phylogenie 2.1.7__py3-none-any.whl → 2.1.9__py3-none-any.whl

phylogenie/generators/alisim.py

@@ -72,7 +72,7 @@ class AliSimDatasetGenerator(DatasetGenerator):
                 )
 
         for leaf in tree.get_leaves():
-            leaf.id += f"|{leaf.get_time()}"
+            leaf.name += f"|{leaf.get_time()}"
         dump_newick(tree, f"{tree_filename}.nwk")
 
         self._generate_one_from_tree(msa_filename, f"{tree_filename}.nwk", rng, d)

phylogenie/generators/configs.py

@@ -1,6 +1,6 @@
 import phylogenie.typings as pgt
+from phylogenie.models import Distribution, StrictBaseModel
 from phylogenie.treesimulator import MutationTargetType
-from phylogenie.utils import Distribution, StrictBaseModel
 
 Integer = str | int
 Scalar = str | pgt.Scalar

phylogenie/generators/dataset.py

@@ -8,7 +8,7 @@ import pandas as pd
 from numpy.random import Generator, default_rng
 from tqdm import tqdm
 
-from phylogenie.utils import Distribution, StrictBaseModel
+from phylogenie.models import Distribution, StrictBaseModel
 
 
 class DataType(str, Enum):
@@ -31,7 +31,7 @@ class DatasetGenerator(ABC, StrictBaseModel):
     def generate_one(
         self,
         filename: str,
-        context: dict[str, Any] | None = None,
+        context: dict[str, Distribution] | None = None,
         seed: int | None = None,
     ) -> dict[str, Any]: ...
 

phylogenie/generators/factories.py

@@ -8,6 +8,7 @@ import phylogenie.generators.configs as cfg
 import phylogenie.generators.typeguards as ctg
 import phylogenie.typeguards as tg
 import phylogenie.typings as pgt
+from phylogenie.models import Distribution
 from phylogenie.skyline import (
     SkylineMatrix,
     SkylineMatrixCoercible,
@@ -16,7 +17,6 @@ from phylogenie.skyline import (
     SkylineVector,
     SkylineVectorCoercible,
 )
-from phylogenie.utils import Distribution
 
 
 def _eval_expression(expression: str, data: dict[str, Any]) -> Any:

phylogenie/generators/trees.py

@@ -19,9 +19,11 @@ from phylogenie.generators.factories import (
     skyline_vector,
 )
 from phylogenie.io import dump_newick
+from phylogenie.models import Distribution
 from phylogenie.tree import Tree
 from phylogenie.treesimulator import (
     Event,
+    Feature,
     Mutation,
     get_BD_events,
     get_BDEI_events,
@@ -30,6 +32,7 @@ from phylogenie.treesimulator import (
     get_contact_tracing_events,
     get_epidemiological_events,
     get_FBD_events,
+    set_features,
     simulate_tree,
 )
 
@@ -51,6 +54,7 @@ class TreeDatasetGenerator(DatasetGenerator):
     init_state: str | None = None
     sampling_probability_at_present: cfg.Scalar = 0.0
     timeout: float = np.inf
+    node_features: list[Feature] | None = None
 
     @abstractmethod
     def _get_events(self, data: dict[str, Any]) -> list[Event]: ...
@@ -77,7 +81,7 @@ class TreeDatasetGenerator(DatasetGenerator):
     def generate_one(
         self,
         filename: str,
-        context: dict[str, Any] | None = None,
+        context: dict[str, Distribution] | None = None,
         seed: int | None = None,
     ) -> dict[str, Any]:
         d = {"file_id": Path(filename).stem}
@@ -86,6 +90,8 @@ class TreeDatasetGenerator(DatasetGenerator):
             try:
                 d.update(data(context, rng))
                 tree = self.simulate_one(d, seed)
+                if self.node_features is not None:
+                    set_features(tree, self.node_features)
                 dump_newick(tree, f"{filename}.nwk")
                 break
             except TimeoutError:

