cobrapy
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opencobra
COBRApy is a package for constraint-based modeling of metabolic networks.
#### 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)....
### 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...
I think this would be an awesome addition to the cobrapy package. Specifically if we ever get to #293 we'll probably want something to reversibly compress / expand cobra models....
## Description of feature **User Defined Constraint:** This new feature from fbc-v3 has been added to COBRApy as well as to JSON and other formats also. A user can now...
## Description of Features 1. **Metadata Classes:** A separate directory for handling metadata information is made inside `cobra/core` directory. Every object derived from SBase can have meta information like annotation...
This PR is solving issue #736 and #706. A new function `_fix_annotation()` has been added which fixes the incorrect annotation format.
### Checklist - [x] There are [no similar issues or pull requests](https://github.com/opencobra/cobrapy/issues) for this yet. Related to the discussion on https://github.com/opencobra/cobrapy/issues/967, in the sense that it is about libraries building...
Hi all, I've created a community model for 156 genomes using carveme, and it's not being read by cobra. This is the error I get: ``` KeyError Traceback (most recent...
For some models it is not possible to apply `deepcopy`, because the reaction names may match reserved names of the gurobi LP format—see [gurobi docs](https://www.gurobi.com/documentation/9.1/refman/lp_format.html): > Also, variable names should...
The documentation is broken (again). In order from most to least important, I think the following points might address this: 1. Instead of generating the auto API documentation on readthedocs...
