[Debian-med-packaging] Bug#938501: Please port smalt to Python3 (Was: Bug#938501: smalt: Python2 removal in sid/bullseye) [EXT]
Hannes Ponstingl
hp3 at sanger.ac.uk
Wed Oct 9 08:56:10 BST 2019
Hi Andreas,
Thank you for pointing me to this issue once more.
Please bear with me until I get a moment to check the patch/update the SMALT test suite to python 3.
It is not a problem, but I have to slot this in with the main obligations of my current role.
Kind regards,
Hannes
On 08/10/2019, 16:33, "Andreas Tille" <andreas at an3as.eu> wrote:
Hi again,
I just took James Bonfield in CC since I'm unsure whether my mail might
have reached someone who is currently working at sanger.ac.uk. Just to
stretch the importance of the issue have a look at the Python2 EOL clock:
https://urldefense.proofpoint.com/v2/url?u=https-3A__pythonclock.org_&d=DwIBAg&c=D7ByGjS34AllFgecYw0iC6Zq7qlm8uclZFI0SqQnqBo&r=XTh5PlieT8KhSRAcJV6w_A&m=KXRG53toHduo0G9U-G8lXQ7R1ZFLgHXlL6pjvR12rzI&s=g-PIxNtQvdPqurLJIeCBAx6cbYUpsQj2kEZ57K5Dhks&e=
In short: Please be so kind and verify the patch linked below and fix
the remaining issues with your deeper knowledge of the code.
Thanks a lot
Andreas.
On Thu, Sep 05, 2019 at 03:39:35PM +0200, Andreas Tille wrote:
> 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://urldefense.proofpoint.com/v2/url?u=https-3A__salsa.debian.org_med-2Dteam_smalt_blob_master_debian_patches_2to3.patch&d=DwIBAg&c=D7ByGjS34AllFgecYw0iC6Zq7qlm8uclZFI0SqQnqBo&r=XTh5PlieT8KhSRAcJV6w_A&m=KXRG53toHduo0G9U-G8lXQ7R1ZFLgHXlL6pjvR12rzI&s=HE73hWE00-z91NAO-Of277mmEjoxLCnPh7ns2AfJt88&e=
>
> 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://urldefense.proofpoint.com/v2/url?u=https-3A__lists.debian.org_debian-2Dpython_2019_07_msg00080.html&d=DwIBAg&c=D7ByGjS34AllFgecYw0iC6Zq7qlm8uclZFI0SqQnqBo&r=XTh5PlieT8KhSRAcJV6w_A&m=KXRG53toHduo0G9U-G8lXQ7R1ZFLgHXlL6pjvR12rzI&s=HjxauC5_s56WX-Za34l9eg_sw_Guf5QO1udZvd6fZys&e=
> >
> > 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://urldefense.proofpoint.com/v2/url?u=https-3A__wiki.debian.org_Python_2Removal&d=DwIBAg&c=D7ByGjS34AllFgecYw0iC6Zq7qlm8uclZFI0SqQnqBo&r=XTh5PlieT8KhSRAcJV6w_A&m=KXRG53toHduo0G9U-G8lXQ7R1ZFLgHXlL6pjvR12rzI&s=Flt2-tweYkXweqyy-FkEpeI7Jh_D46g4Cu2i2_EtLGE&e= , or ask for help on IRC
> > #debian-python, or the debian-python at lists.debian.org mailing list.
> >
> > _______________________________________________
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