openpathsampling · dwhswenson · Dec 31, 2020 · Dec 24, 2020 · Dec 25, 2020 · Dec 25, 2020
diff --git a/openpathsampling/experimental/simstore/test_custom_json.py b/openpathsampling/experimental/simstore/test_custom_json.py
@@ -4,7 +4,6 @@
 
 import numpy as np
 from numpy import testing as npt
-from simtk import unit
 
 from . import test_utils
 

diff --git a/openpathsampling/experimental/storage/ops_storage.py b/openpathsampling/experimental/storage/ops_storage.py
@@ -40,7 +40,11 @@
 from . import snapshots
 from .snapshots_table import SnapshotsTable
 
-from .simtk_unit import simtk_quantity_codec, SimtkQuantityHandler
+try:
+    from .simtk_unit import simtk_quantity_codec, SimtkQuantityHandler
+except ImportError:
+    simtk_quantity_codec = None
+    SimtkQuantityHandler = None
 
 import logging
 logger = logging.getLogger(__name__)
@@ -71,8 +75,10 @@
 ops_schema_sql_metadata = {}
 
 # this defines the simulation object serializer for OPS
-CODECS = DEFAULT_CODECS + [simtk_quantity_codec]
-HANDLERS = DEFAULT_HANDLERS + [SimtkQuantityHandler]
+EXTRA_CODECS = [simtk_quantity_codec] if simtk_quantity_codec else []
+EXTRA_HANDLERS = [SimtkQuantityHandler] if SimtkQuantityHandler else []
+CODECS = DEFAULT_CODECS + EXTRA_CODECS
+HANDLERS = DEFAULT_HANDLERS + EXTRA_HANDLERS
 
 UNSAFE_CODECS = CODECS + [CallableCodec()]
 SAFE_CODECS = CODECS + [CallableCodec({'safemode': True})]

diff --git a/openpathsampling/experimental/storage/test_collective_variables.py b/openpathsampling/experimental/storage/test_collective_variables.py
@@ -119,6 +119,7 @@ class TestMDTrajFunctionCV(object):
     def setup(self):
         if not HAS_MDTRAJ:
             pytest.skip("Unable to import MDTraj")
+        pytest.importorskip('simtk.unit')
 
         self.mdt = md.load(data_filename("ala_small_traj.pdb"))
         top = ops_omm.topology.MDTrajTopology(self.mdt.topology)

diff --git a/openpathsampling/netcdfplus/version.py b/openpathsampling/netcdfplus/version.py
@@ -1,4 +1,4 @@
-short_version = '1.4.0'
+short_version = '1.4.1'
 version = short_version
 full_version = short_version
 git_revision = 'alpha'

diff --git a/openpathsampling/tests/test_features.py b/openpathsampling/tests/test_features.py
@@ -1,12 +1,10 @@
 from __future__ import absolute_import
 from builtins import hex
 from builtins import object
-from nose.tools import (assert_equal, assert_not_equal,
-                        assert_almost_equal, raises, assert_in)
+from nose.tools import raises
 
-from nose.plugins.skip import Skip, SkipTest
-from .test_helpers import (true_func, assert_equal_array_array,
-                           make_1d_traj, assert_items_equal, u)
+from nose.plugins.skip import SkipTest
+from .test_helpers import u
 
 import logging
 
@@ -43,7 +41,7 @@ def test_copy_with_replacement_toy(self):
         assert(toy_copy.velocities[1] == 1.0)
 
     def test_copy_with_replacement_openmm(self):
-        if not paths.integration_tools.HAS_OPENMM:
+        if not paths.integration_tools.HAS_OPENMM or omt is None:
             raise SkipTest
         # test an openmm snapshot
         sys = omt.testsystems.AlanineDipeptideVacuum()
@@ -71,4 +69,4 @@ def test_parameter_error(self):
         init_vel = np.array([3.0, 4.0])
         toy_snap = toy_engine.Snapshot(
             coordinates=init_coord, velocities=init_vel)
-        toy_copy = toy_snap.copy_with_replacement(dummy=0)
+        toy_snap.copy_with_replacement(dummy=0)
diff --git a/openpathsampling/tests/test_helpers.py b/openpathsampling/tests/test_helpers.py
@@ -23,8 +23,6 @@
 except ImportError:
     md = None
 
-from nose.tools import assert_equal, assert_in, assert_true
-#from nose.tools import assert_items_equal
 from pkg_resources import resource_filename
 
 import openpathsampling as paths
@@ -61,20 +59,20 @@ def make_1d_traj(coordinates, velocities=None, engine=None):
     return paths.Trajectory(traj)
 
 def items_equal(truth, beauty):
-    assert_equal(len(truth), len(beauty))
+    assert len(truth) == len(beauty)
     for (t, b) in zip(truth, beauty):
         if t != b:
             return False
     return True
 
 def assert_items_equal(truth, beauty):
-    assert_equal(len(truth), len(beauty))
+    assert len(truth) == len(beauty)
     for (t, b) in zip(truth, beauty):
-        assert_equal(t, b)
+        assert t == b
 
 def assert_items_almost_equal(truth, beauty, tol=10e-7):
     for (t,b) in zip(truth, beauty):
-        assert_equal( abs(t-b) - tol < 0.0, True)
+        assert abs(t-b) - tol < 0.0
 
 
 def assert_equal_array_array(truth, beauty):
@@ -90,9 +88,9 @@ def assert_not_equal_array_array(list_a, list_b):
     return exist_diff
 
 def assert_same_items(list_a, list_b):
-    assert_equal(len(list_a), len(list_b))
+    assert len(list_a) == len(list_b)
     for elem_a in list_a:
-        assert_in(elem_a, list_b)
+        assert elem_a in list_b
 
 
 class MoverWithSignature(paths.PathMover):
@@ -306,18 +304,18 @@ def _wrapper(*args, **kwargs):
     return decorator
 
 def assert_frame_equal(truth, beauty):
-    assert_equal(len(truth.index), len(beauty.index))
-    assert_equal(len(truth.columns), len(beauty.columns))
-    assert_equal(set(truth.index), set(beauty.index))
-    assert_equal(set(truth.columns), set(beauty.columns))
+    assert len(truth.index) == len(beauty.index)
+    assert len(truth.columns) == len(beauty.columns)
+    assert set(truth.index) == set(beauty.index)
+    assert set(truth.columns) == set(beauty.columns)
     for idx in truth.index:
         for col in truth.columns:
             truth_val = truth.loc[idx, col]
             beauty_val = beauty.loc[idx, col]
             if np.isnan(truth_val):
-                assert_true(np.isnan(beauty_val))
+                assert np.isnan(beauty_val)
             else:
-                assert_equal(truth_val, beauty_val)
+                assert truth_val == beauty_val
 
 def A2BEnsemble(volume_a, volume_b, trusted=True):
     # this is a little replacement for the same name that used to be in

diff --git a/setup.cfg b/setup.cfg
@@ -1,6 +1,6 @@
 [metadata]
 name = openpathsampling
-version = 1.4.0
+version = 1.4.1
 description = A Python package for path sampling simulations
 long_description = file: README.md
 long_description_content_type = text/markdown
@@ -49,6 +49,9 @@ test =
     pytest-cov
     coveralls
     ipynbtest
+simstore =
+    sqlalchemy
+    dill
 
 [bdist_wheel]
 universal = 1