phylogenie 3.1.1__tar.gz → 3.1.2__tar.gz

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  1. {phylogenie-3.1.1 → phylogenie-3.1.2}/PKG-INFO +1 -1
  2. {phylogenie-3.1.1 → phylogenie-3.1.2}/phylogenie/treesimulator/io/nexus.py +4 -2
  3. {phylogenie-3.1.1 → phylogenie-3.1.2}/pyproject.toml +1 -1
  4. {phylogenie-3.1.1 → phylogenie-3.1.2}/LICENSE.txt +0 -0
  5. {phylogenie-3.1.1 → phylogenie-3.1.2}/README.md +0 -0
  6. {phylogenie-3.1.1 → phylogenie-3.1.2}/phylogenie/__init__.py +0 -0
  7. {phylogenie-3.1.1 → phylogenie-3.1.2}/phylogenie/draw.py +0 -0
  8. {phylogenie-3.1.1 → phylogenie-3.1.2}/phylogenie/generators/__init__.py +0 -0
  9. {phylogenie-3.1.1 → phylogenie-3.1.2}/phylogenie/generators/alisim.py +0 -0
  10. {phylogenie-3.1.1 → phylogenie-3.1.2}/phylogenie/generators/configs.py +0 -0
  11. {phylogenie-3.1.1 → phylogenie-3.1.2}/phylogenie/generators/dataset.py +0 -0
  12. {phylogenie-3.1.1 → phylogenie-3.1.2}/phylogenie/generators/factories.py +0 -0
  13. {phylogenie-3.1.1 → phylogenie-3.1.2}/phylogenie/generators/trees.py +0 -0
  14. {phylogenie-3.1.1 → phylogenie-3.1.2}/phylogenie/generators/typeguards.py +0 -0
  15. {phylogenie-3.1.1 → phylogenie-3.1.2}/phylogenie/io/__init__.py +0 -0
  16. {phylogenie-3.1.1 → phylogenie-3.1.2}/phylogenie/io/fasta.py +0 -0
  17. {phylogenie-3.1.1 → phylogenie-3.1.2}/phylogenie/main.py +0 -0
  18. {phylogenie-3.1.1 → phylogenie-3.1.2}/phylogenie/mixins.py +0 -0
  19. {phylogenie-3.1.1 → phylogenie-3.1.2}/phylogenie/msa.py +0 -0
  20. {phylogenie-3.1.1 → phylogenie-3.1.2}/phylogenie/py.typed +0 -0
  21. {phylogenie-3.1.1 → phylogenie-3.1.2}/phylogenie/skyline/__init__.py +0 -0
  22. {phylogenie-3.1.1 → phylogenie-3.1.2}/phylogenie/skyline/matrix.py +0 -0
  23. {phylogenie-3.1.1 → phylogenie-3.1.2}/phylogenie/skyline/parameter.py +0 -0
  24. {phylogenie-3.1.1 → phylogenie-3.1.2}/phylogenie/skyline/vector.py +0 -0
  25. {phylogenie-3.1.1 → phylogenie-3.1.2}/phylogenie/treesimulator/__init__.py +0 -0
  26. {phylogenie-3.1.1 → phylogenie-3.1.2}/phylogenie/treesimulator/events/__init__.py +0 -0
  27. {phylogenie-3.1.1 → phylogenie-3.1.2}/phylogenie/treesimulator/events/base.py +0 -0
  28. {phylogenie-3.1.1 → phylogenie-3.1.2}/phylogenie/treesimulator/events/contact_tracing.py +0 -0
  29. {phylogenie-3.1.1 → phylogenie-3.1.2}/phylogenie/treesimulator/events/core.py +0 -0
  30. {phylogenie-3.1.1 → phylogenie-3.1.2}/phylogenie/treesimulator/events/mutations.py +0 -0
  31. {phylogenie-3.1.1 → phylogenie-3.1.2}/phylogenie/treesimulator/features.py +0 -0
  32. {phylogenie-3.1.1 → phylogenie-3.1.2}/phylogenie/treesimulator/gillespie.py +0 -0
  33. {phylogenie-3.1.1 → phylogenie-3.1.2}/phylogenie/treesimulator/io/__init__.py +0 -0
  34. {phylogenie-3.1.1 → phylogenie-3.1.2}/phylogenie/treesimulator/io/newick.py +0 -0
  35. {phylogenie-3.1.1 → phylogenie-3.1.2}/phylogenie/treesimulator/model.py +0 -0
  36. {phylogenie-3.1.1 → phylogenie-3.1.2}/phylogenie/treesimulator/tree.py +0 -0
  37. {phylogenie-3.1.1 → phylogenie-3.1.2}/phylogenie/treesimulator/utils.py +0 -0
  38. {phylogenie-3.1.1 → phylogenie-3.1.2}/phylogenie/typeguards.py +0 -0
  39. {phylogenie-3.1.1 → phylogenie-3.1.2}/phylogenie/typings.py +0 -0
{phylogenie-3.1.1 → phylogenie-3.1.2}/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: 3.1.1
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+ Version: 3.1.2
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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-3.1.1 → phylogenie-3.1.2}/phylogenie/treesimulator/io/nexus.py RENAMED
@@ -32,9 +32,11 @@ def _parse_trees_block(lines: Iterator[str]) -> dict[str, Tree]:
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  else:
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  match = re.match(r"^TREE\s*\*?\s+(\S+)\s*=\s*(.+)$", line, re.IGNORECASE)
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  if match is None:
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- raise ValueError(f"Invalid tree line. Expected 'TREE name = newick'")
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+ raise ValueError(
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+ f"Invalid tree line. Expected 'TREE <name> = <newick>'"
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+ )
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  trees[match.group(1)] = parse_newick(match.group(2), translations)
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- return trees
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+ raise ValueError("Unterminated TREES block.")
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  def load_nexus(nexus_file: str | Path) -> dict[str, Tree]:
{phylogenie-3.1.1 → phylogenie-3.1.2}/pyproject.toml RENAMED
@@ -1,6 +1,6 @@
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  [tool.poetry]
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  name = "phylogenie"
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- version = "3.1.1"
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+ version = "3.1.2"
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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-3.1.1 → phylogenie-3.1.2}/LICENSE.txt RENAMED
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{phylogenie-3.1.1 → phylogenie-3.1.2}/README.md RENAMED
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{phylogenie-3.1.1 → phylogenie-3.1.2}/phylogenie/msa.py RENAMED
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