To do list

[alaindomissy]

Done:

• flotilla PEP8 compliance
• ensure CI travis builds ok
• Auto-release to PyPI via Travis CI Auto-release to PyPI via Travis CI #268
• flotilla fix file format extension for output

Priority 1:

• review and prioritize issues on github
• python 3 compatibility python 3 compatibility #23
• check reproducing (all?) analyses from shalek 2013
• check test coverage and add test examples/ tutorial examples if needed
• Add more examples Add more examples #262

Priority 2:

• swap all test data and tutorial examples, using macaulay 2016 paper instead of shalek 2013
• Cannot setup flotilla on Windows? Cannot setup flotilla on Windows? #318

Priority 3:

• Replace Study objects with xray datasets Replace Study objects with xray datasets #326
• generalize/simplify API for subselection of either cells or features or both
• data prep visualization utilities ex: violin plot for single cell population

Priority 4:

• docker build and instructions update
• ensure docker hub builds ok
• abstract out machine learning visualization abstract out machine learning visualization, metadata-based subsetting, and splicing compute #315 ("cupcake" module)
• abstract out metadata-based sub-setting, and splicing compute abstract out machine learning visualization, metadata-based subsetting, and splicing compute #315
• abstract out splicing compute abstract out machine learning visualization, metadata-based subsetting, and splicing compute #315
• document list of data transform utilities currently available and specific to expected data types: expression values between 0 and 1, ...
• specify what other data types might be useful to support, what data transformation utilities would be useful, prioritize, implement
• review current versions of flotilla and cupcake(?) as support for the upcoming single-cell class, define improvements/additions for that class