Python3 compatibility

docs/conf.py

@@ -45,18 +45,18 @@
 master_doc = 'index'
 
 # General information about the project.
-project = u'TRuML'
-copyright = u'2017, Ryan Suderman'
-author = u'Ryan Suderman'
+project = 'TRuML'
+copyright = '2017, Ryan Suderman'
+author = 'Ryan Suderman'
 
 # The version info for the project you're documenting, acts as replacement for
 # |version| and |release|, also used in various other places throughout the
 # built documents.
 #
 # The short X.Y version.
-version = u'0.1.0'
+version = '0.1.0'
 # The full version, including alpha/beta/rc tags.
-release = u'0.1.0'
+release = '0.1.0'
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.
@@ -141,8 +141,8 @@
 # (source start file, target name, title,
 #  author, documentclass [howto, manual, or own class]).
 latex_documents = [
-    (master_doc, 'TRuML.tex', u'TRuML Documentation',
-     u'Ryan Suderman', 'manual'),
+    (master_doc, 'TRuML.tex', 'TRuML Documentation',
+     'Ryan Suderman', 'manual'),
 ]
 
 
@@ -151,7 +151,7 @@
 # One entry per manual page. List of tuples
 # (source start file, name, description, authors, manual section).
 man_pages = [
-    (master_doc, 'truml', u'TRuML Documentation',
+    (master_doc, 'truml', 'TRuML Documentation',
      [author], 1)
 ]
 
@@ -162,7 +162,7 @@
 # (source start file, target name, title, author,
 #  dir menu entry, description, category)
 texinfo_documents = [
-    (master_doc, 'TRuML', u'TRuML Documentation',
+    (master_doc, 'TRuML', 'TRuML Documentation',
      author, 'TRuML', 'One line description of project.',
      'Miscellaneous'),
 ]

tests/test_actions.py

@@ -67,22 +67,22 @@ def test_interface_map(self):
         idm0 = self.m7.interface_diff_map(self.m9)
         assert len(idm0) == 1
         s0 = objects.Site('a', 1)
-        assert s0 in idm0.keys()
+        assert s0 in list(idm0.keys())
         assert idm0[s0] == (-1, objects.Bond(1))
 
     def test_build_mol_map(self):
         r0_lhs_mols = utils.flatten_pattern([self.p2])
         r0_rhs_mols = utils.flatten_pattern([self.p3])
         mmap0 = objects.Rule._build_mol_map(r0_lhs_mols, r0_rhs_mols)
         assert mmap0[0] is None
-        assert len(mmap0.keys()) == 1
+        assert len(list(mmap0.keys())) == 1
 
         r1_lhs_mols = utils.flatten_pattern([self.p5, self.p6])
         r1_rhs_mols = utils.flatten_pattern([self.p7])
         mmap1 = objects.Rule._build_mol_map(r1_lhs_mols, r1_rhs_mols)
         assert mmap1[0] == 0
         assert mmap1[1] == 1
-        assert len(mmap1.keys()) == 2
+        assert len(list(mmap1.keys())) == 2
 
         r2_lhs_mols = utils.flatten_pattern([self.p4, self.p2, self.p3])
         r2_rhs_mols = utils.flatten_pattern([self.p4, self.p3])

tests/test_convert.py

@@ -1,4 +1,5 @@
 from .context import readers
+import os
 
 
 class TestConvert:
@@ -7,8 +8,9 @@ def __init__(self):
 
     @classmethod
     def setup_class(cls):
-        test0 = "resources/test0.bngl"
-        test1 = "resources/test1.bngl"
+        testdir = os.path.abspath(os.path.dirname(__file__))
+        test0 = os.path.join(testdir, "resources/test0.bngl")
+        test1 = os.path.join(testdir, "resources/test1.bngl")
         cls.bm0 = readers.BNGLReader(test0).parse()
         cls.bm1 = readers.BNGLReader(test1).parse()
 
