try using system-wide headers

bin/cythonize.sh

@@ -1,7 +0,0 @@
-#!/bin/bash
-if [ ! -d ".cythonize" ]; then
-    virtualenv .cythonize
-fi
-. .cythonize/bin/activate
-pip install -U -r requirements.txt
-./bin/cythonize.py $@

build.sh

@@ -0,0 +1,7 @@
+#!/bin/bash
+if [ ! -d ".build" ]; then
+    virtualenv --always-copy .build
+fi
+. .build/bin/activate
+pip install -U -r requirements.txt
+tox $@

setup.py

@@ -172,7 +172,8 @@ if not release:
 def generate_cython():
     cwd = os.path.abspath(os.path.dirname(__file__))
     print('Cythonizing sources')
-    p = subprocess.call([os.path.join(cwd, 'bin', 'cythonize.sh'),
+    p = subprocess.call([sys.executable,
+                         os.path.join(cwd, 'bin', 'cythonize.py'),
                          'spacy'],
                          cwd=cwd)
     if p != 0:
@@ -197,8 +198,8 @@ def setup_package():
     write_version_py()
 
     include_dirs = [
-        os.path.join(sys.prefix, 'include'),
-        get_python_inc(plat_specific=True)]
+        get_python_inc(plat_specific=True),
+        os.path.join(src_path, 'include')]
 
     ext_modules = []
     for mod_name in MOD_NAMES:
@@ -236,15 +237,15 @@ def setup_package():
             shutil.rmtree(include_dir)
         os.mkdir(include_dir)
 
-        # import numpy
-        # shutil.copytree(
-        #     os.path.join(numpy.get_include(), 'numpy'),
-        #     os.path.join(include_dir, 'numpy'))
+        import numpy
+        shutil.copytree(
+            os.path.join(numpy.get_include(), 'numpy'),
+            os.path.join(include_dir, 'numpy'))
 
-        # import murmurhash
-        # shutil.copytree(
-        #     os.path.join(os.path.dirname(murmurhash.__file__), 'headers', 'murmurhash'),
-        #     os.path.join(include_dir, 'murmurhash'))
+        import murmurhash
+        shutil.copytree(
+            os.path.join(os.path.dirname(murmurhash.__file__), 'headers', 'murmurhash'),
+            os.path.join(include_dir, 'murmurhash'))
 
     try:
         setup(**metadata)