def test_compare_evol_h5(self, ref_50iter):
'''Test to compare plothist evolution pdf was generated'''
with mock.patch(
target='argparse.ArgumentParser.parse_args',
return_value=argparse.Namespace(
verbosity='debug',
rcfile=self.cfg_filepath,
input='pdist_ref.h5',
firstdim='0',
plot_output='hist_evol.pdf',
hdf5_output='hist_evol.h5',
plot_contour=False,
title=None,
plotscale='energy',
enerzero='min',
range=None,
postprocess_function=None,
seconddim=None,
first_iter=1,
last_iter=50,
step_iter=None,
west_subcommand=EvolutionPlotHist(1),
),
):
entry_point()
assert os.path.isfile('./hist_evol.pdf'), "The evolution pdf was not generated."
diff = H5Diff('hist_evol_ref.h5', 'hist_evol.h5')
diff.check()
# clean up
os.remove('hist_evol.pdf')
os.remove('hist_evol.h5')
def test_run_w_pdist(self, ref_50iter):
'''Testing if w_pdist runs as expected and the pdist.h5 file looks good.'''
with mock.patch(
target='argparse.ArgumentParser.parse_args',
return_value=argparse.Namespace(
verbosity='debug',
rcfile=self.cfg_filepath,
max_queue_length=None,
we_h5filename=self.h5_filepath,
construct_dataset=None,
dsspecs=None,
group_name='pcoord',
first_iter=1,
last_iter=None,
bins='100',
output='pdist.h5',
ignore_out_of_range=False,
compress=False,
work_manager=None,
n_workers=None,
construct_wdataset=None,
),
):
entry_point()
assert os.path.isfile(
'./pdist.h5'), "The pdist.h5 file was not generated."
diff = H5Diff('pdist_ref.h5', 'pdist.h5')
diff.check()
# clean up
os.remove('pdist.h5')
def test_run_w_init(self, ref_cfg):
'''Tests initialization of a WESTPA simulation system from a prebuilt .cfg'''
# This test is named in such a way so it always runs before test_w_assign.py. It will fail otherwise.
# The argument processing is just looking for an object with these attributes
args = MockArgs(force=True,
rcfile=self.cfg_filepath,
verbosity='verbose')
westpa.rc.process_args(args)
westpa.cli.core.w_init.initialize(
tstates=None,
tstate_file=None,
bstates=['initial,1.0'],
bstate_file=None,
sstates=None,
sstate_file=None,
segs_per_state=1,
shotgun=False,
)
# h5 files contain some internal information that includes timestamps, so I can't just compare md5 checksums
# to ensure that w_init is producing the same output.
# Instead, use my H5Diff class.
# If the checked contents differ, an AssertionError will be raised.
diff = H5Diff(self.ref_h5_filepath, self.h5_filepath)
diff.check()
def test_run_w_multi_west(self, ref_multi):
'''Testing if w_pdist runs as expected and the pdist.h5 file looks good.'''
with mock.patch(
target='argparse.ArgumentParser.parse_args',
return_value=argparse.Namespace(
verbosity='debug',
rcfile=self.cfg_filepath,
max_queue_length=None,
west=self.h5_filepath,
output_file='multi.h5',
master='.',
sims='3',
aux=None,
auxall=True,
no_reweight=False,
),
):
entry_point()
assert os.path.isfile(
'./multi.h5'), "The multi.h5 file was not generated."
diff = H5Diff('multi_aux_ref.h5', 'multi.h5')
diff.check()
# clean up
os.remove('multi.h5')
def test_run_w_direct(self):
'''Testing if w_direct runs as expected and the direct.h5 file looks good.'''
ref_dir = os.path.join(os.path.dirname(__file__), '../refs')
shutil.copy2(os.path.join(ref_dir, 'west_ref.h5'), './west.h5')
os.system('w_direct all')
assert os.path.isfile(
'./direct.h5'), "The direct.h5 file was not generated."
diff = H5Diff(os.path.join(ref_dir, 'direct_ref.h5'), './direct.h5')
diff.check()
os.remove('direct.h5')
os.remove('west.h5')
def check_output(self, arg_idx):
with h5py.File(self.outfile) as f:
assert 'trajectories' in list(f.keys()), "'trajectories' group not in output file"
traj_group = f['trajectories']
# Expected trace groups - successive runs of w_trace with different traces should add
# newly traced groups to output hdf5 file
expected_groups = sorted([self.w.output_pattern % (n_iter, seg_id) for n_iter, seg_id in self.endpoints])
assert list(traj_group.keys()) == expected_groups, "H5 groups ({}) are not as expected ({})".format(
list(traj_group.keys()), expected_groups
)
diff = H5Diff(self.ref_files[arg_idx], self.outfile)
diff.check()
def test_run_w_direct(self, ref_50iter):
with mock.patch(
target='argparse.ArgumentParser.parse_args',
return_value=argparse.Namespace(
verbosity='debug',
rcfile=self.cfg_filepath,
work_manager=None,
max_queue_length=None,
west_subcommand=DAll(1),
we_h5filename=self.h5_filepath,
construct_dataset=None,
dsspecs=None,
output='direct.h5',
kinetics='direct.h5',
first_iter=1,
last_iter=None,
step_iter=None,
assignments='assign_ref.h5',
evolution_mode=None,
subsample=None,
config_from_file=True,
scheme='TEST',
bootstrap=None,
correl=None,
alpha=0.05,
acalpha=None,
nsets=None,
window_frac=1.0,
display_averages=True,
),
):
entry_point()
diff = H5Diff('./direct_ref.h5', './direct.h5')
diff.check()
# clean up
os.remove('direct.h5')
def test_run_w_assign(self, ref_50iter):
args = MockArgs(
verbosity='debug',
rcfile=self.cfg_filepath,
max_queue_length=None,
we_h5filename=self.h5_filepath,
construct_dataset=None,
dsspecs=None,
output='assign.h5',
subsample=None,
config_from_file=True,
scheme='TEST',
)
# This basically some logic that's wrapped up in WESTTool.main() for convenience.
# It needs to be explicitly called like this because the args are captured and set in make_parser_and_process()
# which we don't want to call, because we don't want to make a parser.
# We just want to process the args that "would've" been captured if called from CLI.
tool = w_assign.WAssign()
# Prepare and instantiate work manager
tool.wm_env.process_wm_args(args)
tool.work_manager = tool.wm_env.make_work_manager()
tool.process_all_args(args)
with tool.work_manager:
if tool.work_manager.is_master:
tool.go()
else:
tool.work_manager.run()
diff = H5Diff('./assign_ref.h5', './ANALYSIS/TEST/assign.h5')
diff.check()
# clean up
shutil.rmtree('ANALYSIS')