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monarch-initiative / omim

Data ingest pipeline for OMIM.
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GH Action: Run in ODK #97

Closed joeflack4 closed 1 year ago

joeflack4 commented 1 year ago

Overview

This will ensure dependencies are consistent w/ ODK and will solve #92.

joeflack4 commented 1 year ago

Not sure if this is feasible. If not, close.

matentzn commented 1 year ago

100% we have 1000 GH actions running on ODK, e.g.

https://github.com/obophenotype/bio-attribute-ontology/blob/master/.github/workflows/qc.yml#L22

(the latest version is 1.4.1)

joeflack4 commented 1 year ago

@matentzn I went ahead and opened a PR with initial attempt (#100). I got stuck here:

Ideally I'd like to not change the whole directory structure of the repository to use ODK as more of a software / package management environment. I can do that if it is necessary, but IMO simply including a local robot.jar seems like the much less complex solution in that case.

Also, there are some docs that are a little helpful and give me ideas, but I think the case we want here is simpler / should ideally not require all these changes. However on that note, I should say that even for standard ODK use cases, I think these docs could be better. I think there should be an ordered list of exact steps to follow to set up a new repo or migrate an existing one.

matentzn commented 1 year ago

There is no need to change any directory structure at all! No need to even install anything. Just run your python scripts and robot commands in the container, with no changes at all to your set up!