phylogenie 3.1.9__tar.gz → 3.3.0__tar.gz

{phylogenie-3.1.9/src/phylogenie.egg-info → phylogenie-3.3.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: phylogenie
-Version: 3.1.9
+Version: 3.3.0
 Summary: Generate phylogenetic datasets with minimal setup effort
 Requires-Python: >=3.10
 Description-Content-Type: text/markdown
@@ -23,7 +23,6 @@ Dynamic: license-file
 [![PyPI version](https://img.shields.io/pypi/v/phylogenie)](https://pypi.org/project/phylogenie/)
 ![Downloads](https://img.shields.io/pypi/dm/phylogenie)
 
-
 Phylogenie is a [Python](https://www.python.org/) package designed to easily simulate phylogenetic datasets—such as trees and multiple sequence alignments (MSAs)—with minimal setup effort. Simply specify the distributions from which your parameters should be sampled, and Phylogenie will handle the rest!
 
 ## ✨ Features
@@ -48,8 +47,8 @@ Phylogenie comes packed with useful features, including:
 - **Skyline parameter support** 🪜  
   Support for piece-wise constant parameters.
 
-- **Arithmetic operations on parameters** 🧮  
-  Perform flexible arithmetic operations between parameters directly within the config file.
+- **Operations on parameters** 🧮  
+  Perform flexible operations between parameters directly within the config file.
 
 ## 📦 Installation
 Phylogenie requires [Python](https://www.python.org/) 3.10 to be installed on your system. There are several ways to install Python and managing different Python versions. One popular option is to use [pyenv](https://github.com/pyenv/pyenv).
@@ -73,21 +72,21 @@ Phylogenie relies on [AliSim](https://iqtree.github.io/doc/AliSim) for simulatin
 
 ## 🚀 Quick Start
 
-Once you have installed Phylogenie, check out the [examples](https://github.com/gabriele-marino/phylogenie/tree/main/examples) folder.  
+Once you have installed Phylogenie, check out the [tutorials](https://github.com/gabriele-marino/phylogenie/tree/main/tutorials) folder.  
 It includes a collection of thoroughly commented configuration files, organized as a step-by-step tutorial. These examples will help you understand how to use Phylogenie in practice and can be easily adapted to fit your own workflow.
 
 For quick start, pick your favorite config file and run Phylogenie with:
 ```bash
-phylogenie examples/config_file.yaml
+phylogenie tutorials/config_file.yaml
 ```
 This command will create the output dataset in the folder specified inside the configuration file, including data directories and metadata files for each dataset split defined in the config.
 
 >❗ *Tip*: Can’t choose just one config file?
-You can run them all at once by pointing Phylogenie to the folder! Just use: `phylogenie examples`. In this mode, Phylogenie will automatically find all `.yaml` files in the folder you specified and run for each of them!
+You can run them all at once by pointing Phylogenie to the folder! Just use: `phylogenie tutorials`. In this mode, Phylogenie will automatically find all `.yaml` files in the folder you specified and run for each of them!
 
 ## 📖 Documentation
 
-- The [examples](https://github.com/gabriele-marino/phylogenie/tree/main/examples) folder contains many ready-to-use, extensively commented configuration files that serve as a step-by-step tutorial to guide you through using Phylogenie. You can explore them to learn how it works or adapt them directly to your own workflows.
+- The [tutorials](https://github.com/gabriele-marino/phylogenie/tree/main/tutorials) folder contains many ready-to-use, extensively commented configuration files that serve as a step-by-step tutorial to guide you through using Phylogenie. You can explore them to learn how it works or adapt them directly to your own workflows.
 - A complete user guide and API reference are under development. In the meantime, feel free to [reach out](mailto:gabmarino.8601@email.com) if you have any questions about integrating Phylogenie into your workflows.
 
 ## 📄 License
@@ -98,4 +97,4 @@ 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!
+For help with configuration files, don’t hesitate to reach out — I’m happy to assist!

{phylogenie-3.1.9 → phylogenie-3.3.0}/README.md

@@ -8,7 +8,6 @@
 [![PyPI version](https://img.shields.io/pypi/v/phylogenie)](https://pypi.org/project/phylogenie/)
 ![Downloads](https://img.shields.io/pypi/dm/phylogenie)
 
-
 Phylogenie is a [Python](https://www.python.org/) package designed to easily simulate phylogenetic datasets—such as trees and multiple sequence alignments (MSAs)—with minimal setup effort. Simply specify the distributions from which your parameters should be sampled, and Phylogenie will handle the rest!
 
