HOTFIX: Homo-Dimer Reaction Propensities

[BryanRumsey]

Case 1

This case is impossible to catch since python dictionaries don't support duplicate keys.

r1 = spatialpy.Reaction(
name="r1", reactants={"s1":1, "s1":1}, products={"s1":1, "s2":1}, rate=0.1
)

Case 2

S1 = spatialpy.Species(name="s1", diffusion_coefficient=0.1)
r2 = spatialpy.Reaction(
name="r2", reactants={"s1":1, S1:1}, products={"s1":1, "s2":1}, rate=0.1
)

Propensity Bug

r2
Reactants
s1: 1
Products
s1: 1
s2: 1
Propensity Function: (0.1*s1)

Fixed Propensity

r2
Reactants
s1: 2
Products
s1: 1
s2: 1
Propensity Function: (((0.1*s1)*(s1-1))/vol)

Case 3

r3 = spatialpy.Reaction(
name="r3", reactants={"s1":1}, products={"s1":1, "s2":1}, rate=0.1
)
r3.add_reactant("s1", 1)

Propensity Bug

r3
Reactants
s1: 1
Products
s1: 1
s2: 1
Propensity Function: (0.1*s1)

Fixed Propensity

r3
Reactants
s1: 2
Products
s1: 1
s2: 1
Propensity Function: (((0.1*s1)*(s1-1))/vol)

closes#328