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Solving Installation issues (the Biskit oldnumeric problem)

As some users have noticed, newer versions of numpy are incompatible with one of the main dependencies for pyMDmix installation: Biskit. Biskit uses an older version of numpy (Numeric, or oldnumeric in the code) that is currently obsolete and not supported anymore. Because of that, installation of pyMDmix fails!

But don´t worry, I solved the issue by updating Biskit sourcecode to use standard and well supported numpy functions and installation runs smoothly as it was before. However, to use the updated Biskit version, the code should only be installed using SVN and checking out the trunk source code at sourceforge:

https://sourceforge.net/p/biskit/code/HEAD/tree/trunk

All other means of installation (automatic installation using pymdmix installer, easy_install, pip, or even the ZIP file in sourceforge) will install the previous non-updated version of Biskit. I am working with Raik, the main developer, to update all these other files and means of installation. I will post a new comment as soon as they are working and available.

Sorry for the inconveniences and enjoy the program again!

Daniel

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Uninstalling pyMDMix

Unfortunately, python does not provide an official uninstaller. To uninstall pyMDMix we must locate were the installation took place and manually remove the module folder. Dependencies also need to be uninstalled manually.

This process is also recommended when updating to a newer version of pyMDMix to avoid version clashes.

  •  Locate python packages installation folder. For instance:
daniel@pulp:~>  python -c "import pyMDMix as pm; print pm.__file__"
/home/daniel/.local/lib/python2.7/site-packages/pyMDMix/__init__.py
This tells me the installation directory in my case is: /home/daniel/.local/lib/python2.7/site-packages/
  • Remove all pyMDMix folders inside the installation directory (root privileges might be needed depending on the installation).
daniel@pulp:~> rm -rf /home/daniel/.local/lib/python2.7/site-packages/pyMDMix*
  • Check we are clean. This command should fail:
daniel@pulp:~>python -c "import pyMDMix"
Traceback (most recent call last):
File "<string>", line 1, in <module>
ImportError: No module named pyMDMix