phynetpy 0.2.0__tar.gz

phynetpy-0.2.0/.gitignore

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+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+
+# C extensions
+*.so
+
+# Distribution / packaging
+bin/
+build/
+develop-eggs/
+dist/
+eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+Data/
+Nexus/
+*.egg-info/
+.installed.cfg
+*.egg
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+.tox/
+.coverage
+.cache
+nosetests.xml
+coverage.xml
+
+# Translations
+*.mo
+
+# Mr Developer
+.mr.developer.cfg
+.project
+.pydevproject
+
+# Rope
+.ropeproject
+
+# Django stuff:
+*.log
+*.pot
+
+# Sphinx documentation
+docs/_build/

phynetpy-0.2.0/LICENSE

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+Copyright 2025 Rice University Nakhleh Lab
+
+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.

phynetpy-0.2.0/PKG-INFO

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+Metadata-Version: 2.4
+Name: phynetpy
+Version: 0.2.0
+Summary: A library and framework for Phylogenetics research, data analytics, networks inference, and network tooling.
+Home-page: https://github.com/NakhlehLab/PhyNetPy
+Author: Mark Kessler
+Author-email: mak17@rice.edu
+Project-URL: Bug Reports, https://github.com/NakhlehLab/PhyNetPy/issues
+Project-URL: Source, https://github.com/NakhlehLab/PhyNetPy
+Keywords: phylogenetics,networks,data,biology,graphical modeling,development,methods,statistics,bayesian,python
+Classifier: Development Status :: 3 - Alpha
+Classifier: Intended Audience :: Developers
+Classifier: Intended Audience :: Science/Research
+Classifier: Topic :: Software Development :: Build Tools
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Programming Language :: Python :: 3.8
+Classifier: Programming Language :: Python :: 3.9
+Classifier: Programming Language :: Python :: 3.10
+Requires-Python: >=3.8, <4
+Description-Content-Type: text/markdown
+Requires-Dist: numpy>=1.19.0
+Requires-Dist: scikit-learn>=0.24.0
+Requires-Dist: matplotlib>=3.3.0
+Requires-Dist: networkx>=2.5
+Requires-Dist: biopython>=1.78
+Requires-Dist: python-nexus
+Requires-Dist: newick
+Requires-Dist: scipy>=1.5.0
+Requires-Dist: pulp
+Provides-Extra: dev
+Requires-Dist: check-manifest; extra == "dev"
+Provides-Extra: test
+Requires-Dist: coverage; extra == "test"
+Dynamic: author
+Dynamic: author-email
+Dynamic: classifier
+Dynamic: description
+Dynamic: description-content-type
+Dynamic: home-page
+Dynamic: keywords
+Dynamic: project-url
+Dynamic: provides-extra
+Dynamic: requires-dist
+Dynamic: requires-python
+Dynamic: summary
+
+# PhyNetPy
+
+PhyNetPy is a Python Library that provides some improved methods from PhyloNet, as well as a framework for the development of Bayesian/Simulation based methods and structures.
+
+The current version of this software is v0.1.0, which is the release for the Botany Conference in Boise for July 2023.
+
+This version is unstable, and only meant to provide tutorial functionality. A stable release is planned for September 1, 2023.
+
+To install PhyNetPy, simply open up a command line instance and execute the following:
+`pip install phynetpy`. 
+
+A tutorial and further instructions on how to use PhyNetPy will be made available on our website, https://phylogenomics.rice.edu

phynetpy-0.2.0/README.md

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+# PhyNetPy
+
+PhyNetPy is a Python Library that provides some improved methods from PhyloNet, as well as a framework for the development of Bayesian/Simulation based methods and structures.
+
+The current version of this software is v0.1.0, which is the release for the Botany Conference in Boise for July 2023.
+
+This version is unstable, and only meant to provide tutorial functionality. A stable release is planned for September 1, 2023.
+
+To install PhyNetPy, simply open up a command line instance and execute the following:
+`pip install phynetpy`. 
+
+A tutorial and further instructions on how to use PhyNetPy will be made available on our website, https://phylogenomics.rice.edu

