phylogenie 2.1.21__py3-none-any.whl → 2.1.23__py3-none-any.whl

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]
@@ -50,9 +53,10 @@ def draw_tree(
     coloring: str | Coloring | None = None,
     default_color: Color = "black",
     cmap: str | None = None,
-    show_legend: bool = True,
     vmin: float | None = None,
     vmax: float | None = None,
+    show_legend: bool = True,
+    legend_kwargs: dict[str, Any] | None = None,
     show_hist: bool = True,
     hist_kwargs: dict[str, Any] | None = None,
     hist_axes_kwargs: dict[str, Any] | None = None,
@@ -98,7 +102,9 @@ def draw_tree(
             ]
             if any(color_by not in node.features for node in tree):
                 legend_handles.append(mpatches.Patch(color=default_color, label="NA"))
-            ax.legend(handles=legend_handles)  # pyright: ignore
+            if legend_kwargs is None:
+                legend_kwargs = {}
+            ax.legend(handles=legend_handles, **legend_kwargs)  # pyright: ignore
 
         return _draw_colored_tree(tree, ax, colors)
 

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/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.dist-info → phylogenie-2.1.23.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: phylogenie
-Version: 2.1.21
+Version: 2.1.23
 Summary: Generate phylogenetic datasets with minimal setup effort
 Author: Gabriele Marino
 Author-email: gabmarino.8601@gmail.com

{phylogenie-2.1.21.dist-info → phylogenie-2.1.23.dist-info}/RECORD

@@ -1,5 +1,5 @@
 phylogenie/__init__.py,sha256=8ulA-U7-WnBLNsqRYqPOPrJG8X4ZzyEU02oaDbR_Hxs,2849
-phylogenie/draw.py,sha256=mXCBS5xtJh0zJza8K2QkmRg_YbeCINst0vh6YMv6HQg,4959
+phylogenie/draw.py,sha256=WCjr_HCn-wCuxwkDhHA9Ijl1Sm6av6FBLkyR0MK2bVM,5271
 phylogenie/generators/__init__.py,sha256=zsOxy28-9j9alOQLIgrOAFfmM58NNHO_NEtW-KXQXAY,888
 phylogenie/generators/alisim.py,sha256=0aCLuGInifWgAvfh7zARWSKF4EMw3TjlPXMLSECui0k,2783
 phylogenie/generators/configs.py,sha256=WFoeKpgj9ZQIom7BKqwpgXbriiQGg3jFBMLoD8KButk,1073
@@ -7,7 +7,7 @@ phylogenie/generators/dataset.py,sha256=pPwW9yxm9fkU0PPllFq8EsPlqau8tth-4OatbA_h
 phylogenie/generators/factories.py,sha256=TuVFQWRjq33Hewjw_Lp8tQ0l_IPtqYDyQCNJhtiHpw8,7882
 phylogenie/generators/trees.py,sha256=6tHS013RNRyIsObeYq2Kx9it7Yc0TgiMkeAHbskHzAM,10748
 phylogenie/generators/typeguards.py,sha256=yj4VkhOaUXJ2OrY-6zhOeY9C4yKIQxjZtk2d-vIxttQ,828
-phylogenie/io.py,sha256=nwy8DOknt0HqF9qMeFZHrCmSXpM5AGrU5oajwTtD6vY,3973
+phylogenie/io.py,sha256=vUG2yVtoV98tNHut46uSuB3VPj6s64VDhUp1EaSk0o0,4084
 phylogenie/main.py,sha256=vtvSpQxBNlYABoFQ25czl-l3fIr4QRo3svWVd-jcArw,1170
 phylogenie/models.py,sha256=pCg9ob0RpLUHwM49x4knKxL4FNPr3-EU_6zMXsvxtAg,370
 phylogenie/msa.py,sha256=JDGyZUsAq6-m-SQjoCDjAkAZIxfgyl_PDIhdYn5HOow,2064
@@ -16,7 +16,7 @@ phylogenie/skyline/__init__.py,sha256=7pF4CUb4ZCLzNYJNhOjpuTOLTRhlK7L6ugfccNqjIG
 phylogenie/skyline/matrix.py,sha256=Gl8OgKjtieG0NwPYiPimKI36gefV8fm_OeorjdXxPTs,9146
 phylogenie/skyline/parameter.py,sha256=EM9qlPt0JhMBy3TbztM0dj24BaGNEy8KWKdTObDKhbI,4644
 phylogenie/skyline/vector.py,sha256=bJP7_FNX_Klt6wXqsyfj0KX3VNj6-dIhzCKSJuQcOV0,7115
-phylogenie/tree.py,sha256=mv8Jrb2jzK5q-vx5E1-mAQLagkP4aHgaL6tNpAOPfIE,5194
+phylogenie/tree.py,sha256=P1uM6s32TsODpvNJQIPMix9oj39vGSw_wsHYp2wmy5U,5246
 phylogenie/treesimulator/__init__.py,sha256=yqS2vtYMhdWSXc9RAnX1dd4zAqSQweMLyVKTnJLfGTU,1106
 phylogenie/treesimulator/events/__init__.py,sha256=6zSgZ0MEUMvTK4yPlSolJnRWzCARLS-jYreTzh45mQo,1033
 phylogenie/treesimulator/events/contact_tracing.py,sha256=_nJ85yhgGkeruQgMHvGpDYoyhheBf8M4LgZWiWdi5dY,4801
@@ -28,8 +28,8 @@ phylogenie/treesimulator/model.py,sha256=Nyg6R8XmMwZMSw1-dII81sU9uU7tDe-NMs8v1qK
 phylogenie/typeguards.py,sha256=JtqmbEWJZBRHbWgCvcl6nrWm3VcBfzRbklbTBYHItn0,1325
 phylogenie/typings.py,sha256=GknvAFXyiaWeeYJ8Lk5d6E2VHT-xW6ONEojYbtJYiB8,476
 phylogenie/utils.py,sha256=ehVk_2kvjW8Q_EyM2kxBPHYiK-KlPmZQx7JeVN6Fh-E,5419
-phylogenie-2.1.21.dist-info/LICENSE.txt,sha256=NUrDqElK-eD3I0WqC004CJsy6cs0JgsAoebDv_42-pw,1071
-phylogenie-2.1.21.dist-info/METADATA,sha256=De8Vqs1ngZOKgBdivLw1hWrtMDdtFWLRDW3M4-IAAyg,5477
-phylogenie-2.1.21.dist-info/WHEEL,sha256=sP946D7jFCHeNz5Iq4fL4Lu-PrWrFsgfLXbbkciIZwg,88
-phylogenie-2.1.21.dist-info/entry_points.txt,sha256=Rt6_usN0FkBX1ZfiqCirjMN9FKOgFLG8rydcQ8kugeE,51
-phylogenie-2.1.21.dist-info/RECORD,,
+phylogenie-2.1.23.dist-info/LICENSE.txt,sha256=NUrDqElK-eD3I0WqC004CJsy6cs0JgsAoebDv_42-pw,1071
+phylogenie-2.1.23.dist-info/METADATA,sha256=ym-NHK9hkvBR4kH_KGCnLnckV_iEzvFk0fdMzrkVudQ,5477
+phylogenie-2.1.23.dist-info/WHEEL,sha256=sP946D7jFCHeNz5Iq4fL4Lu-PrWrFsgfLXbbkciIZwg,88
+phylogenie-2.1.23.dist-info/entry_points.txt,sha256=Rt6_usN0FkBX1ZfiqCirjMN9FKOgFLG8rydcQ8kugeE,51
+phylogenie-2.1.23.dist-info/RECORD,,