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

[Tim Booth]

Hi Andreas,

> IMHO python-burrito-filling should be adapted to the latest skbio
> interface.

Yes, but not by us!  SKBio and the Burrito stuff and QIIME and SortMeRNA
are all being developed by the same people under the "biocore" umbrella,
which is why they all live on https://github.com/biocore.  They are
already working to sort it out, and I don't want to duplicate effort.
My concern here is to make the user-facing tools work properly on
Debian/Bio-Linux even if there is a tangle of wires under the hood.

Cheers,

TIM

On Mon, 2015-10-05 at 23:12 +0200, Andreas Tille wrote:
> Hi Tim,
> 
> On Mon, Oct 05, 2015 at 03:55:07PM +0100, Tim Booth wrote:
> > 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?
> 
> Well, I'm using the latest (packaged python-skbio).  From the log
> 
> ...
> Selecting previously unselected package python-skbio.
> Preparing to unpack .../python-skbio_0.4.0-1_amd64.deb ...
> ...
> 
> test_raxml_params (bfillings.tests.test_raxml_v730.RaxmlTests)
> raxml should raise exception if missing required params ... ok
> 
> ======================================================================
> ERROR: bfillings.tests.test_vsearch (unittest.loader.ModuleImportFailure)
> ----------------------------------------------------------------------
> ImportError: Failed to import test module: bfillings.tests.test_vsearch
> Traceback (most recent call last):
>   File "/usr/lib/python2.7/unittest/loader.py", line 254, in _find_tests
>     module = self._get_module_from_name(name)
>   File "/usr/lib/python2.7/unittest/loader.py", line 232, in _get_module_from_name
>     __import__(name)
>   File "bfillings/tests/test_vsearch.py", line 23, in <module>
>     from skbio.parse.sequences import parse_fasta
> ImportError: No module named parse.sequences
> 
> 
> ======================================================================
> ERROR: bfillings.tests.test_blast (unittest.loader.ModuleImportFailure)
> ----------------------------------------------------------------------
> ImportError: Failed to import test module: bfillings.tests.test_blast
> Traceback (most recent call last):
>   File "/usr/lib/python2.7/unittest/loader.py", line 254, in _find_tests
>     module = self._get_module_from_name(name)
>   File "/usr/lib/python2.7/unittest/loader.py", line 232, in _get_module_from_name
>     __import__(name)
>   File "bfillings/tests/test_blast.py", line 18, in <module>
>     from bfillings.blast import (seqs_to_stream, make_subject_match_scorer,
>   File "bfillings/blast.py", line 21, in <module>
>     from skbio.parse.sequences.fasta import FastaFinder, is_fasta_label
> ImportError: No module named parse.sequences.fasta
> 
> 
> ======================================================================
> ERROR: bfillings.tests.test_usearch (unittest.loader.ModuleImportFailure)
> ----------------------------------------------------------------------
> ImportError: Failed to import test module: bfillings.tests.test_usearch
> Traceback (most recent call last):
>   File "/usr/lib/python2.7/unittest/loader.py", line 254, in _find_tests
>     module = self._get_module_from_name(name)
>   File "/usr/lib/python2.7/unittest/loader.py", line 232, in _get_module_from_name
>     __import__(name)
>   File "bfillings/tests/test_usearch.py", line 23, in <module>
>     from skbio.parse.sequences import parse_fasta
> ImportError: No module named parse.sequences
> 
> ...
> 
> 
> IMHO python-burrito-filling should be adapted to the latest skbio
> interface.
> 
> Does this clarify the issue?
> 
> Kind regards
> 
>       Andreas. 
> 

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

Centre for Ecology and Hydrology
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http://environmentalomics.org/bio-linux
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