[setup] use pre-cythonized files, if cython has not been requested du…

…ring build.

Also do not ship ipython notebooks, since there is currently no easy way to make them useable.
Fixes #453.

MANIFEST.in

@@ -29,21 +29,14 @@ prune doc/source/generated
 prune doc/source/api/generated
 
 # ipython notebooks
-graft pyemma-ipython
-recursive-exclude pyemma-ipython .ipynb_checkpoints
+#graft pyemma-ipython
+#recursive-exclude pyemma-ipython .ipynb_checkpoints
 
 # exclude git related files
 recursive-exclude * git .git*
 
 # sources of extensions (incl. cython)
-include pyemma/msm/estimation/dense/*.h
-include pyemma/msm/estimation/sparse/*.h
-include pyemma/msm/estimation/dense/mle_trev_given_pi.c
-include pyemma/msm/estimation/sparse/mle_trev_given_pi.c
-include pyemma/coordinates/clustering/include/clustering.h
-
-#include cython files
-recursive-include pyemma *.pyx
+recursive-include pyemma *.pyx *.h *.c
 
 # do not include eventually present eggs (installed during setup runtime)
 prune .eggs

setup.py

@@ -126,7 +126,7 @@ def extensions():
     else:
         lib_prefix = ''
     regspatial_module = \
-        Extension('pyemma.coordinates.clustering.regspatial', 
+        Extension('pyemma.coordinates.clustering.regspatial',
                   sources=[
                       'pyemma/coordinates/clustering/src/regspatial.c',
                       'pyemma/coordinates/clustering/src/clustering.c'],
@@ -157,6 +157,13 @@ def extensions():
 
     if USE_CYTHON: # if we have cython available now, cythonize module
         exts = cythonize(exts)
+    else:
+        # replace pyx files by their pre generated c code.
+        for e in exts:
+            new_src = []
+            for s in e.sources:
+                new_src.append(s.replace('.pyx', '.c'))
+            e.sources = new_src
 
     if openmp_enabled:
         warnings.warn('enabled openmp')
@@ -291,7 +298,7 @@ def script_entry_points():
         metadata['install_requires'] += ['argparse']
 
     # include ipython notebooks. Will be installed directly in site-packages
-    metadata['packages'] += ['pyemma-ipython']
+    #metadata['packages'] += ['pyemma-ipython']
     #metadata['include_package_data'] = True
 
 try: