committor problems, dependency versions in setup.py

Author: alexrd

csnanalysis/csn.py

@@ -238,13 +238,13 @@ def calc_committors(self,basins,labels=None,basin_labels=None,add_basins=False,t
         else:
             # use trimmed transition matrix
             comm = committor(self.transmat,basins,tol=tol,maxstep=maxstep)
-            full_comm = np.zeros(self.nnodes,dtype=float64)
+            full_comm = np.zeros((self.transmat.shape[0],len(basins)),dtype=float)
             for i,ind in enumerate(self.trim_indices):
                 full_comm[ind] = comm[i]
 
         if labels is None:
             labels = ['p' + str(i) for i in range(len(basins))]
-        for i,b in enumerate(basins):
+        for i in range(len(basins)):
             self.add_attr(labels[i], full_comm[:,i])
 
         if add_basins:

csnanalysis/matrix.py

@@ -137,7 +137,8 @@ def committor(transmat,basins,tol=1e-6,maxstep=20):
     """
 
     # make sink_matrix
-    sink_mat = make_sink(transmat,list(np.array(basins).flatten()))
+    flat_basin_list = [state for b in basins for state in b]
+    sink_mat = make_sink(transmat,flat_basin_list)
 
     sink_results = trans_mult_iter(sink_mat,tol,maxstep)