remove perses atommapper and scorer

[atravitz]

resolves #1635

We communicated to the board that we will be removing these in v1.11.0. My only concern is that I originally said v2.0 in the changelog.

To be thorough, we can give this one more deprecation cycle where we update the changelog to say "will be removed in v1.12.0" so that users have appropriate heads-up.

Checklist

• All new code is appropriately documented (user-facing code must have complete docstrings).
• Added a news entry, or the changes are not user-facing.
• Ran pre-commit: you can run pre-commit locally or comment on this PR with pre-commit.ci autofix.

Manual Tests: these are slow so don't need to be run every commit, only before merging and when relevant changes are made (generally at reviewer-discretion).

• GPU integration tests: failing but unrelated to these changes, issue tracked here: septop resume test failing #2046
• example notebook testing: failing but will be resolved by fix: add dep for example notebook testing #2045
• packaging tests: run this for any large feature PRs or PRs that add test data.

Developers certificate of origin

• I certify that this contribution is covered by the MIT License here and the Developer Certificate of Origin at https://developercertificate.org/.

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 90.61%. Comparing base (903f31c) to head (9a284e5).

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #1943      +/-   ##
==========================================
- Coverage   94.93%   90.61%   -4.32%     
==========================================
  Files         217      212       -5     
  Lines       20774    20572     -202     
==========================================
- Hits        19721    18642    -1079     
- Misses       1053     1930     +877     

Flag	Coverage Δ
fast-tests	90.61% <100.00%> (?)
slow-tests	?

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[atravitz]

(looks like API break check is working as expected @mikemhenry!)

[IAlibay]

One unused fixture (blocking over that one) and one nit, otherwise it looks good to me.

[github-actions]

🚨 API breaking changes detected! 🚨

View workflow run

Griffe output

$ griffe check "openfe" -s src --no-inspection --no-color --verbose -a origin/main
src/openfe/setup/atom_mapping/perses_mapper.py:0: <module>:
Public object was removed

src/openfe/setup/atom_mapping/perses_scorers.py:0: <module>:
Public object was removed

src/openfe/tests/setup/atom_mapping/test_perses_atommapper.py:0: <module>:
Public object was removed

src/openfe/tests/setup/atom_mapping/conftest.py:0: <module>:
Public object was removed

src/openfe/tests/setup/atom_mapping/test_perses_scorers.py:0: <module>:
Public object was removed


$ griffe check "openfecli" -s src --no-inspection --no-color --verbose -a origin/main