phylogenie 2.1.29__py3-none-any.whl → 3.0.0__py3-none-any.whl

phylogenie-3.0.0.dist-info/RECORD

@@ -0,0 +1,40 @@
+phylogenie/__init__.py,sha256=-4GKO2EKgc2GiOhzVRI0SQk6wQZ4AlP7Ron_Lp-s_r0,2913
+phylogenie/draw.py,sha256=6WHLxXXyTKq6pxuPBfDgZfEZti3UkJVhDory2pJzdIc,5499
+phylogenie/generators/__init__.py,sha256=zsOxy28-9j9alOQLIgrOAFfmM58NNHO_NEtW-KXQXAY,888
+phylogenie/generators/alisim.py,sha256=oizyUz2xNKUdO4HrmZFqtVUfzPBN4BRgxgYczofgeYs,2809
+phylogenie/generators/configs.py,sha256=xDIyDgGxuaqdET9wVkpdrXk02jIbibSp8mgxuIcM5qQ,1489
+phylogenie/generators/dataset.py,sha256=Z3a4Mhh6zMTYmhd-aIT3aCaJMTVg4I_QvWWIrCw2l4E,2121
+phylogenie/generators/factories.py,sha256=2mTFdFbbLyV3v79JaOEVtqLOmxQHaOUv1S-Y3vVo7U0,8480
+phylogenie/generators/trees.py,sha256=8dO1CkU34E6mmMAHrYqiLV_VA8r54cSEOo-UzoHiN20,10467
+phylogenie/generators/typeguards.py,sha256=yj4VkhOaUXJ2OrY-6zhOeY9C4yKIQxjZtk2d-vIxttQ,828
+phylogenie/io/__init__.py,sha256=eWDU6YDqAdx6TZlUMmMbsfO8gP3i5HP_cfUe_-0x2FA,69
+phylogenie/io/fasta.py,sha256=CUFO06m7wClprarsMheZojM4Os2NQf3ALYUXSWzfNL0,869
+phylogenie/main.py,sha256=vtvSpQxBNlYABoFQ25czl-l3fIr4QRo3svWVd-jcArw,1170
+phylogenie/mixins.py,sha256=kwxcHGYSS-Frk-r0nwuyILYS1g6NjSOhbUKEYt2g1B0,1319
+phylogenie/msa.py,sha256=JDGyZUsAq6-m-SQjoCDjAkAZIxfgyl_PDIhdYn5HOow,2064
+phylogenie/py.typed,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+phylogenie/skyline/__init__.py,sha256=7pF4CUb4ZCLzNYJNhOjpuTOLTRhlK7L6ugfccNqjIGo,620
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+phylogenie/treesimulator/events/contact_tracing.py,sha256=t64omKEO2d-DfN_dhDJlXp_Kg9egy2ZE346yWjV3ZrA,5148
+phylogenie/treesimulator/events/core.py,sha256=bhgQgi5L-oaHsoWJmUOsTTzWxi0POYxVLoF-KrC8AGQ,8179
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+phylogenie/treesimulator/features.py,sha256=XbuwGw8xjGs2lNhJvvUUvXVtheSTBaSN6qj39tWYEro,1391
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+phylogenie/typeguards.py,sha256=JtqmbEWJZBRHbWgCvcl6nrWm3VcBfzRbklbTBYHItn0,1325
+phylogenie/typings.py,sha256=p694PBe_tk25A6N8vGGWxuqoDtt3nHFUsIYJrwR_76Y,494
+phylogenie-3.0.0.dist-info/LICENSE.txt,sha256=NUrDqElK-eD3I0WqC004CJsy6cs0JgsAoebDv_42-pw,1071
+phylogenie-3.0.0.dist-info/METADATA,sha256=j8dRenC33-Ab4NTcgawv6_kRJbpvC6fyDF2AyD-IeEo,5476
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+phylogenie-3.0.0.dist-info/RECORD,,

