Add test for msmbuildergh-713

msmbuilder/tests/test_ratematrix.py

@@ -17,6 +17,9 @@
 from msmbuilder.example_datasets import MullerPotential
 from msmbuilder.example_datasets import load_doublewell
 from msmbuilder.cluster import NDGrid
+from msmbuilder import utils
+import tempfile
+import shutil
 
 random = np.random.RandomState(0)
 
@@ -457,3 +460,18 @@ def test_doublewell():
                                       sliding_window=sliding_window)
             model.fit(assignments)
             assert model.optimizer_state_.success
+
+
+def test_dump():
+    # gh-713
+    sequence = [0, 0, 0, 1, 1, 1, 0, 0, 2, 2, 0, 1, 1, 1, 2, 2, 2, 2, 2]
+    model = ContinuousTimeMSM(verbose=False)
+    model.fit([sequence])
+
+    d = tempfile.mkdtemp()
+    try:
+        utils.dump(model, '{}/cmodel'.format(d))
+        m2 = utils.load('{}/cmodel'.format(d))
+        np.testing.assert_array_almost_equal(model.transmat_, m2.transmat_)
+    finally:
+        shutil.rmtree(d)

runtests.py

@@ -78,7 +78,7 @@ def main(argv):
     if args.ipython:
         commands = ['ipython']
     else:
-        commands = ['nosetests', '--with-timer']
+        commands = ['nosetests', '--with-timer', '--timer-top-n', '5']
 
         if args.verbose > 0 and not args.no_verbose:
             verbosity = "-{vs}".format(vs="v" * args.verbose)