Cython tidying

[camillescott]

Cythonizes the free floating functions and cleans up some code locations.

• Is it mergeable?
• make test Did it pass the tests?
• make clean diff-cover If it introduces new functionality in
  scripts/ is it tested?
• make format diff_pylint_report cppcheck doc pydocstyle Is it well
  formatted?
• Did it change the command-line interface? Only backwards-compatible
  additions are allowed without a major version increment. Changing file
  formats also requires a major version number increment.
• For substantial changes or changes to the command-line interface, is it
  documented in CHANGELOG.md? See keepachangelog
  for more details.
• Was a spellchecker run on the source code and documentation after
  changes were made?
• Do the changes respect streaming IO? (Are they
  tested for streaming IO?)

[luizirber]

I don't know if you want to cover this here, but we can remove all the from __future__ and sys.version checks from the code (yay!)

[camillescott]

Yeah, already started it on a few files :)

…

On Thu, Sep 7, 2017 at 11:19 AM, Luiz Irber ***@***.***> wrote: I don't know if you want to cover this here, but we can remove all the from __future__ and sys.version checks from the code (yay!) — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#1774 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ACwxrYh0Diq9qg-nMeGKGMhKViU_TlM7ks5sgDOugaJpZM4PPHv1> .

-- Camille Scott Graduate Group for Computer Science Lab for Data Intensive Biology University of California, Davis camille.scott.w@gmail.com

[camillescott]

For @standage: a good example of how to do the new style paired read handling can be found the in sample-reads-randomly script: https://github.com/dib-lab/khmer/pull/1774/files#diff-d7ee671a9cc8a3d7f82adcc860c1850b

Basically, utility function allows handling multiple paired-end samples in either split, interleaved, or single mode seamlessly, using the new Cython-based BrokenPairedReader.

[standage]

Woot! This PR is down from 140 files to 37! :-)