phylogenie/models.py

@@ -1,17 +0,0 @@
-from typing import Any
-
-from pydantic import BaseModel, ConfigDict
-
-
-class StrictBaseModel(BaseModel):
-    model_config = ConfigDict(extra="forbid")
-
-
-class Distribution(BaseModel):
-    type: str
-    model_config = ConfigDict(extra="allow")
-
-    @property
-    def args(self) -> dict[str, Any]:
-        assert self.model_extra is not None
-        return self.model_extra

phylogenie/utils.py

@@ -1,176 +0,0 @@
-from itertools import chain
-from math import comb
-
-from phylogenie.tree import Tree
-
-
-def get_node_leaf_counts(tree: Tree) -> dict[Tree, int]:
-    n_leaves: dict[Tree, int] = {}
-    for node in tree.postorder_traversal():
-        n_leaves[node] = sum(n_leaves[child] for child in node.children) or 1
-    return n_leaves
-
-
-def get_node_depth_levels(tree: Tree) -> dict[Tree, int]:
-    depth_levels: dict[Tree, int] = {}
-    for node in tree:
-        if node.parent is None:
-            depth_levels[node] = 0
-        else:
-            depth_levels[node] = depth_levels[node.parent] + 1
-    return depth_levels
-
-
-def get_node_depths(tree: Tree) -> dict[Tree, float]:
-    depths: dict[Tree, float] = {}
-    for node in tree:
-        if node.parent is None:
-            depths[node] = 0 if node.branch_length is None else node.branch_length
-        else:
-            if node.branch_length is None:
-                raise ValueError(f"Branch length of node {node.name} is not set.")
-            depths[node] = depths[node.parent] + node.branch_length
-    return depths
-
-
-def get_node_height_levels(tree: Tree) -> dict[Tree, int]:
-    height_levels: dict[Tree, int] = {}
-    for node in tree.postorder_traversal():
-        if node.is_leaf():
-            height_levels[node] = 0
-        else:
-            height_levels[node] = max(
-                1 + height_levels[child] for child in node.children
-            )
-    return height_levels
-
-
-def get_node_heights(tree: Tree) -> dict[Tree, float]:
-    heights: dict[Tree, float] = {}
-    for node in tree.postorder_traversal():
-        if node.is_leaf():
-            heights[node] = 0
-        else:
-            if any(child.branch_length is None for child in node.children):
-                raise ValueError(
-                    f"Branch length of one or more children of node {node.name} is not set."
-                )
-            heights[node] = max(
-                child.branch_length + heights[child]  # pyright: ignore
-                for child in node.children
-            )
-    return heights
-
-
-def get_mrca(node1: Tree, node2: Tree) -> Tree:
-    node1_ancestors = set(node1.iter_ancestors())
-    for node2_ancestor in node2.iter_ancestors():
-        if node2_ancestor in node1_ancestors:
-            return node2_ancestor
-    raise ValueError(f"No common ancestor found between node {node1} and node {node2}.")
-
-
-def get_distance(node1: Tree, node2: Tree) -> float:
-    mrca = get_mrca(node1, node2)
-    path = list(chain(node1.iter_ancestors(stop=mrca), node2.iter_ancestors(stop=mrca)))
-    if any(node.branch_length is None for node in path):
-        return len(path)
-    return sum(node.branch_length for node in path)  # pyright: ignore
-
-
-def compute_sackin_index(tree: Tree, normalize: bool = False) -> float:
-    """
-    Compute the Sackin index of a tree.
-
-    Parameters
-    ----------
-    tree : Tree
-        The input tree.
-    normalize : bool, optional
-        Whether to normalize the index between 0 and 1, by default False.
-
-    Returns
-    -------
-    float
-        The Sackin index of the tree.
-
-    References
-    ----------
-    - Kwang-Tsao Shao and Robert R Sokal. Tree Balance. Systematic Zoology, 39(3):266, 1990.
-    """
-    leaves = tree.get_leaves()
-    depth_levels = get_node_depth_levels(tree)
-    sackin_index = sum(depth_levels[leaf] for leaf in leaves)
-    if normalize:
-        n = len(leaves)
-        max_sackin_index = (n + 2) * (n - 1) / 2
-        return (sackin_index - n) / (max_sackin_index - n)
-    return sackin_index
-
-
-def compute_colless_index(tree: Tree, normalize: bool = False) -> float:
-    """
-    Compute the Colless index of a binary tree.
-
-    Parameters
-    ----------
-    tree : Tree
-        The input binary tree.
-    normalize : bool, optional
-        Whether to normalize the index between 0 and 1, by default False.
-
-    Returns
-    -------
-    float
-        The Colless index of the tree.
-
-    References
-    ----------
-    - Donald H. Colless. Review of phylogenetics: the theory and practice of phylogenetic systematics. Systematic Zoology, 31(1):100–104, 1982.
-    """
-    if not tree.is_binary():
-        raise ValueError("Colless index is only defined for binary trees.")
-
-    internal_nodes = tree.get_internal_nodes()
-    if not internal_nodes:
-        raise ValueError(
-            "Tree must have at least one internal node to compute the Colless index."
-        )
-
-    colless_index = 0
-    leaf_counts = get_node_leaf_counts(tree)
-    for node in internal_nodes:
-        left, right = node.children
-        colless_index += abs(leaf_counts[left] - leaf_counts[right])
-    if normalize:
-        n_leaves = len(leaf_counts) - len(internal_nodes)
-        max_colless_index = comb(n_leaves, 2)
-        return colless_index / max_colless_index
-    return colless_index
-
-
-def compute_mean_leaf_pairwise_distance(tree: Tree) -> float:
-    """
-    Compute the mean pairwise distance between all pairs of leaves in the tree.
-
-    Parameters
-    ----------
-    tree : Tree
-        The input tree.
-
-    Returns
-    -------
-    float
-        The mean pairwise distance between all pairs of leaves in the tree.
-    """
-    leaves = tree.get_leaves()
-    n_leaves = len(leaves)
-    if n_leaves < 2:
-        return 0.0
-
-    total_distance = sum(
-        get_distance(leaves[i], leaves[j])
-        for i in range(n_leaves)
-        for j in range(i + 1, n_leaves)
-    )
-    return total_distance / comb(n_leaves, 2)

phylogenie-2.1.29.dist-info/RECORD

@@ -1,39 +0,0 @@
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-phylogenie/draw.py,sha256=jM24oCGkU66IsEm56IAcq0pCSVXC8ltyYJQizNwDJl8,5451
-phylogenie/generators/__init__.py,sha256=zsOxy28-9j9alOQLIgrOAFfmM58NNHO_NEtW-KXQXAY,888
-phylogenie/generators/alisim.py,sha256=1YQLpOG_Bpn9YqExQqEu-wz1MDGCbpPmTdhrBb6TbWc,2820
-phylogenie/generators/configs.py,sha256=zjNnljBBC-d6DTjWjieE8-HnKeE58LAy3moBYiD6NFo,1042
-phylogenie/generators/dataset.py,sha256=kY92diePr2IjiLejHLixJoYRc-2LpM-GBt3wkX9SYvA,2109
-phylogenie/generators/factories.py,sha256=qSz-s7ltQwUf7R6TPZ-5xFyOnnSHkKn0u5IukeysXVU,8544
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-phylogenie/io/fasta.py,sha256=CUFO06m7wClprarsMheZojM4Os2NQf3ALYUXSWzfNL0,869
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-phylogenie/py.typed,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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-phylogenie-2.1.29.dist-info/LICENSE.txt,sha256=NUrDqElK-eD3I0WqC004CJsy6cs0JgsAoebDv_42-pw,1071
-phylogenie-2.1.29.dist-info/METADATA,sha256=mVsGaofekWG_o0Mu2CqYu7RZsEL7MKsY3m5w7wv8hAw,5477
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