Cleanup code - Githubissues

iDrDex / star_api

API access to STARGEO: stargeo.org

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Cleanup code #6

Closed dhimmel closed 8 years ago

dhimmel commented 8 years ago

Clean up code:

Adopt PEP 8 style for imports
Remove large chunks of quoted code

Return a tuple of (sample_df, fold_change, balanced_permutations, permutations) in analysis.perform_analysis.

Remove log file handling from analysis.py. This file location should be set by the calling program.

Remove __main__ statements.

dhimmel commented 8 years ago

Note this pull request will overwrite all changes from idrdex/star_api@278ab2d35584d5f6e94aded80a823b3b5f2cf254. If this commit has important changes those should be manually added back.

dhimmel commented 8 years ago

This pull request includes major modifications.

The repository now contains a python package that can be installed locally in development mode (see #8). See examples/example.ipynb for how to operate.

Creating a package will make the repository easier for users to adapt, and will help remove user-specific analyses from the central package.

iDrDex commented 8 years ago

@Suor, can you change the master branch of idrdex/star_api to exactly dhimmel/starapi@e171dd2b1d62cd6714e0321bee1e199836f8858d. This commit includes the optimized permutation test and has the repo designed as a module.

Suor commented 8 years ago

Merged manually