phylogenie 2.1.21__tar.gz → 2.1.22__tar.gz

{phylogenie-2.1.21 → phylogenie-2.1.22}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: phylogenie
-Version: 2.1.21
+Version: 2.1.22
 Summary: Generate phylogenetic datasets with minimal setup effort
 Author: Gabriele Marino
 Author-email: gabmarino.8601@gmail.com

{phylogenie-2.1.21 → phylogenie-2.1.22}/phylogenie/draw.py

@@ -28,7 +28,10 @@ def _draw_colored_tree(tree: Tree, ax: Axes, colors: Color | dict[Tree, Color])
         if any(node.branch_length is None for node in tree)
         else get_node_depths(tree)
     )
-    ys = {node: i for i, node in enumerate(tree.inorder_traversal())}
+    ys: dict[Tree, float] = {node: i for i, node in enumerate(tree.get_leaves())}
+    for node in tree.postorder_traversal():
+        if node.is_internal():
+            ys[node] = sum(ys[child] for child in node.children) / len(node.children)
 
     for node in tree:
         x1, y1 = xs[node], ys[node]

{phylogenie-2.1.21 → phylogenie-2.1.22}/phylogenie/io.py

@@ -1,3 +1,4 @@
+import re
 from typing import Callable
 
 from phylogenie.msa import MSA, Sequence
@@ -12,54 +13,56 @@ def _parse_newick(newick: str) -> Tree:
     i = 0
     while i < len(newick):
 
-        def _parse_chars(stoppers: list[str]) -> str:
+        def _read_chars(stoppers: list[str]) -> str:
             nonlocal i
             chars = ""
-            while newick[i] not in stoppers:
+            while i < len(newick) and newick[i] not in stoppers:
                 chars += newick[i]
                 i += 1
+            if i == len(newick):
+                raise ValueError(f"Expected one of {stoppers}, got end of string")
             return chars
 
         if newick[i] == "(":
             stack.append(current_nodes)
             current_nodes = []
-        else:
-            id = _parse_chars([":", ",", ")", ";", "["])
-            branch_length = None
-            if newick[i] == ":":
-                i += 1
-                branch_length = float(_parse_chars([",", ")", ";", "["]))
+            i += 1
+            continue
+
+        current_node = Tree(_read_chars(["[", ":", ",", ")", ";"]))
+
+        if newick[i] == "[":
+            i += 1
+            if newick[i] != "&":
+                raise ValueError("Expected '[&' at the start of node features")
+            i += 1
+            features = re.split(r",(?=[^,]+=)", _read_chars(["]"]))
+            i += 1
+            for feature in features:
+                key, value = feature.split("=")
+                try:
+                    current_node.set(key, eval(value))
+                except Exception:
+                    current_node.set(key, value)
 
-            current_node = Tree(id, branch_length)
-            for node in current_children:
-                current_node.add_child(node)
-                current_children = []
-            current_nodes.append(current_node)
+        if newick[i] == ":":
+            i += 1
+            current_node.branch_length = float(_read_chars([",", ")", ";"]))
 
-            if newick[i] == "[":
-                i += 1
-                features = _parse_chars(["]"]).split(":")
-                i += 1
-                if features[0] != "&&NHX":
-                    raise ValueError(f"Expected '&&NHX' for node features.")
-                for feature in features[1:]:
-                    key, value = feature.split("=", 1)
-                    try:
-                        current_node.set(key, eval(value))
-                    except Exception as e:
-                        raise ValueError(
-                            f"Error setting node feature `{key}` to `{value}`: {e}"
-                        )
-
-            if newick[i] == ")":
-                current_children = current_nodes
-                current_nodes = stack.pop()
-            elif newick[i] == ";":
-                return current_node
+        for node in current_children:
+            current_node.add_child(node)
+            current_children = []
+        current_nodes.append(current_node)
+
+        if newick[i] == ")":
+            current_children = current_nodes
+            current_nodes = stack.pop()
+        elif newick[i] == ";":
+            return current_node
 
         i += 1
 
-    raise ValueError("Newick string is invalid.")
+    raise ValueError("Newick string should end with ';'")
 
 
 def load_newick(filepath: str) -> Tree | list[Tree]:
@@ -71,19 +74,23 @@ def load_newick(filepath: str) -> Tree | list[Tree]:
 def _to_newick(tree: Tree) -> str:
     children_newick = ",".join([_to_newick(child) for child in tree.children])
     newick = tree.name
-    if children_newick:
-        newick = f"({children_newick}){newick}"
-    if tree.branch_length is not None:
-        newick += f":{tree.branch_length}"
     if tree.features:
         reprs = {k: repr(v).replace("'", '"') for k, v in tree.features.items()}
         for k, r in reprs.items():
-            if ":" in r or "=" in r or "]" in r:
+            if "," in k or "=" in k or "]" in k:
+                raise ValueError(
+                    f"Invalid feature key `{k}`: keys must not contain ',', '=', or ']'"
+                )
+            if "=" in r or "]" in r:
                 raise ValueError(
-                    f"Cannot serialize feature `{k}` with value `{r}`: contains reserved characters."
+                    f"Invalid value  `{r}` for feature `{k}`: values must not contain '=' or ']'"
                 )
         features = [f"{k}={repr}" for k, repr in reprs.items()]
-        newick += f"[&&NHX:{':'.join(features)}]"
+        newick += f"[&{','.join(features)}]"
+    if children_newick:
+        newick = f"({children_newick}){newick}"
+    if tree.branch_length is not None:
+        newick += f":{tree.branch_length}"
     return newick
 
 

{phylogenie-2.1.21 → phylogenie-2.1.22}/phylogenie/tree.py

@@ -136,16 +136,19 @@ class Tree:
     def get_leaves(self) -> tuple["Tree", ...]:
         return tuple(node for node in self if node.is_leaf())
 
+    def is_internal(self) -> bool:
+        return not self.is_leaf()
+
     def get_internal_nodes(self) -> tuple["Tree", ...]:
-        return tuple(node for node in self if not node.is_leaf())
+        return tuple(node for node in self if node.is_internal())
 
     def is_binary(self) -> bool:
         return all(len(node.children) in (0, 2) for node in self)
 
-    def ladderize(self, criterion: Callable[["Tree"], Any]) -> None:
-        self._children.sort(key=criterion)
+    def ladderize(self, key: Callable[["Tree"], Any]) -> None:
+        self._children.sort(key=key)
         for child in self.children:
-            child.ladderize(criterion)
+            child.ladderize(key)
 
     def copy(self):
         new_tree = Tree(self.name, self.branch_length)

{phylogenie-2.1.21 → phylogenie-2.1.22}/pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "phylogenie"
-version = "2.1.21"
+version = "2.1.22"
 description = "Generate phylogenetic datasets with minimal setup effort"
 authors = ["Gabriele Marino <gabmarino.8601@gmail.com>"]
 readme = "README.md"