Fix Python and PySB flat exporters, add tests (pysb#366)

* Python 3 compatibility in Python exporter
* Unit tests for Python and PySB flat exporters
* A few small fixes to get the tests running

pysb/annotation.py

@@ -1,4 +1,4 @@
-from pysb.core import SelfExporter, Component
+from pysb.core import SelfExporter, Component, Model
 
 class Annotation(object):
 
@@ -33,6 +33,8 @@ def __init__(self, subject, object_, predicate="is"):
     def __repr__(self):
         if isinstance(self.subject, Component):
             subject = self.subject.name
+        elif isinstance(self.subject, Model):
+            subject = 'model'
         else:
             subject = self.subject
         return "%s(%s, %s, %s)" % (self.__class__.__name__, subject,

pysb/examples/fricker_2010_apoptosis.py

@@ -64,8 +64,9 @@
 for flip_m, kf, kr, reversible in (zip(flip_monomers, (kf31,kf32), (kr31,kr32), (False,True))):
     rule = Rule('RLFADD_%s_Binding' % flip_m.name, FADD (rf=ANY, fe=None) + flip_m (fe=None, ee=None) | FADD (rf=ANY, fe=1) % flip_m (fe=1, ee=None), kf, kr)
     if reversible is False:
-        rule.is_reversible = False;
-        rule.rate_reverse = None;
+        rule.is_reversible = False
+        rule.rule_expression.is_reversible = False
+        rule.rate_reverse = None
 
 pC8_HomoD   = pC8 (fe=ANY, ee=1, D384='U') % pC8   (fe=ANY, ee=1, D384='U')
 pC8_HeteroD = pC8 (fe=ANY, ee=1, D384='U') % flipL (fe=ANY, ee=1, D384='U')
@@ -87,8 +88,9 @@
 for flip_m, kf, kr, reversible in (zip(flip_monomers, (kf34,kf35), (kr34,kr35), (False,True))):
     rule = Rule('RLFADD_C8_%s_Binding' % flip_m.name, pC8 (fe=ANY, ee=None, D384='U') + flip_m (fe=ANY, ee=None) | pC8 (fe=ANY, ee=1, D384='U') % flip_m (fe=ANY, ee=1), kf, kr)
     if reversible is False:
-        rule.is_reversible = False;
-        rule.rate_reverse = None;
+        rule.is_reversible = False
+        rule.rule_expression.is_reversible = False
+        rule.rate_reverse = None
 
 Parameter('kc36', 0.223046e-3)
 #Homodimer catalyses Homodimer ?: no p18 is released. Only this "cleaved" p43 homoD is the product that will transform into a p18 + L:R:FADD in later reaction.

pysb/export/python.py

@@ -106,7 +106,7 @@ def export(self):
         code_eqs = '\n'.join(['ydot[%d] = %s;' %
                                  (i, sympy.ccode(self.model.odes[i]))
                               for i in range(len(self.model.odes))])
-        code_eqs = re.sub(r's(\d+)',
+        code_eqs = re.sub(r'__s(\d+)',
                           lambda m: 'y[%s]' % (int(m.group(1))), code_eqs)
         for i, p in enumerate(self.model.parameters):
             code_eqs = re.sub(r'\b(%s)\b' % p.name, 'p[%d]' % i, code_eqs)
@@ -118,7 +118,6 @@ def export(self):
         output.write("# exported from PySB model '%s'\n" % self.model.name)
         output.write(pad(r"""
             import numpy
-            import weave
             import scipy.integrate
             import collections
             import itertools
@@ -128,8 +127,11 @@ def export(self):
             _use_inline = False
             # try to inline a C statement to see if inline is functional
             try:
+                import weave
                 weave.inline('int i;', force=1)
                 _use_inline = True
+            except ImportError:
+                pass
             except distutils.errors.CompileError:
                 pass
 
@@ -214,8 +216,8 @@ def simulate(self, tspan, param_values=None, view=False):
                     self.y = numpy.empty((len(tspan), len(self.y0)))
                     if len(self.observables):
                         self.yobs = numpy.ndarray(len(tspan),
-                                        zip((obs.name for obs in self.observables),
-                                            itertools.repeat(float)))
+                                        list(zip((obs.name for obs in self.observables),
+                                            itertools.repeat(float))))
                     else:
                         self.yobs = numpy.ndarray((len(tspan), 0))
                     self.yobs_view = self.yobs.view(float).reshape(len(self.yobs),

pysb/tests/test_exporters.py

@@ -19,8 +19,9 @@ def test_export():
 
 def check_convert(model, format):
     """ Test exporters run without error """
+    exported_file = None
     try:
-        export.export(model, format)
+        exported_file = export.export(model, format)
     except export.ExpressionsNotSupported:
         pass
     except export.CompartmentsNotSupported:
@@ -34,3 +35,10 @@ def check_convert(model, format):
             pass
         else:
             raise
+
+    if exported_file is not None:
+        if format == 'python':
+            # linspace arguments picked to avoid VODE warning
+            exec(exported_file + 'Model().simulate(tspan=numpy.linspace(0,1,501))\n', {'_use_inline': False})
+        elif format == 'pysb_flat':
+            exec(exported_file, {'__name__': model.name})