Catch errors in bulk charge assignment

[jthorton]

Aims to fix #2021. Currently, this will catch all molecules which raise an error and report the full list at the end of the run.

To fully address the issue I think adding a kwarg like raise_errors would make sense, whereby, by default and in the CLI, errors are raised if any molecule fails to have charges assigned as this is the safest option. Then API users can turn this off if they wish.

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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.
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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
• example notebook testing
• packaging tests: run this for any large feature PRs or PRs that add test data.

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

[jthorton]

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[codecov]

Codecov Report

❌ Patch coverage is 93.54839% with 2 lines in your changes missing coverage. Please review.
✅ Project coverage is 90.29%. Comparing base (7b81d32) to head (76c4dbd).
⚠️ Report is 1 commits behind head on main.

Files with missing lines	Patch %	Lines
...openfe/protocols/openmm_utils/charge_generation.py	87.50%	2 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #2180      +/-   ##
==========================================
- Coverage   95.03%   90.29%   -4.75%     
==========================================
  Files         206      206              
  Lines       20527    20581      +54     
==========================================
- Hits        19508    18583     -925     
- Misses       1019     1998     +979     

Flag	Coverage Δ
fast-tests	90.29% <93.54%> (?)
slow-tests	?

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[jthorton]

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