dependency on python-biopython-sql missing

[Jan T Kim]

1) Ubuntu release: 18.04 LTS (Bionic Beaver)

2) Package versions: python-biopython 1.70+dfsg-4, python-biopython-sql 1.70+dfsg-4 (solves problem)

3) Expected: script that works elsewhere to work on bionic as well

4) What happened: script fails when python-biopython-sql is not installed,
with errors like

  File "/usr/lib/python2.7/dist-packages/Bio/SeqRecord.py", line 440, in __getitem__
    from BioSQL.BioSeq import DBSeqRecord
ImportError: No module named BioSQL.BioSeq

5) Solution and analysis: The offending line (#440) reads

    from BioSQL.BioSeq import DBSeqRecord

Installing python-biopython-sql solves the problem. It thus seems that python-biopython should depend on python-biopython-sql. I notice that python-biopython-sql does depend on python-biopython, so this would introduce a mutual (circular) dependency. A solution to avoid having mutually dependent packages might be to merge python-biopython-sql into the main / base python-biopython package.

[Dylan Aïssi (daissi)]

 Fixed since python-biopython 1.71+dfsg-1 (Cosmic)