[Debian-med-packaging] Bug#1079439: Bug#1079439: python-biopython: autopkgtest stuck on riscv64

[Étienne Mollier]

Hi Reinhard,

Reinhard Tartler, on 2024-08-24:
> Actually, I've been able to compile pystack on the machine
> (see https://github.com/bloomberg/pystack, and amazing tool)
> and was able to get a trace of what the stuck process is doing:

This is a very handy tool and I need to recall about it when
I'll next need it, probably too soon for my taste.  :)

[…]
>     (Python) File "/home/siretart/python-biopython/.pybuild/cpython3_3.12/build/Bio/Align/analysis.py",
> line 484, in _yn00
>         P = expm(Q * t)
>     (Python) File
> "/usr/lib/python3/dist-packages/scipy/linalg/_matfuncs.py", line 358, in
> expm
>         eAw = eAw @ eAw
> 
> I think that indicates that the problematic / looping test is indeed
> Align_condonalign.py?

This is highly plausible.  It was a bold assumption from me to
believe the standard output would be flushed to let us see
whether the test started.  The stack trace is even pointing to
something off in scipy/linalg/_matfunc.py, even more so as scipy
is only suggested by python3-biopython, so it is not available
in the lightweight variant of the autopkgtest, which does run
the test_Align_codonalign.py but doesn't hangup.  And indeed,
here is what I see in test_Align_codonalign.py, starting line
8235:

        try:
            import scipy
        except ImportError:
            # Silently skip the rest of the test
            return

My current conclusion is: it seems to me that Biopython's test
suite revealed something off in SciPy specifically on Risc-V.

Have a nice day,  :)
-- 
  .''`.  Étienne Mollier <emollier at debian.org>
 : :' :  pgp: 8f91 b227 c7d6 f2b1 948c  8236 793c f67e 8f0d 11da
 `. `'   sent from /dev/pts/1, please excuse my verbosity
   `-
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