Christian Diener

Update CDN version?

3

Hi guys. This is more of a request than a bug. Would it be possible to update the CDN version of min.css to something a bit more current. As it...

Behavior of Gene.functional and Reaction.functional is unclear

3

#### Problem description Setting `Gene.functional` does currently not trigger side effects. This leads to reactions with `rxn.functional == False` that still carry flux. The use case for that should be...

Switch SBML parser defaults to not rewriting IDs

20

#### Problem description Reading a SBML model with ASCII codes in the IDs may generate invalid cobrapy IDs during parsing (for instance names including spaces). #### Code Sample That one...

Reaction.summary() broken for some models

6

#### Problem description Reconstructed a model for a course with CARVEME and was surprised that Reaction.summary() errors with a key error. #### Code Sample Create a [minimal, complete, verifiable example](https://stackoverflow.com/help/mcve)....

Allow formatting/content options to be set in the model summary constructor

2

### Checklist - [X] There are [no similar issues or pull requests](https://github.com/opencobra/cobrapy/issues) for this yet. ### Is your feature related to a problem? Please describe it. Summaries look great in...

Exchanges and external compartment don't match in models with SBO terms

3

#### Problem description If a model annotates reactions as exchanges those are picked up by model.exchanges, however, the external compartment detection does not take this into account. So the model...

memory leaks when creating models

18

#### Problem description Tried to debug it for weeks now, but never found a fix. So reporting it here for now... The following code will slowly consume all memory on...

* [X] fix #238 * [X] description of feature/fix * [X] tests added/passed * [X] add an entry to the [next release](../CHANGELOG.rst) While looking at fixing the GLPK scaling output...

Add faster primal, shadow price and reduced cost accessors to the Gurobi interface.

2

* [X] description of feature/fix * [X] tests added/passed * [x] add an entry to the [next release](../CHANGELOG.rst) This adds faster accessors to the interface. This probably only works for...

#### Problem description The coinor_cbc interface will give incorrect solutions. Sometimes this happens on the first optimizations and sometimes on later ones, but it is definitely inconsistent. #### Code Sample...