[Debian-med-packaging] pauvre is missing sklearn despite the package is installed

[Étienne Mollier]

Hi Andreas,

Andreas Tille, on 2020-04-28 13:05:52 +0200:
> On Tue, Apr 28, 2020 at 12:54:00PM +0200, Étienne Mollier wrote:
> > > Keeping reads that satisfy: length >= 0 and meanQual >= 0
> > > /usr/lib/python3.8/_collections_abc.py:832: MatplotlibDeprecationWarning: 
> > > The text.latex.unicode rcparam was deprecated in Matplotlib 3.0 and will be removed in 3.2.
> > >   self[key] = other[key]
> > 
> > The deprecation warning seems unrelated to the crash.
> 
> Yes.  But once you are talking to upstream it might sense to
> forward this as well.

Okay, I forwarded the word:

	https://github.com/conchoecia/pauvre/issues/41
 
> > > plotting in the following window:
> > >         0 <= Q-score (x-axis) <= 14.0
> > >         0 <= length  (y-axis) <= 223383
> > > 
> > > Traceback (most recent call last):
> > >   File "/usr/bin/pauvre", line 11, in <module>
> > >     load_entry_point('pauvre==0.1924', 'console_scripts', 'pauvre')()
> > >   File "/usr/lib/python3/dist-packages/pauvre/pauvre_main.py", line 630, in main
> > >     args.func(parser, args)
> > >   File "/usr/lib/python3/dist-packages/pauvre/pauvre_main.py", line 64, in run_subtool
> > >     submodule.run(args)
> > >   File "/usr/lib/python3/dist-packages/pauvre/marginplot.py", line 403, in run
> > >     margin_plot(df=df.dropna(), **vars(args))
> > >   File "/usr/lib/python3/dist-packages/pauvre/marginplot.py", line 381, in margin_plot
> > >     if kwargs["BASENAME"] is None and not kwargs["path"] is None:
> > > KeyError: 'path'
> > > ...
> > > 
> > > 
> > > The data are obtained from python3-nanoget-examples package.
> > > 
> > > Any idea what might be wrong here?
> > 
> > Checking for the availability of the key in the kwargs prior to
> > dereferencing it seems to help moving forward:
> > 
> > 381:    if kwargs["BASENAME"] is None and "path" in kwargs and not kwargs["path"] is None:
> >                                      +++++++++++++++++++++
> > 
> > Patching pauvre/marginplot.py in python-pauvre and bringing the
> > issue to upstream should do the trick.  I can bring these
> > changes this evening, unless you prefer to work on this this
> > afternoon.
> 
> Thanks for the pointer.  I have sufficient other work to do so I'll
> simply leave this for you. ;-)

Good news, it has already been fixed:

	https://github.com/conchoecia/pauvre/commit/90fbe2f4c190ff897dfc8ae12971d5865682fc8a

Furthermore, applying this patch, I ran the whole test on my
machine, and it went through without erroring, which I suppose
is good news.  :)

While I was at it, I generated a skeleton manual page, since it
was missing.  It's from help2man, so still needs quite some wrap
up though.  Reading quickly through pauvre/pauvre_main.py, there
seem to be sub-option for each sub-commands, so the page might
gain to be completed, but that is better than nothing.

There is the ITP "Closes:" field left to fill, but I believe
that you migth enjoy filling it by yourself since you opened the
request.  ;)

Kind Regards,
-- 
Étienne Mollier <etienne.mollier at mailoo.org>
Fingerprint:  5ab1 4edf 63bb ccff 8b54  2fa9 59da 56fe fff3 882d
Help find cures against the Covid-19 !  Give CPU cycles:
  * Rosetta at home: https://boinc.bakerlab.org/rosetta/
  * Folding at home: https://foldingathome.org/
-------------- next part --------------
A non-text attachment was scrubbed...
Name: signature.asc
Type: application/pgp-signature
Size: 659 bytes
Desc: not available
URL: <http://alioth-lists.debian.net/pipermail/debian-med-packaging/attachments/20200428/b7e9af77/attachment.sig>