--- a/pylearn/sampling/hmc.py	Fri Sep 09 10:53:46 2011 -0400
+++ b/pylearn/sampling/hmc.py	Fri Sep 09 10:54:17 2011 -0400
@@ -16,7 +16,7 @@
 expression graph.
 
 The initialize_dynamics() theano-function does several things:
-1. samples a random velocity for each particle (saving it to self.velocities) 
+1. samples a random velocity for each particle (saving it to self.velocities)
 2. calculates the initial hamiltonian based on those velocities (saving it to
     self.initial_hamiltonian)
 3. saves self.positions to self.initial_positions.
@@ -92,11 +92,11 @@
         pos: theano matrix
             in leapfrog update equations, represents pos(t), position at time t
         vel: theano matrix
-            in leapfrog update equations, represents vel(t - stepsize/2), 
+            in leapfrog update equations, represents vel(t - stepsize/2),
             velocity at time (t - stepsize/2)
         step: theano scalar
             scalar value controlling amount by which to move
-        
+
         Returns
         -------
         rval1: [theano matrix, theano matrix]
@@ -121,7 +121,7 @@
 
     # perform leapfrog updates: the scan op is used to repeatedly compute pos(t_1 + n*sigma) and
     # vel(t_1 + n*sigma + 1/2) for n in [0,n_steps-2].
-    (all_p, all_v), scan_updates = theano.scan(leapfrog, 
+    (all_p, all_v), scan_updates = theano.scan(leapfrog,
             outputs_info=[
                 dict(initial=p_full_step),
                 dict(initial=v_half_step),
@@ -137,7 +137,7 @@
     # function, to avoid drawing the same random numbers each time the function is called. In
     # this case however, we consciously ignore "scan_updates" because we know it is empty.
     assert not scan_updates
-    
+
     # The last velocity returned by the scan op is at time-step: t + n_steps* stepsize - 1/2
     # We therefore perform one more half-step to return vel(t + n_steps*stepsize)
     energy = energy_fn(final_p)
@@ -156,7 +156,7 @@
     initial_v = s_rng.normal(size=positions_shape)
 
     final_p, final_v = simulate_dynamics(
-            initial_p = positions, 
+            initial_p = positions,
             initial_v = initial_v,
             stepsize = stepsize,
             n_steps = n_steps,
@@ -166,10 +166,10 @@
             energy_prev = Print('ep')(hamiltonian(positions, initial_v, energy_fn)),
             energy_next = Print('en')(hamiltonian(final_p, final_v, energy_fn)),
             s_rng=s_rng, shape=(batchsize,))
-    
+
     return Print('accept')(accept), final_p
 
-def mcmc_updates(shrd_pos, shrd_stepsize, shrd_avg_acceptance_rate, final_p, accept, 
+def mcmc_updates(shrd_pos, shrd_stepsize, shrd_avg_acceptance_rate, final_p, accept,
         target_acceptance_rate,
         stepsize_inc,
         stepsize_dec,
@@ -183,9 +183,9 @@
                     accept.dimshuffle(0, *(('x',)*(final_p.ndim-1))),
                     final_p,
                     shrd_pos)),
-            (shrd_stepsize, 
+            (shrd_stepsize,
                 TT.clip(
-                    TT.switch( 
+                    TT.switch(
                         shrd_avg_acceptance_rate > target_acceptance_rate,
                         shrd_stepsize * stepsize_inc,
                         shrd_stepsize * stepsize_dec,
@@ -214,7 +214,7 @@
         self.__dict__.update(kwargs)
 
     @classmethod
-    def new_from_shared_positions(cls, shared_positions, energy_fn, 
+    def new_from_shared_positions(cls, shared_positions, energy_fn,
             initial_stepsize=0.01, target_acceptance_rate=.9, n_steps=20,
             stepsize_dec = 0.98,
             stepsize_min = 0.001,
@@ -222,13 +222,13 @@
             stepsize_inc = 1.02,
             avg_acceptance_slowness = 0.9, # used in geometric avg. 1.0 would be not moving at all
             seed=12345, dtype=theano.config.floatX,
-            shared_positions_shape=None, 
+            shared_positions_shape=None,
             compile_simulate=True):
         """
         :param shared_positions: theano ndarray shared var with many particle [initial] positions
         :param energy_fn:
-            callable such that energy_fn(positions) 
-            returns theano vector of energies.  
+            callable such that energy_fn(positions)
+            returns theano vector of energies.
             The len of this vector is the batchsize.
 
             The sum of this energy vector must be differentiable (with theano.tensor.grad) with
@@ -245,17 +245,17 @@
         s_rng = TT.shared_randomstreams.RandomStreams(seed)
 
         accept, final_p = mcmc_move(
-                s_rng, 
-                shared_positions, 
+                s_rng,
+                shared_positions,
                 energy_fn,
-                stepsize, 
+                stepsize,
                 n_steps,
                 shared_positions_shape)
         simulate_updates = mcmc_updates(
                 shared_positions,
                 stepsize,
-                avg_acceptance_rate, 
-                final_p=final_p, 
+                avg_acceptance_rate,
+                final_p=final_p,
                 accept=accept,
                 stepsize_min=stepsize_min,
                 stepsize_max=stepsize_max,
@@ -298,8 +298,7 @@
         """
         return list(self._updates)
 
-#TODO: 
+#TODO:
 # Consider a heuristic for updating the *MASS* of the particles.  We might want the mass to be
 # such that the momentum is in the same range as the gradient on the energy.  Look at Radford's
 # recent book chapter, maybe there are hints. (2010).
-