phylogenie 2.0.12__tar.gz → 2.0.14__tar.gz

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  1. {phylogenie-2.0.12 → phylogenie-2.0.14}/PKG-INFO +1 -1
  2. {phylogenie-2.0.12 → phylogenie-2.0.14}/phylogenie/__init__.py +6 -0
  3. {phylogenie-2.0.12 → phylogenie-2.0.14}/phylogenie/generators/__init__.py +8 -0
  4. {phylogenie-2.0.12 → phylogenie-2.0.14}/phylogenie/treesimulator/gillespie.py +4 -2
  5. {phylogenie-2.0.12 → phylogenie-2.0.14}/pyproject.toml +1 -1
  6. {phylogenie-2.0.12 → phylogenie-2.0.14}/LICENSE.txt +0 -0
  7. {phylogenie-2.0.12 → phylogenie-2.0.14}/README.md +0 -0
  8. {phylogenie-2.0.12 → phylogenie-2.0.14}/phylogenie/generators/alisim.py +0 -0
  9. {phylogenie-2.0.12 → phylogenie-2.0.14}/phylogenie/generators/configs.py +0 -0
  10. {phylogenie-2.0.12 → phylogenie-2.0.14}/phylogenie/generators/dataset.py +0 -0
  11. {phylogenie-2.0.12 → phylogenie-2.0.14}/phylogenie/generators/factories.py +0 -0
  12. {phylogenie-2.0.12 → phylogenie-2.0.14}/phylogenie/generators/trees.py +0 -0
  13. {phylogenie-2.0.12 → phylogenie-2.0.14}/phylogenie/generators/typeguards.py +0 -0
  14. {phylogenie-2.0.12 → phylogenie-2.0.14}/phylogenie/io.py +0 -0
  15. {phylogenie-2.0.12 → phylogenie-2.0.14}/phylogenie/main.py +0 -0
  16. {phylogenie-2.0.12 → phylogenie-2.0.14}/phylogenie/msa.py +0 -0
  17. {phylogenie-2.0.12 → phylogenie-2.0.14}/phylogenie/py.typed +0 -0
  18. {phylogenie-2.0.12 → phylogenie-2.0.14}/phylogenie/skyline/__init__.py +0 -0
  19. {phylogenie-2.0.12 → phylogenie-2.0.14}/phylogenie/skyline/matrix.py +0 -0
  20. {phylogenie-2.0.12 → phylogenie-2.0.14}/phylogenie/skyline/parameter.py +0 -0
  21. {phylogenie-2.0.12 → phylogenie-2.0.14}/phylogenie/skyline/vector.py +0 -0
  22. {phylogenie-2.0.12 → phylogenie-2.0.14}/phylogenie/tree.py +0 -0
  23. {phylogenie-2.0.12 → phylogenie-2.0.14}/phylogenie/treesimulator/__init__.py +0 -0
  24. {phylogenie-2.0.12 → phylogenie-2.0.14}/phylogenie/treesimulator/events.py +0 -0
  25. {phylogenie-2.0.12 → phylogenie-2.0.14}/phylogenie/treesimulator/model.py +0 -0
  26. {phylogenie-2.0.12 → phylogenie-2.0.14}/phylogenie/typeguards.py +0 -0
  27. {phylogenie-2.0.12 → phylogenie-2.0.14}/phylogenie/typings.py +0 -0
{phylogenie-2.0.12 → phylogenie-2.0.14}/PKG-INFO RENAMED
@@ -1,6 +1,6 @@
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  Metadata-Version: 2.1
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  Name: phylogenie
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- Version: 2.0.12
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+ Version: 2.0.14
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  Summary: Generate phylogenetic datasets with minimal setup effort
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  Author: Gabriele Marino
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  Author-email: gabmarino.8601@gmail.com
{phylogenie-2.0.12 → phylogenie-2.0.14}/phylogenie/__init__.py RENAMED
@@ -8,6 +8,9 @@ from phylogenie.generators import (
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  DatasetGeneratorConfig,
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  EpidemiologicalTreeDatasetGenerator,
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  FBDTreeDatasetGenerator,
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+ SkylineMatrixModel,
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+ SkylineParameterModel,
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+ SkylineVectorModel,
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  TreeDatasetGeneratorConfig,
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  )
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  from phylogenie.io import load_fasta, load_newick
@@ -48,13 +51,16 @@ __all__ = [
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  "FBDTreeDatasetGenerator",
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  "SkylineMatrix",
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  "SkylineMatrixCoercible",
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+ "SkylineMatrixModel",
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  "skyline_matrix",
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  "SkylineParameter",
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  "SkylineParameterLike",
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+ "SkylineParameterModel",
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  "skyline_parameter",
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  "SkylineVector",
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  "SkylineVectorCoercible",
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  "SkylineVectorLike",
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+ "SkylineVectorModel",
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  "skyline_vector",
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  "Tree",
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  "TreeDatasetGeneratorConfig",
{phylogenie-2.0.12 → phylogenie-2.0.14}/phylogenie/generators/__init__.py RENAMED
@@ -3,6 +3,11 @@ from typing import Annotated
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  from pydantic import Field
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  from phylogenie.generators.alisim import AliSimDatasetGenerator
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+ from phylogenie.generators.configs import (
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+ SkylineMatrixModel,
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+ SkylineParameterModel,
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+ SkylineVectorModel,
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+ )
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  from phylogenie.generators.dataset import DatasetGenerator
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  from phylogenie.generators.trees import (
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  BDEITreeDatasetGenerator,
@@ -29,4 +34,7 @@ __all__ = [
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  "BDTreeDatasetGenerator",
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  "BDEITreeDatasetGenerator",
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  "BDSSTreeDatasetGenerator",
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+ "SkylineMatrixModel",
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+ "SkylineParameterModel",
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+ "SkylineVectorModel",
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  ]
{phylogenie-2.0.12 → phylogenie-2.0.14}/phylogenie/treesimulator/gillespie.py RENAMED
@@ -60,9 +60,11 @@ def simulate_tree(
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  if not any(rates):
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  break
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- current_time += rng.exponential(1 / sum(rates))
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- if current_time >= max_time:
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+ time_step = rng.exponential(1 / sum(rates))
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+ if current_time + time_step >= max_time:
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+ current_time = max_time
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  break
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+ current_time += time_step
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  if current_time >= next_change_time:
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  current_time = next_change_time
{phylogenie-2.0.12 → phylogenie-2.0.14}/pyproject.toml RENAMED
@@ -1,6 +1,6 @@
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  [tool.poetry]
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  name = "phylogenie"
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- version = "2.0.12"
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+ version = "2.0.14"
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  description = "Generate phylogenetic datasets with minimal setup effort"
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  authors = ["Gabriele Marino <gabmarino.8601@gmail.com>"]
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  readme = "README.md"
{phylogenie-2.0.12 → phylogenie-2.0.14}/LICENSE.txt RENAMED
File without changes
{phylogenie-2.0.12 → phylogenie-2.0.14}/README.md RENAMED
File without changes