 ## ✨ Features
@@ -33,8 +32,8 @@ Phylogenie comes packed with useful features, including:
 - **Skyline parameter support** 🪜  
   Support for piece-wise constant parameters.
 
-- **Arithmetic operations on parameters** 🧮  
-  Perform flexible arithmetic operations between parameters directly within the config file.
+- **Operations on parameters** 🧮  
+  Perform flexible operations between parameters directly within the config file.
 
 ## 📦 Installation
 Phylogenie requires [Python](https://www.python.org/) 3.10 to be installed on your system. There are several ways to install Python and managing different Python versions. One popular option is to use [pyenv](https://github.com/pyenv/pyenv).
@@ -58,21 +57,21 @@ Phylogenie relies on [AliSim](https://iqtree.github.io/doc/AliSim) for simulatin
 
 ## 🚀 Quick Start
 
-Once you have installed Phylogenie, check out the [examples](https://github.com/gabriele-marino/phylogenie/tree/main/examples) folder.  
+Once you have installed Phylogenie, check out the [tutorials](https://github.com/gabriele-marino/phylogenie/tree/main/tutorials) folder.  
 It includes a collection of thoroughly commented configuration files, organized as a step-by-step tutorial. These examples will help you understand how to use Phylogenie in practice and can be easily adapted to fit your own workflow.
 
 For quick start, pick your favorite config file and run Phylogenie with:
 ```bash
-phylogenie examples/config_file.yaml
+phylogenie tutorials/config_file.yaml
 ```
 This command will create the output dataset in the folder specified inside the configuration file, including data directories and metadata files for each dataset split defined in the config.
 
 >❗ *Tip*: Can’t choose just one config file?
-You can run them all at once by pointing Phylogenie to the folder! Just use: `phylogenie examples`. In this mode, Phylogenie will automatically find all `.yaml` files in the folder you specified and run for each of them!
+You can run them all at once by pointing Phylogenie to the folder! Just use: `phylogenie tutorials`. In this mode, Phylogenie will automatically find all `.yaml` files in the folder you specified and run for each of them!
 
 ## 📖 Documentation
 
-- The [examples](https://github.com/gabriele-marino/phylogenie/tree/main/examples) folder contains many ready-to-use, extensively commented configuration files that serve as a step-by-step tutorial to guide you through using Phylogenie. You can explore them to learn how it works or adapt them directly to your own workflows.
+- The [tutorials](https://github.com/gabriele-marino/phylogenie/tree/main/tutorials) folder contains many ready-to-use, extensively commented configuration files that serve as a step-by-step tutorial to guide you through using Phylogenie. You can explore them to learn how it works or adapt them directly to your own workflows.
 - A complete user guide and API reference are under development. In the meantime, feel free to [reach out](mailto:gabmarino.8601@email.com) if you have any questions about integrating Phylogenie into your workflows.
 
 ## 📄 License
@@ -83,4 +82,4 @@ 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!
+For help with configuration files, don’t hesitate to reach out — I’m happy to assist!

{phylogenie-3.1.9 → phylogenie-3.3.0}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "phylogenie"
-version = "3.1.9"
+version = "3.3.0"
 description = "Generate phylogenetic datasets with minimal setup effort"
 readme = "README.md"
 requires-python = ">=3.10"
@@ -17,7 +17,7 @@ dependencies = [
 dev = [
     "joblib-stubs>=1.5.2.0.20250831",
     "pandas-stubs>=2.3.2.250926",
-    "pyright>=1.1.407",
+    "pyright>=1.1.408",
     "pytest>=8.4.2",
 ]
 
@@ -29,4 +29,4 @@ phylogenie = "phylogenie.main:main"
 
 [build-system]
 requires = ["setuptools>=42"]
-build-backend = "setuptools.build_meta"
+build-backend = "setuptools.build_meta"

