phylozoo 0.1.0__tar.gz

phylozoo-0.1.0/LICENSE.md

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+# MIT License
+
+Copyright (c) 2026 Niels Holtgrefe
+
+Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the “Software”), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED “AS IS”, WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

phylozoo-0.1.0/PKG-INFO

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+Metadata-Version: 2.4
+Name: phylozoo
+Version: 0.1.0
+Summary: A phylogenetic networks analysis package
+Author-email: Niels Holtgrefe <n.a.l.holtgrefe@tudelft.nl>
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Requires-Python: >=3.10
+Description-Content-Type: text/markdown
+License-File: LICENSE.md
+Requires-Dist: numpy>=1.20.0
+Requires-Dist: numba>=0.56.0
+Requires-Dist: networkx>=3.0.0
+Provides-Extra: viz
+Requires-Dist: matplotlib>=3.5.0; extra == "viz"
+Provides-Extra: graphviz
+Requires-Dist: matplotlib>=3.5.0; extra == "graphviz"
+Requires-Dist: pygraphviz; extra == "graphviz"
+Provides-Extra: test
+Requires-Dist: pytest>=7.0.0; extra == "test"
+Requires-Dist: pytest-cov>=4.0.0; extra == "test"
+Requires-Dist: matplotlib>=3.5.0; extra == "test"
+Provides-Extra: dev
+Requires-Dist: pytest>=7.0.0; extra == "dev"
+Requires-Dist: pytest-cov>=4.0.0; extra == "dev"
+Requires-Dist: matplotlib>=3.5.0; extra == "dev"
+Requires-Dist: mypy>=1.0.0; extra == "dev"
+Requires-Dist: black>=23.0.0; extra == "dev"
+Requires-Dist: ruff>=0.1.0; extra == "dev"
+Provides-Extra: docs
+Requires-Dist: sphinx>=7.0.0; extra == "docs"
+Requires-Dist: sphinx-autobuild>=2023.0.0; extra == "docs"
+Requires-Dist: sphinx-rtd-theme>=2.0.0; extra == "docs"
+Requires-Dist: pydata-sphinx-theme>=0.15.0; extra == "docs"
+Requires-Dist: sphinxcontrib-napoleon>=0.7; extra == "docs"
+Requires-Dist: sphinx-copybutton>=0.5.0; extra == "docs"
+Requires-Dist: sphinxcontrib-bibtex>=2.6.0; extra == "docs"
+Requires-Dist: pybtex>=0.24.0; extra == "docs"
+Dynamic: license-file
+
+
+[![PyPI](https://img.shields.io/pypi/v/phylozoo)](https://pypi.org/project/phylozoo/)
+[![License](https://img.shields.io/github/license/nholtgrefe/phylozoo)](https://github.com/nholtgrefe/phylozoo/blob/main/LICENSE.md)
+[![Docs](https://img.shields.io/badge/docs-stable-blue)](https://nholtgrefe.github.io/phylozoo/)
+
+<img src="https://github.com/nholtgrefe/phylozoo/blob/master/docs/source/_static/phylozoo_compact.svg" alt="PhyloZoo" width="375" align="left">
+
+PhyloZoo is a Python package for working with phylogenetic networks and related evolutionary
+data types. PhyloZoo aims to provide the foundational infrastructure for
+phylogenetic network analysis in Python — a common framework that other packages can build on.
+
+<br>
+
+## Key Features
+
+- **Directed & semi-directed networks** — represent phylogenetic networks as fully directed rooted DAGs or as semi-directed/mixed graphs that allow root uncertainty. Both representations are validated on construction to guarantee well-formed phylogenetic objects. Includes a rich library of operations: network classifications, generators, conversions between representations, and much more.
+- **Quartets, splits & distance matrices** — support for quartet systems, split systems, and pairwise distance matrices: the core building blocks for phylogenetic inference and comparison.
+- **Multiple sequence alignments** — store and manipulate sequence data with efficient NumPy-backed arrays, including bootstrapping and site-pattern extraction.
+- **Flexible visualization** — plot networks with different layouts and fine-grained control over styling, labels, and coloring via Matplotlib.
+- **Standard file formats** — read and write common phylogenetic formats including eNewick, DOT, FASTA, and NEXUS, making it easy to integrate with existing workflows.
+- **Performance** — leverages NumPy and optional Numba JIT compilation for computationally intensive algorithms.
+
+
+## Installation
+
+To install the recommended version that includes vizualization, do:
+
+```bash
+pip install phylozoo[viz]
+```
+
+## Documentation
+
+For detailed documentation, installation instructions, tutorials, and API reference, visit the **[PhyloZoo docs](https://nholtgrefe.github.io/phylozoo/)**.
+
+## Citation
+
+If you use PhyloZoo in your research, please cite:
+
+> Niels Holtgrefe (2026). *PhyloZoo*. Available at: https://github.com/nholtgrefe/phylozoo

