phylogenie 3.3.0__tar.gz → 3.3.1__tar.gz

{phylogenie-3.3.0/src/phylogenie.egg-info → phylogenie-3.3.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: phylogenie
-Version: 3.3.0
+Version: 3.3.1
 Summary: Generate phylogenetic datasets with minimal setup effort
 Requires-Python: >=3.10
 Description-Content-Type: text/markdown

{phylogenie-3.3.0 → phylogenie-3.3.1}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "phylogenie"
-version = "3.3.0"
+version = "3.3.1"
 description = "Generate phylogenetic datasets with minimal setup effort"
 readme = "README.md"
 requires-python = ">=3.10"

{phylogenie-3.3.0 → phylogenie-3.3.1}/src/phylogenie/__init__.py

@@ -41,8 +41,8 @@ from phylogenie.treesimulator import (
     Migration,
     Model,
     Sampling,
-    SamplingAtTime,
     TimedEvent,
+    TimedSampling,
     UnboundedPopulationEvent,
     UnboundedPopulationModel,
     UnboundedPopulationTimedEvent,
@@ -98,8 +98,8 @@ __all__ = [
     "Migration",
     "Model",
     "Sampling",
-    "SamplingAtTime",
     "TimedEvent",
+    "TimedSampling",
     "UnboundedPopulationEvent",
     "UnboundedPopulationModel",
     "UnboundedPopulationTimedEvent",

{phylogenie-3.3.0 → phylogenie-3.3.1}/src/phylogenie/generators/_configs.py

@@ -59,7 +59,7 @@ class TimedEventModel(StrictBaseModel):
     times: ManyScalars
 
 
-class SamplingAtTimeModel(TimedEventModel):
+class TimedSamplingModel(TimedEventModel):
     type: Literal[TimedEventType.SAMPLING]
     state: str
     proportion: Scalar
@@ -67,6 +67,6 @@ class SamplingAtTimeModel(TimedEventModel):
 
 
 UnboundedPopulationTimedEventConfig = Annotated[
-    SamplingAtTimeModel,
+    TimedSamplingModel,
     Field(discriminator="type"),
 ]

{phylogenie-3.3.0 → phylogenie-3.3.1}/src/phylogenie/generators/_factories.py

@@ -16,7 +16,7 @@ from phylogenie.skyline import (
     SkylineVector,
     SkylineVectorCoercible,
 )
-from phylogenie.treesimulator import SamplingAtTime, UnboundedPopulationTimedEvent
+from phylogenie.treesimulator import TimedSampling, UnboundedPopulationTimedEvent
 
 
 def eval_expression(
@@ -233,8 +233,8 @@ def data(context: dict[str, cfg.Distribution] | None, rng: Generator) -> dict[st
 def unbounded_population_timed_event(
     config: cfg.TimedEventModel, data: dict[str, Any]
 ) -> UnboundedPopulationTimedEvent:
-    if isinstance(config, cfg.SamplingAtTimeModel):
-        return SamplingAtTime(
+    if isinstance(config, cfg.TimedSamplingModel):
+        return TimedSampling(
             times=many_scalars(config.times, data),
             state=string(config.state, data),
             proportion=scalar(config.proportion, data),

{phylogenie-3.3.0 → phylogenie-3.3.1}/src/phylogenie/treesimulator/__init__.py

@@ -7,8 +7,8 @@ from phylogenie.treesimulator.events import (
     Event,
     Migration,
     Sampling,
-    SamplingAtTime,
     TimedEvent,
+    TimedSampling,
     UnboundedPopulationEvent,
     UnboundedPopulationTimedEvent,
     get_BD_events,
@@ -30,8 +30,8 @@ __all__ = [
     "Event",
     "Migration",
     "Sampling",
-    "SamplingAtTime",
     "TimedEvent",
+    "TimedSampling",
     "UnboundedPopulationEvent",
     "UnboundedPopulationTimedEvent",
     "get_BD_events",

{phylogenie-3.3.0 → phylogenie-3.3.1}/src/phylogenie/treesimulator/events/__init__.py

@@ -7,7 +7,7 @@ from phylogenie.treesimulator.events.unbounded_population import (
     Death,
     Migration,
     Sampling,
-    SamplingAtTime,
+    TimedSampling,
     UnboundedPopulationEvent,
     UnboundedPopulationTimedEvent,
     get_BD_events,
@@ -28,7 +28,7 @@ __all__ = [
     "Death",
     "Migration",
     "Sampling",
-    "SamplingAtTime",
+    "TimedSampling",
     "UnboundedPopulationEvent",
     "UnboundedPopulationTimedEvent",
     "get_BD_events",

{phylogenie-3.3.0 → phylogenie-3.3.1}/src/phylogenie/treesimulator/events/unbounded_population.py

@@ -68,7 +68,7 @@ class Sampling(UnboundedPopulationEvent):
         return f"Sampling(state={self.state}, rate={self.rate}, removal={self.removal})"
 
 
-class SamplingAtTime(UnboundedPopulationTimedEvent):
+class TimedSampling(UnboundedPopulationTimedEvent):
     def __init__(
         self, times: Sequence[float], state: str, proportion: float, removal: bool
     ):
@@ -83,7 +83,7 @@ class SamplingAtTime(UnboundedPopulationTimedEvent):
                 model.sample(individual, time, self.removal)
 
     def __repr__(self) -> str:
-        return f"SamplingAtTime(times={self.times}, state={self.state}, proportion={self.proportion}, removal={self.removal})"
+        return f"TimedSampling(times={self.times}, state={self.state}, proportion={self.proportion}, removal={self.removal})"
 
 
 def get_canonical_events(

{phylogenie-3.3.0 → phylogenie-3.3.1/src/phylogenie.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: phylogenie
-Version: 3.3.0
+Version: 3.3.1
 Summary: Generate phylogenetic datasets with minimal setup effort
 Requires-Python: >=3.10
 Description-Content-Type: text/markdown