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Re: [MoM] lefse migration to python 3

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.


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


> 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



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