phylogenie 2.1.30__tar.gz → 3.1.8__tar.gz

{phylogenie-2.1.30 → phylogenie-3.1.8}/PKG-INFO

@@ -1,21 +1,17 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.4
 Name: phylogenie
-Version: 2.1.30
+Version: 3.1.8
 Summary: Generate phylogenetic datasets with minimal setup effort
-Author: Gabriele Marino
-Author-email: gabmarino.8601@gmail.com
-Requires-Python: >=3.10,<4.0
-Classifier: Programming Language :: Python :: 3
-Classifier: Programming Language :: Python :: 3.10
-Classifier: Programming Language :: Python :: 3.11
-Classifier: Programming Language :: Python :: 3.12
-Requires-Dist: joblib (>=1.4.2,<2.0.0)
-Requires-Dist: matplotlib (>=3.10.6,<4.0.0)
-Requires-Dist: pandas (>=2.2.2,<3.0.0)
-Requires-Dist: pydantic (>=2.11.5,<3.0.0)
-Requires-Dist: pyyaml (>=6.0.2,<7.0.0)
-Requires-Dist: tqdm (>=4.66.4,<5.0.0)
+Requires-Python: >=3.10
 Description-Content-Type: text/markdown
+License-File: LICENSE.txt
+Requires-Dist: joblib>=1.5.2
+Requires-Dist: matplotlib>=3.10.7
+Requires-Dist: pandas>=2.3.3
+Requires-Dist: pydantic>=2.12.3
+Requires-Dist: pyyaml>=6.0.3
+Requires-Dist: tqdm>=4.67.1
+Dynamic: license-file
 
 <p align="center">
 <img src="https://raw.githubusercontent.com/gabriele-marino/phylogenie/main/logo.png" style="width:100%; height:auto;"/>
@@ -103,4 +99,3 @@ This project is licensed under [MIT License](https://raw.githubusercontent.com/g
 For questions, bug reports, or feature requests, please, consider opening an [issue on GitHub](https://github.com/gabriele-marino/phylogenie/issues), or [contact me directly](mailto:gabmarino.8601@email.com).
 
 If you need help with the configuration files, feel free to reach out —  I am always very available and happy to assist!
-

phylogenie-3.1.8/pyproject.toml

@@ -0,0 +1,32 @@
+[project]
+name = "phylogenie"
+version = "3.1.8"
+description = "Generate phylogenetic datasets with minimal setup effort"
+readme = "README.md"
+requires-python = ">=3.10"
+dependencies = [
+    "joblib>=1.5.2",
+    "matplotlib>=3.10.7",
+    "pandas>=2.3.3",
+    "pydantic>=2.12.3",
+    "pyyaml>=6.0.3",
+    "tqdm>=4.67.1",
+]
+
+[dependency-groups]
+dev = [
+    "joblib-stubs>=1.5.2.0.20250831",
+    "pandas-stubs>=2.3.2.250926",
+    "pyright>=1.1.407",
+    "pytest>=8.4.2",
+]
+
+[tool.pyright]
+typeCheckingMode = "strict"
+
+[project.scripts]
+phylogenie = "phylogenie.main:main"
+
+[build-system]
+requires = ["setuptools>=42"]
+build-backend = "setuptools.build_meta"

