Remove TODO comments

[jennyfothergill]

PR Summary:

• all TODO comments were removed and converted to issues.

Fixes #872

PR Checklist

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• Includes appropriate unit test(s)
• Appropriate docstring(s) are added/updated
• Code is (approximately) PEP8 compliant
• Issue(s) raised/addressed?

[codecov]

Codecov Report

Merging #876 (1ded05c) into master (a9d9e3e) will not change coverage.
The diff coverage is 80.00%.

@@           Coverage Diff           @@
##           master     #876   +/-   ##
=======================================
  Coverage   88.39%   88.39%           
=======================================
  Files          62       62           
  Lines        7857     7857           
=======================================
  Hits         6945     6945           
  Misses        912      912           

Impacted Files	Coverage Δ
mbuild/coarse_graining.py	90.67% <ø> (ø)
mbuild/compound.py	97.57% <ø> (ø)
mbuild/conversion.py	89.26% <ø> (ø)
mbuild/coordinate_transform.py	91.60% <ø> (ø)
mbuild/lib/surfaces/amorphous_silica_surface.py	100.00% <ø> (ø)
mbuild/formats/lammpsdata.py	87.65% <66.66%> (ø)
mbuild/formats/protobuf.py	92.00% <100.00%> (ø)
mbuild/pattern.py	90.22% <100.00%> (ø)

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