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microbiomeDB / microbiomeData

An R package containing all of the curated datasets from MicrobiomeDB.org
https://microbiomedb.github.io/microbiomeData/
Apache License 2.0
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AbundanceData to inherit from new CollectionWithMetadata #26

Closed d-callan closed 5 months ago

d-callan commented 6 months ago

depends on https://github.com/VEuPathDB/veupathUtils/pull/42

instigated by the introduction of data types other than abundances by hpi, but i also like it generally. might one day let mbio take more abstract data types as well.

d-callan commented 6 months ago

a real question here, that im still considering... is whether the Collection class from here should move to veupathUtils as well, and have CollectionWithMetadata inherit in turn from it. the naive answer is, yes-duh-dumb-danielle, but im nervous about unintended consequences. i might give it a go next week and see if it turns into a nightmare or not..

d-callan commented 5 months ago

so i made the change to have CollectionWithMetadata inherit from Collection, and the only real consequence is that now when we make AbundanceData objects we have to name them. I think thats fine, probably a good thing anyhow, and well worth this change. thoughts?