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Cython tidying #1774

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Cython tidying #1774

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camillescott
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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
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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
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camillescott commented Sep 7, 2017 via email

This was referenced Sep 8, 2017
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@camillescott
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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.

This was referenced Sep 14, 2017
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Woot! This PR is down from 140 files to 37! :-)

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@camillescott @luizirber @standage