Make Transformation and NonTransformation subclass TransformationBase

[dotsdl]

In some cases it can be awkward for NonTransformation to be a subclass of Transformation, such as in alchemiscale, for cases where NonTransformation should be handled very differently.

Switching to a shared, abstract base class for Transformation and NonTransformation simplifies this.

[pep8speaks]

Hello @dotsdl! Thanks for updating this PR. We checked the lines you've touched for PEP 8 issues, and found:

• In the file gufe/transformations/transformation.py:

Line 75:80: E501 line too long (80 > 79 characters)
Line 283:80: E501 line too long (80 > 79 characters)

Comment last updated at 2024-04-25 06:03:17 UTC

[IAlibay]

Thanks for opening this @dotsdl - as a first initial triage, could you possibly add in a rever rst file with a short summary of this update and any expected API breaks?

[dotsdl]

I can do that, no problem @IAlibay! I also need to fix the broken tests yet as well.

[dotsdl]

To be clear, this isn't blocking anything on alchemiscale; it's just something @ianmkenney and I noticed while working on this one: OpenFreeEnergy/alchemiscale#270

[IAlibay]

@dotsdl possibly a crazy question - does this technically change the gufe keys for transformation objects? I can't remember if it captures the parent class signatures

(partly asking because of the test failures)

[IAlibay]

The follow up question I have is if we need a 1.x gufe policy on key stability?

[dotsdl]

Will pursue a review on this from Alyssa when she starts.

[IAlibay]

This looks good to me, couple of comments though.

[codecov]

Codecov Report

Attention: Patch coverage is 98.14815% with 1 line in your changes missing coverage. Please review.

Project coverage is 98.49%. Comparing base (4ee7647) to head (45583b0).
Report is 1 commits behind head on main.

Files with missing lines	Patch %	Lines
gufe/transformations/transformation.py	98.14%	1 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #311      +/-   ##
==========================================
- Coverage   98.67%   98.49%   -0.18%     
==========================================
  Files          36       36              
  Lines        2117     2131      +14     
==========================================
+ Hits         2089     2099      +10     
- Misses         28       32       +4     

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[dotsdl]

@IAlibay can I get another review from you? I also used this as an opportunity to clean up some docstrings, and adjust the reprs for Transformation and NonTransformation to include the name attribute.

[IAlibay]

lgtm thanks!

[atravitz]

This refactor is a big improvement imo, just a couple docstrings and clarifying questions.

[dotsdl]

pre-commit.ci autofix

[dotsdl]

Thanks @IAlibay and @atravitz! Merged!