phylogenie 1.0.8__py3-none-any.whl → 2.0.0__py3-none-any.whl

phylogenie/core/trees/treesimulator.py

@@ -1,199 +0,0 @@
-from enum import Enum
-from typing import Annotated, Literal
-
-import numpy as np
-from numpy.random import Generator
-from pydantic import Field
-
-import phylogenie.core.configs as cfg
-import phylogenie.typings as pgt
-from phylogenie.backend.treesimulator import (
-    DEFAULT_POPULATION,
-    TreeParams,
-    generate_tree,
-    get_BD_params,
-    get_BDEI_params,
-    get_BDSS_params,
-)
-from phylogenie.core.factories import (
-    int_factory,
-    scalar_factory,
-    skyline_matrix_coercible_factory,
-    skyline_parameter_like_factory,
-    skyline_vector_coercible_factory,
-)
-from phylogenie.core.trees.base import BackendType, TreesGenerator
-
-
-class ParameterizationType(str, Enum):
-    MTBD = "MTBD"
-    BD = "BD"
-    BDEI = "BDEI"
-    BDSS = "BDSS"
-
-
-class TreeSimulatorGenerator(TreesGenerator):
-    backend: Literal[BackendType.TREESIMULATOR] = BackendType.TREESIMULATOR
-    min_tips: cfg.IntConfig
-    max_tips: cfg.IntConfig
-    T: cfg.ScalarConfig = np.inf
-    root_state: str | None = None
-    state_frequencies: list[float] | None = None
-    notification_probability: cfg.SkylineParameterLikeConfig = 0
-    notification_sampling_rate: cfg.SkylineParameterLikeConfig = np.inf
-    allow_irremovable_states: bool = False
-    max_notified_contacts: cfg.IntConfig = 1
-
-    def _generate_one_from_params(
-        self, filename: str, rng: Generator, data: pgt.Data, params: TreeParams
-    ) -> None:
-        root_state = (
-            self.root_state
-            if self.root_state is None
-            else self.root_state.format(**data)
-        )
-        generate_tree(
-            output_file=f"{filename}.nwk",
-            params=params,
-            min_tips=int_factory(self.min_tips, data),
-            max_tips=int_factory(self.max_tips, data),
-            T=scalar_factory(self.T, data),
-            state_frequencies=self.state_frequencies,
-            notification_probability=skyline_parameter_like_factory(
-                self.notification_probability, data
-            ),
-            notification_sampling_rate=skyline_parameter_like_factory(
-                self.notification_sampling_rate, data
-            ),
-            allow_irremovable_states=self.allow_irremovable_states,
-            max_notified_contacts=int_factory(self.max_notified_contacts, data),
-            root_state=root_state,
-            random_seed=int(rng.integers(0, 2**31 - 1)),
-        )
-
-
-class MTBDTreeSimulatorGenerator(TreeSimulatorGenerator):
-    parameterization: Literal[ParameterizationType.MTBD] = ParameterizationType.MTBD
-    populations: str | list[str] = DEFAULT_POPULATION
-    transmission_rates: cfg.SkylineMatrixCoercibleConfig
-    removal_rates: cfg.SkylineVectorCoercibleConfig
-    transition_rates: cfg.SkylineMatrixCoercibleConfig = 0
-    sampling_proportions: cfg.SkylineVectorCoercibleConfig = 1
-
-    def _generate_one(self, filename: str, rng: Generator, data: pgt.Data) -> None:
-        self._generate_one_from_params(
-            filename,
-            rng,
-            data,
-            TreeParams(
-                populations=self.populations,
-                transition_rates=skyline_matrix_coercible_factory(
-                    self.transition_rates, data
-                ),
-                transmission_rates=skyline_matrix_coercible_factory(
-                    self.transmission_rates, data
-                ),
-                removal_rates=skyline_vector_coercible_factory(
-                    self.removal_rates, data
-                ),
-                sampling_proportions=skyline_vector_coercible_factory(
-                    self.sampling_proportions, data
-                ),
-            ),
-        )
-
-
-class BDTreeSimulatorGenerator(TreeSimulatorGenerator):
-    parameterization: Literal[ParameterizationType.BD] = ParameterizationType.BD
-    reproduction_number: cfg.SkylineParameterLikeConfig
-    infectious_period: cfg.SkylineParameterLikeConfig
-    sampling_proportion: cfg.SkylineParameterLikeConfig = 1
-
-    def _generate_one(self, filename: str, rng: Generator, data: pgt.Data) -> None:
-        self._generate_one_from_params(
-            filename,
-            rng,
-            data,
-            get_BD_params(
-                reproduction_number=skyline_parameter_like_factory(
-                    self.reproduction_number, data
-                ),
-                infectious_period=skyline_parameter_like_factory(
-                    self.infectious_period, data
-                ),
-                sampling_proportion=skyline_parameter_like_factory(
-                    self.sampling_proportion, data
-                ),
-            ),
-        )
-
-
-class BDEITreeSimulatorGenerator(TreeSimulatorGenerator):
-    parameterization: Literal[ParameterizationType.BDEI] = ParameterizationType.BDEI
-    reproduction_number: cfg.SkylineParameterLikeConfig
-    infectious_period: cfg.SkylineParameterLikeConfig
-    incubation_period: cfg.SkylineParameterLikeConfig
-    sampling_proportion: cfg.SkylineParameterLikeConfig = 1
-
-    def _generate_one(self, filename: str, rng: Generator, data: pgt.Data) -> None:
-        self._generate_one_from_params(
-            filename,
-            rng,
-            data,
-            get_BDEI_params(
-                reproduction_number=skyline_parameter_like_factory(
-                    self.reproduction_number, data
-                ),
-                infectious_period=skyline_parameter_like_factory(
-                    self.infectious_period, data
-                ),
-                incubation_period=skyline_parameter_like_factory(
-                    self.incubation_period, data
-                ),
-                sampling_proportion=skyline_parameter_like_factory(
-                    self.sampling_proportion, data
-                ),
-            ),
-        )
-
-
-class BDSSTreeSimulatorGenerator(TreeSimulatorGenerator):
-    parameterization: Literal[ParameterizationType.BDSS] = ParameterizationType.BDSS
-    reproduction_number: cfg.SkylineParameterLikeConfig
-    infectious_period: cfg.SkylineParameterLikeConfig
-    superspreading_ratio: cfg.SkylineParameterLikeConfig
-    superspreaders_proportion: cfg.SkylineParameterLikeConfig
-    sampling_proportion: cfg.SkylineParameterLikeConfig = 1
-
-    def _generate_one(self, filename: str, rng: Generator, data: pgt.Data) -> None:
-        self._generate_one_from_params(
-            filename,
-            rng,
-            data,
-            get_BDSS_params(
-                reproduction_number=skyline_parameter_like_factory(
-                    self.reproduction_number, data
-                ),
-                infectious_period=skyline_parameter_like_factory(
-                    self.infectious_period, data
-                ),
-                superspreading_ratio=skyline_parameter_like_factory(
-                    self.superspreading_ratio, data
-                ),
-                superspreaders_proportion=skyline_parameter_like_factory(
-                    self.superspreaders_proportion, data
-                ),
-                sampling_proportion=skyline_parameter_like_factory(
-                    self.sampling_proportion, data
-                ),
-            ),
-        )
-
-
-TreeSimulatorGeneratorConfig = Annotated[
-    MTBDTreeSimulatorGenerator
-    | BDTreeSimulatorGenerator
-    | BDEITreeSimulatorGenerator
-    | BDSSTreeSimulatorGenerator,
-    Field(discriminator="parameterization"),
-]

