[Biopython-dev] Git master branch freeze for Biopython 1.69 release

Fulton, Ben befulton at iu.edu
Fri Apr 7 14:39:20 UTC 2017

Pull request submitted. Did you just copy that comment from the last release email?  ☺ 

I got an error in testing that I don't remember seeing before:

ERROR: test_correct_retrieval_1 (test_MafIO_index.TestSpliceGoodMAF)
Traceback (most recent call last):
  File "C:\Users\befulton\Documents\GIT\biopython\Tests\test_MafIO_index.py", line 398, in test_correct_retrieval_1
    3227479), 1)
  File "C:\Users\befulton\Documents\GIT\biopython\build\lib.win32-3.5\Bio\AlignIO\MafIO.py", line 555, in get_spliced
    fetched = [multiseq for multiseq in self.search(starts, ends)]
  File "C:\Users\befulton\Documents\GIT\biopython\build\lib.win32-3.5\Bio\AlignIO\MafIO.py", line 555, in <listcomp>
    fetched = [multiseq for multiseq in self.search(starts, ends)]
  File "C:\Users\befulton\Documents\GIT\biopython\build\lib.win32-3.5\Bio\AlignIO\MafIO.py", line 530, in search
    (rec_start, rec_end, offset, start, end))
ValueError: Expected 3185728-3185798 @ offset 1974167, found 3185634-3185641

I don't know if it's a Windows thing, or known bug, or something else.

Ben Fulton
Research Technologies
Scientific Applications and Performance Tuning
Indiana University
E-Mail: befulton at iu.edu

-----Original Message-----
From: Biopython-dev [mailto:biopython-dev-bounces+befulton=iu.edu at mailman.open-bio.org] On Behalf Of Peter Cock
Sent: Friday, April 7, 2017 6:37 AM
To: Ben Fulton <ben at benfulton.net>
Cc: Biopython-Dev Mailing List <biopython-dev at mailman.open-bio.org>
Subject: Re: [Biopython-dev] Git master branch freeze for Biopython 1.69 release

Dear Ben,

If you like last time could prepare Biopython 1.69 Windows 32-bit installers for
Python 3.5 and now also Python 3.6, that would be much appreciated.

(Embarrassingly, I still haven't got round to replacing my obsolete
Windows XP machine)

Thank you,


On Fri, Apr 7, 2017 at 11:29 AM, Peter Cock <p.j.a.cock at googlemail.com> wrote:
> OK, what is hopefully going to be the official Biopython 1.69 release
> is now uploaded and tagged on the main repository master branch:
> https://github.com/biopython/biopython/commit/536ead7385084d7547af636eddd6f1706ba2717e
> https://github.com/biopython/biopython/tree/biopython-169
> Likewise I've uploaded the files so far to the official DIST repo for
> the website,
> https://github.com/biopython/DIST/commit/3e14bab2a9235915dd93b33306196029ac17e574
> They are not yet linked to from the website, but you can browse them here:
> https://github.com/biopython/DIST
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