phylogenie 3.0.0__py3-none-any.whl → 3.1.2__py3-none-any.whl

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Files changed (7) hide show
  1. phylogenie/treesimulator/io/nexus.py +4 -2
  2. phylogenie/treesimulator/utils.py +1 -1
  3. {phylogenie-3.0.0.dist-info → phylogenie-3.1.2.dist-info}/METADATA +1 -1
  4. {phylogenie-3.0.0.dist-info → phylogenie-3.1.2.dist-info}/RECORD +7 -7
  5. {phylogenie-3.0.0.dist-info → phylogenie-3.1.2.dist-info}/LICENSE.txt +0 -0
  6. {phylogenie-3.0.0.dist-info → phylogenie-3.1.2.dist-info}/WHEEL +0 -0
  7. {phylogenie-3.0.0.dist-info → phylogenie-3.1.2.dist-info}/entry_points.txt +0 -0
phylogenie/treesimulator/io/nexus.py CHANGED
@@ -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/treesimulator/utils.py CHANGED
@@ -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.dist-info → phylogenie-3.1.2.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: 3.0.0
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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-3.0.0.dist-info → phylogenie-3.1.2.dist-info}/RECORD RENAMED
@@ -27,14 +27,14 @@ phylogenie/treesimulator/features.py,sha256=XbuwGw8xjGs2lNhJvvUUvXVtheSTBaSN6qj3
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  phylogenie/treesimulator/gillespie.py,sha256=ey2hdpJOSpNW88duwK7wTAdYSTnSuTSZ_yhZv9MlNHo,5323
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  phylogenie/treesimulator/io/__init__.py,sha256=rfP-zp8SP8baq5_4dPAr10WH0W6KfoMCxdTZDCSXtzE,185
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  phylogenie/treesimulator/io/newick.py,sha256=8Pr_jixByPOaVch18w-rFt62HYy0U97YMu0H-QSwIy0,3449
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- phylogenie/treesimulator/io/nexus.py,sha256=7g5lHb1GZczdLIXnkOUwjwTYtLZJX_4C-zOD4TW_Dao,1628
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+ phylogenie/treesimulator/io/nexus.py,sha256=wmOueclNRp85Zcs72dpaoKFiDY13TtmEL0mabKYni0w,1703
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  phylogenie/treesimulator/model.py,sha256=L0RsL6H1ynFDPecULniSs4Cs8dvz87ovviQOXFy5Qt0,4580
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  phylogenie/treesimulator/tree.py,sha256=-yMW14018x9dw45TonS6nRlzWcwXcaHv3Jn5HYriLQQ,6009
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- phylogenie/treesimulator/utils.py,sha256=ZA7gZYTBMDyt6Fjv4dVI1a9HUsAtTtzHvDkLE_jUpIw,3416
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+ phylogenie/treesimulator/utils.py,sha256=OxZwVHxN004Jf-kYZ_GfJgIY0beo-0tYq80CuFGQt-M,3416
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  phylogenie/typeguards.py,sha256=JtqmbEWJZBRHbWgCvcl6nrWm3VcBfzRbklbTBYHItn0,1325
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  phylogenie/typings.py,sha256=p694PBe_tk25A6N8vGGWxuqoDtt3nHFUsIYJrwR_76Y,494
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- phylogenie-3.0.0.dist-info/LICENSE.txt,sha256=NUrDqElK-eD3I0WqC004CJsy6cs0JgsAoebDv_42-pw,1071
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- phylogenie-3.0.0.dist-info/METADATA,sha256=j8dRenC33-Ab4NTcgawv6_kRJbpvC6fyDF2AyD-IeEo,5476
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- phylogenie-3.0.0.dist-info/WHEEL,sha256=sP946D7jFCHeNz5Iq4fL4Lu-PrWrFsgfLXbbkciIZwg,88
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- phylogenie-3.0.0.dist-info/entry_points.txt,sha256=Rt6_usN0FkBX1ZfiqCirjMN9FKOgFLG8rydcQ8kugeE,51
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- phylogenie-3.0.0.dist-info/RECORD,,
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+ phylogenie-3.1.2.dist-info/LICENSE.txt,sha256=NUrDqElK-eD3I0WqC004CJsy6cs0JgsAoebDv_42-pw,1071
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+ phylogenie-3.1.2.dist-info/METADATA,sha256=8bNrxXaHWW1N1nWmjDwf8CV9306fDaxguE2xoWmPufU,5476
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+ phylogenie-3.1.2.dist-info/WHEEL,sha256=sP946D7jFCHeNz5Iq4fL4Lu-PrWrFsgfLXbbkciIZwg,88
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+ phylogenie-3.1.2.dist-info/entry_points.txt,sha256=Rt6_usN0FkBX1ZfiqCirjMN9FKOgFLG8rydcQ8kugeE,51
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+ phylogenie-3.1.2.dist-info/RECORD,,