[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 ...)

[Andreas Tille <andreas@an3as.eu>]

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/

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