Fix inconsistent restriction digest cutting behaviour

[manulera]

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Closes #4604

@peterjc I have also refactored the code, since there was some code repeated up to three times in the different _drop functions. Let me know if that makes sense.

[manulera]

Hi @peterjc I am not sure test that does not pass is actually wrong. The failed test can be reproduced with python run_tests.py "Bio.Restriction".

I am not sure, but If I understand the error correctly, it is checking that the output of a.print_that() in the docstring of the file Bio/restricntion/__init__.py matches the actual content of the docstring. The output would of course be much longer than that. Maybe a flag to not run this test in that docstring should be included?

The weird thing is that it passes the test on the previous branch.

Nevermind, it turned out one of the example listed sites should no longer be returned because it produced a cut where not both generated sequences were double strand.

[peterjc]

I would find this easier to read if the fix and the refactoring were done as two separate commits. Would that be easy to do in principle, and is your git knowledge up to it?

(I've not looked at the change, nor quite how the refactoring works - but agree there was duplicated code)

[manulera]

Hi @peterjc I splitted the change as you requested

[peterjc]

The refactoring as a separate commit is much clearer to me - thank you!

[peterjc]

Over to you @MarkusPiotrowski - this looks good to me from a style/technical point of view.

[MarkusPiotrowski]

Yes, I'll have a look at it.

[manulera]

Hi @MarkusPiotrowski just following up on the review request.

[manulera]

Hi @peterjc @MarkusPiotrowski this has been pending since February, not sure if you can find someone else to review the PR. The changes are fairly small:

• Refactor to remove code duplication: 81c0bdb
• Feature implementation (-5 +7 lines) + tests: bb13298
• Refactor of feature based on @peterjc review: a2d2e48