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micom-dev / micom

Python package to study microbial communities using metabolic modeling.
https://micom-dev.github.io/micom
Apache License 2.0
82 stars 17 forks source link

Documentation and default parameters do not match for micom.workflows.grow.grow #120

Closed cdiener closed 8 months ago

cdiener commented 1 year ago

Discussed in https://github.com/micom-dev/micom/discussions/80

Originally posted by **anubhavdas0907** April 14, 2022 Hello Christian, I just wanted to point out that in the documentation for micom.workflows.grow.grow, the default strategy in the code is 'minimal imports', while in the explanation, pFBA is mentioned as default. Kindly edit accordingly. ``` micom.workflows.grow.grow(manifest, model_folder, medium, tradeoff, threads=1, weights=None, strategy='minimal imports', atol=None, rtol=None, presolve=False) ``` strategy : str Computational strategy used to reduce the flux space. Default "pFBA" uses parsimonious FBA, ... Regards Anubhav
cdiener commented 8 months ago

Fixed by #142.