From 455aa75595be456373f17cb42294700349bd76ac Mon Sep 17 00:00:00 2001
From: marscher <m.scherer@fu-berlin.de>
Date: Mon, 27 Jul 2015 18:45:02 +0200
Subject: [PATCH] [setup] use pre-cythonized files, if cython has not been
 requested during build. Also do not ship ipython notebooks, since there is
 currently no easy way to make them useable. Fixes #453.

---
 MANIFEST.in | 13 +++----------
 setup.py    | 11 +++++++++--
 2 files changed, 12 insertions(+), 12 deletions(-)

diff --git a/MANIFEST.in b/MANIFEST.in
index 28eabe9e8..c25963e65 100644
--- a/MANIFEST.in
+++ b/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
diff --git a/setup.py b/setup.py
index f157d29df..7b67c7c71 100755
--- a/setup.py
+++ b/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: