JOSS fixes: resolves jcsutherland issues

[kyleniemeyer]

This PR makes a number of changes to resolve the issues raised by @jcsutherland during his review for our JOSS submission (https://github.com/openjournals/joss-reviews/issues/1543).

In particular, this:

• Closes #56 by more clearly describing input parameter units in the docs, annotating the example input file with comments, and also allowing the user to specify mass fractions
• Closes #57 by moving all reduction inputs to a single YAML file
• Closes #58 and closes #59 by adding better error-checking of reduction inputs (including that any species mentioned are actually present in the model)
• Closes #60 by allowing the user to specify a particular ideal_gas object for reduction, if multiple are present in the CTI file
• Closes #61 by integrating autoignition simulations to steady state by default

[codecov-io]

Codecov Report

Merging #63 into master will increase coverage by 1.7%. The diff coverage is 60.15%.

@@            Coverage Diff            @@
##           master      #63     +/-   ##
=========================================
+ Coverage   65.46%   67.16%   +1.7%     
=========================================
  Files          12       12             
  Lines        1193     1261     +68     
  Branches      299      294      -5     
=========================================
+ Hits          781      847     +66     
- Misses        305      314      +9     
+ Partials      107      100      -7

Impacted Files	Coverage Δ
pymars/tools.py	48.81% <ø> (ø)	:arrow_up:
pymars/pymars.py	0% <0%> (ø)	:arrow_up:
pymars/sensitivity_analysis.py	73.43% <100%> (ø)	:arrow_up:
pymars/drg.py	84.69% <100%> (ø)	:arrow_up:
pymars/pfa.py	87.28% <100%> (ø)	:arrow_up:
pymars/drgep.py	77.56% <100%> (ø)	:arrow_up:
pymars/reduce_model.py	92% <60%> (-8%)	:arrow_down:
pymars/simulation.py	85% <80.82%> (+25%)	:arrow_up:
pymars/sampling.py	67.08% <82.95%> (+10.43%)	:arrow_up:

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