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lanl / PyBNF

An application for parameterization of biological models available in SBML and BNGL formats. Features include parallelization, metaheuristic optimization algorithms, and an adaptive Markov chain Monte Carlo (MCMC) sampling algorithm.
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Verifying installation with demo example ends with KeyError #312

Closed shoepfl closed 2 years ago

shoepfl commented 2 years ago

I installed PyBNF and Bionetgen on my windows computer without any problems or errors.

However, when I want to verify my installation with pybnf -c demo_xml.conf, I get the error:

Sorry, an unknown error occurred: KeyError: 'step' Logs have been saved to bnf_20211208-141351.log. Please report this bug to help us improve PyBNF.

Can someone tell me if the problem is on my installation or on the demo example?

Many thanks in advance.

wshlavacek commented 2 years ago

Thanks for letting us know about this error message There’s a problem in the CONF file The fix is to add a time step to the simulation command So… your installation is probably fine

Sent from my iPhone

On Dec 8, 2021, at 6:24 AM, shoepfl @.***> wrote:

 I installed PyBNF and Bionetgen on my windows computer without any problems or errors.

However, when I want to verify my installation with pybnf -c demo_xml.conf, I get the error:

Sorry, an unknown error occurred: KeyError: 'step' Logs have been saved to bnf_20211208-141351.log. Please report this bug to help us improve PyBNF.

Can someone tell me if the problem is on my installation or on the demo example?

Many thanks in advance.

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wshlavacek commented 2 years ago

The CONF file has been fixed.

shoepfl commented 2 years ago

Thank you very much for the fast response and the fix