phylogenie/io.py

@@ -44,7 +44,12 @@ def _parse_newick(newick: str) -> Tree:
                     raise ValueError(f"Expected '&&NHX' for node features.")
                 for feature in features[1:]:
                     key, value = feature.split("=", 1)
-                    current_node.set(key, eval(value))
+                    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
@@ -65,13 +70,18 @@ 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.id
+    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:
+                raise ValueError(
+                    f"Cannot serialize feature `{k}` with value `{r}`: contains reserved characters."
+                )
         features = [f"{k}={repr}" for k, repr in reprs.items()]
         newick += f"[&&NHX:{':'.join(features)}]"
     return newick

phylogenie/models.py

@@ -0,0 +1,17 @@
+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/plot.py

@@ -0,0 +1,77 @@
+from enum import Enum
+
+import matplotlib.colors as mcolors
+import matplotlib.patches as mpatches
+import matplotlib.pyplot as plt
+
+from phylogenie import Tree
+from phylogenie.tree import Tree
+from phylogenie.utils import get_times
+
+
+class Coloring(str, Enum):
+    DISCRETE = "discrete"
+    CONTINUOUS = "continuous"
+
+
+def plot_tree(
+    tree: Tree,
+    ax: plt.Axes | None = None,  # pyright: ignore
+    color_by: str | None = None,
+    default_color: str = "black",
+    coloring: str | Coloring | None = None,
+    cmap: str | None = None,
+    show_legend: bool = True,
+) -> plt.Axes:  # pyright: ignore
+    if ax is None:
+        ax = plt.gca()
+
+    xs = get_times(tree)
+    ys = {node: i for i, node in enumerate(tree.inorder_traversal())}
+
+    if color_by is not None:
+        features = set(node.get(color_by) for node in tree)
+        if coloring is None and any(isinstance(f, float) for f in features):
+            coloring = Coloring.CONTINUOUS
+        elif coloring is None:
+            coloring = Coloring.DISCRETE
+        if coloring == Coloring.DISCRETE:
+            if any(isinstance(f, float) for f in features):
+                raise ValueError(
+                    "Discrete coloring selected but feature values are not all categorical."
+                )
+            cmap = "tab20" if cmap is None else cmap
+            colormap = plt.get_cmap(cmap, len(features))
+            feature_colors = {
+                f: mcolors.to_hex(colormap(i)) for i, f in enumerate(features)
+            }
+            colors = {node: feature_colors[node.get(color_by)] for node in tree}
+            legend_handles = [
+                mpatches.Patch(color=feature_colors[f], label=str(f)) for f in features
+            ]
+            if show_legend:
+                ax.legend(handles=legend_handles, title=color_by)  # pyright: ignore
+        elif coloring in {Coloring.CONTINUOUS}:
+            cmap = "viridis" if cmap is None else cmap
+            values = list(map(float, features))
+            norm = mcolors.Normalize(vmin=min(values), vmax=max(values))
+            colormap = plt.get_cmap(cmap)
+            colors = {node: colormap(norm(float(node.get(color_by)))) for node in tree}
+        else:
+            raise ValueError(
+                f"Unknown coloring method: {coloring}. Choices are {list(Coloring)}."
+            )
+    else:
+        colors = {node: default_color for node in tree}
+
+    for node in tree:
+        x1, y1 = xs[node.name], ys[node]
+        if node.parent is None:
+            ax.hlines(y=y1, xmin=0, xmax=x1, color=colors[node])  # pyright: ignore
+            continue
+        x0, y0 = xs[node.parent.name], ys[node.parent]
+        ax.vlines(x=x0, ymin=y0, ymax=y1, color=colors[node])  # pyright: ignore
+        ax.hlines(y=y1, xmin=x0, xmax=x1, color=colors[node])  # pyright: ignore
+
+    ax.set_yticks([])  # pyright: ignore
+    return ax

phylogenie/tree.py

@@ -3,8 +3,8 @@ from typing import Any
 
 
 class Tree:
-    def __init__(self, id: str = "", branch_length: float | None = None):
-        self.id = id
+    def __init__(self, name: str = "", branch_length: float | None = None):
+        self.name = name
         self.branch_length = branch_length
         self._parent: Tree | None = None
         self._children: list[Tree] = []
@@ -20,7 +20,7 @@ class Tree:
 
