Add fixed species support

doc/examples/robertson_standalone.py

@@ -8,7 +8,6 @@
 # exported from PySB model 'robertson'
 
 import numpy
-import weave
 import scipy.integrate
 import collections
 import itertools
@@ -18,8 +17,11 @@
 _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
 
@@ -41,7 +43,7 @@ def __init__(self):
         self.sim_param_values = numpy.empty(6)
         self.parameters = [None] * 6
         self.observables = [None] * 3
-        self.initial_conditions = [None] * 3
+        self.initials = [None] * 3
 
         self.parameters[0] = Parameter('k1', 0.040000000000000001)
         self.parameters[1] = Parameter('k2', 30000000)
@@ -54,28 +56,28 @@ def __init__(self):
         self.observables[1] = Observable('B_total', [1], [1])
         self.observables[2] = Observable('C_total', [2], [1])
 
-        self.initial_conditions[0] = Initial(3, 0)
-        self.initial_conditions[1] = Initial(4, 1)
-        self.initial_conditions[2] = Initial(5, 2)
+        self.initials[0] = Initial(3, 0)
+        self.initials[1] = Initial(4, 1)
+        self.initials[2] = Initial(5, 2)
 
     if _use_inline:
 
         def ode_rhs(self, t, y, p):
             ydot = self.ydot
             weave.inline(r'''
-                ydot[0] = -p[0]*y[0] + p[2]*y[1]*y[2];
-                ydot[1] = p[0]*y[0] - p[1]*pow(y[1], 2) - p[2]*y[1]*y[2];
-                ydot[2] = p[1]*pow(y[1], 2);
+                ydot[0] = y[1]*y[2]*p[2] + (y[0]*p[0])*(-1);
+                ydot[1] = y[0]*p[0] + (pow(y[1], 2)*p[1])*(-1) + (y[1]*y[2]*p[2])*(-1);
+                ydot[2] = pow(y[1], 2)*p[1];
                 ''', ['ydot', 't', 'y', 'p'])
             return ydot
 
     else:
 
         def ode_rhs(self, t, y, p):
             ydot = self.ydot
-            ydot[0] = -p[0]*y[0] + p[2]*y[1]*y[2]
-            ydot[1] = p[0]*y[0] - p[1]*pow(y[1], 2) - p[2]*y[1]*y[2]
-            ydot[2] = p[1]*pow(y[1], 2)
+            ydot[0] = y[1]*y[2]*p[2] + (y[0]*p[0])*(-1)
+            ydot[1] = y[0]*p[0] + (pow(y[1], 2)*p[1])*(-1) + (y[1]*y[2]*p[2])*(-1)
+            ydot[2] = pow(y[1], 2)*p[1]
             return ydot
 
 
@@ -90,14 +92,14 @@ def simulate(self, tspan, param_values=None, view=False):
             # create parameter vector from the values in the model
             self.sim_param_values[:] = [p.value for p in self.parameters]
         self.y0.fill(0)
-        for ic in self.initial_conditions:
+        for ic in self.initials:
             self.y0[ic.species_index] = self.sim_param_values[ic.param_index]
         if self.y is None or len(tspan) != len(self.y):
             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),

doc/tutorial.rst

@@ -452,8 +452,8 @@ one shown (output shown below the ``'>>>'``` prompts)::
       {'obsC8': <pysb.core.Observable object at 0x104b2c4d0>,
        'obsBid': <pysb.core.Observable object at 0x104b2c5d0>,
        'obstBid': <pysb.core.Observable object at 0x104b2c6d0>}
-   >>> m.model.initial_conditions
-      [(C8(b=None), Parameter(name='C8_0', value=1000)), (Bid(b=None, S=u), Parameter(name='Bid_0', value=10000))]
+   >>> m.model.initials
+      [Initial(C8(b=None), C8_0), Initial(Bid(b=None, S='u'), Bid_0)]
    >>> m.model.rules
       {'C8_Bid_bind': Rule(name='C8_Bid_bind', reactants=C8(b=None) +
       Bid(b=None, S=None), products=C8(b=1) % Bid(b=1, S=None),

pysb/bng.py

@@ -96,8 +96,10 @@ def _check_model(self):
         """
         if not self.model.rules:
             raise NoRulesError()
-        if not self.model.initial_conditions and not any(r.is_synth() for r
-                                                         in self.model.rules):
+        if (
+            not self.model.initials
+            and not any(r.is_synth() for r in self.model.rules)
+        ):
             raise NoInitialConditionsError()
 
     @classmethod
@@ -778,7 +780,7 @@ def _parse_species(model, line):
     monomer_patterns = []
     for ms in monomer_strings:
         monomer_name, site_strings, monomer_compartment_name = \
-            re.match(r'(\w+)\(([^)]*)\)(?:@(\w+))?', ms).groups()
+            re.match(r'\$?(\w+)\(([^)]*)\)(?:@(\w+))?', ms).groups()
         site_conditions = {}
         if len(site_strings):
             for ss in site_strings.split(','):

pysb/builder.py

@@ -172,9 +172,11 @@ def expression(self, *args, **kwargs):
         self.model.add_component(e)
         return e
 
-    def initial(self, *args):
+    def initial(self, *args, **kwargs):
         """Adds an initial condition to the Builder's model instance."""
-        self.model.initial(*args)
+        i = Initial(*args, _export=False, **kwargs)
+        self.model.add_initial(i)
+        return i
 
     def __getitem__(self, index):
         """Returns the component with the given string index