Re: Fwd: [iva] - Python 3 code depends on pysam

On Mon, Nov 24, 2014 at 5:02 PM, Jorge Sebastião Soares <j.s.soares@gmail.com> wrote:

Hi Ghis

On Mon, Nov 24, 2014 at 4:58 PM, Ghislain Vaillant <ghisvail@gmail.com> wrote:
At worst, can't you just disable the test suite for the Python 3 builds ? Pybuild should allow to do that easily.

Trying that now.

But I would still need to link pysam to the iva package at some point, no?

Regards,

Jorge

2014-11-24 16:36 GMT+00:00 Jorge Sebastião Soares <j.s.soares@gmail.com>:
Hi guys,

So essentially the package build halts when it tries to run the test suite:

This is the error I'm getting when the pysam module is being imported:

root@debian:~/iva-0.10.0# python3.4 setup.py test
running test
running egg_info
writing top-level names to iva.egg-info/top_level.txt
writing iva.egg-info/PKG-INFO
writing dependency_links to iva.egg-info/dependency_links.txt
reading manifest file 'iva.egg-info/SOURCES.txt'
writing manifest file 'iva.egg-info/SOURCES.txt'
running build_ext
Failure: ImportError (No module named 'pysam') ... ERROR

======================================================================
ERROR: Failure: ImportError (No module named 'pysam')
----------------------------------------------------------------------
Traceback (most recent call last):
File "/usr/lib/python3/dist-packages/nose/failure.py", line 39, in runTest
    raise self.exc_val.with_traceback(self.tb)
File "/usr/lib/python3/dist-packages/nose/loader.py", line 414, in loadTestsFromName
    addr.filename, addr.module)
File "/usr/lib/python3/dist-packages/nose/importer.py", line 47, in importFromPath
    return self.importFromDir(dir_path, fqname)
File "/usr/lib/python3/dist-packages/nose/importer.py", line 94, in importFromDir
    mod = load_module(part_fqname, fh, filename, desc)
File "/usr/lib/python3.4/imp.py", line 245, in load_module
    return load_package(name, filename)
File "/usr/lib/python3.4/imp.py", line 217, in load_package
    return methods.load()
File "<frozen importlib._bootstrap>", line 1220, in load
File "<frozen importlib._bootstrap>", line 1200, in _load_unlocked
File "<frozen importlib._bootstrap>", line 1129, in _exec
File "<frozen importlib._bootstrap>", line 1471, in exec_module
File "<frozen importlib._bootstrap>", line 321, in _call_with_frames_removed
File "/tmp/buildd/iva-0.10.0/iva/__init__.py", line 20, in <module>
    from iva import *
File "/tmp/buildd/iva-0.10.0/iva/assembly.py", line 2, in <module>
    import pysam
ImportError: No module named 'pysam'

----------------------------------------------------------------------
Ran 1 test in 0.016s

FAILED (errors=1)

If pysam is python 3 compliant, I'm tempted to create the needed symlinks in python3.4 pointing to pysam in python2.7, eg.

ln -s /usr/lib/python2.7/dist-packages/pysam /usr/lib/python3.4/dist-packages/pysam

I'm sure that this is not the proper way of doing things, so is there any other way I can get pysam to be installed under python3.4 rather than python2.7?

Regards,

Jorge