Master

Created by: magaliruffier

Requirements

• Filling out the template is required. Any pull request that does not include enough information to be reviewed in a timely manner may be closed at the maintainers' discretion;
• Review the contributing guidelines for this repository; remember in particular:
  • do not modify code without testing for regression
  • provide simple unit tests to test the changes
  • if you change the schema you must patch the test databases as well, see Updating the schema
  • the PR must not fail unit testing

Description

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.

Use case

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

Benefits

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The code will not break for the lack of outdated data.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.

Possible Drawbacks

If applicable, describe any possible undesirable consequence of the changes.

None that I can think of.

Testing

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