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 <d...@debian.org> 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 <module>
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
