gimme algorithm doesn't return a reduced model

[Ben-Strain]

hello,

I have tried to apply to gimme algorithm using the following:

#apply gimme algorithm

apply GIMME algorithm on the model

gimme_result = pmodel.integrate_gene_data(data_name="mean_gene_expression", integrator="GIMME", high_exp=0.0001)
context_specific_gem = gimme_result.result_model

it runs and produces an objective function value and flux distribution however the .result_model attribute is empty.
context_specific_gem = {NoneType} None

I was using this package to try and extract context specific models... can you help??

Thank you so much again - the package seems great.

[Ben-Strain]

I fixed this by adding the remove_zero_fluxes to the function. Might want to highlight this in the documentation

[qwerty239qwe]

Sorry that caused some trouble! In the future, the default for remove_zero_fluxes will be set to True to make the behavior more intuitive.
The reason this argument exists is that copying and removing reactions in a duplicated model can sometimes be time-consuming—setting it to False allows users to get just the GIMME fluxes without the extra computational overhead.

I’ll also update the documentation soon—thanks for the helpful suggestion!

[Ben-Strain]

That is great thank you, much appreciated. Some extra documentation about running mCADRE would also be appreciated (e.g. the exact data and format that should be fed to it), I've found this lacking across most available packages. Thank you for all your hard work with this, I think it will defiantly become the defacto python package for running these sort of model extraction pipelines for GeMs

[qwerty239qwe]

Thank you very much for the kind words and feedback—I really appreciate it. I’ll continue working on this and hope the package can truly be helpful to the community and advance the field.
I'll be adding more detailed documentation soon, particularly on running mCADRE and the expected data formats, as I agree this is often lacking. I also plan to include example workflows in upcoming updates to help make things clearer.