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SimStore: Support for OpenMM snapshots #949

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Merged
dwhswenson merged 15 commits into from
Dec 23, 2020
Merged

SimStore: Support for OpenMM snapshots #949

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a67f164
Refactor for attribute handler factories
dwhswenson Dec 1, 2020
51cbccd
redo attribute handlers; integrate for ndarray
dwhswenson Dec 3, 2020
31892e9
complete transition to attribute handlers (numpy)
dwhswenson Dec 3, 2020
1a2ae80
support for simtk units (needs tests)
dwhswenson Dec 3, 2020
c4d0ade
most of the way to storing OpenMM snapshots
dwhswenson Dec 4, 2020
d4546e2
Add engine to StaticContainer/KineticContainer
dwhswenson Dec 4, 2020
b8fa05d
Seems like I can store/load OpenMM snapshots now!
dwhswenson Dec 5, 2020
1523850
move proxy and UUID stuff to their own files
dwhswenson Dec 12, 2020
7224f2e
Fix test for new file locs
dwhswenson Dec 12, 2020
4e29269
docstrings
dwhswenson Dec 12, 2020
c5b6f78
Misc fixes to get the new tutorial to work
dwhswenson Dec 12, 2020
1bf7a16
tests for attribute_handler.py
dwhswenson Dec 19, 2020
9e901bf
Additional test for scalarize_singletons
dwhswenson Dec 19, 2020
8f97732
tests for simstore/simtk-quantity serialization
dwhswenson Dec 20, 2020
62d09d6
integration tests for openmm snapshots
dwhswenson Dec 20, 2020
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tests for attribute_handler.py
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@dwhswenson
dwhswenson committed Dec 19, 2020
commit 1bf7a16d4418baa8cff1ec7a9043aeaa5de5c7a8
50 changes: 50 additions & 0 deletions openpathsampling/experimental/simstore/test_attribute_handlers.py
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import pytest

import numpy as np

from .attribute_handlers import *

class TestStandardHandler(object):
def setup(self):
self.obj = {'str': 'foo',
'int': 42,
'float': 3.14159,
'function': lambda x: x}

@pytest.mark.parametrize('type_str, expected', [
('str', 'str'), ('int', 'int'), ('float', 'float'),
('function', 'function'), ('ndarray.float32(3,2)', None),
])
def test_is_my_type(self, type_str, expected):
assert StandardHandler.is_my_type(type_str) == expected

@pytest.mark.parametrize('type_str', ['str', 'int', 'float', 'function'])
def test_serialization_cycle(self, type_str):
handler = StandardHandler(type_str)
data = self.obj[type_str]
ser = handler.serialize(data)
deser = handler.deserialize(ser)
reser = handler.serialize(deser)
assert data == deser
assert ser == reser


class TestNDArrayHandler(object):
def setup(self):
self.data = np.array([[0.0, 1.0, 2.0], [3.0, 4.0, 5.0]])
self.ndarray_handler = NDArrayHandler(('float32', (2,3)))

@pytest.mark.parametrize('type_str,expected', [
('str', None),
('ndarray.float32(3, 2)', (np.float32, (3, 2))),
('ndarray.float32(3,2)', (np.float32, (3, 2))),
])
def test_is_my_type(self, type_str, expected):
assert NDArrayHandler.is_my_type(type_str) == expected

def test_serialization_cycle(self):
ser = self.ndarray_handler.serialize(self.data)
deser = self.ndarray_handler.deserialize(ser)
np.testing.assert_equal(deser, self.data)
reser = self.ndarray_handler.serialize(deser)
assert ser == reser