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 [email protected] 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!)

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-- Camille Scott

Graduate Group for Computer Science Lab for Data Intensive Biology University of California, Davis

[email protected]

[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! :-)