phylogenie 3.0.0__tar.gz → 3.1.2__tar.gz

{phylogenie-3.0.0 → phylogenie-3.1.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: phylogenie
-Version: 3.0.0
+Version: 3.1.2
 Summary: Generate phylogenetic datasets with minimal setup effort
 Author: Gabriele Marino
 Author-email: gabmarino.8601@gmail.com

{phylogenie-3.0.0 → phylogenie-3.1.2}/phylogenie/treesimulator/io/nexus.py

@@ -32,9 +32,11 @@ def _parse_trees_block(lines: Iterator[str]) -> dict[str, Tree]:
         else:
             match = re.match(r"^TREE\s*\*?\s+(\S+)\s*=\s*(.+)$", line, re.IGNORECASE)
             if match is None:
-                raise ValueError(f"Invalid tree line. Expected 'TREE name = newick'")
+                raise ValueError(
+                    f"Invalid tree line. Expected 'TREE <name> = <newick>'"
+                )
             trees[match.group(1)] = parse_newick(match.group(2), translations)
-    return trees
+    raise ValueError("Unterminated TREES block.")
 
 
 def load_nexus(nexus_file: str | Path) -> dict[str, Tree]:

{phylogenie-3.0.0 → phylogenie-3.1.2}/phylogenie/treesimulator/utils.py

@@ -22,7 +22,7 @@ def get_node_depths(tree: Tree) -> dict[Tree, float]:
     depths: dict[Tree, float] = {tree: tree.depth}
     for node in tree.iter_descendants():
         parent_depth = depths[node.parent]  # pyright: ignore
-        depths[node] = tree.branch_length_or_raise() + parent_depth
+        depths[node] = node.branch_length_or_raise() + parent_depth
     return depths
 
 

{phylogenie-3.0.0 → phylogenie-3.1.2}/pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "phylogenie"
-version = "3.0.0"
+version = "3.1.2"
 description = "Generate phylogenetic datasets with minimal setup effort"
 authors = ["Gabriele Marino <gabmarino.8601@gmail.com>"]
 readme = "README.md"