Merge branch 'master' into development

README.md

@@ -232,7 +232,7 @@ reaction [condensed      =        3e+06 /M/s ] S2 + R -> e51
         $ cat seesaw_ciruit.ssw | peppercorn --dry-run
 
 ## Version
-0.7.1
+0.8
 
 ## Authors
 Stefan Badelt, Casey Grun, Karthik V. Sarma, Brian Wolfe, Seung Woo Shin and Erik Winfree.

peppercornenumerator/objects.py

@@ -12,10 +12,9 @@
 from collections import namedtuple
 
 from dsdobjects import clear_memory
-from dsdobjects import DL_Domain, DSD_Complex, DSD_Reaction, DSD_Macrostate
 from dsdobjects import DSDObjectsError, DSDDuplicationError
+from dsdobjects.core import DL_Domain, DSD_Complex, DSD_Reaction, DSD_Macrostate
 from dsdobjects.utils import split_complex, convert_units
-# not needed here, but passing it on...
 from dsdobjects.utils import make_pair_table, pair_table_to_dot_bracket 
 
 class PepperObjectsError(Exception):

tests/test_enumerator.py

@@ -104,7 +104,7 @@ def test_interface(self):
         enum.dry_run()
         self.assertEqual(sorted(enum.complexes), sorted([X,Y]))
         self.assertEqual(sorted(enum.resting_complexes), sorted([X,Y]))
-        self.assertEqual(sorted(r.canonical for r in enum.resting_macrostates), sorted([X,Y]))
+        self.assertEqual(sorted(r.canonical_complex for r in enum.resting_macrostates), sorted([X,Y]))
 
         with self.assertRaises(DSDObjectsError) as e:
             enum.enumerate()
@@ -146,7 +146,7 @@ def test_named_complexes(self):
         enum.max_reaction_count = 5000
         enum.enumerate()
 
-        self.assertTrue(F in [rms.canonical for rms in enum.resting_macrostates])
+        self.assertTrue(F in [rms.canonical_complex for rms in enum.resting_macrostates])
 
 class TestWrappers(unittest.TestCase):