William Poole

Thanks for suggesting this @ayush9pandey and @farnazmdi. Short answer is that the bulk of Bioscrape was written before Numpyro and similar tools were commonly used and stable. I agree that...

@ayush9pandey I think an error or warning would be fine, maybe in __init__ of the package?

Good idea - I think Zoltan was doing this for BioCRNpyler. If you can set this up and teach it to me, I can add doc-strings to all of bioscrape...

The simulate functions are actually called fairly frequently, especially with interacting lineages. In addition, simulate_single_cell is written in such a way as to reuse memory buffers, which have to be...

Are you using the py_simulate... methods? there are many places we could reset the seed but I think inside one of those wrappers is best, with an optional keyword to...

I think the answer is to reseed the simulation as part of the multiprocessing function. I have not added any reseed functionality to any py_simulate_X functions. This seems like a...

@sclamons what tweaks do you know about for Mac OSX? I've only done this on Windows and Linux which function the same.

@rlwillia: would an algebraic expression with =, stopping the simulation as soon as the expression is true be sufficient? Code for this kind of rule already exists in lineages in...

This is similar to simulating with a population controlled chemostat (something I very much want to implement) - not particularly hard, but would require a whole new lineage simulation loop.

I can walk you through how to implement this if you want to get inside a simulation loop - or I could just do it. It is pretty easy.