     @property
     def features(self) -> dict[str, Any]:
-        return self._features
+        return self._features.copy()
 
     def add_child(self, child: "Tree") -> "Tree":
         child._parent = self
@@ -37,13 +37,15 @@ class Tree:
             node._children.append(self)
 
     def inorder_traversal(self) -> Iterator["Tree"]:
-        if self.children and len(self.children) != 2:
+        if self.is_leaf():
+            yield self
+            return
+        if len(self.children) != 2:
             raise ValueError("Inorder traversal is only defined for binary trees.")
-        if self.children:
-            yield from self.children[0].inorder_traversal()
+        left, right = self.children
+        yield from left.inorder_traversal()
         yield self
-        if self.children:
-            yield from self.children[1].inorder_traversal()
+        yield from right.inorder_traversal()
 
     def preorder_traversal(self) -> Iterator["Tree"]:
         yield self
@@ -55,41 +57,42 @@ class Tree:
             yield from child.postorder_traversal()
         yield self
 
-    def get_node(self, id: str) -> "Tree":
+    def get_node(self, name: str) -> "Tree":
         for node in self:
-            if node.id == id:
+            if node.name == name:
                 return node
-        raise ValueError(f"Node with id {id} not found.")
+        raise ValueError(f"Node with name {name} not found.")
 
     def is_leaf(self) -> bool:
         return not self.children
 
-    def get_leaves(self) -> list["Tree"]:
-        return [node for node in self if not node.children]
+    def get_leaves(self) -> tuple["Tree", ...]:
+        return tuple(node for node in self if not node.children)
+
+    def parse_branch_length(self) -> float:
+        if self.branch_length is None:
+            raise ValueError(f"Branch length of node {self.name} is not set.")
+        return self.branch_length
 
     def get_time(self) -> float:
         parent_time = 0 if self.parent is None else self.parent.get_time()
-        if self.branch_length is None:
-            if self.parent is not None:
-                raise ValueError(
-                    f"Branch length of non-root node {self.id} is not set."
-                )
-            return 0.0
-        return self.branch_length + parent_time
+        return self.parse_branch_length() + parent_time
 
     def set(self, key: str, value: Any) -> None:
         self._features[key] = value
 
+    def update_features(self, features: dict[str, Any]) -> None:
+        self._features.update(features)
+
     def get(self, key: str) -> Any:
-        return self._features.get(key)
+        return self._features[key]
 
     def delete(self, key: str) -> None:
         del self._features[key]
 
     def copy(self):
-        new_tree = Tree(self.id, self.branch_length)
-        for key, value in self._features.items():
-            new_tree.set(key, value)
+        new_tree = Tree(self.name, self.branch_length)
+        new_tree.update_features(self._features)
         for child in self.children:
             new_tree.add_child(child.copy())
         return new_tree
@@ -98,4 +101,4 @@ class Tree:
         return self.preorder_traversal()
 
     def __repr__(self) -> str:
-        return f"TreeNode(id='{self.id}', branch_length={self.branch_length}, features={self.features})"
+        return f"TreeNode(name='{self.name}', branch_length={self.branch_length}, features={self.features})"

phylogenie/treesimulator/__init__.py

@@ -15,8 +15,11 @@ from phylogenie.treesimulator.events import (
     get_contact_tracing_events,
     get_epidemiological_events,
     get_FBD_events,
+    get_mutation_id,
 )
+from phylogenie.treesimulator.features import Feature, set_features
 from phylogenie.treesimulator.gillespie import generate_trees, simulate_tree
+from phylogenie.treesimulator.model import get_node_state
 
 __all__ = [
     "Birth",
@@ -37,4 +40,8 @@ __all__ = [
     "get_FBD_events",
     "generate_trees",
     "simulate_tree",
+    "get_mutation_id",
+    "get_node_state",
+    "Feature",
+    "set_features",
 ]

phylogenie/treesimulator/events/__init__.py

@@ -18,6 +18,7 @@ from phylogenie.treesimulator.events.core import (
 )
 from phylogenie.treesimulator.events.mutations import Mutation
 from phylogenie.treesimulator.events.mutations import TargetType as MutationTargetType
+from phylogenie.treesimulator.events.mutations import get_mutation_id
 
 __all__ = [
     "Birth",
@@ -36,4 +37,5 @@ __all__ = [
     "get_contact_tracing_events",
     "get_epidemiological_events",
     "get_FBD_events",
+    "get_mutation_id",
 ]

phylogenie/treesimulator/events/mutations.py

@@ -1,9 +1,11 @@
+import re
 from copy import deepcopy
 from enum import Enum
 from typing import Type
 
 from numpy.random import Generator
 
+from phylogenie.models import Distribution
 from phylogenie.skyline import SkylineParameterLike
 from phylogenie.treesimulator.events.contact_tracing import (
     BirthWithContactTracing,
@@ -17,7 +19,6 @@ from phylogenie.treesimulator.events.core import (
     Sampling,
 )
 from phylogenie.treesimulator.model import Model
-from phylogenie.utils import Distribution
 
 MUTATION_PREFIX = "MUT-"
 MUTATIONS_KEY = "MUTATIONS"
@@ -29,10 +30,17 @@ def _get_mutation(state: str) -> str | None:
 
 def _get_mutated_state(mutation_id: int, state: str) -> str:
     if state.startswith(MUTATION_PREFIX):
-        state = state.split(".")[1]
+        _, state = state.split(".")
     return f"{MUTATION_PREFIX}{mutation_id}.{state}"
 
 
+def get_mutation_id(node_name: str) -> int:
+    match = re.search(rf"{MUTATION_PREFIX}(\d+)\.", node_name)
+    if match:
+        return int(match.group(1))
+    return 0
+
+
 class TargetType(str, Enum):
     BIRTH = "birth"
     DEATH = "death"
@@ -93,7 +101,7 @@ class Mutation(Event):
             model.add_event(event)
 
     def __repr__(self) -> str:
-        return f"Mutation(state={self.state}, rate={self.rate}, rate_scalers={self.rate_scalers})"
+        return f"Mutation(state={self.state}, rate={self.rate})"
 
 
 TARGETS: dict[TargetType, tuple[Type[Event], ...]] = {

phylogenie/treesimulator/features.py

@@ -0,0 +1,39 @@
+from collections.abc import Iterable
+from enum import Enum
+
+from phylogenie.tree import Tree
+from phylogenie.treesimulator.events import get_mutation_id
+from phylogenie.treesimulator.model import get_node_state
+from phylogenie.utils import get_heights, get_n_tips, get_times
+
+
+def _get_states(tree: Tree) -> dict[str, str]:
+    return {node.name: get_node_state(node.name) for node in tree}
+
+
+def _get_mutations(tree: Tree) -> dict[str, int]:
+    return {node.name: get_mutation_id(node.name) for node in tree}
+
+
+class Feature(str, Enum):
+    STATE = "state"
+    MUTATION = "mutation"
+    N_TIPS = "n_tips"
+    TIME = "time"
+    HEIGHT = "height"
+
+
+FEATURES_EXTRACTORS = {
+    Feature.STATE: _get_states,
+    Feature.MUTATION: _get_mutations,
+    Feature.N_TIPS: get_n_tips,
+    Feature.TIME: get_times,
+    Feature.HEIGHT: get_heights,
+}
+
+
+def set_features(tree: Tree, features: Iterable[Feature]) -> None:
+    for feature in features:
+        feature_maps = FEATURES_EXTRACTORS[feature](tree)
+        for node in tree:
+            node.set(feature.value, feature_maps[node.name])

