Remove dead code with the help of vulture

[david4096]

https://pypi.python.org/pypi/vulture revealed some dead code. You will need to rebuild your test data.

There is also orphaned code that is under test but doesn't present any features that vulture doesn't catch.

@ejacox note I removed the fillEnd functions if you planned on keeping them for something.

[codecov-io]

Codecov Report

Merging #1612 into master will increase coverage by 0.32%. The diff coverage is 100%.

@@            Coverage Diff             @@
##           master    #1612      +/-   ##
==========================================
+ Coverage   86.32%   86.65%   +0.32%     
==========================================
  Files          33       33              
  Lines        7569     7471      -98     
  Branches      935      926       -9     
==========================================
- Hits         6534     6474      -60     
+ Misses        841      805      -36     
+ Partials      194      192       -2

Impacted Files	Coverage Δ
ga4gh/server/datamodel/init.py	97.16% <ø> (+0.25%)	:white_check_mark:
ga4gh/server/datamodel/datasets.py	94.2% <ø> (+1.32%)	:white_check_mark:
ga4gh/server/datamodel/continuous.py	71.71% <ø> (+0.92%)	:white_check_mark:
ga4gh/server/datamodel/genotype_phenotype.py	79.33% <ø> (+2.97%)	:white_check_mark:
ga4gh/server/datarepo.py	90.47% <ø> (+0.68%)	:white_check_mark:
ga4gh/server/repo/models.py	100% <ø> (+0.5%)	:white_check_mark:
ga4gh/server/datamodel/ontologies.py	95.08% <ø> (+1.33%)	:white_check_mark:
ga4gh/server/cli/init.py	100% <ø> (+7.69%)	:white_check_mark:
ga4gh/server/response_builder.py	100% <ø> (ø)	:white_check_mark:
ga4gh/server/exceptions.py	98.58% <ø> (-0.06%)	:x:
... and 4 more

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[ejacox]

It's OK to remove fillEnd, but keep createIndices in rnaseq2ga.

[david4096]

Thanks @ejacox . Did I miss where the code that uses the indices is? You use it in an external script?

[david4096]

I also removed the .whiskey directory that worked with an old Dockerfile.