Remove deprecated variation-related methods

[tgrego]

Description

A few deprecated methods have been deprecated and are due to be removed at release 95.
Those should be removed effective of release 100.
The extra 5 release should be plenty of time for any users to have updated their code.

Use case

See ENSCORESW-3294

Benefits

Less deprecation notices and runtime of our test harness.

Possible Drawbacks

Users still relying on those methods have been getting deprecation notices for a long time, if they did not update their code they will have to do so now.

Testing

Have you added/modified unit tests to test the changes?

yes

If so, do the tests pass/fail?

pass

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

yes

[coveralls]

Coverage decreased (-0.006%) to 81.448% when pulling cfca6b8 on variation_deprecations into c226c1d on master.

[ens-bwalts]

These methods not called from anywhere else in Ensembl. All 12 calls in the test (and the variation adaptor) removed. Wondering if it would make sense to move the lonely get_all_VariationFeatures test into sliceAdaptor.t and removing sliceVariation.t entirely - not enough to request changes but something to consider.

Also agree with GitHub's suggestion that the other reviewer on this be someone from the variation team if they're willing.

Edit: Should have been more clear that I only checked the core repo - ambiguity between Ensembl (the project) and ensembl (the repo). Apologies/

[at7]

We cannot remove those methods from the core API. The webcode API depends on them. They are used here: https://github.com/Ensembl/ensembl-webcode/blob/release/98/modules/EnsEMBL/Web/Query/GlyphSet/Variation.pm#L205-L209
The slice used in the webcode is a compara AlignSlice. If I rewrite the method to be used in the VariationFeatureAdaptor and pass the AlignSlice from the webcode the method doesn't work.

I have never found a solution for this. Do you have an idea? If not I can remove the deprecation message.

[ens-bwalts]

Should have been more clear that I only checked the core repo - ambiguity between Ensembl (the project) and ensembl (the repo). Apologies.

[at7]

I should have removed the deprecation message when I first found out about the compara/web dependency. I don't know why I didn't. Probably because I was hoping to come up with a solution which until today I haven't.

[tgrego]

good thing we asked variation!
I'll close this pull request and we'll think of the next move