phylogenie 2.0.12__py3-none-any.whl → 2.0.14__py3-none-any.whl

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Files changed (8) hide show
  1. phylogenie/__init__.py +6 -0
  2. phylogenie/generators/__init__.py +8 -0
  3. phylogenie/treesimulator/gillespie.py +4 -2
  4. {phylogenie-2.0.12.dist-info → phylogenie-2.0.14.dist-info}/METADATA +1 -1
  5. {phylogenie-2.0.12.dist-info → phylogenie-2.0.14.dist-info}/RECORD +8 -8
  6. {phylogenie-2.0.12.dist-info → phylogenie-2.0.14.dist-info}/LICENSE.txt +0 -0
  7. {phylogenie-2.0.12.dist-info → phylogenie-2.0.14.dist-info}/WHEEL +0 -0
  8. {phylogenie-2.0.12.dist-info → phylogenie-2.0.14.dist-info}/entry_points.txt +0 -0
phylogenie/__init__.py CHANGED
@@ -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/generators/__init__.py CHANGED
@@ -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/treesimulator/gillespie.py CHANGED
@@ -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.dist-info → phylogenie-2.0.14.dist-info}/METADATA 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.dist-info → phylogenie-2.0.14.dist-info}/RECORD RENAMED
@@ -1,5 +1,5 @@
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- phylogenie/__init__.py,sha256=1w_0H9lg7hI3b-NLjKuzc34GbJJGyjLq9LrlogecTzI,1759
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- phylogenie/generators/__init__.py,sha256=zsOxy28-9j9alOQLIgrOAFfmM58NNHO_NEtW-KXQXAY,888
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+ phylogenie/__init__.py,sha256=4BytT42_M1K6T3W9eqHQCrKc6g0Lh5LTQxP8dGIJTsk,1915
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+ phylogenie/generators/__init__.py,sha256=VCpuvmOoY_N6p1h_Q0peYgGIIUIFLsvZT3T7vbHG6w0,1090
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  phylogenie/generators/alisim.py,sha256=dDqlSwLDbRE2u5SZlsq1mArobTBtuk0aeXY3m1N-bWA,2374
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  phylogenie/generators/configs.py,sha256=4jSBUZiFo2GacXWed5dy7lUEkaOWZkZG-KY9vHfhqGU,993
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  phylogenie/generators/dataset.py,sha256=hbkN5McM4BKY7D0hLNaxdoAGsLHac6O-D4sgnZ0wFX4,2618
@@ -17,12 +17,12 @@ phylogenie/skyline/vector.py,sha256=bJP7_FNX_Klt6wXqsyfj0KX3VNj6-dIhzCKSJuQcOV0,
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  phylogenie/tree.py,sha256=dk8Sj1tqyGOunVO2crtIqb0LH-ws-PXqA8SuNcYfVHI,1738
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  phylogenie/treesimulator/__init__.py,sha256=INPU9LrPdUmt3dYGzWDRoRKrPR9xENcHu44pJVUbyNA,525
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  phylogenie/treesimulator/events.py,sha256=X3_0U9qqMpYgh6-7TwQEnlUipANkHz6QTCXlm-qXFQk,9524
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- phylogenie/treesimulator/gillespie.py,sha256=4uMt_-Rr3cRXWGKC8veBIB-uqtKtN-dLbAHKjAi_5Mo,3182
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+ phylogenie/treesimulator/gillespie.py,sha256=NHiBLVlpKdcTPohMr6ehywbPeB8gnn6erEv2bkgvf4c,3268
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  phylogenie/treesimulator/model.py,sha256=XpzAicmg2O6K0Trk5YolH-B_HJZxoSauF2wZOMqp-Iw,5559
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  phylogenie/typeguards.py,sha256=JtqmbEWJZBRHbWgCvcl6nrWm3VcBfzRbklbTBYHItn0,1325
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  phylogenie/typings.py,sha256=O1X6lGKTjJ2YJz3ApQ-rYb_tEJNUIcHdUIeYlSM4s5o,500
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- phylogenie-2.0.12.dist-info/LICENSE.txt,sha256=NUrDqElK-eD3I0WqC004CJsy6cs0JgsAoebDv_42-pw,1071
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- phylogenie-2.0.12.dist-info/METADATA,sha256=sZ7bmfmNAYLAlx1_cUAGzIBEnAGhS6yhFcfzgknh_BQ,5473
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- phylogenie-2.0.12.dist-info/WHEEL,sha256=sP946D7jFCHeNz5Iq4fL4Lu-PrWrFsgfLXbbkciIZwg,88
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- phylogenie-2.0.12.dist-info/entry_points.txt,sha256=Rt6_usN0FkBX1ZfiqCirjMN9FKOgFLG8rydcQ8kugeE,51
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- phylogenie-2.0.12.dist-info/RECORD,,
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+ phylogenie-2.0.14.dist-info/LICENSE.txt,sha256=NUrDqElK-eD3I0WqC004CJsy6cs0JgsAoebDv_42-pw,1071
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+ phylogenie-2.0.14.dist-info/METADATA,sha256=NXOQmoUHSTA2AjrXjt4VKSaM2KO6H2rBF7nrRuGK2f4,5473
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+ phylogenie-2.0.14.dist-info/WHEEL,sha256=sP946D7jFCHeNz5Iq4fL4Lu-PrWrFsgfLXbbkciIZwg,88
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+ phylogenie-2.0.14.dist-info/entry_points.txt,sha256=Rt6_usN0FkBX1ZfiqCirjMN9FKOgFLG8rydcQ8kugeE,51
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+ phylogenie-2.0.14.dist-info/RECORD,,