phylogenie 2.1.5__py3-none-any.whl → 2.1.7__py3-none-any.whl

phylogenie/generators/trees.py

@@ -46,7 +46,7 @@ class ParameterizationType(str, Enum):
 class TreeDatasetGenerator(DatasetGenerator):
     data_type: Literal[DataType.TREES] = DataType.TREES
     min_tips: cfg.Integer = 1
-    max_tips: cfg.Integer = 2**32
+    max_tips: cfg.Integer | None = None
     max_time: cfg.Scalar = np.inf
     init_state: str | None = None
     sampling_probability_at_present: cfg.Scalar = 0.0
@@ -64,7 +64,7 @@ class TreeDatasetGenerator(DatasetGenerator):
         return simulate_tree(
             events=self._get_events(data),
             min_tips=integer(self.min_tips, data),
-            max_tips=integer(self.max_tips, data),
+            max_tips=None if self.max_tips is None else integer(self.max_tips, data),
             max_time=scalar(self.max_time, data),
             init_state=init_state,
             sampling_probability_at_present=scalar(
@@ -98,8 +98,8 @@ class CanonicalTreeDatasetGenerator(TreeDatasetGenerator):
         ParameterizationType.CANONICAL
     )
     states: list[str]
-    sampling_rates: cfg.SkylineVector
-    remove_after_sampling: bool
+    sampling_rates: cfg.SkylineVector = 0
+    remove_after_sampling: bool = False
     birth_rates: cfg.SkylineVector = 0
     death_rates: cfg.SkylineVector = 0
     migration_rates: cfg.SkylineMatrix = None
@@ -122,7 +122,7 @@ class CanonicalTreeDatasetGenerator(TreeDatasetGenerator):
 class FBDTreeDatasetGenerator(TreeDatasetGenerator):
     parameterization: Literal[ParameterizationType.FBD] = ParameterizationType.FBD
     states: list[str]
-    sampling_proportions: cfg.SkylineVector
+    sampling_proportions: cfg.SkylineVector = 0
     diversification: cfg.SkylineVector = 0
     turnover: cfg.SkylineVector = 0
     migration_rates: cfg.SkylineMatrix = None
@@ -218,7 +218,7 @@ class BDTreeDatasetGenerator(TreeDatasetGeneratorForEpidemiology):
     parameterization: Literal[ParameterizationType.BD] = ParameterizationType.BD
     reproduction_number: cfg.SkylineParameter
     infectious_period: cfg.SkylineParameter
-    sampling_proportion: cfg.SkylineParameter = 1
+    sampling_proportion: cfg.SkylineParameter
 
     def _get_base_events(self, data: dict[str, Any]) -> list[Event]:
         return get_BD_events(
@@ -233,7 +233,7 @@ class BDEITreeDatasetGenerator(TreeDatasetGeneratorForEpidemiology):
     reproduction_number: cfg.SkylineParameter
     infectious_period: cfg.SkylineParameter
     incubation_period: cfg.SkylineParameter
-    sampling_proportion: cfg.SkylineParameter = 1
+    sampling_proportion: cfg.SkylineParameter
 
     def _get_base_events(self, data: dict[str, Any]) -> list[Event]:
         return get_BDEI_events(
@@ -250,7 +250,7 @@ class BDSSTreeDatasetGenerator(TreeDatasetGeneratorForEpidemiology):
     infectious_period: cfg.SkylineParameter
     superspreading_ratio: cfg.SkylineParameter
     superspreaders_proportion: cfg.SkylineParameter
-    sampling_proportion: cfg.SkylineParameter = 1
+    sampling_proportion: cfg.SkylineParameter
 
     def _get_base_events(self, data: dict[str, Any]) -> list[Event]:
         return get_BDSS_events(

phylogenie/tree.py

@@ -36,6 +36,15 @@ class Tree:
         if node is not None:
             node._children.append(self)
 
+    def inorder_traversal(self) -> Iterator["Tree"]:
+        if self.children and len(self.children) != 2:
+            raise ValueError("Inorder traversal is only defined for binary trees.")
+        if self.children:
+            yield from self.children[0].inorder_traversal()
+        yield self
+        if self.children:
+            yield from self.children[1].inorder_traversal()
+
     def preorder_traversal(self) -> Iterator["Tree"]:
         yield self
         for child in self.children:

phylogenie/treesimulator/events/core.py

@@ -64,8 +64,8 @@ class Sampling(Event):
 
 def get_canonical_events(
     states: list[str],
-    sampling_rates: SkylineVectorCoercible,
-    remove_after_sampling: bool,
+    sampling_rates: SkylineVectorCoercible = 0,
+    remove_after_sampling: bool = False,
     birth_rates: SkylineVectorCoercible = 0,
     death_rates: SkylineVectorCoercible = 0,
     migration_rates: SkylineMatrixCoercible | None = None,
@@ -100,7 +100,7 @@ def get_canonical_events(
 
 def get_FBD_events(
     states: list[str],
-    sampling_proportions: SkylineVectorCoercible = 1,
+    sampling_proportions: SkylineVectorCoercible = 0,
     diversification: SkylineVectorCoercible = 0,
     turnover: SkylineVectorCoercible = 0,
     migration_rates: SkylineMatrixCoercible | None = None,
@@ -134,7 +134,7 @@ def get_FBD_events(
 
 def get_epidemiological_events(
     states: list[str],
-    sampling_proportions: SkylineVectorCoercible = 1,
+    sampling_proportions: SkylineVectorCoercible,
     reproduction_numbers: SkylineVectorCoercible = 0,
     become_uninfectious_rates: SkylineVectorCoercible = 0,
     migration_rates: SkylineMatrixCoercible | None = None,
@@ -172,7 +172,7 @@ def get_epidemiological_events(
 def get_BD_events(
     reproduction_number: SkylineParameterLike,
     infectious_period: SkylineParameterLike,
-    sampling_proportion: SkylineParameterLike = 1,
+    sampling_proportion: SkylineParameterLike,
 ) -> list[Event]:
     return get_epidemiological_events(
         states=[INFECTIOUS_STATE],
@@ -186,7 +186,7 @@ def get_BDEI_events(
     reproduction_number: SkylineParameterLike,
     infectious_period: SkylineParameterLike,
     incubation_period: SkylineParameterLike,
-    sampling_proportion: SkylineParameterLike = 1,
+    sampling_proportion: SkylineParameterLike,
 ) -> list[Event]:
     return get_epidemiological_events(
         states=[EXPOSED_STATE, INFECTIOUS_STATE],
@@ -202,7 +202,7 @@ def get_BDSS_events(
     infectious_period: SkylineParameterLike,
     superspreading_ratio: SkylineParameterLike,
     superspreaders_proportion: SkylineParameterLike,
-    sampling_proportion: SkylineParameterLike = 1,
+    sampling_proportion: SkylineParameterLike,
 ) -> list[Event]:
     f_SS = superspreaders_proportion
     r_SS = superspreading_ratio

phylogenie/treesimulator/gillespie.py

@@ -11,20 +11,18 @@ from phylogenie.io import dump_newick
 from phylogenie.tree import Tree
 from phylogenie.treesimulator.model import Event, Model
 
-MAX_TIPS = 2**32
-
 
 def simulate_tree(
     events: Sequence[Event],
     min_tips: int = 1,
-    max_tips: int = MAX_TIPS,
+    max_tips: int | None = None,
     max_time: float = np.inf,
     init_state: str | None = None,
     sampling_probability_at_present: float = 0.0,
     seed: int | None = None,
     timeout: float = np.inf,
 ) -> Tree:
-    if max_time == np.inf and max_tips == MAX_TIPS:
+    if max_time == np.inf and max_tips is None:
         raise ValueError("Either max_time or max_tips must be specified.")
 