phylogenie/core/typeguards.py

@@ -1,32 +0,0 @@
-from typing import TypeGuard
-
-import phylogenie.core.configs as cfg
-import phylogenie.typings as pgt
-
-
-def is_list(x: object) -> TypeGuard[list[object]]:
-    return isinstance(x, list)
-
-
-def is_list_of_scalar_configs(x: object) -> TypeGuard[list[cfg.ScalarConfig]]:
-    return is_list(x) and all(isinstance(v, cfg.ScalarConfig) for v in x)
-
-
-def is_list_of_skyline_parameter_like_configs(
-    x: object,
-) -> TypeGuard[list[cfg.SkylineParameterLikeConfig]]:
-    return is_list(x) and all(isinstance(v, cfg.SkylineParameterLikeConfig) for v in x)
-
-
-def is_skyline_vector_coercible_config(
-    x: object,
-) -> TypeGuard[cfg.SkylineVectorCoercibleConfig]:
-    return isinstance(
-        x, str | pgt.Scalar | cfg.SkylineVectorValueModel
-    ) or is_list_of_skyline_parameter_like_configs(x)
-
-
-def is_list_of_skyline_vector_coercible_configs(
-    x: object,
-) -> TypeGuard[list[cfg.SkylineVectorCoercibleConfig]]:
-    return is_list(x) and all(is_skyline_vector_coercible_config(v) for v in x)

