Set likelihoods to use fixed nodes from prior

Author: hyanwong

tsdate/core.py

@@ -402,7 +402,7 @@ def get_fixed(self, arr, edge):
         return arr * liks
 
     def scale_geometric(self, fraction, value):
-        return value**fraction
+        return value ** fraction
 
 
 class LogLikelihoods(Likelihoods):
@@ -686,7 +686,7 @@ def inside_pass(self, *, normalize=True, cache_inside=False, progress=None):
                             "dangling nodes: please simplify it"
                         )
                     daughter_val = self.lik.scale_geometric(
-                        spanfrac, self.lik.make_lower_tri(inside[edge.child])
+                        spanfrac, self.lik.make_lower_tri(inside_values)
                     )
                     edge_lik = self.lik.get_inside(daughter_val, edge)
                 val = self.lik.combine(val, edge_lik)
@@ -1081,8 +1081,6 @@ def get_dates(
 
     :return: tuple(mn_post, posterior, timepoints, eps, nodes_to_date)
     """
-    fixed_nodes = set(tree_sequence.samples())
-
     # Default to not creating approximate priors unless ts has > 1000 samples
     approx_priors = False
     if tree_sequence.num_samples > 1000:
@@ -1110,6 +1108,8 @@ def get_dates(
             )
         priors = priors
 
+    fixed_nodes = set(priors.fixed_node_ids())
+
     if probability_space != base.LOG:
         liklhd = Likelihoods(
             tree_sequence,