Use pythonic names

[cthoyt]

The repository uses very java-flavored names, which makes it less approachable for python programmers. You can read PEP-8's naming conventions guide to get familiar with https://peps.python.org/pep-0008/#naming-conventions

for example, step = lvmod.stepGillespie() feels very java. Python conventions would be to write it as step = lvmod.step_gillespie()

similarly, using the number 2 instead of to is also not very pythonic

jax-smfsb/src/jsmfsb/smfsbSbml.py

Line 12 in 71a139c

def mod2Spn(filename, verb=False):

should be mod_to_spn, or ideally, something that is not an abbreviation

I understand that this might be because you're trying to mimic the interface of smfsb, but this is irrelevant in terms of reviewing this repo

[darrenjw]

OK, I've had a go at this. I don't like unnecessary breaking changes, but I do get your point. I've tried to make consistent changes to both this library and smfsb. Of course they are now both somewhat inconsistent with the R library and the Scala library, but I guess that's inevitable.

[cthoyt]

I'd highly suggest running the following in the root of your repo before considering this issue closed:

ruff check --select N

More information about how PEP-8 naming checks works here: https://docs.astral.sh/ruff/rules/#pep8-naming-n. I guess it might be initially frustrating to get errors like

tests/test_spatial.py:65:5: N806 Variable `N` in function should be lowercase
   |
63 | def test_step_cle_2d():
64 |     M=16
65 |     N=20
   |     ^ N806
66 |     x0 = jnp.zeros((2,M,N))
67 |     lv = jsmfsb.models.lv()

but, people who read your code will highly appreciate not having cryptic variable names everywhere

[darrenjw]

Have had a good go at cleaning up ruff suggestions