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

[Andreas Tille]

Control: tags -1 upsteam
Control: forwarded -1 Hannes Ponstingl <hp3 at sanger.ac.uk>

Hi Hannes,

as you can read below Debian will remove Python2 since it is EOL.
I tried to port your test scripts using the 2to3 tool.  The result
of the automatic conversion can be found here:

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

Unfortunately there are some remaining issues in the test suite which
are probably not very hard to fix.  I wonder whether you might want
to have a look at these and could prepare an official Python3 release
of your nice tool.

Here is the output of the test suite:


PASS: splitReads_test.py
PASS: results_split_test.py
PASS: ouform_cigar_test.py
Traceback (most recent call last):
  File "./sample_test.py", line 154, in <module>
    compare_mapping(oufilnam1, oufilnam3)
  File "./sample_test.py", line 108, in compare_mapping
    if cmp(cig1.qnam, cig2.qnam):
NameError: name 'cmp' is not defined
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
FAIL: mthread_test.py
Traceback (most recent call last):
  File "./ioform_test.py", line 45, in <module>
    samnam = df.unpack(READ_PREFIX + ".sam")
  File "/build/smalt-0.7.6/test/testdata.py", line 71, in unpack
    oufil.write(lin)
TypeError: write() argument must be str, not bytes
FAIL: 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 260: invalid start byte
FAIL: bam_cigar_test.py
=================================
4 of 9 tests failed
Please report to hp3 at sanger.ac.uk
=================================


Kind regards

      Andreas.


On Fri, Aug 30, 2019 at 07:52:50AM +0000, Matthias Klose wrote:
> Package: src:smalt
> Version: 0.7.6-8
> Severity: normal
> Tags: sid bullseye
> User: debian-python at lists.debian.org
> Usertags: py2removal
> 
> Python2 becomes end-of-live upstream, and Debian aims to remove
> Python2 from the distribution, as discussed in
> https://lists.debian.org/debian-python/2019/07/msg00080.html
> 
> Your package either build-depends, depends on Python2, or uses Python2
> in the autopkg tests.  Please stop using Python2, and fix this issue
> by one of the following actions.
> 
> - Convert your Package to Python3. This is the preferred option.  In
>   case you are providing a Python module foo, please consider dropping
>   the python-foo package, and only build a python3-foo package.  Please
>   don't drop Python2 modules, which still have reverse dependencies,
>   just document them.
>   
>   This is the preferred option.
> 
> - If the package is dead upstream, cannot be converted or maintained
>   in Debian, it should be removed from the distribution.  If the
>   package still has reverse dependencies, raise the severity to
>   "serious" and document the reverse dependencies with the BTS affects
>   command.  If the package has no reverse dependencies, confirm that
>   the package can be removed, reassign this issue to ftp.debian.org,
>   make sure that the bug priority is set to normal and retitle the
>   issue to "RM: PKG -- removal triggered by the Python2 removal".
> 
> - If the package has still many users (popcon >= 300), or is needed to
>   build another package which cannot be removed, document that by
>   adding the "py2keep" user tag (not replacing the py2remove tag),
>   using the debian-python at lists.debian.org user.  Also any
>   dependencies on an unversioned python package (python, python-dev)
>   must not be used, same with the python shebang.  These have to be
>   replaced by python2/python2.7 dependencies and shebang.
> 
>   This is the least preferred option.
> 
> If the conversion or removal needs action on another package first,
> please document the blocking by using the BTS affects command, like
> 
>   affects <bug number of blocking py2removal bug> + src:smalt
> 
> If there is no py2removal bug for that reverse-dependency, please file
> a bug on this package (similar to this bug report).
> 
> If there are questions, please refer to the wiki page for the removal:
> https://wiki.debian.org/Python/2Removal, or ask for help on IRC
> #debian-python, or the debian-python at lists.debian.org mailing list.
> 
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