[24.2] Add linters for datatypes

[bernt-matthias]

• tools should only use available datatypes in inputs, outputs and tests
• discourage the use of custom datatypes_conf.xml

How to test the changes?

(Select all options that apply)

• I've included appropriate automated tests.
• This is a refactoring of components with existing test coverage.
• Instructions for manual testing are as follows:
  1. [add testing steps and prerequisites here if you didn't write automated tests covering all your changes]

License

• I agree to license these and all my past contributions to the core galaxy codebase under the MIT license.

[bernt-matthias]

Is this what you thought about @mvdbeek and @nsoranzo? Then I would be happy to get this in.

[bernt-matthias]

Would be interested to know why this did not make it into 24.2? It just feels very unsatisfying to open this months ago, spend time to update the branch multiple times, and make it ready prior to freeze, and even requesting review ahead of time to get this of the list before the busy times during the release.

[jdavcs]

Would be interested to know why this did not make it into 24.2? It just feels very unsatisfying to open this months ago, spend time to update the branch multiple times, and make it ready prior to freeze, and even requesting review ahead of time to get this of the list before the busy times during the release.

I am sorry - this was obviously an oversight. Merging now.

[github-actions]

This PR was merged without a "kind/" label, please correct.

[bernt-matthias]

Something like:

from pkg_resources import resource_filename
DATATYPES_CONF = resource_filename('galaxy.config', 'sample/datatypes_conf.xml.sample')

would again require config being installed?

[mvdbeek]

I think pkg_resources is deprecated, but using galaxy.util.resource_path would be a minor improvement here.

[bernt-matthias]

This seems to rely on importlib.resources, wouldn't this mean that we rely on config again?

[mvdbeek]

You've created a copy by including datatypes_conf.xml.sample" in the manifest, so the galaxy.tool_util.linters package should have that file.