Rename submodules in rmgpy.tools

[mliu49]

Motivation or Problem

The submodules in the tools module are a bit of a mess in terms of naming. The 3.0 release seems like a good opportunity to rename them.

Note that RMG-website imports will need to be updated, as will any other dependencies which use the tools module.

Description of Changes

Rename submodules in rmgpy.tools and update imports in RMG-Py.

• Generally, changed to short, all lowercase names without underscores.
• Test files are identified with capital Test.

Reviewing

Any comments or suggestions about the new names are welcome.

[xiaoruiDong]

@mliu49 Thanks for the contribution! I think it is a good idea to standardize the module names. The changes (using all-lowercase names) are according to PEP-8 nomenclature, right? @amarkpayne, your thoughts?

[amarkpayne]

This is correct according to PEP-8 (https://www.python.org/dev/peps/pep-0008/#package-and-module-names).

I think all of this looks good to go, but should we do the same for the scripts folder? The modules in the script folder are all consistent, but use a different convention.

Rebase and I'll approve and merge

[codecov]

Codecov Report

Merging #1794 into master will increase coverage by 0.06%.
The diff coverage is 75%.

@@            Coverage Diff             @@
##           master    #1794      +/-   ##
==========================================
+ Coverage   42.92%   42.99%   +0.06%     
==========================================
  Files          82       80       -2     
  Lines       21182    21090      -92     
  Branches     5519     5513       -6     
==========================================
- Hits         9093     9067      -26     
+ Misses      11074    11008      -66     
  Partials     1015     1015

Impacted Files	Coverage Δ
rmgpy/tools/diffmodels.py	37.71% <ø> (ø)
rmgpy/tools/mergemodels.py	46.34% <ø> (ø)
rmgpy/tools/canteramodel.py	38.87% <ø> (ø)
rmgpy/tools/ckcsvparser.py	5.06% <ø> (ø)
rmgpy/tools/generatereactions.py	30% <ø> (ø)
rmgpy/rmg/main.py	21.62% <0%> (ø)	⬆️
rmgpy/tools/observablesregression.py	8% <100%> (ø)
rmgpy/tools/regression.py	29.76% <100%> (ø)	⬆️

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[mliu49]

Should be good to go once tests pass.

[amarkpayne]

Thanks for the PR @mliu49 !