cobrapy
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opencobra
COBRApy is a package for constraint-based modeling of metabolic networks.
> We should make a benchmark action in the CI. That would be a good way to track those issues. _Originally posted by @cdiener in https://github.com/opencobra/cobrapy/issues/997#issuecomment-683314766_ What is a good...
We should strive to test on all solvers and this gives us the ability to at least test with CPLEX in a limited setting.
We decided some time ago to drop Python 2.7 and only support 3.6 and later versions. Our legacy codebase offers many opportunities for cleaning up old syntax. --- ## Check...
So far, we have been using pep8 for style checks. This has been deprecated for ages and I finally replaced it with flake8 in #969. However, flake8 checks are much...
This function is a modified version of the existing gapfilling algorithm adapted to the multi-strain workflow. In such workflows, strain-specific models are built through a reductionist approach with comparative genomics...
Add `find_active_reactions.py` and a `test_find_active_reactions.py`. Had some discussion with @ChristianLieven and @Midnighter before. Said it might be nice to add these functions for finding active reactions (primarily for finding reactions...
I believe cobrapy doesn't provide FCA out-of-the-box yet. Thought I'd initiate the discussion. Any request for having this? Would love to have a PR for the same.
#### Problem description The model has groups that contain members (list of reactions). However, the reactions do not have a groups field, and the subsystems is always an empty string....
#### Problem description Trying to open model of Y.Lipolytica iMK735 and returns the following error: [y_lipolytica_iMK735.zip](https://github.com/opencobra/cobrapy/files/4864511/y_lipolytica_iMK735.zip) ```python cplex.exceptions.errors.CplexSolverError: CPLEX Error 1236: Control character in string. ``` I am not using...
https://github.com/opencobra/cobrapy/blob/4129a13b0055477e85bec5c0c4e0cf72b4641c7c/cobra/io/sbml.py#L1055 Is this the expected outcome, that the gene **fbc:label** is equal to **fbc:id** ? Because the ID is mutated with prefix "G_" the label is also mutated, looking back...
