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refactor: organize repo as standard-GEM #232
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@edkerk @mihai-sysbio I realized a problem (in this repo) with changing |
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I guess that was my question: what would be the advantage of following said standard? It will probably take some extra work on the yeast-GEM side (solving this memote problem + some conflicts with master), so would be good to know the benefits of doing it :)
No idea, but I'm not a fan of having both folders @Midnighter would it be possible to adapt the travis deploy script to catch this file migration when computing the history report? e.g. try to run memote on |
Let me see if I understood the issue: the path to the
is the behaviour that the latest version of the model gets added to the database, or that all previous versions are run sequentially? Also, from what I'm seeing in the |
@BenjaSanchez following a standard that is adopted across open-sourced GEMs facilitates automation, be it integration into different websites or workflows. If we were to imagine that such a standard is already in place, the standard could eg be taking care of running |
@mihai-sysbio sounds indeed very nice. As the shift from
not really sure how it works: maybe @Midnighter can shed some light here. Hopefully it is the former, so that we can run the history for everything so far in
yes, as the branch of memote has still not been merged (#162 was in standby). I will be working on re-implementing it in the coming weeks now that BiGG ids are implemented and the model can be properly loaded with cobrapy. |
I am great fan of how @BenjaSanchez the automated validation mentioned above in the thread needs some repositories to start adopting the standard (chicken and egg). It looks like Another core feature of the |
@mihai-sysbio nice to see there is some automated validation starting in |
After a call with @Midnighter I confirmed that indeed we can switch the model file path, but only after memote is running in the repo (as otherwise the history report command won't work for all of the old commits). Currently there's issue opencobra/memote#689 that needs to be handled but as soon as that is done we can move forward. @mihai-sysbio I like your idea of moving from Travis CI to GH actions (I read online that it performs faster, which is crucial for our setup), however I have no experience with the latter. Would you be interested in helping me to set it up? We can have a call to discuss the nuts and bolts ;) |
With opencobra/memote#689 closed, yeast-GEM can be transferred to |
Will close when merged with |
Description of the issue:
Efforts are made to standardize the format of [Git(Hub)] repositories containing genome-scale models:
standard-GEM
. This is being discussed and formalized at https://github.com/MetabolicAtlas/standard-GEM.yeast-GEM
largely already complies withstandard-GEM
, so applying the latest guidelines will not result in drastic changes.Any comments on the
standard-GEM
format should be discussed on that repo: https://github.com/MetabolicAtlas/standard-GEM/issues.Main changes:
Note that this is a non-exhaustive list, and
standard-GEM
is still under development.ComplementaryScripts
-->code
;ComplementaryData
-->data
;modelFiles
-->model
).README.md
..standard-GEM.md
template.The text was updated successfully, but these errors were encountered: