Re: Python-pysam for unstable?

[Afif Elghraoui <afif@ghraoui.name>]

Hi, Andreas,

On السبت 11 تـمـوز 2015 02:11, Andreas Tille wrote:
> > On الجمعـة 10 تـمـوز 2015 08:22, Andreas Tille wrote:
>       ^^^^^^^^^^^^^^^^^
> Pretty cool - I was not aware that xterm can display this, at least
> I notice it the first time. :-)

:)

> However, what I'm doing to run the autopkg test - which I would call the
> wimp method - is just
>
>      cd debian/tests
>      sh run-nose-tests
>
> This runs the test on the local machine and not in a chroot - so it might
> run successfully but fail in a chroot.  But if this runs its a good sign.
> Unfortunately I get:
>
> $ sh run-nose-tests
> In file included from /tmp/python-pysam-test.YwEQqG/_compile_test.c:243:0:
> /usr/lib/python2.7/dist-packages/pysam/htslib_util.h:12:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
>   int hts_get_verbosity();
>   ^
> E.
> ======================================================================
> ERROR: testCount (compile_test.BAMTest)
> ----------------------------------------------------------------------
> Traceback (most recent call last):
>    File "/tmp/python-pysam-test.YwEQqG/compile_test.py", line 32, in testCount
>      pysam.Samfile(self.input_filename))
>    File "pysam/calignmentfile.pyx", line 311, in pysam.calignmentfile.AlignmentFile.__cinit__ (pysam/calignmentfile.c:4943)
>    File "pysam/calignmentfile.pyx", line 353, in pysam.calignmentfile.AlignmentFile._open (pysam/calignmentfile.c:5660)
>    File "pysam/calignmentfile.pyx", line 480, in pysam.calignmentfile.AlignmentFile._open (pysam/calignmentfile.c:6923)
> IOError: file `pysam_data/ex1.bam` not found
>
> ----------------------------------------------------------------------
> Ran 2 tests in 0.727s
>
> FAILED (errors=1)

So I just noticed a python-pysam-tests.README.Debian. These are 
apparently not autopkgtests. As written, these are tests intended for 
the user to run after the python-pysam-tests package is installed.

The pysam_data folder is indeed created by that package (in 
/usr/share/doc/python-pysam-tests/) and does hold the data, but I think 
this is not at all the correct way to proceed for many many reasons. So 
I will revamp the test packaging and report back.

However, maybe you can go ahead and upload to unstable to try to prevent 
autoremoval from testing--- the known issue here is not with the actual 
package (at least the main packages); just the arrangement of the test 
suite code. If I finish before hearing back from you, I will include it 
in the current unreleased revision.

> So somehow we can reproduce a problem quite simple (same with python3).

Thanks for shedding light on this. I always try to avoid ad-hoc methods 
like that to avoid cluttering my system, but it helps in this case.

Regards
Afif

--
Afif Elghraoui | عفيف الغراوي
http://afif.ghraoui.name