phylozoo-0.1.0/README.md

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+
+[![PyPI](https://img.shields.io/pypi/v/phylozoo)](https://pypi.org/project/phylozoo/)
+[![License](https://img.shields.io/github/license/nholtgrefe/phylozoo)](https://github.com/nholtgrefe/phylozoo/blob/main/LICENSE.md)
+[![Docs](https://img.shields.io/badge/docs-stable-blue)](https://nholtgrefe.github.io/phylozoo/)
+
+<img src="https://github.com/nholtgrefe/phylozoo/blob/master/docs/source/_static/phylozoo_compact.svg" alt="PhyloZoo" width="375" align="left">
+
+PhyloZoo is a Python package for working with phylogenetic networks and related evolutionary
+data types. PhyloZoo aims to provide the foundational infrastructure for
+phylogenetic network analysis in Python — a common framework that other packages can build on.
+
+<br>
+
+## Key Features
+
+- **Directed & semi-directed networks** — represent phylogenetic networks as fully directed rooted DAGs or as semi-directed/mixed graphs that allow root uncertainty. Both representations are validated on construction to guarantee well-formed phylogenetic objects. Includes a rich library of operations: network classifications, generators, conversions between representations, and much more.
+- **Quartets, splits & distance matrices** — support for quartet systems, split systems, and pairwise distance matrices: the core building blocks for phylogenetic inference and comparison.
+- **Multiple sequence alignments** — store and manipulate sequence data with efficient NumPy-backed arrays, including bootstrapping and site-pattern extraction.
+- **Flexible visualization** — plot networks with different layouts and fine-grained control over styling, labels, and coloring via Matplotlib.
+- **Standard file formats** — read and write common phylogenetic formats including eNewick, DOT, FASTA, and NEXUS, making it easy to integrate with existing workflows.
+- **Performance** — leverages NumPy and optional Numba JIT compilation for computationally intensive algorithms.
+
+
+## Installation
+
+To install the recommended version that includes vizualization, do:
+
+```bash
+pip install phylozoo[viz]
+```
+
+## Documentation
+
+For detailed documentation, installation instructions, tutorials, and API reference, visit the **[PhyloZoo docs](https://nholtgrefe.github.io/phylozoo/)**.
+
+## Citation
+
+If you use PhyloZoo in your research, please cite:
+
+> Niels Holtgrefe (2026). *PhyloZoo*. Available at: https://github.com/nholtgrefe/phylozoo

phylozoo-0.1.0/pyproject.toml

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+[build-system]
+requires = ["setuptools>=61.0"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "phylozoo"
+dynamic = ["version"]
+authors = [
+    {name = "Niels Holtgrefe", email = "n.a.l.holtgrefe@tudelft.nl"},
+]
+description = "A phylogenetic networks analysis package"
+readme = "README.md"
+requires-python = ">=3.10"
+classifiers = [
+    "License :: OSI Approved :: MIT License",
+    "Programming Language :: Python :: 3",
+    "Programming Language :: Python :: 3.10",
+    "Programming Language :: Python :: 3.11",
+]
+dependencies = [
+    "numpy>=1.20.0",
+    "numba>=0.56.0",
+    "networkx>=3.0.0",
+]
+
+[project.optional-dependencies]
+viz = [
+    "matplotlib>=3.5.0",
+]
+graphviz = [
+    "matplotlib>=3.5.0",
+    "pygraphviz",
+]
+test = [
+    "pytest>=7.0.0",
+    "pytest-cov>=4.0.0",
+    "matplotlib>=3.5.0",
+]
+dev = [
+    "pytest>=7.0.0",
+    "pytest-cov>=4.0.0",
+    "matplotlib>=3.5.0",
+    "mypy>=1.0.0",
+    "black>=23.0.0",
+    "ruff>=0.1.0",
+]
+docs = [
+    "sphinx>=7.0.0",
+    "sphinx-autobuild>=2023.0.0",
+    "sphinx-rtd-theme>=2.0.0",
+    "pydata-sphinx-theme>=0.15.0",
+    "sphinxcontrib-napoleon>=0.7",
+    "sphinx-copybutton>=0.5.0",
+    "sphinxcontrib-bibtex>=2.6.0",
+    "pybtex>=0.24.0",
+]
+
+[tool.setuptools]
+package-dir = {"" = "src"}
+
+[tool.setuptools.dynamic]
+version = {attr = "phylozoo.__version__"}
+
+[tool.setuptools.packages.find]
+where = ["src"]
+
+[tool.pytest.ini_options]
+testpaths = ["tests"]
+python_files = ["test_*.py", "*_test.py"]
+python_classes = ["Test*"]
+python_functions = ["test_*"]
+addopts = [
+    "-v",
+    "--strict-markers",
+    "--tb=short",
+    "--import-mode=importlib",
+]
+filterwarnings = [
+    "ignore:Empty network.*no nodes.*:UserWarning",
+    "ignore:Single-node network.*:UserWarning",
+    "ignore:Validity is not fully checked for MixedPhyNetworks.*:UserWarning",
+]
+
+[tool.mypy]
+python_version = "3.10"
+warn_return_any = true
+warn_unused_configs = true
+disallow_untyped_defs = false
+disallow_incomplete_defs = false
+check_untyped_defs = true
+no_implicit_optional = true
+warn_redundant_casts = true
+warn_unused_ignores = true
+warn_no_return = true
+
+[tool.black]
+line-length = 100
+target-version = ['py310', 'py311']
+
+[tool.ruff]
+line-length = 100
+target-version = "py310"
+

