* updated the setup.py to use setuptools to avoid issues with the egg…

…-info files. This was a bit trickier because of the cython code.

* also discovered compilation bug when linking to a static hdf5 library (version 1.8.11 or higher) and made a note in the README

README

@@ -25,3 +25,15 @@ In the future, autogen and configure may be updated to automatically run python
 More information about the package can be found here:
 
 https://wiki.phenogenomics.ca/display/MICePub/minc-stuffs+(formerly+mice-minc-tools)
+
+Known bugs:
+-----------
+From: http://www.unidata.ucar.edu/support/help/MailArchives/netcdf/msg11875.html
+> In 1.8.11, hdf5 added the capability to use plugins which are dynamically
+> loaded.  If linking with shareable libraries, then the -ldl is already
+> present due to the mechanisms of shareable libraries; however, if using
+> static libraries, the -ldl needs to be added manually which is not
+> currently being done in configure.
+
+after running ./autogen.sh and if you're linking against a static hdf5 library (1.8.11 or later)
+you might have to add -ldl as a flag when linking. This can be done in the configure file

setup.py

@@ -1,10 +1,17 @@
 #!/usr/bin/env python
 
-from distutils.core import setup
+from setuptools import setup
 from distutils.extension import Extension
 from Cython.Distutils import build_ext
 import numpy
 
+# setuptools DWIM monkey-patch madness
+# http://mail.python.org/pipermail/distutils-sig/2007-September/thread.html#8204
+import sys
+if 'setuptools.extension' in sys.modules:
+    m = sys.modules['setuptools.extension']
+    m.Extension.__dict__ = m._Extension.__dict__
+
 setup(name="python-stuffs",
       version='0.1.5',
       scripts=["python/TFCE",