phylogenie/treesimulator/gillespie.py

@@ -1,6 +1,6 @@
 import os
 import time
-from collections.abc import Sequence
+from collections.abc import Iterable, Sequence
 
 import joblib
 import numpy as np
@@ -9,6 +9,7 @@ from tqdm import tqdm
 
 from phylogenie.io import dump_newick
 from phylogenie.tree import Tree
+from phylogenie.treesimulator.features import Feature, set_features
 from phylogenie.treesimulator.model import Event, Model
 
 
@@ -69,7 +70,7 @@ def simulate_tree(
             if (
                 not any(rates)
                 or max_tips is not None
-                and model.n_sampled > max_tips
+                and model.n_sampled >= max_tips
                 or target_n_tips is not None
                 and model.n_sampled >= target_n_tips
             ):
@@ -101,12 +102,13 @@ def simulate_tree(
 def generate_trees(
     output_dir: str,
     n_trees: int,
-    events: list[Event],
+    events: Sequence[Event],
     min_tips: int = 1,
-    max_tips: int = 2**32,
+    max_tips: int | None = None,
     max_time: float = np.inf,
     init_state: str | None = None,
     sampling_probability_at_present: float = 0.0,
+    node_features: Iterable[Feature] | None = None,
     seed: int | None = None,
     n_jobs: int = -1,
     timeout: float = np.inf,
@@ -114,7 +116,7 @@ def generate_trees(
     def _simulate_tree(seed: int) -> Tree:
         while True:
             try:
-                return simulate_tree(
+                tree = simulate_tree(
                     events=events,
                     min_tips=min_tips,
                     max_tips=max_tips,
@@ -124,6 +126,9 @@ def generate_trees(
                     seed=seed,
                     timeout=timeout,
                 )
+                if node_features is not None:
+                    set_features(tree, node_features)
+                return tree
             except TimeoutError:
                 print("Simulation timed out, retrying with a different seed...")
             seed += 1

phylogenie/treesimulator/model.py

@@ -11,6 +11,13 @@ from phylogenie.skyline import SkylineParameterLike, skyline_parameter
 from phylogenie.tree import Tree
 
 
+@dataclass
+class Individual:
+    id: int
+    node: Tree
+    state: str
+
+
 class Event(ABC):
     def __init__(self, state: str, rate: SkylineParameterLike):
         self.state = state
@@ -30,11 +37,17 @@ class Event(ABC):
     def apply(self, model: "Model", time: float, rng: Generator) -> None: ...
 
 
-@dataclass
-class Individual:
-    id: int
-    node: Tree
-    state: str
+def _get_node_name(node_id: int, state: str) -> str:
+    return f"{node_id}|{state}"
+
+
+def get_node_state(node_name: str) -> str:
+    try:
+        return node_name.split("|")[1]
+    except IndexError:
+        raise ValueError(
+            f"Invalid node name: {node_name} (expected format 'id|state')."
+        )
 
 
 class Model:
@@ -61,7 +74,8 @@ class Model:
 
     def _get_new_node(self, state: str) -> Tree:
         self._next_node_id += 1
-        return Tree(f"{self._next_node_id}|{state}")
+        node = Tree(_get_node_name(self._next_node_id, state))
+        return node
 
     def _get_new_individual(self, state: str) -> Individual:
         self._next_individual_id += 1
@@ -74,7 +88,7 @@ class Model:
 
