Phosphorylation generates duplicate ODE

[formersbach]

Description:

If "is phosphorylated" reaction rule is used with a unphosphorylated species that has been previously used, a second ODE is mistakenly generated.

Reproduce:

Text file containing:

TNFR phosphorylates Ikk --> pIkk   
Ikk is phosphorylated <--> pIkk
pIkk is phosphorylated <--> ppIkk

Convert to model:

from biomass import Text2Model, create_model
model = Text2Model("test.txt")
model.convert(overwrite=True)
model = create_model(test)

Proposed changes:

Add missing format string in line 1099:

elif "dydt[V.{phosphorylated_form}]" in eq:

to

elif f"dydt[V.{phosphorylated_form}]" in eq:

[himoto]

Hi @formersbach, thanks for your report.
I created a pull request #184 to resolve this issue.