[Debian-med-packaging] Bug#883860: python-biopython: SeqRecord broken on Debian packages when python-biopython-sql package is not installed

[Kai Blin]

Package: python-biopython
Version: 1.68+dfsg-3
Severity: important
Tags: upstream

Dear Maintainer,

Upstream Biopython introduced a hard dependency from the Bio.SeqRecord
class on BioSQL with commit 48cd6bc1. This causes the __getitem__
method to fail unless python-biopython-sql is also installed. As the
-sql package also pulls in mysql, that can be undesirable.

I've reported this bug upstream as
https://github.com/biopython/biopython/issues/1471 already.

That bug report also contains a reproducer that works on current Debian
stretch.

I have not tested with the 1.70 packages available in unstable as the
code causing the issue is present in that version as well.

Best regards,
Kai

-- System Information:
Debian Release: 9.1
  APT prefers stable-updates
  APT policy: (500, 'stable-updates'), (500, 'stable')
Architecture: amd64 (x86_64)

Kernel: Linux 4.4.0-93-generic (SMP w/8 CPU cores)
Locale: LANG=C, LC_CTYPE=C (charmap=ANSI_X3.4-1968), LANGUAGE=C (charmap=ANSI_X3.4-1968)
Shell: /bin/sh linked to /usr/bin/dash
Init: unable to detect

Versions of packages python-biopython depends on:
ii  libc6                             2.24-11+deb9u1
ii  python                            2.7.13-2
ii  python-numpy [python-numpy-abi9]  1:1.12.1-3
ii  python-reportlab                  3.3.0-2

Versions of packages python-biopython recommends:
ii  ncbi-blast+           2.6.0-1
ii  python-biopython-doc  1.68+dfsg-3

Versions of packages python-biopython suggests:
pn  bwa                <none>
pn  clustalo           <none>
pn  clustalw           <none>
pn  dialign            <none>
pn  dssp               <none>
pn  emboss             <none>
pn  fasttree           <none>
pn  mafft              <none>
pn  muscle             <none>
pn  phylip             <none>
pn  phyml              <none>
pn  prank              <none>
pn  probcons           <none>
pn  python-matplotlib  <none>
pn  python-mysqldb     <none>
ii  python-pil         4.0.0-4
pn  python-psycopg2    <none>
pn  python-rdflib      <none>
ii  python-renderpm    3.3.0-2
pn  python-scipy       <none>
pn  python-tk          <none>
pn  raxml              <none>
pn  samtools           <none>
pn  t-coffee           <none>
pn  wise               <none>

-- no debconf information