Created by: magaliruffier
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- do not modify code without testing for regression
- provide simple unit tests to test the changes
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Using one or more sentences, describe in detail the proposed changes.
The xref pipeline is heavily biased towards species with manual annotation, relying on data from so-called vega databases. These databases are no longer available and the pipeline should be compatible with any species across the taxonomic tree. These changes remove the expectation of vega data in the code, as well as updating the documentation/comments to not mention it.
Describe the problem. Please provide an example representing the motivation behind the need for having these changes in place.
the OfficialNaming module uses hard-coded lists of sources to consider, which includes deprecated Vega sources. If the code cannot find these, it can fail. Removing all use of vega sources, both in code and comments, makes it clearer and less error-prone
If applicable, describe the advantages the changes will have.
The code will not break for the lack of outdated data. There will be less confusion as to what should be done about vega data.
If applicable, describe any possible undesirable consequence of the changes.
None that I can think of.
Have you added/modified unit tests to test the changes?
The pipeline was run on a set of vertebrates, including species that used to expect vega data and species without.
If so, do the tests pass/fail? All ran successfully
Have you run the entire test suite and no regression was detected? NA