class Test_W_Trace_Args(unittest.TestCase, CommonToolTest):
'''Class to test w_trace works with different positional arguments (of the form n_iter:seg_id [n_iter:seg_id])
This class tests that a) w_trace works with different numbers of positional arguments, b) that the output file is set up
correctly AND the data from subsequent traces is appended (in other words, if there is an existing output file, it
is not overwritten each time trace is called), and c) that the content of the h5 files generated match the content of previously
generated reference files.'''
arg_combos = [['20:0'], ['20:1', '20:2']]
ref_files = ['refs/trajs_ref_20_0.h5', 'refs/trajs_ref_full.h5']
test_name = 'W_TRACE'
def test_args(self):
'''Testing arg combos: w_trace runs as expected'''
self.args_so_far = []
self.endpoints = []
self.outfile = self.mktemp(prefix='trace')
outarg = '-o={}'.format(self.outfile)
for idx, args in enumerate(self.arg_combos):
self.w = WTraceTool()
self.args_so_far.extend(args)
args.append(outarg)
self.w.make_parser_and_process(args=args)
self.endpoints.extend(self.w.endpoints)
args.remove(outarg)
test_outcome, err = self.check_runs_with_args(idx)
yield self.check_args, test_outcome, err, args
del self.w
yield self.check_args, test_outcome, err, args
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_args(self):
'''Testing arg combos: w_trace runs as expected'''
self.args_so_far = []
self.endpoints = []
self.outfile = self.mktemp(prefix='trace')
outarg = '-o={}'.format(self.outfile)
for idx, args in enumerate(self.arg_combos):
self.w = WTraceTool()
self.args_so_far.extend(args)
args.append(outarg)
self.w.make_parser_and_process(args=args)
self.endpoints.extend(self.w.endpoints)
args.remove(outarg)
test_outcome, err = self.check_runs_with_args(idx)
return self.check_args, test_outcome, err, args
del self.w
return self.check_args, test_outcome, err, args