@@ -37,5 +39,5 @@ def test_bmodel0_convert(self):
 
     def test_bmodel1_convert(self):
         krules = [r for rule in self.bm1.rules for r in rule.convert()]
-        print '\n'.join([r.write_as_kappa() for r in krules])
+        print('\n'.join([r.write_as_kappa() for r in krules]))
         assert len(krules) == 29

tests/test_misc.py

@@ -90,7 +90,7 @@ def test_graph_builder(self):
         graph = readers.BNGLReader.parse_cpattern(self.pattern, [self.md0, self.md1])._build_graph()
         assert len(graph.nodes()) == 3
         assert len(graph.edges()) == 2
-        assert graph.node[1]['name'] == 'A:xb_yb'
+        assert graph.nodes[1]['name'] == 'A:xb_yb'
         assert graph[0][1]['name'] == 'x-x'
 
         graph2 = readers.BNGLReader.parse_cpattern(self.pattern2, [self.md2, self.md3])._build_graph()
@@ -129,7 +129,7 @@ def test_contains_variable(self):
         assert self.rate2.contains_variable('rate')
 
     def test_factors(self):
-        print self.rule6._unique_reactant_indices()
+        print(self.rule6._unique_reactant_indices())
         assert self.rule6._unique_reactant_indices() == {0: 2}
         assert self.rule6.rate_factor(True) == 0.5
-        assert self.rule6.rate_factor(False) == 2.0
+        assert self.rule6.rate_factor(False) == 2.0

tests/test_parse.py

@@ -63,20 +63,20 @@ def test_rule_parse(self):
         assert len(rule4s) == 1
         assert rule4s[0].rev
         rule5s = readers.KappaReader.parse_rule(self.rule5, mds)
-        print rule5s[0]
+        print(rule5s[0])
         assert len(rule5s[0].lhs) == 1
         assert len(rule5s[0].lhs[0]) == 1
         assert rule5s[0].lhs[0][0] == objects.PlaceHolderMolecule()
         assert rule5s[0].rev
         rule6s = readers.KappaReader.parse_rule(self.rule6, mds)
-        print rule6s
+        print(rule6s)
         assert len(rule6s[0].rhs) == 1
         assert len(rule6s[0].rhs[0]) == 1
         assert rule6s[0].rhs[0][0] == objects.PlaceHolderMolecule()
         assert rule6s[0].delmol
         rule7s = readers.KappaReader.parse_rule(self.rule7, mds)
         assert len(rule7s[0].rhs) == 2
-        print rule7s[0].rhs
+        print(rule7s[0].rhs)
         assert isinstance(rule7s[0].rhs[1][0], objects.PlaceHolderMolecule)
 
     def test_cpattern_parse(self):
@@ -200,7 +200,7 @@ def test_mol_parse(self):
         assert mol1.write_as_bngl() == "Mol(a,b~U,b~P)"
         mol2 = readers.BNGLReader.parse_molecule(self.mol2, [pmdef3])
         assert mol2.write_as_bngl() == "Mol(a,b~?!+)"
-        print mol2.write_as_kappa()
+        print(mol2.write_as_kappa())
         assert mol2.write_as_kappa() == "Mol(a[.],b{#}[_])"
 
     @raises(rbexceptions.NotAMoleculeException)

tests/test_print.py

@@ -206,6 +206,7 @@ def test_rule(self):
         assert self.rule6.write_as_kappa() == r"B(b[.]),B(b[.]) -> B(b[1]),B(b[1]) @ 3 * 0.5"
         assert self.rule6.write_as_bngl() == r"B(b)+B(b) -> B(b!1).B(b!1) 3 * 2.0"
         assert self.rule6.write_as_bngl(dot=True) == r"B(b).B(b) -> B(b!1).B(b!1) 3 * 2.0"
+        print(self.rule7.write_as_kappa())
         assert self.rule7.write_as_kappa() == r"B(b[1]),B(b[1]) -> B(b[.]),. @ 3 * 0.5"
         assert self.rule7.write_as_bngl() == r"B(b!1).B(b!1) -> B(b) 3 * 2.0"
         assert self.rule8.write_as_bngl() == r"B(b) -> B(b)+B(b) 3"
@@ -218,9 +219,9 @@ def test_molecule_conversion_determinism(self):
             assert x[i - 1] < x[i]
 
     def test_rule_expansion(self):
-        print self.rule3.write_as_bngl(from_bngl=True)
+        print(self.rule3.write_as_bngl(from_bngl=True))
         x = self.rule3.convert()
-        print '\n'.join(sorted([y.write_as_kappa() for y in set(x)]))
+        print('\n'.join(sorted([y.write_as_kappa() for y in set(x)])))
         assert len(x) == 36
 
     def test_obs(self):