Include missing BayesLogit headers

Author: Allen Riddell

MANIFEST.in

@@ -8,3 +8,6 @@ global-exclude *.so
 global-exclude *.pyc
 global-exclude .git*
 global-exclude *.png
+
+# Exclude .R files in BayesLogit
+global-exclude *.R

README.rst

@@ -1,5 +1,5 @@
-horizont: Dynamic topic models
-==============================
+horizont: Topic models in Python
+================================
 
 .. image:: https://travis-ci.org/ariddell/horizont.png
         :target: https://travis-ci.org/ariddell/horizont

horizont/__init__.py

@@ -10,4 +10,4 @@
 logger.addHandler(logging.NullHandler())
 
 # following PEP 386
-__version__ = "0.0.4"
+__version__ = "0.0.5"

horizont/_random.pyx

@@ -1,4 +1,8 @@
 # distutils: language = c++
+#cython: language_level=3
+#cython: boundscheck=False
+#cython: wraparound=False
+
 from cython.operator cimport dereference as deref
 from libc.math cimport sqrt
 

setup.py

@@ -1,5 +1,5 @@
 #-----------------------------------------------------------------------------
-# Copyright (c) 2013, Allen B. Riddell
+# Copyright (c) 2013-2014, Allen B. Riddell
 #
 # This file is licensed under Version 3.0 of the GNU General Public
 # License. See LICENSE for a text of the license.
@@ -71,22 +71,16 @@ def find_version(*parts):
     cython = False
 
 
-# use CheckSDist strategy from pandas
 class CheckSDist(sdist):
     """Custom sdist that ensures Cython has compiled all pyx files to c."""
 
-    _pyxfiles = ['horizont/_lda.pyx']
-
     def initialize_options(self):
         sdist.initialize_options(self)
-
-        '''
-self._pyxfiles = []
-for root, dirs, files in os.walk('pandas'):
-for f in files:
-if f.endswith('.pyx'):
-self._pyxfiles.append(pjoin(root, f))
-'''
+        self._pyxfiles = []
+        for root, dirs, files in os.walk('horizont'):
+            for f in files:
+                if f.endswith('.pyx'):
+                    self._pyxfiles.append(os.path.join(root, f))
 
     def run(self):
         if 'cython' in cmdclass:
@@ -115,9 +109,7 @@ def run(self):
 
 include_gsl_dir = os.environ.get('GSL_INC_DIR', "/usr/include/")
 lib_gsl_dir = os.environ.get('GSL_LIB_DIR', "/usr/lib/")
-random_include_dirs = ["horizont/BayesLogit/Code/C",
-                       "horizont/RNG",
-                       include_gsl_dir]
+random_include_dirs = ["horizont/BayesLogit/Code/C", "horizont/RNG", include_gsl_dir]
 random_library_dirs = [lib_gsl_dir]
 random_libraries = ['gsl', 'gslcblas']
 
@@ -147,6 +139,17 @@ def run(self):
 import numpy
 include_dirs = [numpy.get_include()]
 
+# package data
+package_data_pats = ['*.hpp', '*.pxd', '*.pyx', 'tests/*.dat', 'tests/*.ldac']
+
+# get every file under horizont/BayesLogit/Code/C/", "horizont/RNG/"
+package_data_pats += sum(
+    [[os.path.join(path.replace('horizont/', ''), fn) for fn in files]
+     for path, dirs, files in os.walk('horizont/BayesLogit/Code/C/')], [])
+
+package_data_pats += sum(
+    [[os.path.join(path.replace('horizont/', ''), fn) for fn in files]
+     for path, dirs, files in os.walk('horizont/RNG/')], [])
 
 ###########################################################################
 # Setup proper
@@ -165,5 +168,5 @@ def run(self):
       classifiers=CLASSIFIERS,
       ext_modules=extensions,
       include_dirs=include_dirs,
-      package_data={'horizont.tests': ['ap.dat', 'ch.ldac']},
+      package_data={'horizont' : package_data_pats},
       platforms='any')