Installing MDAnalysis

[GoogleCodeExporter]

What steps will reproduce the problem?
1. git clone https://code.google.com/p/mdanalysis
2. cd mdanalysis
3. git fetch --all
4. git checkout -b develop origin/develop
5. git pull
6. cd package
7. python setup.py install --user

What is the expected output? What do you see instead?

I get the following error (same error when trying to install the master branch):

Traceback (most recent call last):
  File "setup.py", line 45, in <module>
    use_setuptools()
  File "mdanalysis18sep/mdanalysis/package/ez_setup.py", line 116, in use_setuptools
    return _do_download(version, download_base, to_dir, download_delay)
  File "mdanalysis18sep/mdanalysis/package/ez_setup.py", line 103, in _do_download
    import setuptools
  File "build/bdist.linux-x86_64/egg/setuptools/__init__.py", line 2, in <module>
    # The Python Imaging Library.
  File "build/bdist.linux-x86_64/egg/setuptools/extension.py", line 5, in <module>
  File "build/bdist.linux-x86_64/egg/setuptools/dist.py", line 7, in <module>
  File "build/bdist.linux-x86_64/egg/setuptools/command/__init__.py", line 8, in <module>
    #
  File "build/bdist.linux-x86_64/egg/setuptools/command/install_scripts.py", line 3, in <module>
  File "build/bdist.linux-x86_64/egg/pkg_resources.py", line 3027, in <module>

  File "build/bdist.linux-x86_64/egg/pkg_resources.py", line 741, in subscribe

  File "build/bdist.linux-x86_64/egg/pkg_resources.py", line 3027, in <lambda>

  File "build/bdist.linux-x86_64/egg/pkg_resources.py", line 2514, in activate
    return [dep for dep in self._dep_map if dep]
  File "build/bdist.linux-x86_64/egg/pkg_resources.py", line 2094, in declare_namespace

  File "build/bdist.linux-x86_64/egg/pkg_resources.py", line 2064, in _handle_ns

  File "/usr/lib64/python2.7/pkgutil.py", line 246, in load_module
    mod = imp.load_module(fullname, self.file, self.filename, self.etc)
  File "/users/ardita/.local/lib/python2.7/site-packages/pyPcazip-1.0-py2.7.egg/MDPlus/__init__.py", line 2, in <module>
    from MDAnalysis import *
  File "mdanalysis18sep/mdanalysis/package/MDAnalysis/__init__.py", line 224, in <module>
    from coordinates.core import writer as Writer
  File "mdanalysis18sep/mdanalysis/package/MDAnalysis/coordinates/__init__.py", line 600, in <module>
    import PDB, PQR, DCD, CRD, XTC, TRR, GRO, XYZ, TRJ, PDBQT, LAMMPS, DMS, TRZ, MOL2
  File "/users/ardita/mdanalysis18sep/mdanalysis/package/MDAnalysis/coordinates/PDB.py", line 222, in <module>
    import MDAnalysis.core.util as util
AttributeError: 'module' object has no attribute 'core'

What version of the product are you using? On what operating system?

I have these problems on a system with the following characteristics:
Linux version 3.11.10-100.fc18.x86_64 (mockbuild@bkernel02) (gcc version 4.7.2 
20121109 (Red Hat 4.7.2-8) (GCC) ) #1 SMP Mon Dec 2 20:28:38 UTC 2013

Could anyone please have a look at this? 
Thank you very much.

Kind regards,
Ardita

Original issue reported on code.google.com by ardita.s...@gmail.com on 18 Sep 2014 at 9:26

[GoogleCodeExporter]

Hrrm.  It works for me, I'm using setuptools 3.3.  Maybe check what version 
you're using* and update it**

*
import setuptools
setuptools.__version__

** 
pip install -U setuptools

Original comment by richardjgowers on 18 Sep 2014 at 11:57

[GoogleCodeExporter]

I get the following error:

>>> import setuptools
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/usr/lib/python2.7/site-packages/setuptools/__init__.py", line 2, in <module>
    from setuptools.extension import Extension, Library
  File "/usr/lib/python2.7/site-packages/setuptools/extension.py", line 5, in <module>
    from setuptools.dist import _get_unpatched
  File "/usr/lib/python2.7/site-packages/setuptools/dist.py", line 6, in <module>
    from setuptools.command.install import install
  File "/usr/lib/python2.7/site-packages/setuptools/command/__init__.py", line 8, in <module>
    from setuptools.command import install_scripts
  File "/usr/lib/python2.7/site-packages/setuptools/command/install_scripts.py", line 3, in <module>
    from pkg_resources import Distribution, PathMetadata, ensure_directory
  File "/usr/lib/python2.7/site-packages/pkg_resources.py", line 2897, in <module>
    add_activation_listener(lambda dist: dist.activate())
  File "/usr/lib/python2.7/site-packages/pkg_resources.py", line 712, in subscribe
    callback(dist)
  File "/usr/lib/python2.7/site-packages/pkg_resources.py", line 2897, in <lambda>
    add_activation_listener(lambda dist: dist.activate())
  File "/usr/lib/python2.7/site-packages/pkg_resources.py", line 2332, in activate
    map(declare_namespace, self._get_metadata('namespace_packages.txt'))
  File "/usr/lib/python2.7/site-packages/pkg_resources.py", line 1920, in declare_namespace
    _handle_ns(packageName, path_item)
  File "/usr/lib/python2.7/site-packages/pkg_resources.py", line 1890, in _handle_ns
    loader.load_module(packageName); module.__path__ = path
  File "/usr/lib64/python2.7/pkgutil.py", line 246, in load_module
    mod = imp.load_module(fullname, self.file, self.filename, self.etc)
  File "/users/ardita/.local/lib/python2.7/site-packages/pyPcazip-1.0-py2.7.egg/MDPlus/__init__.py", line 2, in <module>
    from MDAnalysis import *
  File "MDAnalysis/__init__.py", line 224, in <module>
    from coordinates.core import writer as Writer
  File "MDAnalysis/coordinates/__init__.py", line 600, in <module>
    import PDB, PQR, DCD, CRD, XTC, TRR, GRO, XYZ, TRJ, PDBQT, LAMMPS, DMS, TRZ, MOL2
  File "MDAnalysis/coordinates/PDB.py", line 222, in <module>
    import MDAnalysis.core.util as util
AttributeError: 'module' object has no attribute 'core'

Original comment by ardita.s...@gmail.com on 18 Sep 2014 at 2:40

[GoogleCodeExporter]

I actually fixed these problems that were due to an older version of setuptools.

Thanks a lot for the support,
Ardita

Original comment by ardita.s...@gmail.com on 18 Sep 2014 at 3:50

[GoogleCodeExporter]

Great, enjoy!

Original comment by richardjgowers on 18 Sep 2014 at 4:42

• Changed state: Done