From c8a246be7ca847f9e509dc09efef3d3dd036ab29 Mon Sep 17 00:00:00 2001
From: Jacob Schreiber <jmschreiber91@gmail.com>
Date: Sat, 26 Sep 2015 22:27:14 -0700
Subject: [PATCH] ENH hmm cleanup

---
 pomegranate/hmm.pyx | 38 +++++++++++++++++---------------------
 1 file changed, 17 insertions(+), 21 deletions(-)

diff --git a/pomegranate/hmm.pyx b/pomegranate/hmm.pyx
index dff542db..f5e188f4 100644
--- a/pomegranate/hmm.pyx
+++ b/pomegranate/hmm.pyx
@@ -13,11 +13,25 @@ import networkx
 import tempfile
 import warnings
 
+from .base cimport Model
+from .base cimport State
+from .distributions cimport Distribution
+from .distributions cimport MultivariateDistribution
+from .distributions cimport DiscreteDistribution
+from .utils cimport _log
+from .utils cimport pair_lse
+
 from libc.stdlib cimport calloc
 from libc.stdlib cimport free
 from libc.string cimport memcpy
 from libc.string cimport memset
 
+import numpy
+cimport numpy
+
+from joblib import Parallel
+from joblib import delayed
+
 if sys.version_info[0] > 2:
 	# Set up for Python 3
 	xrange = range
@@ -25,19 +39,6 @@ if sys.version_info[0] > 2:
 else:
 	izip = it.izip
 
-import numpy
-cimport numpy
-
-from base cimport Model
-from base cimport State
-from distributions cimport Distribution
-from distributions cimport MultivariateDistribution
-from distributions cimport DiscreteDistribution
-from joblib import Parallel
-from joblib import delayed
-from utils cimport _log
-from utils cimport pair_lse
-
 try:
 	import pygraphviz
 	from matplotlib import pyplot
@@ -63,13 +64,6 @@ def log(value):
 		to_return[ value == 0 ] = NEGINF
 		return to_return
 	return _log( value )
-		
-def exp(value):
-	"""
-	Return e^value, or 0 if the value is - infinity.
-	"""
-	
-	return numpy.exp(value)
 
 def log_probability( model, samples, n_jobs=1, parallel=None ):
 	"""Return the log probability of samples given a model."""
@@ -88,7 +82,9 @@ cdef class HiddenMarkovModel( Model ):
 	"""
 
 	cdef public object start, end
-	cdef public int start_index, end_index, silent_start
+	cdef public int start_index
+	cdef public int end_index
+	cdef public int silent_start
 	cdef double* in_transition_pseudocounts
 	cdef double* out_transition_pseudocounts
 	cdef double [:] state_weights