phylogenie 3.0.0__tar.gz → 3.1.1__tar.gz

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  1. {phylogenie-3.0.0 → phylogenie-3.1.1}/PKG-INFO +1 -1
  2. {phylogenie-3.0.0 → phylogenie-3.1.1}/phylogenie/treesimulator/utils.py +1 -1
  3. {phylogenie-3.0.0 → phylogenie-3.1.1}/pyproject.toml +1 -1
  4. {phylogenie-3.0.0 → phylogenie-3.1.1}/LICENSE.txt +0 -0
  5. {phylogenie-3.0.0 → phylogenie-3.1.1}/README.md +0 -0
  6. {phylogenie-3.0.0 → phylogenie-3.1.1}/phylogenie/__init__.py +0 -0
  7. {phylogenie-3.0.0 → phylogenie-3.1.1}/phylogenie/draw.py +0 -0
  8. {phylogenie-3.0.0 → phylogenie-3.1.1}/phylogenie/generators/__init__.py +0 -0
  9. {phylogenie-3.0.0 → phylogenie-3.1.1}/phylogenie/generators/alisim.py +0 -0
  10. {phylogenie-3.0.0 → phylogenie-3.1.1}/phylogenie/generators/configs.py +0 -0
  11. {phylogenie-3.0.0 → phylogenie-3.1.1}/phylogenie/generators/dataset.py +0 -0
  12. {phylogenie-3.0.0 → phylogenie-3.1.1}/phylogenie/generators/factories.py +0 -0
  13. {phylogenie-3.0.0 → phylogenie-3.1.1}/phylogenie/generators/trees.py +0 -0
  14. {phylogenie-3.0.0 → phylogenie-3.1.1}/phylogenie/generators/typeguards.py +0 -0
  15. {phylogenie-3.0.0 → phylogenie-3.1.1}/phylogenie/io/__init__.py +0 -0
  16. {phylogenie-3.0.0 → phylogenie-3.1.1}/phylogenie/io/fasta.py +0 -0
  17. {phylogenie-3.0.0 → phylogenie-3.1.1}/phylogenie/main.py +0 -0
  18. {phylogenie-3.0.0 → phylogenie-3.1.1}/phylogenie/mixins.py +0 -0
  19. {phylogenie-3.0.0 → phylogenie-3.1.1}/phylogenie/msa.py +0 -0
  20. {phylogenie-3.0.0 → phylogenie-3.1.1}/phylogenie/py.typed +0 -0
  21. {phylogenie-3.0.0 → phylogenie-3.1.1}/phylogenie/skyline/__init__.py +0 -0
  22. {phylogenie-3.0.0 → phylogenie-3.1.1}/phylogenie/skyline/matrix.py +0 -0
  23. {phylogenie-3.0.0 → phylogenie-3.1.1}/phylogenie/skyline/parameter.py +0 -0
  24. {phylogenie-3.0.0 → phylogenie-3.1.1}/phylogenie/skyline/vector.py +0 -0
  25. {phylogenie-3.0.0 → phylogenie-3.1.1}/phylogenie/treesimulator/__init__.py +0 -0
  26. {phylogenie-3.0.0 → phylogenie-3.1.1}/phylogenie/treesimulator/events/__init__.py +0 -0
  27. {phylogenie-3.0.0 → phylogenie-3.1.1}/phylogenie/treesimulator/events/base.py +0 -0
  28. {phylogenie-3.0.0 → phylogenie-3.1.1}/phylogenie/treesimulator/events/contact_tracing.py +0 -0
  29. {phylogenie-3.0.0 → phylogenie-3.1.1}/phylogenie/treesimulator/events/core.py +0 -0
  30. {phylogenie-3.0.0 → phylogenie-3.1.1}/phylogenie/treesimulator/events/mutations.py +0 -0
  31. {phylogenie-3.0.0 → phylogenie-3.1.1}/phylogenie/treesimulator/features.py +0 -0
  32. {phylogenie-3.0.0 → phylogenie-3.1.1}/phylogenie/treesimulator/gillespie.py +0 -0
  33. {phylogenie-3.0.0 → phylogenie-3.1.1}/phylogenie/treesimulator/io/__init__.py +0 -0
  34. {phylogenie-3.0.0 → phylogenie-3.1.1}/phylogenie/treesimulator/io/newick.py +0 -0
  35. {phylogenie-3.0.0 → phylogenie-3.1.1}/phylogenie/treesimulator/io/nexus.py +0 -0
  36. {phylogenie-3.0.0 → phylogenie-3.1.1}/phylogenie/treesimulator/model.py +0 -0
  37. {phylogenie-3.0.0 → phylogenie-3.1.1}/phylogenie/treesimulator/tree.py +0 -0
  38. {phylogenie-3.0.0 → phylogenie-3.1.1}/phylogenie/typeguards.py +0 -0
  39. {phylogenie-3.0.0 → phylogenie-3.1.1}/phylogenie/typings.py +0 -0
{phylogenie-3.0.0 → phylogenie-3.1.1}/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: 3.0.0
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+ Version: 3.1.1
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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-3.0.0 → phylogenie-3.1.1}/phylogenie/treesimulator/utils.py RENAMED
@@ -22,7 +22,7 @@ def get_node_depths(tree: Tree) -> dict[Tree, float]:
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  depths: dict[Tree, float] = {tree: tree.depth}
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  for node in tree.iter_descendants():
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  parent_depth = depths[node.parent] # pyright: ignore
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- depths[node] = tree.branch_length_or_raise() + parent_depth
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+ depths[node] = node.branch_length_or_raise() + parent_depth
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  return depths
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{phylogenie-3.0.0 → phylogenie-3.1.1}/pyproject.toml RENAMED
@@ -1,6 +1,6 @@
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  [tool.poetry]
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  name = "phylogenie"
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- version = "3.0.0"
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+ version = "3.1.1"
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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-3.0.0 → phylogenie-3.1.1}/LICENSE.txt RENAMED
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{phylogenie-3.0.0 → phylogenie-3.1.1}/README.md RENAMED
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{phylogenie-3.0.0 → phylogenie-3.1.1}/phylogenie/msa.py RENAMED
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