Updates to setup.py

Add a cleanall, and try to make the cython build things in the correct
place.

setup.py

@@ -5,10 +5,15 @@ SimPEG is a python package for simulation and gradient based
 parameter estimation in the context of geophysical applications.
 """
 
+import numpy as np
+
+import os
+import sys
+import subprocess
+
 from distutils.core import setup
 from setuptools import find_packages
 from distutils.extension import Extension
-import numpy as np
 
 CLASSIFIERS = [
 'Development Status :: 4 - Beta',
@@ -26,14 +31,31 @@ CLASSIFIERS = [
 'Natural Language :: English',
 ]
 
+args = sys.argv[1:]
 
-from distutils.core import setup
+# Make a `cleanall` rule to get rid of intermediate and library files
+if "cleanall" in args:
+    print "Deleting cython files..."
+    # Just in case the build directory was created by accident,
+    # note that shell=True should be OK here because the command is constant.
+    subprocess.Popen("rm -rf build", shell=True, executable="/bin/bash")
+    subprocess.Popen("find . -name \*.c -type f -delete", shell=True, executable="/bin/bash")
+    subprocess.Popen("find . -name \*.so -type f -delete", shell=True, executable="/bin/bash")
+    # Now do a normal clean
+    sys.argv[sys.argv.index('cleanall')] = "clean"
+
+# We want to always use build_ext --inplace
+if args.count("build_ext") > 0 and args.count("--inplace") == 0:
+    sys.argv.insert(sys.argv.index("build_ext")+1, "--inplace")
 
 try:
     from Cython.Build import cythonize
+    from Cython.Distutils import build_ext
+    cythonKwargs = dict(cmdclass={'build_ext': build_ext})
     USE_CYTHON = True
 except Exception, e:
     USE_CYTHON = False
+    cythonKwargs = dict()
 
 ext = '.pyx' if USE_CYTHON else '.c'
 
@@ -41,9 +63,9 @@ cython_files = [
                     "SimPEG/Utils/interputils_cython",
                     "SimPEG/Mesh/TreeUtils"
                ]
-extensions = [Extension(f, [f+ext]) for f in cython_files]
+extensions = [Extension(f, [f+ext], include_dirs=[np.get_include()]) for f in cython_files]
 
-if USE_CYTHON:
+if USE_CYTHON and "cleanall" not in args:
     from Cython.Build import cythonize
     extensions = cythonize(extensions)
 
@@ -71,6 +93,6 @@ setup(
     classifiers=CLASSIFIERS,
     platforms = ["Windows", "Linux", "Solaris", "Mac OS-X", "Unix"],
     use_2to3 = False,
-    include_dirs=[np.get_include()],
-    ext_modules = extensions
+    ext_modules = extensions,
+    **cythonKwargs
 )