Input/Output of Statmech Calculations

[nateharms]

When creating Arkane input files for species and transition states, we would first check to make sure that an Arkane input file was created and if it was created, we would not create a new one on the assumption that this was correct. This PR allows for new files to be written and if an old file exists, it will be written as a backup file in case a user wants to keep it.

[codecov[bot]]

Codecov Report

Merging #83 into master will increase coverage by 0.74%. The diff coverage is 72.13%.

@@            Coverage Diff             @@
##           master      #83      +/-   ##
==========================================
+ Coverage   65.18%   65.93%   +0.74%     
==========================================
  Files          27       27              
  Lines        4774     4899     +125     
==========================================
+ Hits         3112     3230     +118     
- Misses       1662     1669       +7     

Impacted Files	Coverage Δ
autotst/data/inputoutput.py	65.25% <ø> (ø)
autotst/job/job.py	44.01% <ø> (-0.09%)	:arrow_down:
autotst/calculator/statmech.py	72.30% <67.92%> (+1.33%)	:arrow_up:
autotst/species.py	72.14% <100.00%> (-0.05%)	:arrow_down:
autotst/reaction.py	81.80% <0.00%> (-0.40%)	:arrow_down:
autotst/geometry.py	91.30% <0.00%> (+2.17%)	:arrow_up:
autotst/conformer/systematic.py	83.09% <0.00%> (+8.59%)	:arrow_up:

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[davidfarinajr]

@nateharms, can you rebase this branch onto master? I think there are some commits here we already merged in

[nateharms]

Okay, I rebased

[nateharms]

Because this PR is a little old, here's a summary of the changes:

calculator/statmech.py

• Added a few imports
• Added former rotor treatment for stable species
• Added a try / except for running kinetics with rotors and then without if Arkane fails

species.py

• reorganized when certain attributes are set

data/inputoutput.py

• added TemplateReaction to the read_kinetics_file method

job/job.py

• removed an import

environment.yml

• added a matplotlib requirement to fix errors that we currently have

[nateharms]

@skrsna could you give this one a look over too?

[nateharms]

@skrsna the corrections that you requested were made. When you get a chance, can you approve this PR?