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Allow working with pbzip2 compressed files #4559

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merged 4 commits into from Sep 6, 2017

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@mvdbeek
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commented Sep 5, 2017

This adds supprt for uploading and uncompressing pbzip2 compressed
files by exchanging the bz2 module with bz2file (recommended as workaround in
https://docs.python.org/2/library/bz2.html). The problem was reported by
@alpapan in #4538 and this commit should fix #4538.

Depends on galaxyproject/starforge#147 for the
bz2file wheel.

Allow working with pbzip2 compressed files
This adds supprt for uploading and uncompressing pbzip2 compressed
files by exchanging the bz2 module with bz2file (recommended as workaround in
https://docs.python.org/2/library/bz2.html). The problem was reported by
@alpapan in #4538 and this commit should fix #4538.

Depends on galaxyproject/starforge#147 for the
bz2file wheel.
@nsoranzo

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commented Sep 5, 2017

Thanks @mvdbeek! According to https://docs.python.org/3.7/library/bz2.html#bz2.BZ2File , support for the multi-stream files produced by pbzip2 was added in Python 3.3. Can you modify the imports and the requirements files to use bz2file only for Python < 3.3?

@mvdbeek mvdbeek force-pushed the mvdbeek:use_bzip2file branch from 50d411e to 4f138ab Sep 5, 2017

@mvdbeek mvdbeek force-pushed the mvdbeek:use_bzip2file branch from 4f138ab to cccf79a Sep 5, 2017

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commented Sep 5, 2017

Thanks again, LGTM! My only doubt is if we should instead use the environment markers in pinned-requirements.txt , i.e.:

bz2file==0.98; python_version < '3.3'
@mvdbeek

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commented Sep 5, 2017

I didn't know we could do that! If it works then I think we should do it.

@nsoranzo

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commented Sep 5, 2017

Ping our pip expert @natefoo

@mvdbeek mvdbeek force-pushed the mvdbeek:use_bzip2file branch from 14ced53 to 8c4716e Sep 5, 2017

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commented Sep 5, 2017

Yes, we pip install -r requirements.txt, so the full requirements syntax is supported. This looks great, thanks @mvdbeek!

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commented Sep 5, 2017

Awesome, thanks!

@nsoranzo nsoranzo merged commit 486f436 into galaxyproject:dev Sep 6, 2017

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@mvdbeek mvdbeek deleted the mvdbeek:use_bzip2file branch Jun 12, 2018

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