phylogenie 2.1.25__py3-none-any.whl → 2.1.27__py3-none-any.whl

phylogenie/__init__.py

@@ -31,9 +31,9 @@ from phylogenie.treesimulator import (
     BirthWithContactTracing,
     Death,
     Event,
+    EventType,
     Migration,
     Mutation,
-    MutationTargetType,
     Sampling,
     SamplingWithContactTracing,
     generate_trees,
@@ -85,9 +85,9 @@ __all__ = [
     "BirthWithContactTracing",
     "Death",
     "Event",
+    "EventType",
     "Migration",
     "Mutation",
-    "MutationTargetType",
     "Sampling",
     "SamplingWithContactTracing",
     "get_BD_events",

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.treesimulator import EventType
 
 Integer = str | int
 Scalar = str | pgt.Scalar
@@ -29,6 +29,10 @@ SkylineVector = str | pgt.Scalar | pgt.Many[SkylineParameter] | SkylineVectorMod
 SkylineMatrix = str | pgt.Scalar | pgt.Many[SkylineVector] | SkylineMatrixModel | None
 
 
-class Mutation(StrictBaseModel):
-    rate: Scalar
-    rate_scalers: dict[MutationTargetType, Distribution]
+class Event(StrictBaseModel):
+    state: str | None = None
+    rate: SkylineParameter
+
+
+class Mutation(Event):
+    rate_scalers: dict[EventType, Distribution]

phylogenie/generators/factories.py

@@ -17,7 +17,7 @@ from phylogenie.skyline import (
     SkylineVector,
     SkylineVectorCoercible,
 )
-from phylogenie.treesimulator import Mutation
+from phylogenie.treesimulator import EventType, Mutation
 
 
 def _eval_expression(expression: str, data: dict[str, Any]) -> Any:
@@ -222,11 +222,23 @@ def distribution(x: Distribution, data: dict[str, Any]) -> Distribution:
     return Distribution(type=x.type, **args)
 
 
-def mutation(x: cfg.Mutation, data: dict[str, Any]) -> Mutation:
-    return Mutation(
-        scalar(x.rate, data),
-        {k: distribution(v, data) for k, v in x.rate_scalers.items()},
-    )
+def mutations(
+    x: list[cfg.Mutation],
+    data: dict[str, Any],
+    states: set[str],
+    rates_to_log: list[EventType] | None,
+) -> list[Mutation]:
+    mutations: list[Mutation] = []
+    for m in x:
+        rate = skyline_parameter(m.rate, data)
+        rate_scalers = {k: distribution(v, data) for k, v in m.rate_scalers.items()}
+        if m.state is None:
+            mutations.extend(
+                Mutation(s, rate, rate_scalers, rates_to_log) for s in states
+            )
+        else:
+            mutations.append(Mutation(m.state, rate, rate_scalers, rates_to_log))
+    return mutations
 
 
 def data(context: dict[str, Distribution] | None, rng: Generator) -> dict[str, Any]:

phylogenie/generators/trees.py

@@ -12,7 +12,7 @@ from phylogenie.generators.dataset import DatasetGenerator, DataType
 from phylogenie.generators.factories import (
     data,
     integer,
-    mutation,
+    mutations,
     scalar,
     skyline_matrix,
     skyline_parameter,
@@ -23,6 +23,7 @@ from phylogenie.models import Distribution
 from phylogenie.tree import Tree
 from phylogenie.treesimulator import (
     Event,
+    EventType,
     Feature,
     get_BD_events,
     get_BDEI_events,
@@ -47,7 +48,8 @@ class ParameterizationType(str, Enum):
 