     def _set_branch_length(self, node: Tree, time: float) -> None:
         if node.branch_length is not None:
-            raise ValueError(f"Branch length of node {node.id} is already set.")
+            raise ValueError(f"Branch length of node {node.name} is already set.")
         node.branch_length = (
             time if node.parent is None else time - node.parent.get_time()
         )
@@ -108,12 +122,12 @@ class Model:
     def sample(self, id: int, time: float, removal: bool) -> None:
         individual = self._population[id]
         if removal:
-            self._sampled.add(individual.node.id)
+            self._sampled.add(individual.node.name)
             self.remove(id, time)
         else:
             sample_node = self._get_new_node(individual.state)
             sample_node.branch_length = 0.0
-            self._sampled.add(sample_node.id)
+            self._sampled.add(sample_node.name)
             individual.node.add_child(sample_node)
             self._stem(individual, time)
 
@@ -123,7 +137,7 @@ class Model:
     def get_sampled_tree(self) -> Tree:
         tree = self._tree.copy()
         for node in list(tree.postorder_traversal()):
-            if node.id not in self._sampled and not node.children:
+            if node.name not in self._sampled and not node.children:
                 if node.parent is None:
                     raise ValueError("No samples in the tree.")
                 else:

phylogenie/utils.py

@@ -1,17 +1,28 @@
-from typing import Any
+from phylogenie.tree import Tree
 
-from pydantic import BaseModel, ConfigDict
 
+def get_n_tips(tree: Tree) -> dict[str, int]:
+    n_tips: dict[str, int] = {}
+    for node in tree.postorder_traversal():
+        n_tips[node.name] = (
+            1 if node.is_leaf() else sum(n_tips[child.name] for child in node.children)
+        )
+    return n_tips
 
-class StrictBaseModel(BaseModel):
-    model_config = ConfigDict(extra="forbid")
 
+def get_times(tree: Tree) -> dict[str, float]:
+    times: dict[str, float] = {}
+    for node in tree:
+        parent_time = 0 if node.parent is None else times[node.parent.name]
+        times[node.name] = node.parse_branch_length() + parent_time
+    return times
 
-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
+def get_heights(tree: Tree) -> dict[str, int]:
+    heights: dict[str, int] = {}
+    for node in tree.postorder_traversal():
+        if node.is_leaf():
+            heights[node.name] = 0
+        else:
+            heights[node.name] = 1 + max(heights[child.name] for child in node.children)
+    return heights

{phylogenie-2.1.7.dist-info → phylogenie-2.1.9.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: phylogenie
-Version: 2.1.7
+Version: 2.1.9
 Summary: Generate phylogenetic datasets with minimal setup effort
 Author: Gabriele Marino
 Author-email: gabmarino.8601@gmail.com
@@ -10,6 +10,7 @@ Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.11
 Classifier: Programming Language :: Python :: 3.12
 Requires-Dist: joblib (>=1.4.2,<2.0.0)
+Requires-Dist: matplotlib (>=3.10.6,<4.0.0)
 Requires-Dist: pandas (>=2.2.2,<3.0.0)
 Requires-Dist: pydantic (>=2.11.5,<3.0.0)
 Requires-Dist: pyyaml (>=6.0.2,<7.0.0)

