Skip to content

Restructure file functions #14

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
dwhswenson merged 6 commits into from
Mar 3, 2020
Merged

Restructure file functions #14

Changes from 1 commit
Commits
Show all changes
6 commits
Select commit Hold shift + click to select a range
d638dcf
make strip-snapshots stuff more reusable
dwhswenson Feb 16, 2020
a44578f
(temporarily) remove strip_snapshots
dwhswenson Feb 25, 2020
748705b
add file_copying and start to its tests
dwhswenson Feb 28, 2020
7033c0d
tests for precomputing CVs
dwhswenson Mar 2, 2020
3ae0ce1
remaining tests for file_copying
dwhswenson Mar 2, 2020
222bd2f
remove references to strip-snapshots
dwhswenson Mar 2, 2020
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
Prev Previous commit
Next Next commit
tests for precomputing CVs
  • Loading branch information
@dwhswenson
dwhswenson committed Mar 2, 2020
commit 7033c0da0b444eb5cf5b2fd71a525ae0e361950e
56 changes: 53 additions & 3 deletions paths_cli/tests/test_file_copying.py
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,11 +1,41 @@
import os

import tempfile
from unittest.mock import MagicMock, patch
import pytest


import openpathsampling as paths
from openpathsampling.tests.test_helpers import make_1d_traj

from paths_cli.file_copying import *

class Test_PRECOMPUTE_CVS(object):
pass
def setup(self):
self.tmpdir = tempfile.mkdtemp()
self.storage_filename = os.path.join(self.tmpdir, "test.nc")
self.storage = paths.Storage(self.storage_filename, mode='w')
snap = make_1d_traj([1])[0]
self.storage.save(snap)
self.cv_x = paths.CoordinateFunctionCV("x", lambda s: s.xyz[0][0])
self.cv_y = paths.CoordinateFunctionCV("y", lambda s: s.xyz[0][1])
self.storage.save([self.cv_x, self.cv_y])

def teardown(self):
self.storage.close()

for filename in os.listdir(self.tmpdir):
os.remove(os.path.join(self.tmpdir, filename))
os.rmdir(self.tmpdir)

@pytest.mark.parametrize('getter', ['x', None, '--'])
def test_get(self, getter):
expected = {'x': [self.cv_x],
None: [self.cv_x, self.cv_y],
'--': []}[getter]
getter = [] if getter is None else [getter] # CLI gives a list
cvs = PRECOMPUTE_CVS.get(self.storage, getter)
assert len(cvs) == len(expected)
assert set(cvs) == set(expected)


@pytest.mark.parametrize('blocksize', [2, 3, 5, 10, 12])
Expand All @@ -22,8 +52,28 @@ def test_make_blocks(blocksize):


class TestPrecompute(object):
def setup(self):
class RunOnceFunction(object):
def __init__(self):
self.previously_seen = set([])

def __call__(self, snap):
if snap in self.previously_seen:
raise AssertionError("Second CV eval for " + str(snap))
self.previously_seen.update({snap})
return snap.xyz[0][0]

self.cv = paths.FunctionCV("test", RunOnceFunction())
traj = paths.tests.test_helpers.make_1d_traj([2, 1])
self.snap = traj[0]
self.other_snap = traj[1]

def test_precompute_cvs(self):
pytest.skip()
precompute_cvs([self.cv], [self.snap])
assert self.cv.f.previously_seen == {self.snap}
recalced = self.cv(self.snap) # AssertionError if func called
assert recalced == 2
assert self.cv.diskcache_enabled is True

def test_precompute_cvs_and_inputs(self):
pytest.skip()
Expand Down