Use snakemake to manage mavis scheduling

[creisle]

• replace mavis scheduler with snakemake
• use JSON config for snakemake instead of many command line arguments

Note: This will set up for the next PR which will dockerize the whole thing to make future extensions of mavis simpler

[codecov[bot]]

Codecov Report

Merging #241 (d99112a) into develop_v3 (f3c76b7) will decrease coverage by 6.22%. The diff coverage is 64.95%.

@@              Coverage Diff               @@
##           develop_v3     #241      +/-   ##
==============================================
- Coverage       81.49%   75.26%   -6.23%     
==============================================
  Files              57       53       -4     
  Lines           10319     8726    -1593     
  Branches            0     2277    +2277     
==============================================
- Hits             8409     6568    -1841     
+ Misses           1910     1686     -224     
- Partials            0      472     +472     

Flag	Coverage Δ
unittests	75.26% <64.95%> (-6.23%)	:arrow_down:

Flags with carried forward coverage won't be shown. Click here to find out more.

Impacted Files	Coverage Δ
mavis/pairing/main.py	13.88% <28.57%> (-70.49%)	:arrow_down:
mavis/cluster/main.py	10.56% <30.43%> (-78.87%)	:arrow_down:
mavis/validate/main.py	12.79% <42.85%> (+1.67%)	:arrow_up:
mavis/summary/main.py	8.90% <46.66%> (+0.51%)	:arrow_up:
mavis/config.py	69.82% <59.09%> (-18.37%)	:arrow_down:
mavis/annotate/main.py	12.92% <68.75%> (-0.41%)	:arrow_down:
mavis/overlay.py	75.90% <75.90%> (ø)
mavis/main.py	81.67% <81.96%> (-4.86%)	:arrow_down:
mavis/annotate/file_io.py	76.44% <100.00%> (-10.05%)	:arrow_down:
mavis/constants.py	74.89% <100.00%> (-18.73%)	:arrow_down:
... and 40 more

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[creisle]

Ignore the coverage checks for now. When this is run locally the coverage is 89%. I'm not sure why codecov isn't picking up all the coverage but I am looking into it. I think it has to do with multi-processing during tests