Path: csiph.com!goblin2!goblin.stu.neva.ru!aioe.org!bofh.it!news.nic.it!robomod
From: Andreas Tille <andreas@an3as.eu>
Newsgroups: linux.debian.maint.python
Subject: [Urgent help needed ] python-pysam broken - may be  Python3 3.6.3 to  3.6.4~rc1 transition issue (Was: Uploaded new version 1.6 of htslib,  samtools & bcftools ...)
Date: Thu, 14 Dec 2017 18:00:01 +0100
Message-ID: <uWF1v-1ee-3@gated-at.bofh.it>
References: <uWF1v-1ee-5@gated-at.bofh.it> <uWF1v-1ee-7@gated-at.bofh.it> <uWF1v-1ee-9@gated-at.bofh.it> <uWF1v-1ee-11@gated-at.bofh.it> <uWF1v-1ee-13@gated-at.bofh.it> <uWF1v-1ee-15@gated-at.bofh.it> <uWF1v-1ee-17@gated-at.bofh.it> <uWF1v-1ee-19@gated-at.bofh.it> <uWF1v-1ee-21@gated-at.bofh.it> <uWF1v-1ee-23@gated-at.bofh.it>
X-Mailbox-Line: From debian-python-request@lists.debian.org  Thu Dec 14 16:58:53 2017
Old-Return-Path: <andreas@an3as.eu>
X-Amavis-Spam-Status: No, score=-6.99 tagged_above=-10000 required=5.3 tests=[BAYES_00=-2, LDO_WHITELIST=-5, MURPHY_DRUGS_REL8=0.02, T_RP_MATCHES_RCVD=-0.01] autolearn=unavailable autolearn_force=no
X-Policyd-Weight: using cached result; rate: -6.1
MIME-Version: 1.0
Content-Type: text/plain; charset=us-ascii
Content-Disposition: inline
User-Agent: NeoMutt/20170113 (1.7.2)
X-Mailing-List: <debian-python@lists.debian.org> archive/latest/15403
List-ID: <debian-python.lists.debian.org>
List-URL: <https://lists.debian.org/debian-python/>
List-Archive: https://lists.debian.org/msgid-search/20171214165835.o6w7jdx247ejgy2s@an3as.eu
Approved: robomod@news.nic.it
Lines: 77
Organization: linux.* mail to news gateway
Sender: robomod@news.nic.it
X-Original-Cc: debian-python@lists.debian.org
X-Original-Date: Thu, 14 Dec 2017 17:58:35 +0100
X-Original-Message-ID: <20171214165835.o6w7jdx247ejgy2s@an3as.eu>
X-Original-References: <20171212214714.GM29307@mapreri.org> <E93DDBDB-FBB0-417C-A516-6CEDEEBE647F@glasgow.ac.uk> <20171213115347.GP29307@mapreri.org> <20171213120321.abnwpbpe5syrpsc7@an3as.eu> <20171213154044.GQ29307@mapreri.org> <20171213154936.3belsp5q2thhvaw2@an3as.eu> <20171214123133.GS29307@mapreri.org> <20171214132646.hxe2b4y3yy4phl3o@an3as.eu> <20171214133052.GT29307@mapreri.org> <20171214134218.zfbwwfehm3aqrjl6@an3as.eu>
Xref: csiph.com linux.debian.maint.python:10009

Hi,

as I reported yesterday, I've tested python-pysam 0.13.0+ds-1 as in Git
yesterday with the new samtools 1.6 package.  (For those who need a
prove here is the fill build[1].)  Unfortunately if I build today the
package does not build any more.  The python2 tests are running fine but
if it comes to python3 I get:


...
==================================== ERRORS ====================================
__ ERROR collecting .pybuild/pythonX.Y_3.6/build/tests/AlignedSegment_test.py __
ImportError while importing test module '/build/python-pysam-0.13.0+ds/.pybuild/pythonX.Y_3.6/build/tests/AlignedSegment_test.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
tests/AlignedSegment_test.py:2: in <module>
    import pysam
pysam/__init__.py:28: in <module>
    from pysam.samtools import *
pysam/samtools.py:1: in <module>
    from utils import PysamDispatcher
E   ModuleNotFoundError: No module named 'utils'
__ ERROR collecting .pybuild/pythonX.Y_3.6/build/tests/AlignmentFile_test.py ___
tests/AlignmentFile_test.py:25: in <module>
    import pysam
pysam/__init__.py:9: in <module>
    import pysam.libcutils as libcutils
E   AttributeError: module 'pysam' has no attribute 'libcutils'
 ERROR collecting .pybuild/pythonX.Y_3.6/build/tests/StreamFiledescriptors_test.py.
tests/StreamFiledescriptors_test.py:8: in <module>
    from pysam import AlignmentFile
pysam/__init__.py:9: in <module>
    import pysam.libcutils as libcutils
E   AttributeError: module 'pysam' has no attribute 'libcutils'
___ ERROR collecting .pybuild/pythonX.Y_3.6/build/tests/VariantFile_test.py ____
tests/VariantFile_test.py:4: in <module>
    import pysam
pysam/__init__.py:9: in <module>
    import pysam.libcutils as libcutils
E   AttributeError: module 'pysam' has no attribute 'libcutils'
_____ ERROR collecting .pybuild/pythonX.Y_3.6/build/tests/compile_test.py ______
ImportError while importing test module '/build/python-pysam-0.13.0+ds/.pybuild/pythonX.Y_3.6/build/tests/compile_test.py'.
Hint: make sure your test modules/packages have valid Python names.
...


When comparing the build log of today with the one from yesterday
I see differences in the Python versions:


-Preparing to unpack .../50-libpython-dev_2.7.14-3_amd64.deb ...
-Unpacking libpython-dev:amd64 (2.7.14-3) ...
+Preparing to unpack .../49-libpython-dev_2.7.14-4_amd64.deb ...
+Unpacking libpython-dev:amd64 (2.7.14-4) ...
...
-Setting up python3 (3.6.3-2) ...
-Setting up python3-dev (3.6.3-2) ...
-Setting up python3-pkg-resources (38.2.4-1) ...
-Setting up python3-all (3.6.3-2) ...
+Setting up python3 (3.6.4~rc1-1) ...
+Setting up python3-pkg-resources (38.2.4-2) ...
+Setting up python3-all (3.6.4~rc1-1) ...


So may be we are hit by a Python3 3.6.3 to 3.6.4~rc1 issue?

Does anybody have a clue?

Kind regards

        Andreas.


[1] https://people.debian.org/~tille/packages/python-pysam/

-- 
http://fam-tille.de