Transition from Python 2 to 3

[nateharms]

This PR address recent changes in RMG to move from Python 2 to 3. This transition was needed for a while, but RMG (one of the dependencies) needed to be moved to Python 3 before we were able to make this transition ourself.

Summary of changes:

• all camelCase variables and methods were transitioned to snake_case formatting (with the exception of Arkane input files and jobs)
• database files were updated to transition camelCase to snake_case
• The setting of variables for TS and Conformer objects was refactored for python 3

ToDo:

• [x] update the environment.yml file to use the new RMG 3 (when the binary gets released)
• [x] add krsna's openbabel to the environment file
• [x] assert that TravisCI is able to pass the tests when the RMG 3 binary is released

[codecov[bot]]

Codecov Report

Merging #43 into master will decrease coverage by 1.1%. The diff coverage is 57.95%.

@@            Coverage Diff             @@
##           master      #43      +/-   ##
==========================================
- Coverage   64.32%   63.21%   -1.11%     
==========================================
  Files          27       27              
  Lines        4647     4654       +7     
==========================================
- Hits         2989     2942      -47     
- Misses       1658     1712      +54

Impacted Files	Coverage Δ
autotst/data/updateTest.py	54.54% <ø> (ø)	:arrow_up:
autotst/calculator/vibrational_analysis.py	86.3% <100%> (ø)	:arrow_up:
autotst/calculator/orca.py	83.69% <100%> (ø)	:arrow_up:
autotst/conformer/systematicTest.py	96.66% <100%> (ø)	:arrow_up:
autotst/calculator/gaussianTest.py	95.23% <100%> (+0.07%)	:arrow_up:
autotst/job/jobTest.py	98.59% <100%> (+5.56%)	:arrow_up:
autotst/__init__.py	100% <100%> (ø)	:arrow_up:
autotst/calculator/orcaTest.py	97.14% <100%> (ø)	:arrow_up:
autotst/data/baseTest.py	99.01% <100%> (ø)	:arrow_up:
autotst/speciesTest.py	98.75% <100%> (ø)	:arrow_up:
... and 19 more

---

Continue to review full report at Codecov.

Legend - Click here to learn more Δ = absolute <relative> (impact), ø = not affected, ? = missing data Powered by Codecov. Last update 02f5f8a...239798d. Read the comment docs.