Bugs

[freiburgermsu]

Hello!

I merged the upstream MSpy into my fork and was reacquainted with some bugs that I corrected in my fork. A few of them here:

1. Self is already passed as an argument (here and here) by calling the function from the Class object, so explicitly listing the argument (when the function does not accept any other argument) will cause an error.
2. The model. is missing from these calls, where the Class object does not directly store the metabolites.
3. I believe that rxn.id is a string here, and not a function, so this would throw an error.
4. There are many instances of editing an objective (e.g. here and here) after it has been assigned to a model, which I believe does not track the changes to the model and therefore deviates from the author's intentions of editing the model objective.
5. The group variable in this line is never defined. I think that the author intended to extract the matched regex content in m, so group should be replaced with m.

I will share more bugs through this medium, since it seems to be more amenable than a PR with my whole fork.

Thank you :) Andrew

[Fxe]

I believe these are all related @cshenry