[Debian-med-packaging] Bug#996794: ncbi-acc-download: autopkgtest failure with python-biopython 1.79+dfsg-1~0exp0 in experimental

[Étienne Mollier]

Hi Aaron, Hi Andreas,

Andreas Tille, on 2021-10-19:
> Am Tue, Oct 19, 2021 at 07:55:07AM -0400 schrieb Aaron M. Ucko:
> > Étienne Mollier <emollier at emlwks999.eu> writes:
> > 
> > > 	E         - LOCUS       NC_007194                 60 bp    DNA     linear   CON 03-APR-2018
> > > 	E         ?                                  ^^^^^^^                            ^^ ^^^   ^^
> > > 	E         + LOCUS       NC_007194            4918979 bp    DNA     linear   CON 11-NOV-2009
> > > 	E         ?                                  ^^^^^^^                            ^^ ^^^   ^^
> > 
> > It looks like this test is intended to work offline (as required) and
> > yield short mock records, but for some reason winds up fetching
> > full-length live data instead.

As always, thanks for your analysis!  I confirm the test suite
works offline, so withdraw my suspicion.

> Strangely enough this issue seems to depend from the biopython version.
> Any idea what might be wrong here?

After some digging, I found one possible cause of breakage.
Since biopython 1.79, Bio.Seq.UnknownSeq is deprecated [1], so
it might be possible that ncbi-acc-download does not parse the
instanciation of that class very well.

[1]: https://github.com/biopython/biopython/blob/master/DEPRECATED.rst#biosequnknownseq

Looks like I would want to take the issue upstream.

Have a nice day,  :)
-- 
Étienne Mollier <emollier at emlwks999.eu>
Fingerprint:  8f91 b227 c7d6 f2b1 948c  8236 793c f67e 8f0d 11da
Sent from /dev/tty1, please excuse my verbosity.
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