phylogenie-1.0.8.dist-info/RECORD

@@ -1,39 +0,0 @@
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-phylogenie/backend/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-phylogenie/backend/remaster/__init__.py,sha256=g1oMKi6SX60Geq_e2AjBlf7-pDvLfrsT3gW6AORdbMo,509
-phylogenie/backend/remaster/generate.py,sha256=jDtcZyi6ifptRopeuGCHETzVz_NyK4UC3HiNPwQPzbg,6109
-phylogenie/backend/remaster/reactions.py,sha256=oc2ZY9WtTajbOWjARDmA0JnS255tbVeMt1DmyCUp95M,5904
-phylogenie/backend/treesimulator.py,sha256=pJmSX_0EOFngJTCxh36qTap1llYIZq4p9azQ9PIjlo4,5469
-phylogenie/configs.py,sha256=HtRUWZ-zNq1--zTBWL3QFXX27Ybw5x1qSWcmx7Sz8YA,125
-phylogenie/core/__init__.py,sha256=pvQMohKFAPaSvujw7H5sQJn7SOSqENQUHECuVfUBVNg,402
-phylogenie/core/configs.py,sha256=9tUYWrmdDn_Gg6xnywCDcGDEk0gne0vYqFH9dXixJbM,1042
-phylogenie/core/context/__init__.py,sha256=ZiCweJgf1REKbhZTfHuzz1lIgVmio9bTYW3-srOUqUo,168
-phylogenie/core/context/configs.py,sha256=TEJZykoNLy-77nVWqjrZuoFhJLRggJuFA_GLMPDrUVM,570
-phylogenie/core/context/distributions.py,sha256=zQrUXDqQH_Goz0jGFb1tUMUU0YPOG4rMIilR8DDmQp4,3037
-phylogenie/core/context/factories.py,sha256=I6J3e_ZWdETehiSXH9pCVPBuun6vHpuyC48zjayKMX8,1752
-phylogenie/core/dataset.py,sha256=mgPAexXTat6x7YB9-BI6d5HWwrAvt8xydmiWVzwVD3M,2431
-phylogenie/core/factories.py,sha256=DwuocGd48Ham7wD7uyGnGA0tHvXhzuP1Ji0PW5-onwM,7397
-phylogenie/core/msas/__init__.py,sha256=-2XjTmiTA6zAwiLs2ksKecCrSbNLheo7KKjDyvuLipg,207
-phylogenie/core/msas/alisim.py,sha256=TG4LAHJaH3rGWa3cwXzX6MgaXuh2tLzhdoALyOkoiXY,1047
-phylogenie/core/msas/base.py,sha256=Mw7bI4PU7J4b5mrsd0kMkJVJk7bqmJQZFtZ91I8oRS0,1597
-phylogenie/core/trees/__init__.py,sha256=epKgJ-EI04kBEuS4kfBcnsAj7dMObT1T742peBAnB78,335
-phylogenie/core/trees/base.py,sha256=sNBCJRtWGYaMog4WoyAkrK4F2SXrgjXrxjuVQ6Ae5Js,305
-phylogenie/core/trees/remaster/__init__.py,sha256=FfgXYjkeosb22Anbp78re2NssWtNcNNaj7hFQZx8JLE,116
-phylogenie/core/trees/remaster/configs.py,sha256=d4EqowYMb5I2TfBTgNf9H_X1t8aNCYJbh1RQmFoDxs4,362
-phylogenie/core/trees/remaster/factories.py,sha256=qla4pg4OgfE5lwQZuP3bEaMt7xIF4P6fQ1Z0IPpFxUs,812
-phylogenie/core/trees/remaster/generator.py,sha256=UJO9ymxHE3lS62RgyJ-cS2Tc_RbHgxeGggx_Ses6k4Q,7259
-phylogenie/core/trees/treesimulator.py,sha256=RpyRvXAHLHEOU9Ub9Yg61au7xP_rnbC7N0va43gbbx8,7319
-phylogenie/core/typeguards.py,sha256=wEBYJZZ_Q_bY7ZJSh00AXJeyc1X8ZoysoOiLwo24N1w,990
-phylogenie/main.py,sha256=n_joau3dWJIq0ZMHe4a_1_2GigTFagkfzUFuQEMlyRI,1158
-phylogenie/py.typed,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-phylogenie/skyline/__init__.py,sha256=7pF4CUb4ZCLzNYJNhOjpuTOLTRhlK7L6ugfccNqjIGo,620
-phylogenie/skyline/matrix.py,sha256=T2g_MtfrqXVVGug40Nka1Q0YrpIi4KKx72Z573J-V18,7999
-phylogenie/skyline/parameter.py,sha256=CJ5OEyRQG2Tg1WJWQ1IpfX-6hjJv80Zj8lMoRke5nnQ,4648
-phylogenie/skyline/vector.py,sha256=Zh6HWoziXQFKDz-XvVE2e_Tw1706NrbwcvBpyPpw_cc,7120
-phylogenie/typeguards.py,sha256=WBOSJSaOC8VDtrYoA2w_AYEXTpyKdCfmsM29KaKXl3A,1350
-phylogenie/typings.py,sha256=93VRedBxrpzXkT4uaNu_1JiMzsOjp7fUy4kLv_eYxUE,565
-phylogenie-1.0.8.dist-info/LICENSE.txt,sha256=NUrDqElK-eD3I0WqC004CJsy6cs0JgsAoebDv_42-pw,1071
-phylogenie-1.0.8.dist-info/METADATA,sha256=eEc-ZuAO-y2SKsjHYxqSxRwqMYZ4Y_Hr8wzk49x9I4k,6291
-phylogenie-1.0.8.dist-info/WHEEL,sha256=sP946D7jFCHeNz5Iq4fL4Lu-PrWrFsgfLXbbkciIZwg,88
-phylogenie-1.0.8.dist-info/entry_points.txt,sha256=Rt6_usN0FkBX1ZfiqCirjMN9FKOgFLG8rydcQ8kugeE,51
-phylogenie-1.0.8.dist-info/RECORD,,