phylogenie-3.1.8/setup.cfg

@@ -0,0 +1,4 @@
+[egg_info]
+tag_build = 
+tag_date = 0
+

{phylogenie-2.1.30 → phylogenie-3.1.8/src}/phylogenie/__init__.py

@@ -1,4 +1,11 @@
-from phylogenie.draw import Coloring, draw_tree
+from phylogenie.draw import (
+    draw_colored_dated_tree_categorical,
+    draw_colored_dated_tree_continuous,
+    draw_colored_tree_categorical,
+    draw_colored_tree_continuous,
+    draw_dated_tree,
+    draw_tree,
+)
 from phylogenie.generators import (
     AliSimDatasetGenerator,
     BDEITreeDatasetGenerator,
@@ -11,8 +18,8 @@ from phylogenie.generators import (
     FBDTreeDatasetGenerator,
     TreeDatasetGeneratorConfig,
 )
-from phylogenie.io import dump_newick, load_fasta, load_newick, load_nexus
-from phylogenie.msa import MSA
+from phylogenie.io import dump_fasta, load_fasta
+from phylogenie.msa import MSA, Sequence
 from phylogenie.skyline import (
     SkylineMatrix,
     SkylineMatrixCoercible,
@@ -25,41 +32,51 @@ from phylogenie.skyline import (
     skyline_parameter,
     skyline_vector,
 )
-from phylogenie.tree import Tree
 from phylogenie.treesimulator import (
     Birth,
     BirthWithContactTracing,
     Death,
     Event,
     EventType,
+    Feature,
     Migration,
     Mutation,
     Sampling,
     SamplingWithContactTracing,
+    Tree,
+    compute_mean_leaf_pairwise_distance,
+    compute_sackin_index,
+    dump_newick,
     generate_trees,
     get_BD_events,
     get_BDEI_events,
     get_BDSS_events,
     get_canonical_events,
     get_contact_tracing_events,
+    get_distance,
     get_epidemiological_events,
     get_FBD_events,
-    simulate_tree,
-)
-from phylogenie.utils import (
-    compute_colless_index,
-    compute_mean_leaf_pairwise_distance,
-    compute_sackin_index,
-    get_distance,
     get_mrca,
+    get_mutation_id,
     get_node_depth_levels,
     get_node_depths,
     get_node_height_levels,
     get_node_heights,
     get_node_leaf_counts,
+    get_node_state,
+    load_newick,
+    load_nexus,
+    set_features,
+    simulate_tree,
 )
 
 __all__ = [
+    "draw_colored_dated_tree_categorical",
+    "draw_colored_dated_tree_continuous",
+    "draw_colored_tree_categorical",
+    "draw_colored_tree_continuous",
+    "draw_dated_tree",
+    "draw_tree",
     "AliSimDatasetGenerator",
     "BDEITreeDatasetGenerator",
     "BDSSTreeDatasetGenerator",
@@ -69,51 +86,54 @@ __all__ = [
     "DatasetGeneratorConfig",
     "EpidemiologicalTreeDatasetGenerator",
     "FBDTreeDatasetGenerator",
+    "TreeDatasetGeneratorConfig",
+    "dump_fasta",
+    "load_fasta",
+    "MSA",
+    "Sequence",
     "SkylineMatrix",
     "SkylineMatrixCoercible",
-    "skyline_matrix",
     "SkylineParameter",
     "SkylineParameterLike",
-    "skyline_parameter",
     "SkylineVector",
     "SkylineVectorCoercible",
     "SkylineVectorLike",
+    "skyline_matrix",
+    "skyline_parameter",
     "skyline_vector",
-    "Tree",
-    "TreeDatasetGeneratorConfig",
     "Birth",
     "BirthWithContactTracing",
     "Death",
     "Event",
     "EventType",
+    "Feature",
     "Migration",
     "Mutation",
     "Sampling",
     "SamplingWithContactTracing",
+    "Tree",
+    "compute_mean_leaf_pairwise_distance",
+    "compute_sackin_index",
+    "dump_newick",
+    "generate_trees",
     "get_BD_events",
     "get_BDEI_events",
     "get_BDSS_events",
     "get_canonical_events",
     "get_contact_tracing_events",
+    "get_distance",
     "get_epidemiological_events",
     "get_FBD_events",
-    "generate_trees",
-    "simulate_tree",
-    "dump_newick",
-    "load_nexus",
-    "load_fasta",
-    "load_newick",
-    "MSA",
-    "Coloring",
-    "draw_tree",
-    "compute_colless_index",
-    "compute_mean_leaf_pairwise_distance",
-    "compute_sackin_index",
-    "get_distance",
     "get_mrca",
-    "get_node_depths",
+    "get_mutation_id",
     "get_node_depth_levels",
-    "get_node_heights",
+    "get_node_depths",
     "get_node_height_levels",
+    "get_node_heights",
     "get_node_leaf_counts",
+    "get_node_state",
+    "load_newick",
+    "load_nexus",
+    "set_features",
+    "simulate_tree",
 ]