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

[Andreas Tille]

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. 

-- 
http://fam-tille.de