 class TreeDatasetGenerator(DatasetGenerator):
     data_type: Literal[DataType.TREES] = DataType.TREES
-    mutations: list[cfg.Mutation] | None = None
+    mutations: list[cfg.Mutation] = Field(default_factory=lambda: [])
+    rates_to_log: list[EventType] | None = None
     min_tips: cfg.Integer = 1
     max_tips: cfg.Integer | None = None
     max_time: cfg.Scalar = np.inf
@@ -67,14 +69,11 @@ class TreeDatasetGenerator(DatasetGenerator):
             if self.init_state is None
             else self.init_state.format(**data)
         )
-        mutations = (
-            None
-            if self.mutations is None
-            else [mutation(m, data) for m in self.mutations]
-        )
+        events = self._get_events(data)
+        states = {e.state for e in events}
+        events += mutations(self.mutations, data, states, self.rates_to_log)
         return simulate_tree(
-            events=self._get_events(data),
-            mutations=mutations,
+            events=events,
             min_tips=integer(self.min_tips, data),
             max_tips=None if self.max_tips is None else integer(self.max_tips, data),
             max_time=scalar(self.max_time, data),

phylogenie/treesimulator/__init__.py

@@ -3,7 +3,9 @@ from phylogenie.treesimulator.events import (
     BirthWithContactTracing,
     Death,
     Event,
+    EventType,
     Migration,
+    Mutation,
     Sampling,
     SamplingWithContactTracing,
     get_BD_events,
@@ -13,22 +15,20 @@ 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
-from phylogenie.treesimulator.mutations import Mutation
-from phylogenie.treesimulator.mutations import TargetType as MutationTargetType
-from phylogenie.treesimulator.mutations import get_mutation_id
 
 __all__ = [
     "Birth",
     "BirthWithContactTracing",
     "Death",
     "Event",
+    "EventType",
     "Migration",
     "Mutation",
-    "MutationTargetType",
     "Sampling",
     "SamplingWithContactTracing",
     "get_BD_events",

phylogenie/treesimulator/events/__init__.py

@@ -1,4 +1,4 @@
-from phylogenie.treesimulator.events.base import Event
+from phylogenie.treesimulator.events.base import Event, EventType
 from phylogenie.treesimulator.events.contact_tracing import (
     BirthWithContactTracing,
     SamplingWithContactTracing,
@@ -16,12 +16,14 @@ from phylogenie.treesimulator.events.core import (
     get_epidemiological_events,
     get_FBD_events,
 )
+from phylogenie.treesimulator.events.mutations import Mutation, get_mutation_id
 
 __all__ = [
     "Birth",
     "BirthWithContactTracing",
     "Death",
     "Event",
+    "EventType",
     "Migration",
     "Sampling",
     "SamplingWithContactTracing",
@@ -32,4 +34,6 @@ __all__ = [
     "get_contact_tracing_events",
     "get_epidemiological_events",
     "get_FBD_events",
+    "Mutation",
+    "get_mutation_id",
 ]

phylogenie/treesimulator/events/base.py

@@ -1,4 +1,6 @@
 from abc import ABC, abstractmethod
+from enum import Enum
+from typing import Any
 
 import numpy as np
 from numpy.random import Generator
@@ -7,10 +9,22 @@ from phylogenie.skyline import SkylineParameterLike, skyline_parameter
 from phylogenie.treesimulator.model import Model
 
 
+class EventType(str, Enum):
+    BIRTH = "birth"
+    DEATH = "death"
+    MIGRATION = "migration"
+    SAMPLING = "sampling"
+    MUTATION = "mutation"
+
+
 class Event(ABC):
+    type: EventType
+
     def __init__(self, state: str, rate: SkylineParameterLike):
         self.state = state
         self.rate = skyline_parameter(rate)
+        if any(v < 0 for v in self.rate.value):
+            raise ValueError("Event rates must be non-negative.")
 
     def draw_individual(self, model: Model, rng: Generator) -> int:
         return rng.choice(model.get_population(self.state))
@@ -23,4 +37,6 @@ class Event(ABC):
         return rate * n_individuals
 
     @abstractmethod
-    def apply(self, model: Model, time: float, rng: Generator) -> None: ...
+    def apply(
+        self, model: Model, events: "list[Event]", time: float, rng: Generator
+    ) -> dict[str, Any] | None: ...

phylogenie/treesimulator/events/contact_tracing.py

@@ -1,11 +1,12 @@
 from collections import defaultdict
 from collections.abc import Sequence
+from copy import deepcopy
 
 import numpy as np
 from numpy.random import Generator
 
 from phylogenie.skyline import SkylineParameterLike, skyline_parameter
-from phylogenie.treesimulator.events.base import Event
+from phylogenie.treesimulator.events.base import Event, EventType
 from phylogenie.treesimulator.events.core import Birth, Death, Migration, Sampling
 from phylogenie.treesimulator.model import Model
 
@@ -13,20 +14,22 @@ CT_POSTFIX = "-CT"
 CONTACTS_KEY = "CONTACTS"
 
 
-def _get_CT_state(state: str) -> str:
+def get_CT_state(state: str) -> str:
     return f"{state}{CT_POSTFIX}"
 
 
-def _is_CT_state(state: str) -> bool:
+def is_CT_state(state: str) -> bool:
     return state.endswith(CT_POSTFIX)
 
 
 class BirthWithContactTracing(Event):
+    type = EventType.BIRTH
+
     def __init__(self, state: str, rate: SkylineParameterLike, child_state: str):
         super().__init__(state, rate)
         self.child_state = child_state
 
-    def apply(self, model: Model, time: float, rng: Generator) -> None:
+    def apply(self, model: Model, events: list[Event], time: float, rng: Generator):
         individual = self.draw_individual(model, rng)
         new_individual = model.birth_from(individual, self.child_state, time)
         if CONTACTS_KEY not in model.context:
@@ -39,6 +42,8 @@ class BirthWithContactTracing(Event):
 
 
 class SamplingWithContactTracing(Event):
+    type = EventType.SAMPLING
+
     def __init__(
         self,
         state: str,
@@ -50,7 +55,7 @@ class SamplingWithContactTracing(Event):
         self.max_notified_contacts = max_notified_contacts
         self.notification_probability = skyline_parameter(notification_probability)
 
-    def apply(self, model: Model, time: float, rng: Generator) -> None:
+    def apply(self, model: Model, events: list[Event], time: float, rng: Generator):
         individual = self.draw_individual(model, rng)
         model.sample(individual, time, True)
         population = model.get_population()
@@ -61,8 +66,8 @@ class SamplingWithContactTracing(Event):
             if contact in population:
                 state = model.get_state(contact)
                 p = self.notification_probability.get_value_at_time(time)
-                if not _is_CT_state(state) and rng.random() < p:
-                    model.migrate(contact, _get_CT_state(state), time)
+                if not is_CT_state(state) and rng.random() < p:
+                    model.migrate(contact, get_CT_state(state), time)
 
     def __repr__(self) -> str:
         return f"SamplingWithContactTracing(state={self.state}, rate={self.rate}, max_notified_contacts={self.max_notified_contacts}, notification_probability={self.notification_probability})"
@@ -80,17 +85,24 @@ def get_contact_tracing_events(
     sampling_rate_after_notification = skyline_parameter(
         sampling_rate_after_notification
     )
-    for event in events:
-        state, rate = event.state, event.rate
+    for event in [deepcopy(e) for e in events]:
         if isinstance(event, Migration):
             ct_events.append(event)
             ct_events.append(
-                Migration(_get_CT_state(state), rate, _get_CT_state(event.target_state))
+                Migration(
+                    get_CT_state(event.state),
+                    event.rate,
+                    get_CT_state(event.target_state),
+                )
             )
         elif isinstance(event, Birth):
-            ct_events.append(BirthWithContactTracing(state, rate, event.child_state))
             ct_events.append(
-                BirthWithContactTracing(_get_CT_state(state), rate, event.child_state)
+                BirthWithContactTracing(event.state, event.rate, event.child_state)
+            )
+            ct_events.append(
+                BirthWithContactTracing(
+                    get_CT_state(event.state), event.rate, event.child_state
+                )
             )
         elif isinstance(event, Sampling):
             if not event.removal:
@@ -99,7 +111,10 @@ def get_contact_tracing_events(
                 )
             ct_events.append(
                 SamplingWithContactTracing(
-                    state, rate, max_notified_contacts, notification_probability
+                    event.state,
+                    event.rate,
+                    max_notified_contacts,
+                    notification_probability,
                 )
             )
         elif isinstance(event, Death):
@@ -116,7 +131,7 @@ def get_contact_tracing_events(
     ):
         ct_events.append(
             SamplingWithContactTracing(
-                _get_CT_state(state),
+                get_CT_state(state),
                 sampling_rate_after_notification,
                 max_notified_contacts,
                 notification_probability,

phylogenie/treesimulator/events/core.py

@@ -7,7 +7,7 @@ from phylogenie.skyline import (
     skyline_matrix,
     skyline_vector,
 )
-from phylogenie.treesimulator.events.base import Event
+from phylogenie.treesimulator.events.base import Event, EventType
 from phylogenie.treesimulator.model import Model
 
 INFECTIOUS_STATE = "I"
@@ -16,11 +16,13 @@ SUPERSPREADER_STATE = "S"
 
 
 class Birth(Event):
+    type = EventType.BIRTH
+
     def __init__(self, state: str, rate: SkylineParameterLike, child_state: str):
         super().__init__(state, rate)
         self.child_state = child_state
 
-    def apply(self, model: Model, time: float, rng: Generator) -> None:
+    def apply(self, model: Model, events: list[Event], time: float, rng: Generator):
         individual = self.draw_individual(model, rng)
         model.birth_from(individual, self.child_state, time)
 
@@ -29,7 +31,9 @@ class Birth(Event):
 
 
 class Death(Event):
-    def apply(self, model: Model, time: float, rng: Generator) -> None:
+    type = EventType.DEATH
+
+    def apply(self, model: Model, events: list[Event], time: float, rng: Generator):
         individual = self.draw_individual(model, rng)
         model.remove(individual, time)
 
@@ -38,11 +42,13 @@ class Death(Event):
 
 
 class Migration(Event):
+    type = EventType.MIGRATION
+
     def __init__(self, state: str, rate: SkylineParameterLike, target_state: str):
         super().__init__(state, rate)
         self.target_state = target_state
 
-    def apply(self, model: Model, time: float, rng: Generator) -> None:
+    def apply(self, model: Model, events: list[Event], time: float, rng: Generator):
         individual = self.draw_individual(model, rng)
         model.migrate(individual, self.target_state, time)
 
@@ -51,11 +57,13 @@ class Migration(Event):
 
 
 class Sampling(Event):
+    type = EventType.SAMPLING
+
     def __init__(self, state: str, rate: SkylineParameterLike, removal: bool):
         super().__init__(state, rate)
         self.removal = removal
 
-    def apply(self, model: Model, time: float, rng: Generator) -> None:
+    def apply(self, model: Model, events: list[Event], time: float, rng: Generator):
         individual = self.draw_individual(model, rng)
         model.sample(individual, time, self.removal)
 

phylogenie/treesimulator/{mutations.py → events/mutations.py}

@@ -1,22 +1,17 @@
 import re
 from copy import deepcopy
-from enum import Enum
-from typing import Any, Type
+from typing import Any
 
 from numpy.random import Generator
 
 from phylogenie.models import Distribution
+from phylogenie.skyline import SkylineParameterLike
+from phylogenie.treesimulator.events.base import Event, EventType
 from phylogenie.treesimulator.events.contact_tracing import (
     BirthWithContactTracing,
     SamplingWithContactTracing,
 )
-from phylogenie.treesimulator.events.core import (
-    Birth,
-    Death,
-    Event,
-    Migration,
-    Sampling,
-)
+from phylogenie.treesimulator.events.core import Birth, Death, Migration, Sampling
 from phylogenie.treesimulator.model import Model
 
 MUTATION_PREFIX = "MUT-"
@@ -40,27 +35,19 @@ def get_mutation_id(node_name: str) -> int:
     return 0
 
 
-class TargetType(str, Enum):
-    BIRTH = "birth"
-    DEATH = "death"
-    MIGRATION = "migration"
-    SAMPLING = "sampling"
-
-
-EVENT_TARGET_TYPES: dict[Type[Event], TargetType] = {
-    Birth: TargetType.BIRTH,
-    BirthWithContactTracing: TargetType.BIRTH,
-    Death: TargetType.DEATH,
-    Migration: TargetType.MIGRATION,
-    Sampling: TargetType.SAMPLING,
-    SamplingWithContactTracing: TargetType.SAMPLING,
-}
+class Mutation(Event):
+    type = EventType.MUTATION
 
-
-class Mutation:
-    def __init__(self, rate: float, rate_scalers: dict[TargetType, Distribution]):
-        self.rate = rate
+    def __init__(
+        self,
+        state: str,
+        rate: SkylineParameterLike,
+        rate_scalers: dict[EventType, Distribution],
+        rates_to_log: list[EventType] | None = None,
+    ):
+        super().__init__(state, rate)
         self.rate_scalers = rate_scalers
+        self.rates_to_log = [] if rates_to_log is None else rates_to_log
 
     def apply(
         self, model: Model, events: list[Event], time: float, rng: Generator
@@ -70,11 +57,10 @@ class Mutation:
         model.context[NEXT_MUTATION_ID] += 1
         mutation_id = model.context[NEXT_MUTATION_ID]
 
-        individual = rng.choice(model.get_population())
-        state = model.get_state(individual)
-        model.migrate(individual, _get_mutated_state(mutation_id, state), time)
+        individual = self.draw_individual(model, rng)
+        model.migrate(individual, _get_mutated_state(mutation_id, self.state), time)
 
-        rate_scalers: dict[TargetType, float] = {
+        rate_scalers: dict[EventType, float] = {
             target_type: getattr(rng, rate_scaler.type)(**rate_scaler.args)
             for target_type, rate_scaler in self.rate_scalers.items()
         }
@@ -83,22 +69,30 @@ class Mutation:
         for event in [
             deepcopy(e)
             for e in events
-            if _get_mutation(state) == _get_mutation(e.state)
+            if _get_mutation(self.state) == _get_mutation(e.state)
         ]:
             event.state = _get_mutated_state(mutation_id, event.state)
+
             if isinstance(event, Birth | BirthWithContactTracing):
                 event.child_state = _get_mutated_state(mutation_id, event.child_state)
+                metadata_key = f"birth_rate_from_{event.state}_to_{event.child_state}"
             elif isinstance(event, Migration):
                 event.target_state = _get_mutated_state(mutation_id, event.target_state)
-            elif not isinstance(event, Death | Sampling | SamplingWithContactTracing):
+                metadata_key = (
+                    f"migration_rate_from_{event.state}_to_{event.target_state}"
+                )
+            elif isinstance(
+                event, Mutation | Death | Sampling | SamplingWithContactTracing
+            ):
+                metadata_key = f"{event.type}_rate_for_{event.state}"
+            else:
                 raise ValueError(
                     f"Mutation not implemented for event of type {type(event)}."
                 )
 
-            target_type = EVENT_TARGET_TYPES[type(event)]
-            if target_type in rate_scalers:
-                event.rate *= rate_scalers[target_type]
-                metadata[f"{MUTATION_PREFIX}{mutation_id}.{target_type}.rate.value"] = (
+            event.rate *= rate_scalers.get(event.type, 1)
+            if event.type in self.rates_to_log:
+                metadata[metadata_key] = (
                     event.rate.value[0]
                     if len(event.rate.value) == 1
                     else list(event.rate.value)
@@ -109,4 +103,4 @@ class Mutation:
         return metadata
 
     def __repr__(self) -> str:
-        return f"Mutation(rate={self.rate}, rate_scalers={self.rate_scalers})"
+        return f"Mutation(state={self.state}, rate={self.rate}, rate_scalers={self.rate_scalers})"

phylogenie/treesimulator/features.py

@@ -2,8 +2,8 @@ from collections.abc import Iterable
 from enum import Enum
 
 from phylogenie.tree import Tree
+from phylogenie.treesimulator.events.mutations import get_mutation_id
 from phylogenie.treesimulator.model import get_node_state
-from phylogenie.treesimulator.mutations import get_mutation_id
 from phylogenie.utils import (
     get_node_depth_levels,
     get_node_depths,

phylogenie/treesimulator/gillespie.py

@@ -14,12 +14,10 @@ from phylogenie.tree import Tree
 from phylogenie.treesimulator.events import Event
 from phylogenie.treesimulator.features import Feature, set_features
 from phylogenie.treesimulator.model import Model
-from phylogenie.treesimulator.mutations import Mutation
 
 
 def simulate_tree(
     events: Sequence[Event],
-    mutations: Sequence[Mutation] | None = None,
     min_tips: int = 1,
     max_tips: int | None = None,
     max_time: float = np.inf,
@@ -43,9 +41,6 @@ def simulate_tree(
     elif init_state not in states:
         raise ValueError(f"Init state {init_state} not found in event states: {states}")
 
-    if mutations is None:
-        mutations = []
-
     rng = default_rng(seed)
     start_clock = time.perf_counter()
     while True:
@@ -72,7 +67,7 @@ def simulate_tree(
             instantaneous_events = [e for e, r in zip(run_events, rates) if r == np.inf]
             if instantaneous_events:
                 event = instantaneous_events[rng.integers(len(instantaneous_events))]
-                event.apply(model, current_time, rng)
+                event.apply(model, run_events, current_time, rng)
                 continue
 
             if (
@@ -84,7 +79,6 @@ def simulate_tree(
             ):
                 break
 
-            rates.extend(m.rate for m in mutations)
             time_step = rng.exponential(1 / sum(rates))
             if current_time + time_step >= next_change_time:
                 current_time = next_change_time
@@ -95,13 +89,11 @@ def simulate_tree(
                 break
             current_time += time_step
 
-            targets = run_events + list(mutations)
-            target_idx = np.searchsorted(np.cumsum(rates) / sum(rates), rng.random())
-            target = targets[int(target_idx)]
-            if isinstance(target, Event):
-                target.apply(model, current_time, rng)
-            else:
-                metadata.update(target.apply(model, run_events, current_time, rng))
+            event_idx = np.searchsorted(np.cumsum(rates) / sum(rates), rng.random())
+            event = run_events[int(event_idx)]
+            event_metadata = event.apply(model, run_events, current_time, rng)
+            if event_metadata is not None:
+                metadata.update(event_metadata)
 
         for individual in model.get_population():
             if rng.random() < sampling_probability_at_present:

{phylogenie-2.1.25.dist-info → phylogenie-2.1.27.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: phylogenie
-Version: 2.1.25
+Version: 2.1.27
 Summary: Generate phylogenetic datasets with minimal setup effort
 Author: Gabriele Marino
 Author-email: gabmarino.8601@gmail.com

{phylogenie-2.1.25.dist-info → phylogenie-2.1.27.dist-info}/RECORD

@@ -1,11 +1,11 @@
-phylogenie/__init__.py,sha256=KV83hJ153WAwCIWEPWXtSsqdI_ncojxiXzt1X_lC7SU,2879
+phylogenie/__init__.py,sha256=FdNHTw1U1eYDz8w_EOvk9R0rdOXvCMAgbm7ilXs6Fog,2861
 phylogenie/draw.py,sha256=37eQDK8TKmL8bxSzXvi7jNvrR7ulj7MByR5MA1FtyyE,5317
 phylogenie/generators/__init__.py,sha256=zsOxy28-9j9alOQLIgrOAFfmM58NNHO_NEtW-KXQXAY,888
 phylogenie/generators/alisim.py,sha256=1YQLpOG_Bpn9YqExQqEu-wz1MDGCbpPmTdhrBb6TbWc,2820
-phylogenie/generators/configs.py,sha256=Xp8kk8sDy3EzKSgfdsVuMep1zEvdVX6U86yFgn6MS1I,999
+phylogenie/generators/configs.py,sha256=zjNnljBBC-d6DTjWjieE8-HnKeE58LAy3moBYiD6NFo,1042
 phylogenie/generators/dataset.py,sha256=kY92diePr2IjiLejHLixJoYRc-2LpM-GBt3wkX9SYvA,2109
-phylogenie/generators/factories.py,sha256=A-r33L5eYe2Shc-o7y6RHe8GoAcTTQw61249_lzC1BY,8123
-phylogenie/generators/trees.py,sha256=HrrSxpejURs2DXrV5PBm3OuD9RgSbSu_YBI_ukWbEcA,10119
+phylogenie/generators/factories.py,sha256=qSz-s7ltQwUf7R6TPZ-5xFyOnnSHkKn0u5IukeysXVU,8544
+phylogenie/generators/trees.py,sha256=zsmL3_YUUwtn-_NrGSvwZVSGIm9kpf8SPHxoQCIT_hE,10168
 phylogenie/generators/typeguards.py,sha256=yj4VkhOaUXJ2OrY-6zhOeY9C4yKIQxjZtk2d-vIxttQ,828
 phylogenie/io/__init__.py,sha256=gtRYtDdZSTlWCj3I4vmMJSAs93jdz5RySkCakD3sxlQ,214
 phylogenie/io/fasta.py,sha256=IWtNb_RQLR6kvS0G826wB9SodkCGfugddoUHx78Yrec,837
@@ -20,20 +20,20 @@ phylogenie/skyline/matrix.py,sha256=v4SitY7VbXprqlqQckjWTzW5hwRmCyIF595R6IJMxWw,
 phylogenie/skyline/parameter.py,sha256=TVqkqirGXNN-VP8hnIJACPkOxUan6LkGa5o_JcPfwbY,4834
 phylogenie/skyline/vector.py,sha256=60jtp7PieiEaEH0Tp6zNjNKjyzpN_nT5uwBUXbgeATk,7261
 phylogenie/tree.py,sha256=P1uM6s32TsODpvNJQIPMix9oj39vGSw_wsHYp2wmy5U,5246
-phylogenie/treesimulator/__init__.py,sha256=5UF2S3Evos0-7GJVSQxx6SICaKxcrmU7o1T8JS_cMKk,1246
-phylogenie/treesimulator/events/__init__.py,sha256=5ncG2JMh7RcSgG5BPR012UujxoTrczD0YCv-khSGSHM,792
-phylogenie/treesimulator/events/base.py,sha256=ruyje6lOgBVcsxzqLcEkvjX8TetvHk2xXqTCSz4apKM,875
-phylogenie/treesimulator/events/contact_tracing.py,sha256=bFu00rj5t1ToTuTwzFOqdttodyBAQ9VqUbZpAbvTMSg,4849
-phylogenie/treesimulator/events/core.py,sha256=rALA4LVXsWbtRn0R-SOoAD9w9zDLxmzwzGcQetTVtWU,7997
-phylogenie/treesimulator/features.py,sha256=wWD1aLs4qpFmw7GZpGolhfk7Ym6v9g-cIv2c717cLKU,1359
-phylogenie/treesimulator/gillespie.py,sha256=Xj-ntrhPVH6vMuAe7-Q7x1gA5Zr6xoYoeVLnZQKfcRU,6005
+phylogenie/treesimulator/__init__.py,sha256=0wU1PECAcM5rBg5MmeA3poWgfGDzqHySmSJjJs1wkPw,1088
+phylogenie/treesimulator/events/__init__.py,sha256=w2tJ0D2WB5AiCbr3CsKN6vdADueiAEMzd_ve0rpa4zg,939
+phylogenie/treesimulator/events/base.py,sha256=Rb9qO0EURKGbFPv_KuRrzZv5Krl1ZEMj8ASHXlBLhbI,1259
+phylogenie/treesimulator/events/contact_tracing.py,sha256=QqinLfQmBBi6qF3nFE_Qsiyd6RUG0RJqxiBOKK0nRGE,5196
+phylogenie/treesimulator/events/core.py,sha256=bhgQgi5L-oaHsoWJmUOsTTzWxi0POYxVLoF-KrC8AGQ,8179
+phylogenie/treesimulator/events/mutations.py,sha256=fGxxeXhiFrMAaS-s_vd42aVBZ6XQiRjpW9uJUATNk1E,3752
+phylogenie/treesimulator/features.py,sha256=nNfv0kPudAZnrnufIVuFCR_VEJSP-6fZ2L-VG5_-Fqo,1366
+phylogenie/treesimulator/gillespie.py,sha256=_O1TqK-LOjH6k8ZSos-CbVQ7wJZPzf1Awv_1DXt0NYE,5730
 phylogenie/treesimulator/model.py,sha256=lhDwmBFQ8Qh8qVGZPgED0vehtPC3DE7_CgCV_8rPB-A,4641
-phylogenie/treesimulator/mutations.py,sha256=Wv0qJqjGAMNTYftiCCaSXfZQA6pj8pSrmrOLyTI86ko,3635
 phylogenie/typeguards.py,sha256=JtqmbEWJZBRHbWgCvcl6nrWm3VcBfzRbklbTBYHItn0,1325
 phylogenie/typings.py,sha256=p694PBe_tk25A6N8vGGWxuqoDtt3nHFUsIYJrwR_76Y,494
 phylogenie/utils.py,sha256=ehVk_2kvjW8Q_EyM2kxBPHYiK-KlPmZQx7JeVN6Fh-E,5419
-phylogenie-2.1.25.dist-info/LICENSE.txt,sha256=NUrDqElK-eD3I0WqC004CJsy6cs0JgsAoebDv_42-pw,1071
-phylogenie-2.1.25.dist-info/METADATA,sha256=smzOlX4LSGx_MzMBneW1humdTaUL8FG-TekNtKS1AtE,5477
-phylogenie-2.1.25.dist-info/WHEEL,sha256=sP946D7jFCHeNz5Iq4fL4Lu-PrWrFsgfLXbbkciIZwg,88
-phylogenie-2.1.25.dist-info/entry_points.txt,sha256=Rt6_usN0FkBX1ZfiqCirjMN9FKOgFLG8rydcQ8kugeE,51
-phylogenie-2.1.25.dist-info/RECORD,,
+phylogenie-2.1.27.dist-info/LICENSE.txt,sha256=NUrDqElK-eD3I0WqC004CJsy6cs0JgsAoebDv_42-pw,1071
+phylogenie-2.1.27.dist-info/METADATA,sha256=UUZTU3YJ5yrAzQZ8EiiVsTmhuZzKNiGU_roQazkf3Mo,5477
+phylogenie-2.1.27.dist-info/WHEEL,sha256=sP946D7jFCHeNz5Iq4fL4Lu-PrWrFsgfLXbbkciIZwg,88
+phylogenie-2.1.27.dist-info/entry_points.txt,sha256=Rt6_usN0FkBX1ZfiqCirjMN9FKOgFLG8rydcQ8kugeE,51
+phylogenie-2.1.27.dist-info/RECORD,,