Move parse_command_line_arguments to util.py

[amarkpayne]

rmg.py is not installed as a module in the conda binary, so we cannot import this function

Motivation or Problem

Fixes #1716

Description of Changes

Move parse_commnad_line_arguments inside of rmgpy.util where it can be imported for binary installations

[amarkpayne]

This PR can be reviewed, but let's hold off on merging this for now

[codecov]

Codecov Report

Merging #1717 into master will not change coverage.
The diff coverage is 100%.

@@           Coverage Diff           @@
##           master    #1717   +/-   ##
=======================================
  Coverage   41.66%   41.66%           
=======================================
  Files         176      176           
  Lines       30215    30215           
  Branches     6256     6256           
=======================================
  Hits        12588    12588           
  Misses      16703    16703           
  Partials      924      924

Impacted Files	Coverage Δ
rmgpy/tools/generate_reactions.py	30% <100%> (ø)	⬆️

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[codecov]

Codecov Report

Merging #1717 into master will not change coverage.
The diff coverage is 100%.

@@           Coverage Diff           @@
##           master    #1717   +/-   ##
=======================================
  Coverage   32.65%   32.65%           
=======================================
  Files          87       87           
  Lines       26158    26158           
  Branches     6874     6874           
=======================================
  Hits         8541     8541           
+ Misses      16656    16645   -11     
- Partials      961      972   +11

Impacted Files	Coverage Δ
rmgpy/tools/generate_reactions.py	30% <100%> (ø)	⬆️
rmgpy/data/statmech.py	42.39% <0%> (ø)	⬆️
rmgpy/rmg/pdep.py	12.21% <0%> (ø)	⬆️
rmgpy/reaction.py	0% <0%> (ø)	⬆️
rmgpy/data/kinetics/family.py	48.49% <0%> (ø)	⬆️
rmgpy/yml.py	15.71% <0%> (ø)	⬆️
rmgpy/data/kinetics/database.py	50.73% <0%> (ø)	⬆️
rmgpy/rmg/input.py	34.34% <0%> (ø)	⬆️
rmgpy/molecule/molecule.py	0% <0%> (ø)	⬆️
rmgpy/statmech/ndTorsions.py	59.89% <0%> (ø)	⬆️

---

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[xiaoruiDong]

Hi @amarkpayne. I am sorry that I just see this PR. I will have a quick review by today, and please let me know when it is okay to be merged. Thanks!

[xiaoruiDong]

@amarkpayne Thanks for the contribution. There is only one minor comment.

[xiaoruiDong]

Do we still need 'from rmg import *?After changing,main()is the only function imported and is not used inrmgTest.py`

[mliu49]

I think this looks good. Once it's merged, I think you can cherry-pick it to the v2.5.0 branch as well.