[Debian-med-packaging] Bug#1024425: python-pysam ftbfs with python3.11 reduced severity

[Étienne Mollier]

Nilesh Patra, on 2022-12-01:
> On Tue, 29 Nov 2022 22:30:10 +0100 =?utf-8?Q?=C3=89tienne?= Mollier <emollier at emlwks999.eu> wrote:
> > Control: severity -1 important
> > 
> > Hi,
> > 
> > I just uploaded python-pysam 0.20 with python3-dev support only
> > for the time being.  This can be raised later on when python3.11
> > becomes the default, or a last time when python3.10 is to be
> > dropped.
> 
> Unfortunately this is a rabbit hole, and breaks other stuff, see Bug#1025116.

Ouch, I haven't accounted for that.  I'm suddenly somewhat
concerned that packages marked "Depends" below can be
potentially affected one way or another, even if not detected as
such by autopkgtest or an archive rebuild (yet):

	$ apt rdepends python3-pysam
	python3-pysam
	Reverse Depends:
	  Depends: python3-deeptools (>= 0.14.0)
	  Depends: python3-seqcluster
	  Depends: python3-bcbio
	  Depends: yanosim
	  Depends: umis
	  Depends: tiddit
	  Depends: svim
	  Depends: sniffles
	  Depends: sga
	  Depends: python3-sqt
	  Depends: python3-vcf
	  Enhances: python-pysam-tests
	  Depends: python3-pybedtools
	  Depends: python3-pbcore
	  Depends: python3-nanoget
	  Depends: ariba (>= 0.9.1)
	  Depends: python3-cooler
	  Depends: pycoqc
	  Depends: python3-pbsuite-utils
	  Depends: pbhoney
	  Depends: paleomix
	  Depends: optimir
	  Depends: nanosv
	  Recommends: nanopolish
	  Depends: python3-mirtop
	  Depends: metaphlan
	  Depends: mcaller
	  Depends: mapdamage
	  Depends: lumpy-sv
	  Depends: iva
	  Depends: insilicoseq
	  Depends: python3-htseq
	  Depends: gasic
	  Depends: fitgcp
	  Recommends: med-bio-dev
	  Suggests: med-bio
	  Depends: cutesv
	  Depends: cnvkit
	  Depends: circlator
	  Depends: catfishq
	  Depends: bamkit
	  Depends: atropos

> Ofcourse, there is a work around for that bug as well (i.e. just test with default
> pyvers) but, this would need fixing soonish*
> 
> * T&C applied

I don't expect being able to address the root issue, and I'm
unsure right now how timely I would be able to bring reverse
dependencies into shape to stick to python3.10 yet; possibly
something to do in upcoming python sprint…

Nevertheless, thanks for raising this,
-- 
Étienne Mollier <emollier at emlwks999.eu>
Fingerprint:  8f91 b227 c7d6 f2b1 948c  8236 793c f67e 8f0d 11da
Sent from /dev/pts/4, please excuse my verbosity.
On air: Steve Unruh - challenging
-------------- next part --------------
A non-text attachment was scrubbed...
Name: signature.asc
Type: application/pgp-signature
Size: 833 bytes
Desc: not available
URL: <http://alioth-lists.debian.net/pipermail/debian-med-packaging/attachments/20221130/a4fb3354/attachment.sig>