[Debian-med-packaging] Bug#1044060: More qiime related issues affecting q2-quality-control (Was: Help needed to port qiime to Python3.12)

[Andreas Tille]

Hi again,

Am Sun, Feb 18, 2024 at 12:25:49PM +0100 schrieb Andreas Tille:
> I just realised that a new qiime version is out.  I will upgrade
> to latest upstream and see how this might affect this issue

The new qiime upstream version does not change anything.  After I
switched q2-* packages to run autopkgtest for `py3versions -s` I
realised the problem below exist in several of the q2-* packages so its
rather no Pandas issue but a Python3.12 problem which in parallel to the
Pandas migration showed up.

If you might have any hint how to deal with these (no matter for the
old or the new qiime package since I assume the patch will apply
to both, it would be really appreciated.
 
Kind regards
    Andreas.
 
> Am Sun, Feb 18, 2024 at 12:11:04PM +0100 schrieb Andreas Tille:
> > Control: tags -1 help
> > 
> > Hi again,
> > 
> > I hope to approach the last remaining Pandas issue for the qiime
> > ecosystem.  As it has become obvious in the q2-types package I'm now
> > facing pretty similar errors when running the q2-quality-control
> > package which can be seen in full length in Salsa-CI[3] and contains
> > errors like:
> > 
> > E           AttributeError: 'ProvenancePath' object has no attribute '_drv'
> > E       AttributeError: 'ProvenancePath' object has no attribute '_raw_paths'
> > E           AttributeError: 'ProvenancePath' object has no attribute '_str'
> > E           AttributeError: 'OutPath' object has no attribute '_str'
> > 
> > This all goes back to the qiime package but I admit I have no idea
> > how to fix this.
> > 
> > Kind regards
> >      Andreas.
> > 
> > 
> > [3] https://salsa.debian.org/med-team/q2-quality-control/-/jobs/5320775#L700
> > 
> > Am Sat, Feb 17, 2024 at 11:36:41AM +0100 schrieb Andreas Tille:
> > > Hi,
> > > 
> > > as reported in a qiime2 issue[1] there is some problem with Python3.12
> > > in the tests of the q2-* packages which are all using the qiime package.
> > > This problem is currently hidden from the tests made by Python3.12
> > > porters but it became obvious now on Salsa CI[2].  I tried to fiddle
> > > around a bit with the qiime code but with no success at all.  Any help
> > > would be welcome.
> > > 
> > > Kind regards
> > >     Andreas.
> > > 
> > > [1] https://github.com/qiime2/qiime2/issues/751
> > > [2] https://salsa.debian.org/med-team/q2-types/-/jobs/5313640#L900
> > > 
> > > -- 
> > > http://fam-tille.de
> > 
> > -- 
> > http://fam-tille.de
> 
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