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" <[email protected]> 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 <[email protected]> >>>> >>>> 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 [email protected] >>>> ================================= >>>> >>>> >>>> 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: [email protected] >>>>> 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 [email protected] 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 [email protected] mailing list. >>>>> >>>>> _______________________________________________ >>>>> Debian-med-packaging mailing list >>>>> [email protected] >>>>> https://urldefense.proofpoint.com/v2/url?u=https-3A__alioth-2Dlists.debian.net_cgi-2Dbin_mailman_listinfo_debian-2Dmed-2Dpackaging&d=DwIBAg&c=D7ByGjS34AllFgecYw0iC6Zq7qlm8uclZFI0SqQnqBo&r=wodoR_G062E4YLZ-xu5t6g&m=XK--XBUkRyktzXOkgsZpq_yu16VL7H7Y75QlpOEnwGc&s=QNdw7jPPPozYeLfZMk5O-mjcTGurrKIidxWrdwjOlao&e= >>>> >>>> -- >>>> 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= >>>> >>>> _______________________________________________ >>>> Debian-med-packaging mailing list >>>> [email protected] >>>> https://urldefense.proofpoint.com/v2/url?u=https-3A__alioth-2Dlists.debian.net_cgi-2Dbin_mailman_listinfo_debian-2Dmed-2Dpackaging&d=DwIBAg&c=D7ByGjS34AllFgecYw0iC6Zq7qlm8uclZFI0SqQnqBo&r=wodoR_G062E4YLZ-xu5t6g&m=XK--XBUkRyktzXOkgsZpq_yu16VL7H7Y75QlpOEnwGc&s=QNdw7jPPPozYeLfZMk5O-mjcTGurrKIidxWrdwjOlao&e= >>> >>> -- >>> 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 ([email protected]) >> 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.
