Refactor

[chrisjonesBSU]

Major refactor that changes and expands the API, workflows, functionality and structure.

[codecov]

Codecov Report

Merging #10 (35c41df) into main (0658f92) will increase coverage by 0.87%.
The diff coverage is 92.33%.

Additional details and impacted files

@@            Coverage Diff             @@
##             main      #10      +/-   ##
==========================================
+ Coverage   88.72%   89.59%   +0.87%     
==========================================
  Files          19       31      +12     
  Lines        1055     1971     +916     
==========================================
+ Hits          936     1766     +830     
- Misses        119      205      +86     

Files Changed	Coverage Δ
hoomd_polymers/assets/forcefields/__init__.py	100.00% <ø> (ø)
hoomd_polymers/assets/molecule_files/__init__.py	100.00% <ø> (ø)
hoomd_polymers/modules/utils.py	0.00% <ø> (ø)
hoomd_polymers/utils/actions.py	59.18% <0.00%> (ø)
hoomd_polymers/library/simulations/tensile.py	20.00% <28.57%> (ø)
hoomd_polymers/base/simulation.py	85.18% <59.72%> (ø)
hoomd_polymers/utils/utils.py	50.00% <60.00%> (ø)
hoomd_polymers/base/system.py	81.70% <81.70%> (ø)
hoomd_polymers/utils/exceptions.py	84.61% <84.61%> (ø)
hoomd_polymers/utils/ff_utils.py	88.88% <88.88%> (ø)
... and 20 more

[chrisjonesBSU]

We made a branch called alpha, which has the original working code. We will merge the major refactor and start new PRs from there.