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
