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[MoM] phyx upstream update & changes (Was: Re: [MoM] lefse migration to python 3)

Hello Andreas,

Quick email before I head to bed as I stayed up until early morning to
ensure upstream for phyx was noted about the test issue, pushed a
satisfactory release and then updating the package :).

The issue was due to precision and how the test factored this in when it
came to check / comparison. Upstream has fixed this so all 41 tests pass
on my system. I left your current autopkgtest implementation as it is
late and I didn't want to remove your work so integrate this in.

Kind regards,
Shayan Doust

On 11/09/2019 21:35, Andreas Tille wrote:
> Hi Shayan,
> On Wed, Sep 11, 2019 at 05:34:19PM +0100, Shayan Doust wrote:
>>> plot_cladogram comparative fail
>> I cannot reproduce this and I just did a clean build and installed a
>> fresh *.deb. I did however do some refinements and any fails will result
>> in script execution which will display the output so please pull.
> Ahhh,
> plot_cladogram comparative fail. Instead, I get:
> Traceback (most recent call last):
>   File "/usr/bin/plot_cladogram", line 5, in <module>
>     from pylab import *
> ModuleNotFoundError: No module named 'pylab'
> This uncovered a new missing Depends!  This again proves the sense
> of even very simple tests.
>>> I've observed your commits to phyx but did not acted upon it since you
>>> did not confirmed that you are ready here.
>> More about this: this is ready. Both the run_tests.py and gui interface
>> work. A note about the run_tests.py. Before the conversion, 9 tests
>> failed (I think 31 passed) and after the conversion, there is the same
>> failure rate.
> Confirmed according to
>    https://buildd.debian.org/status/fetch.php?pkg=phyx&arch=amd64&ver=0.999%2Bds-1&stamp=1539857991&raw=0
>> Not sure if this is some upstream fault because I have not
>> been able to get a fresh upstream copy and directly test the
>> run_tests.py, but I assume it will be the same as what I get now.
> That's correct - may be we should contact upstream about this anyway.  I
> simply created an autopkgtest from Phyxed_Manual.tex (via sed + minor
> editing).  If the tools send correct exit codes this should work.
> Kind regards
>        Andreas. 

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