Add a charges argument to QCC calcs

[jennyfothergill]

fixes #8

• [x] fix failing unit tests
• [ ] add unit tests for system -- I think I'm going to skip this because all the functions inside are already tested. Eventually I should add a test system with acceptors.
• [x] update p3ht workflow
• [x] update docstrings

[codecov[bot]]

Codecov Report

Merging #10 (297b5d0) into master (395ac89) will decrease coverage by 1.15%. The diff coverage is 47.61%.

@@            Coverage Diff             @@
##           master      #10      +/-   ##
==========================================
- Coverage   85.88%   84.72%   -1.16%     
==========================================
  Files           8        9       +1     
  Lines         751      766      +15     
==========================================
+ Hits          645      649       +4     
- Misses        106      117      +11     

Impacted Files	Coverage Δ
morphct/kmc_analyze.py	77.04% <ø> (ø)
morphct/system.py	0.00% <0.00%> (ø)
morphct/chromophores.py	93.10% <66.66%> (-0.71%)	:arrow_down:
morphct/execute_qcc.py	84.10% <77.77%> (-0.93%)	:arrow_down:
morphct/__version__.py	100.00% <100.00%> (ø)

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[jennyfothergill]

OK, so I decided to go a little ham on this update, but I think the result is a little cleaner and easier to use, hopefully. I added a system object that contains objects that are getting used repeatedly. I also wrote the visualization functions into the system object. Testing with ITIC allowed me to catch some errors that only popped up with acceptors. I'll update the PR summary with my next steps.

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