[Debian-med-packaging] Bug#938501: Please port smalt to Python3 (Was: Bug#938501: smalt: Python2 removal in sid/bullseye) [EXT]

[Andreas Tille]

On Wed, Oct 09, 2019 at 08:47:14AM +0000, Hannes Ponstingl wrote:
> Hi Zemin, James, Andreas,
> 
> Python was used for the test code (and internally there was a python interface to some of the C code).
> I will update that to python 3 - not a problem, just bear with me.

That's perfectly correct and it might be that just the test suite fails
while smalt is perfectly fine since untouched.  I tried to port these tests
to Python3 with the following patch:

   https://salsa.debian.org/med-team/smalt/blob/master/debian/patches/2to3.patch

This leads to:


make  check-TESTS
make[4]: Entering directory '/build/smalt-0.7.6/test'
PASS: splitReads_test.py
PASS: results_split_test.py
PASS: ouform_cigar_test.py
mappings don't match for read 'SIM_000000000_MAL11_001337747_10_F_75m/1'
FAIL: sample_test.py
PASS: cigar_test.py
Discrepancy:
cigar:A:60 SIM_000000000_MAL11_001337747_10_F_75m/1 1 75 + MAL11 1337747 1337821 + 75 M 75
cigar:A:60 SIM_000000000_MAL11_001337747_10_F_75m/1 1 75 + MAL11 1337747 1337821 + 75 M 75
cigA1.mapq=60 > MAPQ_THRESH=6 and cigB1.mapq=60 > MAPQ_THRESH=6
FAIL: mthread_test.py
PASS: ioform_test.py
PASS: xali_test.py
Traceback (most recent call last):
  File "./bam_cigar_test.py", line 254, in <module>
    isOK = testSAMfilesAreIdentical(sambamnam, samoufilnam)
  File "./bam_cigar_test.py", line 149, in testSAMfilesAreIdentical
    linA = infilA.readline()
  File "/usr/lib/python3.7/codecs.py", line 322, in decode
    (result, consumed) = self._buffer_decode(data, self.errors, final)
UnicodeDecodeError: 'utf-8' codec can't decode byte 0xff in position 366: invalid start byte
FAIL: bam_cigar_test.py
=================================
3 of 9 tests failed
Please report to hp3 at sanger.ac.uk
=================================


Since we would really like to use the complete test suite I'd love to
get this fixed.  Can you help out here?

Kind regards

      Andreas.

-- 
http://fam-tille.de