Control: tags -1 upsteam
Control: forwarded -1 Hannes Ponstingl <h...@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 h...@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-pyt...@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-pyt...@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-pyt...@lists.debian.org mailing list.
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