Remove reaction tagging for output and add new options to help

RuleWorld / nfsim

A general-purpose, stochastic, biochemical reaction simulator for large reaction networks

http://michaelsneddon.net/nfsim/

MIT License

14 stars 9 forks source link

Remove reaction tagging for output and add new options to help #31

Closed rasi closed 2 years ago

rasi commented 2 years ago

I removed the tagging of reactions since this relied on a customized version of PySB and BioNetGen that is unnecessary. Instead, all reactions are output to a file when the -rxnlog switch is given along with a filename.
I added the new options to the help message printed when NFsim -help is run.

rasi commented 2 years ago

@ASinanSaglam Will it be possible to merge this pull request before releasing the next version? The changes are minor and clean up the output files and the help message for the connectivity code that you already merged. That way, we can use the release for all our new simulations.

ASinanSaglam commented 2 years ago

Yes, I have made a release for the old version, I'll merge these and try to make a release with the final changes tomorrow. The BNG release with that new NFSim will be next week and pip install bionetgen should work for those simulations after that.