phylogenie-2.1.9.dist-info/RECORD

@@ -0,0 +1,35 @@
+phylogenie/__init__.py,sha256=T2mRLsYtoLlWt8GlxrrUnfXJ9XVioq7hTvVq3uJpwQI,2215
+phylogenie/generators/__init__.py,sha256=zsOxy28-9j9alOQLIgrOAFfmM58NNHO_NEtW-KXQXAY,888
+phylogenie/generators/alisim.py,sha256=G7p6tfcDWncg4xl3NhEXxgikcZDUi_RdE33zWn_CvzY,2704
+phylogenie/generators/configs.py,sha256=WFoeKpgj9ZQIom7BKqwpgXbriiQGg3jFBMLoD8KButk,1073
+phylogenie/generators/dataset.py,sha256=pPwW9yxm9fkU0PPllFq8EsPlqau8tth-4OatbA_hEHo,2120
+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/main.py,sha256=vtvSpQxBNlYABoFQ25czl-l3fIr4QRo3svWVd-jcArw,1170
+phylogenie/models.py,sha256=pCg9ob0RpLUHwM49x4knKxL4FNPr3-EU_6zMXsvxtAg,370
+phylogenie/msa.py,sha256=JDGyZUsAq6-m-SQjoCDjAkAZIxfgyl_PDIhdYn5HOow,2064
+phylogenie/plot.py,sha256=9lXZokOi7sJ1HLDPQArzjODnQLL_nv16Fr7AtP-5eFE,2869
+phylogenie/py.typed,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+phylogenie/skyline/__init__.py,sha256=7pF4CUb4ZCLzNYJNhOjpuTOLTRhlK7L6ugfccNqjIGo,620
+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=63A--s8C8K685KzZ_3hslkKM-lpqSM39-VFIuwBlIjk,3257
+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
+phylogenie/treesimulator/events/core.py,sha256=RF7oHzAjkU675PnczaVc66d9gNrHBL-IhmVHtcy7MKE,7949
+phylogenie/treesimulator/events/mutations.py,sha256=erEvgfiv_X3G_DwK9Hqu-fAR8otupfwq66cp5tRZamM,3591
+phylogenie/treesimulator/features.py,sha256=f1t7DE_dw8MhD-FAzQr0j8pxHdvLENy5AQeAjJyOjOQ,1082
+phylogenie/treesimulator/gillespie.py,sha256=LZHB2Ko147E78LoUCtN_BN7NYO1xhMYRy5PUZbN93c0,5283
+phylogenie/treesimulator/model.py,sha256=Ct0lfn6maKtjuFxivWx1MbFHvH3Y-fiJ0XXMdkN3Cak,5775
+phylogenie/typeguards.py,sha256=JtqmbEWJZBRHbWgCvcl6nrWm3VcBfzRbklbTBYHItn0,1325
+phylogenie/typings.py,sha256=GknvAFXyiaWeeYJ8Lk5d6E2VHT-xW6ONEojYbtJYiB8,476
+phylogenie/utils.py,sha256=JDe6_8-9AFYf7SuTrqUXTZ7n3CA-goQGg9vTi5UcHB8,878
+phylogenie-2.1.9.dist-info/LICENSE.txt,sha256=NUrDqElK-eD3I0WqC004CJsy6cs0JgsAoebDv_42-pw,1071
+phylogenie-2.1.9.dist-info/METADATA,sha256=V-aDacuPL0dfohsDmU69cvzHakcf6RfdDvrgK3zSCgc,5476
+phylogenie-2.1.9.dist-info/WHEEL,sha256=sP946D7jFCHeNz5Iq4fL4Lu-PrWrFsgfLXbbkciIZwg,88
+phylogenie-2.1.9.dist-info/entry_points.txt,sha256=Rt6_usN0FkBX1ZfiqCirjMN9FKOgFLG8rydcQ8kugeE,51
+phylogenie-2.1.9.dist-info/RECORD,,

phylogenie-2.1.7.dist-info/RECORD

@@ -1,32 +0,0 @@
-phylogenie/__init__.py,sha256=T2mRLsYtoLlWt8GlxrrUnfXJ9XVioq7hTvVq3uJpwQI,2215
-phylogenie/generators/__init__.py,sha256=zsOxy28-9j9alOQLIgrOAFfmM58NNHO_NEtW-KXQXAY,888
-phylogenie/generators/alisim.py,sha256=6IQEn8zNoVSLdHLRT1HBnrv1wfZzYaT-38SQNXE_MU4,2702
-phylogenie/generators/configs.py,sha256=AiiFS6rpH9BPwDKCkT4SVrRzfLFFrwRCJM4CRj0Srdk,1072
-phylogenie/generators/dataset.py,sha256=loVKC_1G7gzkPDN9W3GF-Rj9od8AeOJgIC0aJJa-4KA,2110
-phylogenie/generators/factories.py,sha256=OKCNg9jwF2KahZCJKTdJVxhLTeLNBDMOqJs7XSVXTqY,7881
-phylogenie/generators/trees.py,sha256=KEDvyrfMjUPWwyp1xnhWpatNnjmDLPhSSQl6Msx19Ms,10508
-phylogenie/generators/typeguards.py,sha256=yj4VkhOaUXJ2OrY-6zhOeY9C4yKIQxjZtk2d-vIxttQ,828
-phylogenie/io.py,sha256=y7nQIvLgCvqELsXFKfm1GgKJO_saoQ-7zQpE3Kvajzc,3509
-phylogenie/main.py,sha256=vtvSpQxBNlYABoFQ25czl-l3fIr4QRo3svWVd-jcArw,1170
-phylogenie/msa.py,sha256=JDGyZUsAq6-m-SQjoCDjAkAZIxfgyl_PDIhdYn5HOow,2064
-phylogenie/py.typed,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-phylogenie/skyline/__init__.py,sha256=7pF4CUb4ZCLzNYJNhOjpuTOLTRhlK7L6ugfccNqjIGo,620
-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=JM4ZccuIh0wesSZ5igK3Wi57dX1peJmj8N0KZdGov9Y,3174
-phylogenie/treesimulator/__init__.py,sha256=XG_xwETKWgDmCihqNUFCcMHtFg4WvZu5qbqWn9Dndt8,879
-phylogenie/treesimulator/events/__init__.py,sha256=UGfvXOVJ_ZAkk_8sBPihjmxciiaEnXZEPFIY53sttWI,940
-phylogenie/treesimulator/events/contact_tracing.py,sha256=_nJ85yhgGkeruQgMHvGpDYoyhheBf8M4LgZWiWdi5dY,4801
-phylogenie/treesimulator/events/core.py,sha256=RF7oHzAjkU675PnczaVc66d9gNrHBL-IhmVHtcy7MKE,7949
-phylogenie/treesimulator/events/mutations.py,sha256=xkXUIppbLIWZqKwVf-hi7d-_pS42TG2EPVfJA_grxBg,3443
-phylogenie/treesimulator/gillespie.py,sha256=EfEbuMBQSk9izamBPaQ9rNKA4NvtrI3XVm891G2iMeM,5014
-phylogenie/treesimulator/model.py,sha256=0Im6cFTlpMlJrSP4pTTKtvLT9qrQWV8MSTesAsBxT8g,5422
-phylogenie/typeguards.py,sha256=JtqmbEWJZBRHbWgCvcl6nrWm3VcBfzRbklbTBYHItn0,1325
-phylogenie/typings.py,sha256=GknvAFXyiaWeeYJ8Lk5d6E2VHT-xW6ONEojYbtJYiB8,476
-phylogenie/utils.py,sha256=pCg9ob0RpLUHwM49x4knKxL4FNPr3-EU_6zMXsvxtAg,370
-phylogenie-2.1.7.dist-info/LICENSE.txt,sha256=NUrDqElK-eD3I0WqC004CJsy6cs0JgsAoebDv_42-pw,1071
-phylogenie-2.1.7.dist-info/METADATA,sha256=CZ_2VR75BnBKObxMlc0LZR1sIApDeZMw3IRCuUPT2zM,5432
-phylogenie-2.1.7.dist-info/WHEEL,sha256=sP946D7jFCHeNz5Iq4fL4Lu-PrWrFsgfLXbbkciIZwg,88
-phylogenie-2.1.7.dist-info/entry_points.txt,sha256=Rt6_usN0FkBX1ZfiqCirjMN9FKOgFLG8rydcQ8kugeE,51
-phylogenie-2.1.7.dist-info/RECORD,,