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.
