Path: csiph.com!news.mixmin.net!aioe.org!bofh.it!news.nic.it!robomod From: Sergio Durigan Junior Newsgroups: linux.debian.bugs.dist,linux.debian.maint.python Subject: Bug#937177: obitools: Python2 removal in sid/bullseye Date: Sat, 07 Mar 2020 07:10:01 +0100 Message-ID: References: X-Mailbox-Line: From debian-bugs-dist-request@lists.debian.org Sat Mar 7 06:00:08 2020 Old-Return-Path: X-Spam-Flag: NO Reply-To: Sergio Durigan Junior , 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 help upstream sid X-Debian-Pr-Source: obitools X-Spam-Bayes: score:0.0000 Tokens: new, 8; hammy, 150; neutral, 319; spammy, 0. spammytokens: hammytokens:0.000-+--python3, 0.000-+--H*ct:application, 0.000-+--H*ct:protocol, 0.000-+--H*ct:micalg, 0.000-+--H*ct:signed X-URL: http://blog.sergiodj.net User-Agent: Gnus/5.13 (Gnus v5.13) Emacs/26.1 (gnu/linux) MIME-Version: 1.0 Content-Type: multipart/signed; boundary="=-=-="; micalg=pgp-sha512; protocol="application/pgp-signature" X-Greylist: delayed 2683 seconds by postgrey-1.36 at buxtehude; Sat, 07 Mar 2020 05:57:17 UTC X-Debian-Message: from BTS X-Mailing-List: archive/latest/1588961 List-ID: List-URL: Approved: robomod@news.nic.it Lines: 166 Organization: linux.* mail to news gateway Sender: robomod@news.nic.it X-Original-Cc: Scott Kitterman , 937177@bugs.debian.org, Debian Python , Olivier Sallou X-Original-Date: Sat, 07 Mar 2020 00:12:19 -0500 X-Original-Message-ID: <87v9ngg34c.fsf@paluero> X-Original-References: <20796275.IfHCMGFBT2@l5580> <20200112171910.GB32667@an3as.eu> <20200112171910.GB32667@an3as.eu> Xref: csiph.com linux.debian.bugs.dist:998734 linux.debian.maint.python:12352 --=-=-= Content-Type: text/plain Content-Transfer-Encoding: quoted-printable On Sunday, January 12 2020, Andreas Tille wrote: > On Sun, Jan 12, 2020 at 07:27:59AM -0500, Scott Kitterman wrote: >> On Fri, 30 Aug 2019 07:28:59 +0000 Matthias Klose wrot= e: >> This=20 >> package is blocking several others. Would it be best to remove it? It = can=20 >> 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=3Dpybuild > I: pybuild base:217: cd /build/obitools-1.2.13+dfsg/.pybuild/cpython3_3.7= _obitools/build; python3.7 -m unittest discover -v=20 > obitools (unittest.loader._FailedTest) ... ERROR > > =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D > 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_p= ath > package =3D 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 Hey Andreas, I cannot reproduce this bug when building inside a clean schroot (unstable). I don't know if the reason is because I don't have python3.7 installed in the schroot anymore (it was removed recently, and python3.8 is the default), or because there's something else different. > FAILED (errors=3D1) > E: pybuild pybuild:341: test: plugin distutils failed with: exit code=3D1= : cd /build/obitools-1.2.13+dfsg/.pybuild/cpython3_3.7_obitools/build; pyth= on3.7 -m unittest discover -v=20 > 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 sta= tus 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=20 > 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 = =3D > ./.pybuild/cpython3_3.7_obitools/build/obitools/options/_bioseqfilter.cpy= thon-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.cpyt= hon-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.cpyth= on-37m-x86_64-linux-gnu.so > ./.pybuild/cpython3_3.7_obitools/build/obitools/align/_nwsdnabyprot.cpyth= on-37m-x86_64-linux-gnu.so > ./.pybuild/cpython3_3.7_obitools/build/obitools/align/_assemble.cpython-3= 7m-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.cpytho= n-37m-x86_64-linux-gnu.so > ./.pybuild/cpython3_3.7_obitools/build/obitools/align/_gprofilenws.cpytho= n-37m-x86_64-linux-gnu.so > ./.pybuild/cpython3_3.7_obitools/build/obitools/align/_dynamic.cpython-37= m-x86_64-linux-gnu.so > ./.pybuild/cpython3_3.7_obitools/build/obitools/align/_nws.cpython-37m-x8= 6_64-linux-gnu.so > ./.pybuild/cpython3_3.7_obitools/build/obitools/align/_lcs.cpython-37m-x8= 6_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-3= 7m-x86_64-linux-gnu.so > ./.pybuild/cpython3_3.7_obitools/build/obitools/format/_format.cpython-37= m-x86_64-linux-gnu.so > ./.pybuild/cpython3_3.7_obitools/build/obitools/format/genericparser/_gen= ericparser.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-3= 7m-x86_64-linux-gnu.so > > > The problem is that the former build system using python2.7 and cython ha= d created > > obitools: /usr/lib/python2.7/dist-packages/obitools/_obitools.x86_64-li= nux-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. FWIW, I have the same list of .so files. Cheers, =2D-=20 Sergio GPG key ID: 237A 54B1 0287 28BF 00EF 31F4 D0EB 7628 65FC 5E36 Please send encrypted e-mail if possible http://sergiodj.net/ --=-=-= Content-Type: application/pgp-signature; name="signature.asc" -----BEGIN PGP SIGNATURE----- iQIzBAEBCgAdFiEEI3pUsQKHKL8A7zH00Ot2KGX8XjYFAl5jLTMACgkQ0Ot2KGX8 XjZQGhAArJz9vT9DpYsTpXsjotvL0SS+uIG21mGM/a8YS3ya/A2THb9zXl/KZVPN 9AuMgEz67qSyWAAkTYYlWEWNMR+hOmV4riPetDwpfW1StJFF2v3RxVeJDCOUL3+/ /6eRVKxXGKYkCk1aoDVVVTdLW58ZLa7rVXkS+Gl+lWzbnJna7TQ28FbTKMZFXcZs MTreMVIhINygvUqF/Yeh7AlHnHddNuTbjffTEErchS43hFDnNjQYKDuaSGo9iiDX wSP3uz821Ar6ZpDotjKNR7gTt243Bbr3I6m3AXZ/clKPdNumxjysNoX4Jnmu2aP4 ULitG0wEu+cGL/r5mzYJUsO6RLAnPMC2bP4V6osJBqwC1dlsDZUPDtNaswwYcXdT FhEoS/VeYUz+A4LDrd79kgj3EIP+MTnG7Io2DUVmVvNKUKJZjWNkvyVNdL5pnZAn ijhbOR5hp/p2AyuYoKBJbwI0nht9r4LhOGYrd23PRa2JBWrhRVvZKfE/acDP7Znp hztH+ckOtaTvgklYxd8PXpi6w3d/ki6s178NMBR/NHPJc5jaDk77FmgZat/pp6aX jLuWdkBg08iaPK3lGnVt3nn9wATU4JOOjdcsAzviZZ195elFyXrIDZxrsPpCZ7Vw ygsQ3iend2QDRxgNsuJzlfpTL7mIEc3JECI9HFar0xmtsI+X8F0= =3spG -----END PGP SIGNATURE----- --=-=-=--