.path.relpath(path, directory)
ref_path = os.path.join(ref_directory, rel_path)
if os.path.exists(ref_path):
if os.path.splitext(ref_path)[-1] == '.gro':
utils.assert_gro_equal(path, ref_path)
compare(path, ref_path)
else:
extra_files.append(rel_path)
for root, dirs, files in os.walk(ref_directory):
for single_file in [f for f in files if f not in ignore]:
path = os.path.join(root, single_file)
rel_path = os.path.relpath(path, ref_directory)
ref_path = os.path.join(directory, rel_path)
if not os.path.exists(ref_path):
missing_files.append(rel_path)
assert not bool(extra_files), (
"The following files are unexpected: {}".format(extra_files))
assert not bool(missing_files), (
"The following files are missing: {}".format(missing_files))
def test_equal(self):
"""
Make sure that identical files do not fail.
"""
with utils.tempdir():
with open('ref.gro', 'w') as outfile:
print(textwrap.dedent(self.ref_gro_content),
file=outfile, end='')
utils.assert_gro_equal('ref.gro', 'ref.gro')
def test_equal(self):
"""
Make sure that identical files do not fail.
"""
with utils.tempdir():
with open('ref.gro', 'w') as outfile:
print(textwrap.dedent(self.ref_gro_content),
file=outfile,
end='')
utils.assert_gro_equal('ref.gro', 'ref.gro')
def test_diff_in_tolerance(self):
"""
Make sure that small errors in coordinates are not caught.
"""
gro_content = """\
INSANE! Membrane UpperLeaflet>POPC=1 LowerLeaflet>POPC=1
4
1POPC NC3 1 2.111 14.647 11.951
1POPC PO4 2 2.177 14.644 11.651
1POPC GL1 3 2.128 14.642 11.352 # Is within tolerance
1POPC GL2 4 1.961 14.651 11.351
10 10 10"""
with utils.tempdir():
with open('ref.gro', 'w') as outfile:
print(textwrap.dedent(self.ref_gro_content),
file=outfile, end='')
with open('content.gro', 'w') as outfile:
print(textwrap.dedent(gro_content), file=outfile, end='')
utils.assert_gro_equal('content.gro', 'ref.gro')
def test_diff_in_tolerance(self):
"""
Make sure that small errors in coordinates are not caught.
"""
gro_content = """\
INSANE! Membrane UpperLeaflet>POPC=1 LowerLeaflet>POPC=1
4
1POPC NC3 1 2.111 14.647 11.951
1POPC PO4 2 2.177 14.644 11.651
1POPC GL1 3 2.128 14.642 11.352 # Is within tolerance
1POPC GL2 4 1.961 14.651 11.351
10 10 10"""
with utils.tempdir():
with open('ref.gro', 'w') as outfile:
print(textwrap.dedent(self.ref_gro_content),
file=outfile,
end='')
with open('content.gro', 'w') as outfile:
print(textwrap.dedent(gro_content), file=outfile, end='')
utils.assert_gro_equal('content.gro', 'ref.gro')
def run_and_compare(arguments,
input_dir,
ref_gro,
ref_top,
ref_stdout,
ref_stderr,
runner=_run_external):
"""
Run program and compare its output against a reference
"""
# Create the command as a list for subprocess.Popen.
# The arguments can be pass to the current function as a string or as a
# list of arguments. If they are passed as a string, they need to be
# converted to a list.
arguments = _arguments_as_list(arguments)
# The name of the output file must be provided to program for program to
# work. Since we also need that file name, let's get it from program's
# arguments.
## Magic here -- Expect DRAGONS
gro_output = _output_from_arguments(arguments, option='-o')
if ref_top is not None:
top_output = _output_from_arguments(arguments, option='-p')
# We want program to run in a temporary directory. This allows to keep the
# file system clean, and it avoids mixing output of different tests.
with utils.tempdir():
out, err, returncode = run_program(arguments, input_dir, runner=runner)
assert not returncode
assert os.path.exists(gro_output)
if os.path.splitext(gro_output)[-1] == '.gro':
utils.assert_gro_equal(gro_output, ref_gro)
else:
compare(gro_output, ref_gro)
compare(utils.ContextStringIO(out), ref_stdout)
compare(utils.ContextStringIO(err), ref_stderr)
if ref_top is not None:
compare(top_output, ref_top)