     if max_time == np.inf and sampling_probability_at_present:
@@ -49,9 +47,11 @@ def simulate_tree(
         current_time = 0.0
         change_times = sorted(set(t for e in events for t in e.rate.change_times))
         next_change_time = change_times.pop(0) if change_times else np.inf
-        target_n_tips = (
-            rng.integers(min_tips, max_tips + 1) if max_time == np.inf else None
-        )
+        if max_time == np.inf:
+            assert max_tips is not None
+            target_n_tips = rng.integers(min_tips, max_tips + 1)
+        else:
+            target_n_tips = None
 
         while current_time < max_time:
             if time.perf_counter() - start_clock > timeout:
@@ -68,7 +68,8 @@ def simulate_tree(
 
             if (
                 not any(rates)
-                or model.n_sampled > max_tips
+                or max_tips is not None
+                and model.n_sampled > max_tips
                 or target_n_tips is not None
                 and model.n_sampled >= target_n_tips
             ):
@@ -91,7 +92,9 @@ def simulate_tree(
             if rng.random() < sampling_probability_at_present:
                 model.sample(individual, current_time, True)
 
-        if min_tips <= model.n_sampled <= max_tips:
+        if min_tips <= model.n_sampled and (
+            max_tips is None or model.n_sampled <= max_tips
+        ):
             return model.get_sampled_tree()
 
 
@@ -127,7 +130,7 @@ def generate_trees(
 
     if os.path.exists(output_dir):
         raise FileExistsError(f"Output directory {output_dir} already exists")
-    os.makedirs(output_dir, exist_ok=True)
+    os.makedirs(output_dir)
 
     rng = default_rng(seed)
     jobs = joblib.Parallel(n_jobs=n_jobs, return_as="generator_unordered")(

{phylogenie-2.1.5.dist-info → phylogenie-2.1.7.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: phylogenie
-Version: 2.1.5
+Version: 2.1.7
 Summary: Generate phylogenetic datasets with minimal setup effort
 Author: Gabriele Marino
 Author-email: gabmarino.8601@gmail.com
@@ -24,6 +24,8 @@ Description-Content-Type: text/markdown
 
 [![AliSim](https://img.shields.io/badge/Powered%20by-AliSim-orange?style=flat-square)](https://iqtree.github.io/doc/AliSim)
 [![PyPI version](https://img.shields.io/pypi/v/phylogenie)](https://pypi.org/project/phylogenie/)
+![Downloads](https://img.shields.io/pypi/dm/phylogenie)
+
 
 Phylogenie is a [Python](https://www.python.org/) package designed to easily simulate phylogenetic datasets—such as trees and multiple sequence alignments (MSAs)—with minimal setup effort. Simply specify the distributions from which your parameters should be sampled, and Phylogenie will handle the rest!
 

{phylogenie-2.1.5.dist-info → phylogenie-2.1.7.dist-info}/RECORD

@@ -4,7 +4,7 @@ phylogenie/generators/alisim.py,sha256=6IQEn8zNoVSLdHLRT1HBnrv1wfZzYaT-38SQNXE_M
 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=q03WPG82M4ucp-jyjoKEBy7TKMBzD3RkKn8hS0G0-i0,10463
+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
@@ -14,19 +14,19 @@ phylogenie/skyline/__init__.py,sha256=7pF4CUb4ZCLzNYJNhOjpuTOLTRhlK7L6ugfccNqjIG
 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=KTx3m_tJPdeBqA5i0SA3dwCIobxsFcJwZFunMfDmVBY,2791
+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=JokGmieAv2xEX7KsjBWZr05jHN1jB-XZbpxe9gwdbDA,7953
+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=xdfiiMAsdC4ybLwmT6njC6ZrbgCeEptpuNX23Gnf-Vc,4877
+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-2.1.5.dist-info/LICENSE.txt,sha256=NUrDqElK-eD3I0WqC004CJsy6cs0JgsAoebDv_42-pw,1071
-phylogenie-2.1.5.dist-info/METADATA,sha256=BIpsttapT2FwTo_rFg7AALZigoBVms5w9Q_pFTSGSus,5375
-phylogenie-2.1.5.dist-info/WHEEL,sha256=sP946D7jFCHeNz5Iq4fL4Lu-PrWrFsgfLXbbkciIZwg,88
-phylogenie-2.1.5.dist-info/entry_points.txt,sha256=Rt6_usN0FkBX1ZfiqCirjMN9FKOgFLG8rydcQ8kugeE,51
-phylogenie-2.1.5.dist-info/RECORD,,
+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,,