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wormjam-consortium / wormjam

Website/Repository containing the WormJam genome scale model
https://wormjam.life
Creative Commons Attribution 4.0 International
4 stars 11 forks source link

Cleaning repository #36

Closed michaelwitting closed 3 years ago

michaelwitting commented 4 years ago

I would like to clean up the repository, e.g. the model version folder. Furthermore we should add a general description of the repository to the README.md

michaelwitting commented 4 years ago

We could orient ourselves on https://github.com/SysBioChalmers/Human-GEM

michaelwitting commented 4 years ago

I would like to move all auxillary scripts and code to a folder scripts, e.g. scripts | R | Java | Python

Fine? @JakeHattwell

I guess we should keep the travis scripts in a separate folder

JakeHattwell commented 4 years ago

I agree. The Java folder can be removed as we don't use any of the Java Scripts anymore. I have them backed up, and they're retrievable via git. The docs folder can also go

I think having the scripts folder is a good idea. What about:

travis - the CI pipeline curation - the active curation files supporting_data - any DB tables or reference files we have scripts - as you suggested

In regards to model versions, I think the best thing to do would be if we created a "legacy" release of the repository, which I can then give a permanent DOI, then remove the folder. Old model files can the be retrieved either through the legacy release on Zenodo by non-technical users or accessed with git for technical users.

michaelwitting commented 4 years ago

Yes... Let's archive the current version before we clean up anything. I agree with your folder structure. Model versioning might be done by having GitHub release, right?

JakeHattwell commented 4 years ago

Yes, I can set that up - when we make the release, we can use Zenodo to mint a DOI and archive it. Shall I do this ASAP?

I've checked the comparisons, and currently the repository has no online differences between devel and devel_michael. Can we delete the devel_michael branch in favour of forking the repository to work on once it's been transferred to the WormJam organisation?

michaelwitting commented 4 years ago

Yes, let's use Zenodo and you can delete the devel_michael branch. I will archive also everything here on my PC and start with the fresh repository from the WormJam organisation.

JakeHattwell commented 3 years ago

The devel branch of the repository has been cleaned up in c6f5dc55e182f4bdcbae05d21239f46cbd8264c1

I'll close this following the cleanup of the master branch