{phylogenie-3.1.9 → phylogenie-3.3.0}/src/phylogenie/__init__.py

@@ -18,7 +18,8 @@ from phylogenie.generators import (
     FBDTreeDatasetGenerator,
     TreeDatasetGeneratorConfig,
 )
-from phylogenie.io import dump_fasta, load_fasta
+from phylogenie.io import dump_fasta, dump_newick, load_fasta, load_newick, load_nexus
+from phylogenie.main import run
 from phylogenie.msa import MSA, Sequence
 from phylogenie.skyline import (
     SkylineMatrix,
@@ -32,41 +33,26 @@ from phylogenie.skyline import (
     skyline_parameter,
     skyline_vector,
 )
+from phylogenie.tree_node import TreeNode
 from phylogenie.treesimulator import (
     Birth,
-    BirthWithContactTracing,
     Death,
     Event,
-    EventType,
-    Feature,
     Migration,
-    Mutation,
+    Model,
     Sampling,
-    SamplingWithContactTracing,
-    Tree,
-    compute_mean_leaf_pairwise_distance,
-    compute_sackin_index,
-    dump_newick,
+    SamplingAtTime,
+    TimedEvent,
+    UnboundedPopulationEvent,
+    UnboundedPopulationModel,
+    UnboundedPopulationTimedEvent,
     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,
-    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,
 )
 
@@ -88,7 +74,11 @@ __all__ = [
     "FBDTreeDatasetGenerator",
     "TreeDatasetGeneratorConfig",
     "dump_fasta",
+    "dump_newick",
     "load_fasta",
+    "load_newick",
+    "load_nexus",
+    "run",
     "MSA",
     "Sequence",
     "SkylineMatrix",
@@ -101,39 +91,24 @@ __all__ = [
     "skyline_matrix",
     "skyline_parameter",
     "skyline_vector",
+    "TreeNode",
     "Birth",
-    "BirthWithContactTracing",
     "Death",
     "Event",
-    "EventType",
-    "Feature",
     "Migration",
-    "Mutation",
+    "Model",
     "Sampling",
-    "SamplingWithContactTracing",
-    "Tree",
-    "compute_mean_leaf_pairwise_distance",
-    "compute_sackin_index",
-    "dump_newick",
+    "SamplingAtTime",
+    "TimedEvent",
+    "UnboundedPopulationEvent",
+    "UnboundedPopulationModel",
+    "UnboundedPopulationTimedEvent",
     "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",
-    "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",
 ]

phylogenie-3.3.0/src/phylogenie/_mixins.py

@@ -0,0 +1,87 @@
+from collections.abc import Mapping
+from types import MappingProxyType
+from typing import Any
+
+
+class MetadataMixin:
+    """
+    Provide a dictionary-backed metadata interface.
+
+    This mixin exposes read-only access to metadata and helper methods for
+    mutating key/value annotations in a consistent way.
+    """
+
+    def __init__(self):
+        self._metadata: dict[str, Any] = {}
+
+    @property
+    def metadata(self) -> Mapping[str, Any]:
+        """
+        Return a read-only view of metadata.
+
+        Returns
+        --------
+        Mapping[str, Any]
+            An immutable view of the metadata dictionary.
+        """
+        return MappingProxyType(self._metadata)
+
+    def set(self, key: str, value: Any):
+        """
+        Set a metadata key to a value.
+
+        Parameters
+        -----------
+        key : str
+            Metadata key to set.
+        value : Any
+            Value to store under the key.
+        """
+        self._metadata[key] = value
+
+    def update(self, metadata: Mapping[str, Any]):
+        """
+        Merge a mapping of metadata into the existing metadata.
+
+        Parameters
+        -----------
+        metadata : Mapping[str, Any]
+            Key/value pairs to merge into metadata.
+        """
+        self._metadata.update(metadata)
+
+    def get(self, key: str, default: Any = None) -> Any:
+        """
+        Fetch a metadata value with an optional default.
+
+        Parameters
+        -----------
+        key : str
+            Metadata key to retrieve.
+        default : Any, optional
+            Value to return if the key is missing.
+        """
+        return self._metadata.get(key, default)
+
+    def delete(self, key: str):
+        """
+        Delete a metadata key.
+
+        Parameters
+        -----------
+        key : str
+            Metadata key to delete.
+        """
+        del self._metadata[key]
+
+    def clear(self):
+        """
+        Remove all metadata entries.
+        """
+        self._metadata.clear()
+
+    def __getitem__(self, key: str) -> Any:
+        return self._metadata[key]
+
+    def __setitem__(self, key: str, value: Any) -> None:
+        self._metadata[key] = value

phylogenie-3.1.9/src/phylogenie/typeguards.py → phylogenie-3.3.0/src/phylogenie/_typeguards.py

@@ -1,7 +1,7 @@
 from collections.abc import Sequence
 from typing import Any, TypeGuard
 
-import phylogenie.typings as pgt
+import phylogenie._typings as pgt
 
 
 def is_many(x: Any) -> TypeGuard[pgt.Many[Any]]: