feat: support Mw/kcat models from GECKO 3.0 #10
Merged
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Description
As risen by @edkerk, the matlab toolbox GECKO 3.0 has changed the specification of stoichiometric coefficients for enzymes (see here). The coefficients which were previously$\frac1 {k_{cat}}$ has been changed to be $\frac {M_w} {k_{cat}}$ .
Geckopy should remain compatible with GECKO, so it should support this coefficient fashion.
Implementation
This PR achieves (shallow) interoperability at the document level; i. e., the writing and reading function of SBML now accept a flag to read SBML models with the GECKO3 encoding. The default remains the same (i.e., legacy encoding) and the inner workings of geckopy are still in$\frac1 {k_{cat}}$ .
Reading and writing with the$\frac {M_w} {k_{cat}}$ will raise an error if no $M_w$ is found in a protein. For reading, this relies on the annotation attribute, using "mw" as the field (to follow the name used in GECKO3 YAML, see this example). A test was implemented for reading and writing with this format.
I had to remove support for python 3.6 since Github Actions does not support it for
ubuntu-latest
(and it is deprecated anyways). python3.10 was not added to CI but it should in the future (see #11).