Add Exception or similar for metabolites without associated reactions

[PyLaRi24]

Is your feature request related to a problem? Please describe.
When a metabolite without associated reactions was added to the model, an error appears when I try to do any Analysis. This Is not a huge issue, as I can easily remove the metabolite since it does not impact what I do in CNApy. It would be nice to not have to delete information from the model though.

Describe the solution you'd like
Some sort of exception or similar, so that instead of an error there would be a warning and the analysis continues on.

Describe alternatives you've considered
As I'm not quite sure where exactly the error comes from the only alternative is to delete the metabolite from the model.

Additional context

Note that I'm using CNApy 1.2.8, but cnapy-1.2.7 is my environment name.

[Paulocracy]

Hello and thank you for opening this issue :-) And yes, you're right that this annoying behavior with "orphaned" metabolites should be fixed :3 Luckily, the COBRA-k package (causing this issue as it does not like such ophaned entities) already has a function to solve this, I just forgot to use it :-( but it will be included in the next CNApy version.

In the meantime, if I'm not mistaken, you can fix this yourself by adding cobrak_model = delete_orphaned_metabolites_and_enzymes(cobrak_model) as new line after line 260 in thermodynamics_dialog.py, and from cobrak.utilities import delete_orphaned_metabolites_and_enzymes in the imports at the beginning of the file.

[PyLaRi24]

Awesome, I'll try that. Thanks for your help! :D