Path: csiph.com!aioe.org!bofh.it!news.nic.it!robomod From: Andreas Tille Newsgroups: linux.debian.bugs.dist,linux.debian.maint.python Subject: Bug#937177: obitools: Python2 removal in sid/bullseye Date: Sun, 12 Jan 2020 18:30:01 +0100 Message-ID: References: X-Original-To: Scott Kitterman , 937177@bugs.debian.org X-Mailbox-Line: From debian-bugs-dist-request@lists.debian.org Sun Jan 12 17:24:10 2020 Old-Return-Path: X-Spam-Flag: NO X-Spam-Score: 0.25 Reply-To: Andreas Tille , 937177@bugs.debian.org Resent-To: debian-bugs-dist@lists.debian.org Resent-Cc: Debian Med Packaging Team X-Debian-Pr-Message: followup 937177 X-Debian-Pr-Package: src:obitools X-Debian-Pr-Keywords: bullseye upstream sid X-Debian-Pr-Source: obitools X-Spam-Bayes: score:0.0000 Tokens: new, 77; hammy, 150; neutral, 172; spammy, 0. spammytokens: hammytokens:0.000-+--python3, 0.000-+--python27, 0.000-+--python2.7, 0.000-+--H*u:1.10.1, 0.000-+--H*UA:1.10.1 MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Disposition: inline User-Agent: Mutt/1.10.1 (2018-07-13) X-Debian-Message: from BTS X-Mailing-List: archive/latest/1578760 List-ID: List-URL: Approved: robomod@news.nic.it Lines: 98 Organization: linux.* mail to news gateway Sender: robomod@news.nic.it X-Original-Cc: Debian Python , Olivier Sallou X-Original-Date: Sun, 12 Jan 2020 18:19:10 +0100 X-Original-Message-ID: <20200112171910.GB32667@an3as.eu> X-Original-References: <20796275.IfHCMGFBT2@l5580> <20796275.IfHCMGFBT2@l5580> Xref: csiph.com linux.debian.bugs.dist:991001 linux.debian.maint.python:12204 Control: tags -1 help Hi Scott, On Sun, Jan 12, 2020 at 07:27:59AM -0500, Scott Kitterman wrote: > On Fri, 30 Aug 2019 07:28:59 +0000 Matthias Klose wrote: > ... > > I don't see any evidence of upstream progress on converting to python3. This seems to be correct. > This > package is blocking several others. Would it be best to remove it? It can > always be re-introduced if a python3 port appears. Since some time I've pushed a 2to3 based port to Git. I've now fixed some issues of this and I wonder whether we might give it a try to do the port inside Debian. For the moment I'm running into the following issue: dh_auto_test -O--buildsystem=pybuild I: pybuild base:217: cd /build/obitools-1.2.13+dfsg/.pybuild/cpython3_3.7_obitools/build; python3.7 -m unittest discover -v obitools (unittest.loader._FailedTest) ... ERROR ====================================================================== ERROR: obitools (unittest.loader._FailedTest) ---------------------------------------------------------------------- ImportError: Failed to import test module: obitools Traceback (most recent call last): File "/usr/lib/python3.7/unittest/loader.py", line 470, in _find_test_path package = self._get_module_from_name(name) File "/usr/lib/python3.7/unittest/loader.py", line 377, in _get_module_from_name __import__(name) File "/build/obitools-1.2.13+dfsg/.pybuild/cpython3_3.7_obitools/build/obitools/__init__.py", line 23, in from _obitools import BioSequence,NucSequence,AASequence, \ ModuleNotFoundError: No module named '_obitools' ---------------------------------------------------------------------- Ran 1 test in 0.000s FAILED (errors=1) E: pybuild pybuild:341: test: plugin distutils failed with: exit code=1: cd /build/obitools-1.2.13+dfsg/.pybuild/cpython3_3.7_obitools/build; python3.7 -m unittest discover -v dh_auto_test: pybuild --test -i python{version} -p 3.7 returned exit code 13 make: *** [debian/rules:15: build] Error 255 dpkg-buildpackage: error: debian/rules build subprocess returned exit status 2 I: copying local configuration E: Failed autobuilding of package I: user script /var/cache/pbuilder/build/cow.1543005/tmp/hooks/C99_failed_build starting Installing convenience apps: mc less bash-completion root@energija:/# cd build/obitools-1.2.13+dfsg/ root@energija:/build/obitools-1.2.13+dfsg# find . -name "*.so" ./.pybuild/cpython3_3.7_obitools/build/obitools/options/_options.cpython-37m-x86_64-linux-gnu.so = ./.pybuild/cpython3_3.7_obitools/build/obitools/options/_bioseqfilter.cpython-37m-x86_64-linux-gnu.so ./.pybuild/cpython3_3.7_obitools/build/obitools/profile/_profile.cpython-37m-x86_64-linux-gnu.so ./.pybuild/cpython3_3.7_obitools/build/obitools/utils/_utils.cpython-37m-x86_64-linux-gnu.so ./.pybuild/cpython3_3.7_obitools/build/obitools/_obitools.cpython-37m-x86_64-linux-gnu.so ./.pybuild/cpython3_3.7_obitools/build/obitools/tools/_solexapairend.cpython-37m-x86_64-linux-gnu.so ./.pybuild/cpython3_3.7_obitools/build/obitools/fasta/_fasta.cpython-37m-x86_64-linux-gnu.so ./.pybuild/cpython3_3.7_obitools/build/obitools/align/_upperbond.cpython-37m-x86_64-linux-gnu.so ./.pybuild/cpython3_3.7_obitools/build/obitools/align/_rassemble.cpython-37m-x86_64-linux-gnu.so ./.pybuild/cpython3_3.7_obitools/build/obitools/align/_freeendgapfm.cpython-37m-x86_64-linux-gnu.so ./.pybuild/cpython3_3.7_obitools/build/obitools/align/_nwsdnabyprot.cpython-37m-x86_64-linux-gnu.so ./.pybuild/cpython3_3.7_obitools/build/obitools/align/_assemble.cpython-37m-x86_64-linux-gnu.so ./.pybuild/cpython3_3.7_obitools/build/obitools/align/_freeendgap.cpython-37m-x86_64-linux-gnu.so ./.pybuild/cpython3_3.7_obitools/build/obitools/align/_qsrassemble.cpython-37m-x86_64-linux-gnu.so ./.pybuild/cpython3_3.7_obitools/build/obitools/align/_gprofilenws.cpython-37m-x86_64-linux-gnu.so ./.pybuild/cpython3_3.7_obitools/build/obitools/align/_dynamic.cpython-37m-x86_64-linux-gnu.so ./.pybuild/cpython3_3.7_obitools/build/obitools/align/_nws.cpython-37m-x86_64-linux-gnu.so ./.pybuild/cpython3_3.7_obitools/build/obitools/align/_lcs.cpython-37m-x86_64-linux-gnu.so ./.pybuild/cpython3_3.7_obitools/build/obitools/align/_qsassemble.cpython-37m-x86_64-linux-gnu.so ./.pybuild/cpython3_3.7_obitools/build/obitools/align/_profilenws.cpython-37m-x86_64-linux-gnu.so ./.pybuild/cpython3_3.7_obitools/build/obitools/align/_codonnws.cpython-37m-x86_64-linux-gnu.so ./.pybuild/cpython3_3.7_obitools/build/obitools/format/_format.cpython-37m-x86_64-linux-gnu.so ./.pybuild/cpython3_3.7_obitools/build/obitools/format/genericparser/_genericparser.cpython-37m-x86_64-linux-gnu.so ./.pybuild/cpython3_3.7_obitools/build/obitools/fastq/_fastq.cpython-37m-x86_64-linux-gnu.so ./.pybuild/cpython3_3.7_obitools/build/obitools/word/_binary.cpython-37m-x86_64-linux-gnu.so ./.pybuild/cpython3_3.7_obitools/build/obitools/word/_readindex.cpython-37m-x86_64-linux-gnu.so The problem is that the former build system using python2.7 and cython had created obitools: /usr/lib/python2.7/dist-packages/obitools/_obitools.x86_64-linux-gnu.so But now with python3.7 and cython3 the result are single dynamic libs. I'd love to give at least the test suite a try so if I get some hint how to create that single _obitools.x86_64-linux-gnu.so instead of those many *.so libs I could possibly run the test and see how it performs. Kind regards Andreas. -- http://fam-tille.de