vendor perses atom mapper

[mikemhenry]

The main motivation of this PR is that perses is not really maintained upstream.
Really the only part of perses we (optionally) use is the atom mapper and scorer.
This part of the code has no new deps, which means that you can use the perses atom mapper and scorer without installing perses (which brings in many unneeded deps).

Fixes #1635

Checklist

• Added a news entry

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/.

[mikemhenry]

pre-commit.ci autofix

[codecov]

Codecov Report

❌ Patch coverage is 8.15710% with 608 lines in your changes missing coverage. Please review.
✅ Project coverage is 88.82%. Comparing base (fcf0229) to head (8888b5d).

Files with missing lines	Patch %	Lines
openfe/vendor/perses/_atom_mapping.py	7.23%	603 Missing ⚠️
openfe/setup/atom_mapping/perses_mapper.py	60.00%	2 Missing ⚠️
...fe/tests/setup/atom_mapping/test_perses_scorers.py	33.33%	2 Missing ⚠️
openfe/setup/atom_mapping/perses_scorers.py	75.00%	1 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #1637      +/-   ##
==========================================
- Coverage   95.34%   88.82%   -6.52%     
==========================================
  Files         183      184       +1     
  Lines       15779    16422     +643     
==========================================
- Hits        15044    14587     -457     
- Misses        735     1835    +1100     

Flag	Coverage Δ
fast-tests	88.82% <8.15%> (?)
slow-tests	?

Flags with carried forward coverage won't be shown. Click here to find out more.

☔ View full report in Codecov by Sentry.
📢 Have feedback on the report? Share it here.

🚀 New features to boost your workflow:

• ❄️ Test Analytics: Detect flaky tests, report on failures, and find test suite problems.

[IAlibay]

I strongly veto this addition, we can discuss when I'm back next week.

[mikemhenry]

pre-commit.ci autofix

[github-actions]

No API break detected ✅