phylozoo-0.1.0/setup.cfg

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+[egg_info]
+tag_build = 
+tag_date = 0
+

phylozoo-0.1.0/src/phylozoo/__init__.py

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+"""
+PhyloZoo: A phylogenetic analysis package.
+
+This package provides tools for working with phylogenetic networks, trees,
+and related structures.
+"""
+
+__version__ = "0.1.0"
+
+# Import core classes for convenient access
+from .core import (
+    # Networks
+    DirectedPhyNetwork,
+    SemiDirectedPhyNetwork,
+    # Structures
+    Split,
+    SplitSystem,
+    # Distance
+    DistanceMatrix,
+    # Sequence
+    MSA,
+    # Quartet
+    Quartet,
+    QuartetProfile,
+    QuartetProfileSet,
+)
+
+# Import alias modules to register them
+# These allow: from phylozoo.core.dnetwork import ... instead of from phylozoo.core.network.dnetwork import ...
+from .core import dnetwork  # noqa: F401
+from .core import sdnetwork  # noqa: F401
+
+__all__ = [
+    "__version__",
+    # Core - Networks
+    "DirectedPhyNetwork",
+    "SemiDirectedPhyNetwork",
+    # Core - Structures
+    "Split",
+    "SplitSystem",
+    # Core - Distance
+    "DistanceMatrix",
+    # Core - Sequence
+    "MSA",
+    # Core - Quartet
+    "Quartet",
+    "QuartetProfile",
+    "QuartetProfileSet",
+]

phylozoo-0.1.0/src/phylozoo/core/__init__.py

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+"""
+Core module for PhyloZoo.
+
+This module contains fundamental data structures and classes used throughout
+the package.
+"""
+
+from .network import DirectedPhyNetwork, SemiDirectedPhyNetwork
+from .split import Split, SplitSystem, WeightedSplitSystem
+from .distance import DistanceMatrix
+from .sequence import MSA
+from .quartet import Quartet, QuartetProfile, QuartetProfileSet
+
+__all__ = [
+    # Networks
+    "DirectedPhyNetwork",
+    "SemiDirectedPhyNetwork",
+    # Split structures
+    "Split",
+    "SplitSystem",
+    "WeightedSplitSystem",
+    # Distance
+    "DistanceMatrix",
+    # Sequence
+    "MSA",
+    # Quartet
+    "Quartet",
+    "QuartetProfile",
+    "QuartetProfileSet",
+]
+

phylozoo-0.1.0/src/phylozoo/core/distance/__init__.py

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+"""
+Distance module.
+
+This module provides classes and functions for working with distance matrices. A
+distance matrix represents pairwise distances between a set of labeled items, where
+distances satisfy properties such as symmetry and non-negativity. The public API
+(DistanceMatrix and the classifications, operations, io submodules) is re-exported
+here; the implementation is split across the base, classifications, operations,
+and io submodules.
+"""
+
+from .base import DistanceMatrix
+from . import classifications, operations, io
+
+__all__ = [
+    "DistanceMatrix",
+    "classifications",
+    "operations",
+    "io",
+]