version bump

neherlab · Sep 21, 2022 · 6adb3d1 · 6adb3d1
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diff --git a/changelog.md b/changelog.md
@@ -1,3 +1,8 @@
+# 0.9.4: bug fix and performance improvments
+
+ * avoid negative variance associated with branch lengths in tree regression. This could happen in rare cases when marginal time tree estimation returned short negative branch length and the variance was estimated as being proportional to branch length. Variances in the `TreeRegression` clock model are now always non-negative.
+ * downsample the grid during multiplication of distribution objects. This turned out to be an issue for trees with very large polytomies. In these cases, a large number of distributions get multiplied which resulted in grid sizes above 100000 points. Grid sizes are now downsampled to the average grid size.
+
 # 0.9.3
 
  * Add extra error class for "unknown" (==unhandled) errors

diff --git a/treetime/__init__.py b/treetime/__init__.py
@@ -1,4 +1,4 @@
-version="0.9.3"
+version="0.9.4"
 ## Here we define an error class for TreeTime errors, MissingData, UnknownMethod and NotReady errors
 ## are all due to incorrect calling of TreeTime functions or input data that does not fit our base assumptions.
 ## Errors marked as TreeTimeUnknownErrors might be due to data not fulfilling base assumptions or due

diff --git a/treetime/clock_tree.py b/treetime/clock_tree.py
@@ -690,7 +690,7 @@ def _cleanup():
 
                 msg_parent_to_node =None
                 if node.marginal_pos_Lx is not None:
-                    if len(parent.clades)<3:
+                    if len(parent.clades)<5:
                         # messages from the complementary subtree (iterate over all sister nodes)
                         complementary_msgs = [parent.date_constraint] if parent.date_constraint is not None else []
                         complementary_msgs.extend([sister.marginal_pos_Lx for sister in parent.clades