feat: memote #239
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feat: memote #239
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* Add new GPRs for transport rxns * Add a function for updating those GPRs to model
* Update new GPRs for those transport rxns
update the function
Update the confidence scores for those reactions of transport rxns. Note: r_0475, r_1667, r_1729, r_1805, r_2025, r_2064, r_4403 ,r_4435, r_4484, r_4598, r_4599 rxn confidence scores were also changed due to they have gRrules
Doc/citation guidelines
Add a title for the data file
Add a exchange reaction for Ca 2+
change the function to let Ca2+ can enter into the cell freely update in the model
… update fix the rxnconfidence scores for those reactions in this update:exchange reactions: NAN; reactions for modeling: 1
Fix biomass: Add Ca(2+) into Biomass
for new release
Add transport rxn GPR
* remove rows with no formulas (redundant) * remove undesired ' characters * some bugs in function
as complex carbohydrates have varying length, it's best to use the monomeric form
fix-met.prop: correct metFormulas
…dding a transport reaction
This is to update the model to include fatty acid esters produced during alcoholic fermentation in the cytoplasm and extracellular membrane via the protein medium-chain fatty acid ethyl ester synthase/esterase 2.
fix-correct a gene name for one rxn
a couple were corrected to their neutral form
write PR number as reference in each note
no evidence to support it
fix: FA ester additions
both correspond to only one KEGG pathway: https://www.genome.jp/kegg-bin/show_pathway?map00010
fix: combine glycolysis + gluconeogenesis
xml changes due to opencobra/cobratoolbox#1631
* change in yml: use of quotes for fields (SysBioChalmers/RAVEN#309) * adpated saveYeastModel to be compliant with new exporting structure introduced in SysBioChalmers/RAVEN#303 (temporal)
after COBRA (opencobra/cobratoolbox#1604) and RAVEN (SysBioChalmers/RAVEN#313) added functionality for them
Chore: update COBRA+RAVEN toolboxes
4 tasks
- using RAVEN PR #338
feat: add yaml validation
- note that format of requirements.txt changed since pip-tools 5.5.0+
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I was thinking that I should add a GH workflow to memote in addition to or instead of the Travis CI one. I'm glad that you're already going ahead with that. |
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@Midnighter that would be great. This very large PR has been in progress for a long time, but finally it passes all checks. It would be nice to merge it and let subsequent ideas/issues surface as different PRs. |
1 task
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Main improvements in this PR:
As a follow-up to #162, this PR merges in the
develandfeat/yaml-validationbranches in order to convert the Travis CI pipeline that runs memote to GH Actions. Just as before, thehistory_report.htmlgets commited to thegh-pagesbranch automatically.