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Merged
dwhswenson merged 10 commits into from
Dec 17, 2020
Merged

New command: md #35

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fbe73da
Add md command
dwhswenson Dec 8, 2020
98f3868
Add tests for md
dwhswenson Dec 9, 2020
830ef03
cleanup
dwhswenson Dec 9, 2020
6125554
tests for md command
dwhswenson Dec 9, 2020
00b83cc
more test coverage
dwhswenson Dec 9, 2020
586f1a7
docstrings
dwhswenson Dec 9, 2020
8df4a54
Add progress reporting to md command
dwhswenson Dec 9, 2020
fb91628
Merge remote-tracking branch 'upstream/master' into md
dwhswenson Dec 10, 2020
38e01ba
Merge remote-tracking branch 'upstream/master' into md
dwhswenson Dec 11, 2020
8e9fa46
more tests; docstrings
dwhswenson Dec 15, 2020
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more test coverage
  • Loading branch information
@dwhswenson
dwhswenson committed Dec 9, 2020
commit 00b83cc118453283ee827ce5485297a6265364e5
3 changes: 0 additions & 3 deletions paths_cli/commands/md.py
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Original file line number Diff line number Diff line change
Expand Up @@ -66,9 +66,6 @@ def __call__(self, trajectory, trusted=False):
if not done]
# TODO: update on how many ensembles left, what frame number we are

if not unsatisfied:
return False

start = -1
while self._check_previous_frame(trajectory, start, unsatisfied):
start -= 1
Expand Down
34 changes: 27 additions & 7 deletions paths_cli/tests/commands/test_md.py
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Expand Up @@ -31,9 +31,9 @@ def setup(self):
]).named('transition'),
]
self.ensembles = {ens.name: ens for ens in ensembles}
traj_vals = [-0.1, 1.1, 0.5, -0.2, 0.1, -0.3, 0.4, 1.4, -1.0]
self.trajectory = make_1d_traj(traj_vals)
self.engine = CalvinistDynamics(traj_vals)
self.traj_vals = [-0.1, 1.1, 0.5, -0.2, 0.1, -0.3, 0.4, 1.4, -1.0]
self.trajectory = make_1d_traj(self.traj_vals)
self.engine = CalvinistDynamics(self.traj_vals)
self.satisfied_when_traj_len = {
"len1": 1,
"len3": 3,
Expand Down Expand Up @@ -76,6 +76,10 @@ def test_call(self, traj_len, expected, trusted):
# only test call count if we're trusted
assert mock.call_count == expected_calls

def test_long_traj_untrusted(self):
traj = make_1d_traj(self.traj_vals + [1.0, 1.2, 1.3, 1.4])
assert self.conditions(traj) is False

def test_generate(self):
init_snap = self.trajectory[0]
traj = self.engine.generate(init_snap, self.conditions)
Expand Down Expand Up @@ -118,17 +122,25 @@ def test_md(md_fixture):
assert results.output == expected_output
assert results.exit_code == 0

def test_md_main(md_fixture):
@pytest.mark.parametrize('inp', ['nsteps', 'ensemble'])
def test_md_main(md_fixture, inp):
tempdir = tempfile.mkdtemp()
try:
store_name = os.path.join(tempdir, "md.nc")
storage = paths.Storage(store_name, mode='w')
engine, ensemble, snapshot = md_fixture
engine, ens, snapshot = md_fixture
if inp == 'nsteps':
nsteps, ensembles = 5, None
elif inp == 'ensemble':
nsteps, ensembles = None, [ens]
else:
raise RuntimeError("pytest went crazy")

traj, foo = md_main(
output_storage=storage,
engine=engine,
ensembles=[ensemble],
nsteps=None,
ensembles=ensembles,
nsteps=nsteps,
initial_frame=snapshot
)
assert isinstance(traj, paths.Trajectory)
Expand All @@ -140,3 +152,11 @@ def test_md_main(md_fixture):
os.remove(store_name)
os.rmdir(tempdir)

def test_md_main_error(md_fixture):
engine, ensemble, snapshot = md_fixture
with pytest.raises(RuntimeError):
md_main(output_storage=None,
engine=engine,
ensembles=[ensemble],
nsteps=5,
initial_frame=snapshot)