Lower and upper bounds overwriting on save

[ym2877]

https://github.com/opencobra/cobrapy/blob/4ef4d797d234e6b7153a1eabca0d9bc1d75a7d9e/src/cobra/io/sbml.py#L1281-L1286

Hi! I'm not sure if this is the intended behavior, but these lines of code are overwriting and replacing all absolute bounds that were changed prior to saving the model. So for example, if I have a model with the following reactions-

-1000 < reactionA  < 1000
-1000 < reactionB  < 1000
-1000 < reactionC  < 1000

If I were to try changing the bounds of just reaction C with reactionC.bounds = (-2000,4000), the bounds of all reactions upon saving the model (and subsequently reading it from file) would be-

-2000 < reactionA  < 4000
-2000 < reactionB  < 4000
-2000 < reactionC  < 4000

instead of

-1000 < reactionA  < 1000
-1000 < reactionB  < 1000
-2000 < reactionC  < 4000

If this is indeed the intended behavior, I'd argue it doesn't make much sense and entirely defeats the purpose of having a global configuration object altogether. It's especially strange considering these changes only kick in when trying to save a model a file. With the way the code is written now, the lower_bound and upper_bound configurations are entirely ignored once 1 reaction is added to the model.

Suggested fix is removing the first if clause like so-

min_value = config.lower_bound 
max_value = config.upper_bound 

[cdiener]

Yes that's true. Looks like strange behavior to me as well.

[ym2877]

@cdiener any updates on this? Should I go ahead and make a PR with this fix?