Use new algo for truncating priors

Author: hyanwong

tsdate/base.py

@@ -159,6 +159,9 @@ def normalize(self):
         else:
             raise RuntimeError("Probability space is not", LIN, "or", LOG)
 
+    def is_fixed(self, node_id):
+        return self.row_lookup[node_id] < 0
+
     def __getitem__(self, node_id):
         index = self.row_lookup[node_id]
         if index < 0:

tsdate/prior.py

@@ -1032,14 +1032,10 @@ def shape_scale_from_mean_var(mean, var):
 
 def _truncate_priors(ts, priors, progress=False):
     """
-    Truncate priors for the nodes listed in truncate_nodes (or all nonfixed nodes
-    if truncate_nodes is None) so they conform to the age of fixed nodes in the tree
-    sequence
+    Truncate priors for all nonfixed nodes
+    so they conform to the age of fixed nodes in the tree sequence
     """
     tables = ts.tables
-    truncate_nodes = priors.nonfixed_node_ids()
-    # ensure truncate_nodes is ordered by node time
-    truncate_nodes = truncate_nodes[np.argsort(tables.nodes.time[truncate_nodes])]
 
     fixed_nodes = priors.fixed_node_ids()
     fixed_times = tables.nodes.time[fixed_nodes]
@@ -1055,29 +1051,32 @@ def _truncate_priors(ts, priors, progress=False):
     constrained_min_times = np.zeros_like(tables.nodes.time)
     # Set the min times of fixed nodes to those in the tree sequence
     constrained_min_times[fixed_nodes] = fixed_times
-    constrained_max_times = np.full_like(constrained_min_times, np.inf)
-
-    parents = tables.edges.parent
-    nd_children = tables.edges.child[np.argsort(parents)]
-    parents = sorted(parents)
-    parents_unique = np.unique(parents, return_index=True)
-    parent_indices = parents_unique[1][np.isin(parents_unique[0], truncate_nodes)]
-    for index, nd in tqdm(
-        enumerate(truncate_nodes), desc="Constrain Ages", disable=not progress
+
+    # Traverse through the ARG, ensuring children come before parents.
+    # This can be done by iterating over groups of edges with the same parent
+    new_parent_edge_idx = np.concatenate(
+        (
+            [0],
+            np.where(np.diff(tables.edges.parent) != 0)[0] + 1,
+            [tables.edges.num_rows],
+        )
+    )
+    for edges_start, edges_end in zip(
+        new_parent_edge_idx[:-1], new_parent_edge_idx[1:]
     ):
-        if index + 1 != len(truncate_nodes):
-            children_index = np.arange(parent_indices[index], parent_indices[index + 1])
-        else:
-            children_index = np.arange(parent_indices[index], ts.num_edges)
-        children = nd_children[children_index]
-        time = np.max(constrained_min_times[children])
-        # The constrained time of the node should be the age of the oldest child
-        if constrained_min_times[nd] <= time:
-            constrained_min_times[nd] = time
-        nearest_time = np.argmin(np.abs(timepoints - time))
-        lookup_index = priors.row_lookup[int(nd)]
-        grid_data[lookup_index][:nearest_time] = zero_value
-    assert np.all(constrained_min_times < constrained_max_times)
+        parent = tables.edges.parent[edges_start]
+        child_ids = tables.edges.child[edges_start:edges_end]  # May contain dups
+        oldest_child_time = np.max(constrained_min_times[child_ids])
+        if oldest_child_time > constrained_min_times[parent]:
+            if priors.is_fixed(parent):
+                raise ValueError(
+                    "Invalid fixed times: time for"
+                    + f"fixed node {parent} is younger than some of its descendants"
+                )
+            constrained_min_times[parent] = oldest_child_time
+        if constrained_min_times[parent] > 0 and not priors.is_fixed(parent):
+            nearest_time = np.argmin(np.abs(timepoints - constrained_min_times[parent]))
+            grid_data[priors.row_lookup[parent]][:nearest_time] = zero_value
 
     rowmax = grid_data[:, 1:].max(axis=1)
     if priors.probability_space == "linear":
@@ -1138,7 +1137,7 @@ def build_grid(
     :param dict node_var_override: is a dict mapping node IDs to a variance value.
         Any nodes listed here will be treated as non-fixed nodes whose prior is not
         calculated from the conditional coalescent but instead are allocated a prior
-        whose mean is thenode time in the tree sequence and whose variance is the
+        whose mean is the node time in the tree sequence and whose variance is the
         value in this dictionary. This allows sample nodes to be treated as nonfixed
         nodes, and therefore dated. If ``None`` (default) then all sample nodes are
         treated as occurring ata  fixed time (as if this were an empty dict).