phynetpy-0.2.0/phynetpy.egg-info/PKG-INFO

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+Metadata-Version: 2.4
+Name: phynetpy
+Version: 0.2.0
+Summary: A library and framework for Phylogenetics research, data analytics, networks inference, and network tooling.
+Home-page: https://github.com/NakhlehLab/PhyNetPy
+Author: Mark Kessler
+Author-email: mak17@rice.edu
+Project-URL: Bug Reports, https://github.com/NakhlehLab/PhyNetPy/issues
+Project-URL: Source, https://github.com/NakhlehLab/PhyNetPy
+Keywords: phylogenetics,networks,data,biology,graphical modeling,development,methods,statistics,bayesian,python
+Classifier: Development Status :: 3 - Alpha
+Classifier: Intended Audience :: Developers
+Classifier: Intended Audience :: Science/Research
+Classifier: Topic :: Software Development :: Build Tools
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Programming Language :: Python :: 3.8
+Classifier: Programming Language :: Python :: 3.9
+Classifier: Programming Language :: Python :: 3.10
+Requires-Python: >=3.8, <4
+Description-Content-Type: text/markdown
+Requires-Dist: numpy>=1.19.0
+Requires-Dist: scikit-learn>=0.24.0
+Requires-Dist: matplotlib>=3.3.0
+Requires-Dist: networkx>=2.5
+Requires-Dist: biopython>=1.78
+Requires-Dist: python-nexus
+Requires-Dist: newick
+Requires-Dist: scipy>=1.5.0
+Requires-Dist: pulp
+Provides-Extra: dev
+Requires-Dist: check-manifest; extra == "dev"
+Provides-Extra: test
+Requires-Dist: coverage; extra == "test"
+Dynamic: author
+Dynamic: author-email
+Dynamic: classifier
+Dynamic: description
+Dynamic: description-content-type
+Dynamic: home-page
+Dynamic: keywords
+Dynamic: project-url
+Dynamic: provides-extra
+Dynamic: requires-dist
+Dynamic: requires-python
+Dynamic: summary
+
+# PhyNetPy
+
+PhyNetPy is a Python Library that provides some improved methods from PhyloNet, as well as a framework for the development of Bayesian/Simulation based methods and structures.
+
+The current version of this software is v0.1.0, which is the release for the Botany Conference in Boise for July 2023.
+
+This version is unstable, and only meant to provide tutorial functionality. A stable release is planned for September 1, 2023.
+
+To install PhyNetPy, simply open up a command line instance and execute the following:
+`pip install phynetpy`. 
+
+A tutorial and further instructions on how to use PhyNetPy will be made available on our website, https://phylogenomics.rice.edu

phynetpy-0.2.0/phynetpy.egg-info/SOURCES.txt

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+.DS_Store
+.gitignore
+LICENSE
+README.md
+pyproject.toml
+setup.cfg
+setup.py
+phynetpy.egg-info/PKG-INFO
+phynetpy.egg-info/SOURCES.txt
+phynetpy.egg-info/dependency_links.txt
+phynetpy.egg-info/requires.txt
+phynetpy.egg-info/top_level.txt
+src/PhyNetPy/Alphabet.py
+src/PhyNetPy/BirthDeath.py
+src/PhyNetPy/GTR.py
+src/PhyNetPy/GeneTrees.py
+src/PhyNetPy/GraphUtils.py
+src/PhyNetPy/MSA.py
+src/PhyNetPy/Matrix.py
+src/PhyNetPy/Network.py
+src/PhyNetPy/NetworkMoves.py
+src/PhyNetPy/NetworkParser.py
+src/PhyNetPy/Newick.py
+src/PhyNetPy/PhyloNet.py
+src/PhyNetPy/Validation.py
+src/PhyNetPy/__init__.py
+src/PhyNetPy/test_alphabet.py
+src/PhyNetPy/test_birthdeath.py
+src/PhyNetPy/test_network.py
+src/PhyNetPy/validation_demo.py

