phylogenie 2.1.10__tar.gz → 2.1.11__tar.gz

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  1. {phylogenie-2.1.10 → phylogenie-2.1.11}/PKG-INFO +1 -1
  2. {phylogenie-2.1.10 → phylogenie-2.1.11}/phylogenie/__init__.py +3 -0
  3. {phylogenie-2.1.10 → phylogenie-2.1.11}/phylogenie/plot.py +4 -0
  4. {phylogenie-2.1.10 → phylogenie-2.1.11}/pyproject.toml +1 -1
  5. {phylogenie-2.1.10 → phylogenie-2.1.11}/LICENSE.txt +0 -0
  6. {phylogenie-2.1.10 → phylogenie-2.1.11}/README.md +0 -0
  7. {phylogenie-2.1.10 → phylogenie-2.1.11}/phylogenie/generators/__init__.py +0 -0
  8. {phylogenie-2.1.10 → phylogenie-2.1.11}/phylogenie/generators/alisim.py +0 -0
  9. {phylogenie-2.1.10 → phylogenie-2.1.11}/phylogenie/generators/configs.py +0 -0
  10. {phylogenie-2.1.10 → phylogenie-2.1.11}/phylogenie/generators/dataset.py +0 -0
  11. {phylogenie-2.1.10 → phylogenie-2.1.11}/phylogenie/generators/factories.py +0 -0
  12. {phylogenie-2.1.10 → phylogenie-2.1.11}/phylogenie/generators/trees.py +0 -0
  13. {phylogenie-2.1.10 → phylogenie-2.1.11}/phylogenie/generators/typeguards.py +0 -0
  14. {phylogenie-2.1.10 → phylogenie-2.1.11}/phylogenie/io.py +0 -0
  15. {phylogenie-2.1.10 → phylogenie-2.1.11}/phylogenie/main.py +0 -0
  16. {phylogenie-2.1.10 → phylogenie-2.1.11}/phylogenie/models.py +0 -0
  17. {phylogenie-2.1.10 → phylogenie-2.1.11}/phylogenie/msa.py +0 -0
  18. {phylogenie-2.1.10 → phylogenie-2.1.11}/phylogenie/py.typed +0 -0
  19. {phylogenie-2.1.10 → phylogenie-2.1.11}/phylogenie/skyline/__init__.py +0 -0
  20. {phylogenie-2.1.10 → phylogenie-2.1.11}/phylogenie/skyline/matrix.py +0 -0
  21. {phylogenie-2.1.10 → phylogenie-2.1.11}/phylogenie/skyline/parameter.py +0 -0
  22. {phylogenie-2.1.10 → phylogenie-2.1.11}/phylogenie/skyline/vector.py +0 -0
  23. {phylogenie-2.1.10 → phylogenie-2.1.11}/phylogenie/tree.py +0 -0
  24. {phylogenie-2.1.10 → phylogenie-2.1.11}/phylogenie/treesimulator/__init__.py +0 -0
  25. {phylogenie-2.1.10 → phylogenie-2.1.11}/phylogenie/treesimulator/events/__init__.py +0 -0
  26. {phylogenie-2.1.10 → phylogenie-2.1.11}/phylogenie/treesimulator/events/contact_tracing.py +0 -0
  27. {phylogenie-2.1.10 → phylogenie-2.1.11}/phylogenie/treesimulator/events/core.py +0 -0
  28. {phylogenie-2.1.10 → phylogenie-2.1.11}/phylogenie/treesimulator/events/mutations.py +0 -0
  29. {phylogenie-2.1.10 → phylogenie-2.1.11}/phylogenie/treesimulator/features.py +0 -0
  30. {phylogenie-2.1.10 → phylogenie-2.1.11}/phylogenie/treesimulator/gillespie.py +0 -0
  31. {phylogenie-2.1.10 → phylogenie-2.1.11}/phylogenie/treesimulator/model.py +0 -0
  32. {phylogenie-2.1.10 → phylogenie-2.1.11}/phylogenie/typeguards.py +0 -0
  33. {phylogenie-2.1.10 → phylogenie-2.1.11}/phylogenie/typings.py +0 -0
  34. {phylogenie-2.1.10 → phylogenie-2.1.11}/phylogenie/utils.py +0 -0
{phylogenie-2.1.10 → phylogenie-2.1.11}/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: 2.1.10
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+ Version: 2.1.11
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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-2.1.10 → phylogenie-2.1.11}/phylogenie/__init__.py RENAMED
@@ -12,6 +12,7 @@ from phylogenie.generators import (
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  )
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  from phylogenie.io import dump_newick, load_fasta, load_newick
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  from phylogenie.msa import MSA
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+ from phylogenie.plot import Coloring, plot_tree
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  from phylogenie.skyline import (
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  SkylineMatrix,
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  SkylineMatrixCoercible,
@@ -90,4 +91,6 @@ __all__ = [
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  "load_fasta",
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  "load_newick",
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  "MSA",
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+ "Coloring",
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+ "plot_tree",
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  ]
{phylogenie-2.1.10 → phylogenie-2.1.11}/phylogenie/plot.py RENAMED
@@ -58,6 +58,10 @@ def plot_tree(
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  norm = mcolors.Normalize(vmin=min(values), vmax=max(values))
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  colormap = plt.get_cmap(cmap)
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  colors = {node: colormap(norm(float(node.get(color_by)))) for node in tree}
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+
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+ sm = plt.cm.ScalarMappable(cmap=colormap, norm=norm)
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+ fig = ax.get_figure()
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+ fig.colorbar(sm, ax=ax, label=color_by) # pyright: ignore
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  else:
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  raise ValueError(
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  f"Unknown coloring method: {coloring}. Choices are {list(Coloring)}."
{phylogenie-2.1.10 → phylogenie-2.1.11}/pyproject.toml RENAMED
@@ -1,6 +1,6 @@
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  [tool.poetry]
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  name = "phylogenie"
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- version = "2.1.10"
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+ version = "2.1.11"
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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-2.1.10 → phylogenie-2.1.11}/LICENSE.txt RENAMED
File without changes
{phylogenie-2.1.10 → phylogenie-2.1.11}/README.md RENAMED
File without changes