Use python dict to support bngl hash type arguments in console actions

[ortega2247]

This adds support to use bngl hash type arguments like max_stoich that are passed to generate_network. I use f-strings because i feel it is easier to read, but most of the code in pysb uses the old string formatting (% operator). Comments, feedback, and requests are more than welcome

from pysb.examples.bax_pore import model
from pysb.bng import generate_equations

generate_equations(model, **{'max_stoich':{"BAX":1}})
model.species

That caps the number of BAX molecules in a complex to 1

[alubbock]

Looks good - please could you add a small test for this to the BNG test suite? Similar to the example you give on the PR. Thanks!

[ortega2247]

Just added the requested test. Also, I change the exporters so that the generate_equation is only called when the model has not generated the equations before. I think that can be good for large models that take a long time to generate equations and so we don't have to generate equations again if we want to export the model to some other format. This also facilitates the export of models' equations that has been generated using arguments like max_stoich

[alubbock]

Thanks @ortega2247. I've made a few small suggestions in the inline comments.

[jmuhlich]

This is unwieldy and not really using the benefit of f-strings. Also re-using the local v variable is a bit confusing. How about something like this (not tested) :

args_string = ",".join(f"{k}=>{v}" for k, v in bng_param.items())
par_string = f"{k}=>{args_string}"

[jmuhlich]

Should we perform some validation on the kwargs keys and values here to make sure we don't emit invalid BNGL? If the BNG parser fails due to invalid BNGL here the error will probably be hard for the user to make sense of. The keys should be validated against the regex that matches whatever BNG accepts there, but I'm not sure what the value syntax is.

[codecov-commenter]

Codecov Report

Merging #539 (9a7586f) into master (d58da94) will increase coverage by 0.05%.
The diff coverage is 100.00%.

@@            Coverage Diff             @@
##           master     #539      +/-   ##
==========================================
+ Coverage   80.20%   80.25%   +0.05%     
==========================================
  Files         101      101              
  Lines       10661    10678      +17     
==========================================
+ Hits         8551     8570      +19     
+ Misses       2110     2108       -2     

Impacted Files	Coverage Δ
pysb/bng.py	93.10% <100.00%> (+0.11%)	⬆️
pysb/tests/test_bng.py	100.00% <100.00%> (ø)
pysb/generator/bng.py	97.21% <0.00%> (+0.79%)	⬆️

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