opencobra cobrapy issues

opencobra / cobrapy

COBRApy is a package for constraint-based modeling of metabolic networks.

http://opencobra.github.io/cobrapy/

GNU General Public License v2.0

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issues

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Fix the GPR copy in Python 3.13

#1412 cdiener opened 4 days ago
1
[BUG] model.copy() fails with python 3.13.0

#1411 mpredl opened 6 days ago
0
[BUG] FVA doesn work on windows 11 and Python 3.12.7

#1410 merlin-von-deggendorf opened 1 month ago
2
[BUG] Error when validating AGORA2 Ecoli model with memote

#1409 NatashaJorge closed 1 month ago
2
`write_to_sbml()` fails with `TypeError`

#1408 hariszaf opened 1 month ago
0
remove reference to old Python2-era simplejson

#1407 a-detiste closed 2 months ago
2
[BUG] Numpy update broke load_matlab_model

#1406 cjrodriguez98 closed 2 months ago
2
[Feature] Verbosity Option in `read_sbml_model` or similar.

#1405 ggmirandac opened 2 months ago
1
Support CARVEME and GAPSEQ external IDs

#1404 cdiener closed 2 months ago
0
[Feature] property overload Reaction.lower_bounds/upper_bounds

#1403 oxinabox opened 2 months ago
1
remove reference to old Python2-era simplejson

#1402 a-detiste closed 2 months ago
0
Do not error on duplicate boundary addition

#1401 oxinabox closed 3 months ago
0
[Feature] way to add_boundary if not already present

#1398 oxinabox closed 3 months ago
6
Upgrade GitHub workflows

#1397 Midnighter closed 3 months ago
0
[Feature] Handle reaction removal in the objective

#1396 cdiener opened 4 months ago
0
SBML parsing fails on invalid GPRs

#1394 tamascogustavo closed 5 months ago
2
[Feature] Nullspace calculation similar to COBRA (MATLAB)

#1393 dagl1 opened 5 months ago
11
Gapfilling failed in context manager (infeasible)

#1392 wshao1 opened 6 months ago
3
I cannot install Cobrapy in Anacoda I get this error "chr(c) # raise ValueError for invalid code error: incomplete escape \U at position 28" What should I do?

#1391 zahraaaaaaaaaaaaaaaaaaaa opened 6 months ago
1
Model optimization by integrating growth rate data from biolog

#1388 hites77 closed 7 months ago
0
[BUG] No biomass flux when another objective is added for FBA analysis

#1386 hites77 closed 7 months ago
3
Question about iCN900 from BiGG

#1384 amarsh26 closed 8 months ago
0
fix(core): catch missing reduced costs and shadow prices.

#1383 Palaract closed 7 months ago
1
[BUG] using gurobi on non-linear optimization

#1381 lbugnon closed 7 months ago
3
Stable release of docs broken [BUG]

#1379 gregmedlock opened 9 months ago
1
Fix style

#1378 Midnighter closed 9 months ago
0
fix: reaction bounds in _add_cycle_free function

#1375 alexpan00 closed 9 months ago
5
Error assigning the bounds in _add_cycle_free

#1374 alexpan00 closed 9 months ago
1
Introduction of general constraint in Gurobipy breaks Cobrapy assumption [BUG]

#1372 Palaract closed 7 months ago
4
Adding new metabolites

#1371 amarsh26 closed 11 months ago
4
Use correct accessor for SBML group name

#1369 cdiener closed 7 months ago
1
enable redirects for Biomodels download

#1368 cdiener closed 1 year ago
1
[BUG] Biomodels web io access broekn due to redirects

#1367 cdiener closed 1 year ago
0
Enable the hybrid solver interface

#1366 cdiener closed 1 year ago
2
chore: allow broader range of pandas versions

#1364 Midnighter closed 1 year ago
0
chore: update actions

#1363 Midnighter closed 1 year ago
0
upgrading dependency to allow pandas>=2.0

#1362 eladnoor closed 1 year ago
1
Update depinfo

#1361 Midnighter closed 1 year ago
2
Hello I am new to python and Cobra, i would be grateful if you can provide me with steps to open an XML file from the computer and/or from online database, i tried the commands on Cobra documentation but i can't apply it.

#1356 Rahmaabubakr closed 1 year ago
0
AttributeError: 'list' object has no attribute 'items'

#1354 QixingWei closed 5 months ago
8
[Suggestion] drop suppport for Python 3.7

#1352 Midnighter closed 1 year ago
1
find_gene_knockout_reactions error

#1351 Laminsecin closed 5 months ago
1
gurobipy.Model.addConstr() DeprecationWarning

#1348 wshao1 closed 1 year ago
4
Make COBRApy compatible with pydantic version 2

#1346 teddygroves closed 1 year ago
1
Incompatibility with pydantic version 2

#1345 teddygroves closed 1 year ago
6
Flux-Samplig: Cannot escape sampling region, model seems to be numerically unstable. Reporting the model

#1344 brunorbqi closed 5 months ago
2
Model valid but cannot be loaded

#1343 HASaunders closed 1 year ago
2
how to handle mixed-integer programming (MIP) problems with the glpk, cplex or/and gurobi solvers in python/with cobrapy?

#1342 helehera closed 1 year ago
3
fix the objective in CycleFreeFlux

#1341 cdiener closed 1 year ago
4
Fix broken test for utils.solver with symengine

#1340 cdiener closed 1 year ago
2