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

[Étienne Mollier]

Hi Andreas,

Andreas Tille, on 2020-04-27 23:09:55 +0200:
> pauvre marginplot -f nanotest/reads.fastq.gz -y --filt_minqual 7 --fileform svg
> 
> ...
> 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.

> 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.

Kind Regards,
-- 
Étienne Mollier <etienne.mollier at mailoo.org>
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