Deprecation of DBFile and Utils/Collector.pm

Created by: tgrego

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.

This ticket is to resolve ENSCORESW-3089

According to ENSREGULATION-280, the following core modules can be removed: Bio/EnsEMBL/DBFile/CollectionAdaptor.pm Bio/EnsEMBL/DBFile/FileAdaptor.pm Bio/EnsEMBL/Utils/Collector.pm

This PR deprecates those modules for removal on Ensembl Release 100.

Use case

Describe the problem. Please provide an example representing the motivation behind the need for having these changes in place.

Benefits

If applicable, describe the advantages the changes will have. Slimmer API. There were no tests for this code, which means improved coverage.

Possible Drawbacks

If applicable, describe any possible undesirable consequence of the changes. Nobody should be using this anymore, so no drawbacks.

Testing

Have you added/modified unit tests to test the changes? No

If so, do the tests pass/fail?

Have you run the entire test suite and no regression was detected? Yes