[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 09:47:14 BST 2019
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.
Best,
Hannes
On 09/10/2019, 09:38, "Zemin Ning" <zn1 at sanger.ac.uk> wrote:
Thanks Andreas.
Hannes has moved to other teams a few years ago. In my memory, Python was
not used in the main SMALT code. However, it might be used in some testing
cases. I don't know if Hannes has the time to fix it.
Best regards,
Zemin
On Tue, 8 Oct 2019, Andreas Tille wrote:
> Hi James,
>
> thanks for forwarding. I agree that its probably a small issue
> in the Python3 code. Hope Zemin will be able to fix it soon.
> @Zemin: Please feel free to ask for help from our Python team
> in case you might run into any trouble.
>
> Kind regards
> Andreas.
>
>
> On Tue, Oct 08, 2019 at 05:24:47PM +0100, James Bonfield wrote:
>> Hi all,
>>
>> Hannes is still around, but has moved jobs. I'm including Zemin Ning
>> in this reply whose team Hannes was in when he wrote Smalt.
>>
>> I don't know the extent of the issue having not used Smalt myself, but
>> the main tool itself is C so I doubt the python bit is a major
>> component.
>>
>> Regardless, it's not something I'm involved with personally.
>>
>> James
>>
>>
>> On Tue, Oct 08, 2019 at 05:33:42PM +0200, Andreas Tille 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=wodoR_G062E4YLZ-xu5t6g&m=XK--XBUkRyktzXOkgsZpq_yu16VL7H7Y75QlpOEnwGc&s=1ojoaFsu0HVyuhxGkiUBSnPjQJLSXJQyv1jrE-FfnMw&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=wodoR_G062E4YLZ-xu5t6g&m=XK--XBUkRyktzXOkgsZpq_yu16VL7H7Y75QlpOEnwGc&s=j7oR-RSaMB5DM2SvBCK63XeKcftyATF9QB_A56HxSCs&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=wodoR_G062E4YLZ-xu5t6g&m=XK--XBUkRyktzXOkgsZpq_yu16VL7H7Y75QlpOEnwGc&s=Xgujf6sRlZuNDRpgPdw-HM2EVf1K2YRkzazDPAt9sK4&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=wodoR_G062E4YLZ-xu5t6g&m=XK--XBUkRyktzXOkgsZpq_yu16VL7H7Y75QlpOEnwGc&s=LtGkMxuth36_KHtGeql2HwKH7xEIKZ6BNAP0GOH9aDE&e= , or ask for help on IRC
>>>>> #debian-python, or the debian-python at lists.debian.org mailing list.
>>>>>
>>>>> _______________________________________________
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>>>>> Debian-med-packaging at alioth-lists.debian.net
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>>>>
>>>> --
>>>> https://urldefense.proofpoint.com/v2/url?u=http-3A__fam-2Dtille.de&d=DwIBAg&c=D7ByGjS34AllFgecYw0iC6Zq7qlm8uclZFI0SqQnqBo&r=wodoR_G062E4YLZ-xu5t6g&m=XK--XBUkRyktzXOkgsZpq_yu16VL7H7Y75QlpOEnwGc&s=vbfIEwXiPAwzyQefpXbHmZpdmW1CI-xSYZm96PkCsmw&e=
>>>>
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>>>
>>> --
>>> https://urldefense.proofpoint.com/v2/url?u=http-3A__fam-2Dtille.de&d=DwIBAg&c=D7ByGjS34AllFgecYw0iC6Zq7qlm8uclZFI0SqQnqBo&r=wodoR_G062E4YLZ-xu5t6g&m=XK--XBUkRyktzXOkgsZpq_yu16VL7H7Y75QlpOEnwGc&s=vbfIEwXiPAwzyQefpXbHmZpdmW1CI-xSYZm96PkCsmw&e=
>>
>> --
>> James Bonfield (jkb at sanger.ac.uk)
>> The Sanger Institute, Hinxton, Cambs, CB10 1SA
>>
>>
>> --
>> The Wellcome Sanger Institute is operated by Genome Research
>> Limited, a charity registered in England with number 1021457 and a
>> company registered in England with number 2742969, whose registered
>> office is 215 Euston Road, London, NW1 2BE.
>>
>
> --
> https://urldefense.proofpoint.com/v2/url?u=http-3A__fam-2Dtille.de&d=DwIBAg&c=D7ByGjS34AllFgecYw0iC6Zq7qlm8uclZFI0SqQnqBo&r=3I_p6ZxdWYkfke7BGXRytA&m=jvxTSvXv20nWY_BYG1f0G4HCsvR_lRdqywIhvCGBnMI&s=C0YBsqEJzoB7n-zxstKVL7D7AGjU73TWp2UYbiQpDrQ&e=
>
--
The Wellcome Sanger Institute is operated by Genome Research
Limited, a charity registered in England with number 1021457 and a
company registered in England with number 2742969, whose registered
office is 215 Euston Road, London, NW1 2BE.
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