Check the ability to pass user charges

[IAlibay]

Adds a test that both manually checks charge assignment (good for us) and that user supplied charges will get all the way through to the HTF (good for users).

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

Patch coverage: 100.00% and project coverage change: +0.06% 🎉

Comparison is base (ff7bb16) 92.01% compared to head (901b2ef) 92.07%.
Report is 4 commits behind head on main.

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #524      +/-   ##
==========================================
+ Coverage   92.01%   92.07%   +0.06%     
==========================================
  Files         113      113              
  Lines        6850     6904      +54     
==========================================
+ Hits         6303     6357      +54     
  Misses        547      547              

Files Changed	Coverage Δ
...tests/protocols/test_openmm_equil_rfe_protocols.py	90.90% <100.00%> (+1.11%)	⬆️

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

[IAlibay]

Anyone got any ideas why RTD is broken here?

[mikemhenry]

AttributeError: 'TocTree' object has no attribute 'get_toctree_ancestors'

Smells like we need to add a pin, looks like the issue is here pydata/pydata-sphinx-theme#1412

I will give CI a bump since that might be all we need (since a new release was cut hours ago)

[mikemhenry]

@IAlibay you should be good now :)

[IAlibay]

cheers @mikemhenry !