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biosimulators / Biosimulators_utils

Utilities for building standardized command-line interfaces for biosimulation software packages
https://docs.biosimulators.org/Biosimulators_utils
MIT License
4 stars 6 forks source link

Check for perl before loading BioNetGen files #103

Closed luciansmith closed 2 years ago

luciansmith commented 2 years ago

If perl isn't on the user's system, loading a BioNetGen file will fail with "The system cannot find the file specified". It will appear as if the bionetgen file itself was unable to be found. However, the problem is actually that when BNG initializes itself, it runs a perl command, which thows the FileNotFoundError if perl isn't present. It might be nice to check for the existence of perl before trying to load the file. (As it was, I assumed that the file in question was the bionetgen file, which was not the case.)

jonrkarr commented 2 years ago

This is really a BioNetGen issue. I recommend posting this to RuleWorld/PyBioNetGen

luciansmith commented 2 years ago

Oh, I guess I got the wrong repository; https://github.com/RuleWorld/bionetgen/issues/244 I assume they'll transfer the issue when they get to it.

I don't know how responsive BNG is to this sort of thing, so figured I'd go ahead and post it here as a low-priority enhancement in the meantime.

jonrkarr commented 2 years ago

I could add this here, but I'd prefer not to assume that PyBioNetGen necessarily relies on Perl since they're moving toward a separate BioNetGen library that won't be implemented with Perl.

Sanan has been fairly responsive to feedback.

luciansmith commented 2 years ago

Fair enough! Let's just go with the filed issue, then, and drop this.

jonrkarr commented 2 years ago

This related to open issues I submitted:

I created a new issue for this: