Merge branch 'hotfix/violinplot_numbers'

* hotfix/violinplot_numbers:
  fix (n=#) in violinplot
  test passing??
  test Study.save() works!!!
  fixing up datapackage stuf
  add more datapackage attributes to reading the datapackage
  Add option to not load species data
  add all datapackage parameters to study object
  remove pooled samples from data
  remove pdb/set_trace()
  mapped_reads --> number_mapped
  initial commit of properly saving datapackages
remove pdb.set_trace()
Add filter for minimum number of samples per group for NMF space positions
Only subset, do not standardize for expression binify
add default colors in metadata for phenotypes
Merge branch 'master' of github.com:YeoLab/flotilla
Merge branch 'release/0.1.0'

* release/0.1.0: (26 commits)
  Never standardize SplicingData, since it's already standardized from 0 to 1
  remove big block of commented code
  if feature_data is None, make an empty DataFrame for feature subsetting
  fix expressiondata and study tests
  actually move expression threshold
  move expression threshold cutoff to before log-transforming data
  move expression threshold to be on the raw data, not hte logged data
  Make sure set1 is only hex, not rgb colors
  Convert randomly assigned phenotype colors to hex colors from rgb
  Fix violinplots when there are not outlier cells, and
  Made "version" a required argument to Study (so "save" of a study bumps the version number correctly)
  fix feature_subset fixture for plot_pca test
  add test gene list
  fix test_external, remove test_ipython_interact
  Add official version
  increase scope of data_dir fixture
  Add tests for list_link, and pca with list subsets
  Add whether or not the decomposition is featurewise to the call, to know whether or not to draw violinplots
  Fix classifier plotting bug
  remove pdb call
  ...
Merge branch 'master' into release/0.1.0

PCA fixes: when there are no outliers, add minimum cells for NMF transitions, default colors for metadata

* master:
  remove pdb.set_trace()
Merge branch 'release/0.1.0' into dev

* release/0.1.0:
  Never standardize SplicingData, since it's already standardized from 0 to 1
  remove big block of commented code
  if feature_data is None, make an empty DataFrame for feature subsetting
  fix expressiondata and study tests
  actually move expression threshold
  move expression threshold cutoff to before log-transforming data
  move expression threshold to be on the raw data, not hte logged data
  Make sure set1 is only hex, not rgb colors
  Convert randomly assigned phenotype colors to hex colors from rgb
  Fix violinplots when there are not outlier cells, and
  Made "version" a required argument to Study (so "save" of a study bumps the version number correctly)
  fix feature_subset fixture for plot_pca test
  add test gene list
  fix test_external, remove test_ipython_interact
  Add official version
  increase scope of data_dir fixture
  remove pdb.set_trace()
fix default marker style
Merge remote-tracking branch 'origin/dev' into dev

* origin/dev: