phylogenie 2.0.8__py3-none-any.whl → 2.0.10__py3-none-any.whl

phylogenie/generators/configs.py

@@ -1,6 +1,9 @@
 from pydantic import BaseModel, ConfigDict
 
 import phylogenie.typings as pgt
+from phylogenie.skyline import SkylineMatrix as _SkylineMatrix
+from phylogenie.skyline import SkylineParameter as _SkylineParameter
+from phylogenie.skyline import SkylineVector as _SkylineVector
 
 
 class Distribution(BaseModel):
@@ -34,6 +37,10 @@ class SkylineMatrixModel(StrictBaseModel):
     change_times: ManyScalars
 
 
-SkylineParameter = Scalar | SkylineParameterModel
-SkylineVector = str | pgt.Scalar | list[SkylineParameter] | SkylineVectorModel
-SkylineMatrix = str | pgt.Scalar | list[SkylineVector] | SkylineMatrixModel | None
+SkylineParameter = Scalar | SkylineParameterModel | _SkylineParameter
+SkylineVector = (
+    str | pgt.Scalar | list[SkylineParameter] | SkylineVectorModel | _SkylineVector
+)
+SkylineMatrix = (
+    str | pgt.Scalar | list[SkylineVector] | SkylineMatrixModel | None | _SkylineMatrix
+)

phylogenie/generators/dataset.py

@@ -41,19 +41,21 @@ class DatasetGenerator(ABC, cfg.StrictBaseModel):
         self._generate_one(filename=filename, rng=default_rng(seed), data=data)
 
     def _generate(self, rng: Generator, n_samples: int, output_dir: str) -> None:
-        data_dir = os.path.join(output_dir, DATA_DIRNAME)
-        if os.path.exists(data_dir):
-            print(f"Output directory {data_dir} already exists. Skipping.")
-            return
-        os.makedirs(data_dir)
-
         data: list[dict[str, Any]] = [{} for _ in range(n_samples)]
         if self.context is not None:
+            data_dir = os.path.join(output_dir, DATA_DIRNAME)
             for d, (k, v) in product(data, self.context.items()):
                 args = v.model_extra if v.model_extra is not None else {}
                 d[k] = np.array(getattr(rng, v.type)(**args)).tolist()
             df = pd.DataFrame([{"file_id": str(i), **d} for i, d in enumerate(data)])
             df.to_csv(os.path.join(output_dir, METADATA_FILENAME), index=False)
+        else:
+            data_dir = output_dir
+
+        if os.path.exists(data_dir):
+            print(f"Output directory {data_dir} already exists. Skipping.")
+            return
+        os.makedirs(data_dir)
 
         joblib.Parallel(n_jobs=self.n_jobs)(
             joblib.delayed(self.generate_one)(

phylogenie/generators/factories.py

@@ -80,6 +80,8 @@ def one_or_many_scalars(
 def skyline_parameter(
     x: cfg.SkylineParameter, data: dict[str, Any]
 ) -> SkylineParameterLike:
+    if isinstance(x, SkylineParameter):
+        return x
     if isinstance(x, cfg.Scalar):
         return scalar(x, data)
     return SkylineParameter(
@@ -91,6 +93,8 @@ def skyline_parameter(
 def skyline_vector(
     x: cfg.SkylineVector, data: dict[str, Any]
 ) -> SkylineVectorCoercible:
+    if isinstance(x, SkylineVector):
+        return x
     if isinstance(x, str):
         e = _eval_expression(x, data)
         if tg.is_one_or_many_scalars(e):
@@ -151,7 +155,8 @@ def skyline_matrix(
 ) -> SkylineMatrixCoercible | None:
     if x is None:
         return None
-
+    if isinstance(x, SkylineMatrix):
+        return x
     if isinstance(x, str):
         e = _eval_expression(x, data)
         if tg.is_one_or_many_2D_scalars(e):

phylogenie/treesimulator/gillespie.py

@@ -6,7 +6,7 @@ from numpy.random import default_rng
 from phylogenie.skyline import SkylineParameterLike
 from phylogenie.tree import Tree
 from phylogenie.treesimulator.events import Event, get_contact_tracing_events
-from phylogenie.treesimulator.model import Model, is_CT_state
+from phylogenie.treesimulator.model import Model
 
 
 def simulate_tree(
@@ -29,6 +29,8 @@ def simulate_tree(
     if max_tips is None and max_time == np.inf:
         raise ValueError("Either max_tips or max_time must be specified.")
 
+    root_states = list({e.state for e in events})
+
     if notification_probability:
         events = get_contact_tracing_events(
             events,
@@ -38,7 +40,6 @@ def simulate_tree(
         )
 
     n_tries = 0
-    root_states = [e.state for e in events if not is_CT_state(e.state)]
     while max_tries is None or n_tries < max_tries:
         root_state = init_state if init_state is not None else rng.choice(root_states)
         model = Model(root_state, max_notified_contacts, notification_probability, rng)

{phylogenie-2.0.8.dist-info → phylogenie-2.0.10.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: phylogenie
-Version: 2.0.8
+Version: 2.0.10
 Summary: Generate phylogenetic datasets with minimal setup effort
 Author: Gabriele Marino
 Author-email: gabmarino.8601@gmail.com

{phylogenie-2.0.8.dist-info → phylogenie-2.0.10.dist-info}/RECORD

@@ -1,9 +1,9 @@
 phylogenie/__init__.py,sha256=1w_0H9lg7hI3b-NLjKuzc34GbJJGyjLq9LrlogecTzI,1759
 phylogenie/generators/__init__.py,sha256=zsOxy28-9j9alOQLIgrOAFfmM58NNHO_NEtW-KXQXAY,888
 phylogenie/generators/alisim.py,sha256=dDqlSwLDbRE2u5SZlsq1mArobTBtuk0aeXY3m1N-bWA,2374
-phylogenie/generators/configs.py,sha256=5ZWdKhRUjlNifw7QKXbooKV1fElqfCk_jBGxfcjh8do,969
-phylogenie/generators/dataset.py,sha256=k6RYJpgxOL8a_yMq98WUF-dcJv8TwxaWnde0k13M4J0,2525
-phylogenie/generators/factories.py,sha256=O8wqL-PvZps0Dq6mQa_PTi4vBvky5LkQIy1jjfOUm-4,6944
+phylogenie/generators/configs.py,sha256=DAwJbAJ-1ZUTEvhPE5zs58KsIOA88gcRtrqVx0zONi4,1234
+phylogenie/generators/dataset.py,sha256=OB51YI9ilo-lrw8ETCDQAFh9iXWtPLBRyLg4JOjMi7c,2577
+phylogenie/generators/factories.py,sha256=lXGlN8DXFZmFNN5WwTpE8J80jWj01Zx6MkAYHrAvlTs,7108
 phylogenie/generators/trees.py,sha256=jukaVXGcPGzDBEYMGJ1MKqWt4XbAB5EEfuHXDpwKTqM,9173
 phylogenie/generators/typeguards.py,sha256=Qph6ZnQ7wDMUNvB0VWQKlq42f8wkKOnM42cfMqhNov4,862
 phylogenie/io.py,sha256=ZXlofnSh7FX5UJiP0svRHrTraMSNgKa1GiAv0bMz7jU,2854
@@ -17,12 +17,12 @@ phylogenie/skyline/vector.py,sha256=bJP7_FNX_Klt6wXqsyfj0KX3VNj6-dIhzCKSJuQcOV0,
 phylogenie/tree.py,sha256=dk8Sj1tqyGOunVO2crtIqb0LH-ws-PXqA8SuNcYfVHI,1738
 phylogenie/treesimulator/__init__.py,sha256=INPU9LrPdUmt3dYGzWDRoRKrPR9xENcHu44pJVUbyNA,525
 phylogenie/treesimulator/events.py,sha256=X3_0U9qqMpYgh6-7TwQEnlUipANkHz6QTCXlm-qXFQk,9524
-phylogenie/treesimulator/gillespie.py,sha256=Fn-PyVICx3pWtpHko7rf6omf_kqOkkpebSJy56oPKnQ,3216
+phylogenie/treesimulator/gillespie.py,sha256=4uMt_-Rr3cRXWGKC8veBIB-uqtKtN-dLbAHKjAi_5Mo,3182
 phylogenie/treesimulator/model.py,sha256=XpzAicmg2O6K0Trk5YolH-B_HJZxoSauF2wZOMqp-Iw,5559
 phylogenie/typeguards.py,sha256=JtqmbEWJZBRHbWgCvcl6nrWm3VcBfzRbklbTBYHItn0,1325
 phylogenie/typings.py,sha256=O1X6lGKTjJ2YJz3ApQ-rYb_tEJNUIcHdUIeYlSM4s5o,500
-phylogenie-2.0.8.dist-info/LICENSE.txt,sha256=NUrDqElK-eD3I0WqC004CJsy6cs0JgsAoebDv_42-pw,1071
-phylogenie-2.0.8.dist-info/METADATA,sha256=VQdW_kK48caMP7UJDFDXi1RoY0vfOXnTSXrB-TXUmPU,5472
-phylogenie-2.0.8.dist-info/WHEEL,sha256=sP946D7jFCHeNz5Iq4fL4Lu-PrWrFsgfLXbbkciIZwg,88
-phylogenie-2.0.8.dist-info/entry_points.txt,sha256=Rt6_usN0FkBX1ZfiqCirjMN9FKOgFLG8rydcQ8kugeE,51
-phylogenie-2.0.8.dist-info/RECORD,,
+phylogenie-2.0.10.dist-info/LICENSE.txt,sha256=NUrDqElK-eD3I0WqC004CJsy6cs0JgsAoebDv_42-pw,1071
+phylogenie-2.0.10.dist-info/METADATA,sha256=YQSy1_-Vkuan10JzF5IkKTxs4fWRbUzhMUDYfk143k8,5473
+phylogenie-2.0.10.dist-info/WHEEL,sha256=sP946D7jFCHeNz5Iq4fL4Lu-PrWrFsgfLXbbkciIZwg,88
+phylogenie-2.0.10.dist-info/entry_points.txt,sha256=Rt6_usN0FkBX1ZfiqCirjMN9FKOgFLG8rydcQ8kugeE,51
+phylogenie-2.0.10.dist-info/RECORD,,