Array copy bugfix

[bas-rustenburg]

This uses deepcopy for numpy arrays used inside attempt_state_change. Potentially the main cause of #124

A short description of the problem:

If you index a list in python with my_list[:], this returns a copy of the entire list. For numpy arrays, it returns a reference to the array. This leads to unexpected side effects when copying is intended. I've replaced array slices with deepcopy in several places in the code where copy was the intended behavior.

[jchodera]

You've probably gone a little overkill here, but there shouldn't be any issues with this. Thanks for fixing this!

[codecov-io]

Codecov Report

Merging #126 into master will increase coverage by 0.02%. The diff coverage is 80%.

@@            Coverage Diff             @@
##           master     #126      +/-   ##
==========================================
+ Coverage   59.65%   59.68%   +0.02%     
==========================================
  Files          36       36              
  Lines        5109     5112       +3     
==========================================
+ Hits         3048     3051       +3     
  Misses       2061     2061

Impacted Files	Coverage Δ
protons/app/driver.py	85.49% <100%> (ø)	:arrow_up:
protons/app/samsreporter.py	95.5% <100%> (+0.05%)	:arrow_up:
protons/app/ncmcreporter.py	77.35% <50%> (+0.21%)	:arrow_up:
protons/app/titrationreporter.py	85.18% <66.66%> (+0.13%)	:arrow_up:

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[bas-rustenburg]

I'm going to rerun those ion simulations and see if this fixes the accumulation bug.