[Debian-med-packaging] Last step NanoPlot

[Étienne Mollier]

Étienne Mollier, on 2020-04-29 20:00:54 +0200:
> Looking at the first error in the output of the test, nanoplot
> seems to expect an "orca" program in the user's path, which has
> nothing to do with the screen reader unfortunately.  Said
> program is suggested to be installed through conda:
> 
> 	$ conda install -c plotly plotly-orca
> 
> Or having a look at the project page on Github for other
> installation methods:
> 
> 	https://github.com/plotly/orca

Hi Andreas

Moving forward on this topic, during autopkgtest the orca
executable is required to export figures as static images, but
after visual inspection of test data, the lack of of this
component does not impede the core usage of NanoPlot (although
there is an export capability missing indeed, and it produces a
lot of trace during the execution of the program).

After some testing, it turned out to be unrelated to:
> The second set of errors looks like the following issue, and
> might be data dependent, but there could be a chance it is
> related to the error hereover:
> 
> 	https://github.com/wdecoster/NanoPlot/issues/177

Feeding the test with alignment_fasta.bam instead of
alignment.bam showed that some dataset was triggering the error
and not others indeed.  In the next version of NanoPlot, the
upstream author removed the need to use the statsmodels python
library, which is causing the bug, so just cherry picked that:

	https://github.com/wdecoster/NanoPlot/commit/da185a2e9d4f494987aedeb1eb15374cdbf99d7a

As long as python3-statsmodels is *not installed* on the
machine, it does the job.  However, if the package is pulled for
whatever reason, then the problem comes back.  I don't know what
the best approach would be to solve this properly, for the
moment.


On a side note, I took example on what you did for python-pauvre
in producing a manual page.  A long sequence of characters to
describe a set ended up pulling another lintian warning, so I
did some manual changes to relax the format of sets of options,
and allow well formatted manual pages.  It goes a bit against
the automation, will it do anyway ?

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