[Debian-med-packaging] Packages dependeing from python-skbio (Was: Bug#800739: ITP: python-burrito-fillings -- burrito application controllers for bioinformatics)

[Tim Booth]

Hi Andreas,

As I said when I finished wrestling with this knot of packages, the
whole thing with QIIME needing PyCogent and Burrito and SKBio is just a
horrible mess.  I had to make it work because it's my job, but I'm not
surprised this has arisen in Debian.  Anybody wanting to run QIIME or
SortMeRNA plus a tool that wants SKBio 0.3+ will be hitting the same
problem, no matter how they install things.

Before considering options, could you tell me what package(s) require
the new SKBio 0.4?  What are we actually breaking here?

Cheers,

TIM

On Sat, 2015-10-03 at 08:03 +0200, Andreas Tille wrote:
> Hi Tim,
> 
> I'm afraid I'm beaten by the same issue as mentioned here
> 
>     https://lists.debian.org/debian-med/2015/08/msg00019.html
> 
> I get
> 
> $ grep "Error.*parse\.sequences" python-burrito-fillings_0.1.1-1_amd64.build 
> ImportError: No module named parse.sequences
> ImportError: No module named parse.sequences.fasta
> ImportError: No module named parse.sequences
> ImportError: No module named parse.sequences
> ImportError: No module named parse.sequences
> ImportError: No module named parse.sequences
> ImportError: No module named parse.sequences.fasta
> ImportError: No module named parse.sequences
> ImportError: No module named parse.sequences
> ImportError: No module named parse.sequences
> ImportError: No module named parse.sequences.fasta
> ImportError: No module named parse.sequences
> ImportError: No module named parse.sequences
> 
> 
> Do you have any sensible recommendation how to proceed with the
> python-skbio package if the packages we are interested in remain
> depending on an outdated version?
> 
> Kind regards
> 
>         Andreas.
> 
> On Sat, Oct 03, 2015 at 07:39:26AM +0200, Andreas Tille wrote:
> > Package: wnpp
> > Severity: wishlist
> > Owner: Andreas Tille <tille at debian.org>
> > 
> > * Package name    : python-burrito-fillings
> >   Version         : 0.1.1
> >   Upstream Author : burrito development team <gregcaporaso at gmail.com>
> > * URL             : https://github.com/biocore/burrito/
> > * License         : BSD
> >   Programming Lang: Python
> >   Description     : burrito application controllers for bioinformatics
> >  The burrito-fillings project provides wrappers for bioinformatics tools
> >  using the burrito framework.
> >  .
> >  burrito-fillings (canonically pronounced boar-ee-toe phil-ings; python
> >  package name bfillings) contains burrito CommandLineApplication
> >  subclasses (i.e., application controllers) for bioinformatics
> >  applications. This is intended to be a temporary package for the
> >  application controllers that are used in QIIME as we figure out which of
> >  these we will continue to support.
> > 
> > 
> > Remark: This precondition to upgrade qiime was prepared by Tim Booth from
> > BioLinux in
> >    svn://anonscm.debian.org/debian-med/trunk/packages/python-burrito-fillings/trunk/
> > and is now taken over by the Debian Med team.
> > 
> > _______________________________________________
> > Debian-med-packaging mailing list
> > Debian-med-packaging at lists.alioth.debian.org
> > http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-packaging
> > 
> 

-- 
Tim Booth <tbooth at ceh.ac.uk>

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