phynetpy-0.2.0/phynetpy.egg-info/dependency_links.txt

@@ -0,0 +1 @@
+

phynetpy-0.2.0/phynetpy.egg-info/requires.txt

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+numpy>=1.19.0
+scikit-learn>=0.24.0
+matplotlib>=3.3.0
+networkx>=2.5
+biopython>=1.78
+python-nexus
+newick
+scipy>=1.5.0
+pulp
+
+[dev]
+check-manifest
+
+[test]
+coverage

phynetpy-0.2.0/phynetpy.egg-info/top_level.txt

@@ -0,0 +1 @@
+phynetpy

phynetpy-0.2.0/pyproject.toml

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+[build-system]
+requires = ["setuptools>=61", "wheel", "setuptools_scm"]
+build-backend = "setuptools.build_meta"
+
+

phynetpy-0.2.0/setup.cfg

@@ -0,0 +1,7 @@
+[metadata]
+license_files = LICENSE.txt
+
+[egg_info]
+tag_build = 
+tag_date = 0
+

phynetpy-0.2.0/setup.py

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+# Always prefer setuptools over distutils
+from setuptools import setup, find_packages
+import pathlib
+
+here = pathlib.Path(__file__).parent.resolve()
+
+# Get the long description from the README file
+long_description = (here / "README.md").read_text(encoding="utf-8")
+
+# Arguments marked as "Required" below must be included for upload to PyPI.
+# Fields marked as "Optional" may be commented out.
+
+setup(
+    # This is the name of your project. The first time you publish this
+    # package, this name will be registered for you. It will determine how
+    # users can install this project, e.g.:
+    #
+    # $ pip install sampleproject
+    #
+    # And where it will live on PyPI: https://pypi.org/project/sampleproject/
+    #
+    # There are some restrictions on what makes a valid project name
+    # specification here:
+    # https://packaging.python.org/specifications/core-metadata/#name
+    name="phynetpy",  # Required
+    # Versions should comply with PEP 440:
+    # https://www.python.org/dev/peps/pep-0440/
+    #
+    # For a discussion on single-sourcing the version across setup.py and the
+    # project code, see
+    # https://packaging.python.org/guides/single-sourcing-package-version/
+    version="0.2.0",  # Required
+    # This is a one-line description or tagline of what your project does. This
+    # corresponds to the "Summary" metadata field:
+    # https://packaging.python.org/specifications/core-metadata/#summary
+    description="A library and framework for Phylogenetics research, data analytics, networks inference, and network tooling.",  # Optional
+    # This is an optional longer description of your project that represents
+    # the body of text which users will see when they visit PyPI.
+    #
+    # Often, this is the same as your README, so you can just read it in from
+    # that file directly (as we have already done above)
+    #
+    # This field corresponds to the "Description" metadata field:
+    # https://packaging.python.org/specifications/core-metadata/#description-optional
+    long_description=long_description,  # Optional
+    # Denotes that our long_description is in Markdown; valid values are
+    # text/plain, text/x-rst, and text/markdown
+    #
+    # Optional if long_description is written in reStructuredText (rst) but
+    # required for plain-text or Markdown; if unspecified, "applications should
+    # attempt to render [the long_description] as text/x-rst; charset=UTF-8 and
+    # fall back to text/plain if it is not valid rst" (see link below)
+    #
+    # This field corresponds to the "Description-Content-Type" metadata field:
+    # https://packaging.python.org/specifications/core-metadata/#description-content-type-optional
+    long_description_content_type="text/markdown",  # Optional (see note above)
+    # This should be a valid link to your project's main homepage.
+    #
+    # This field corresponds to the "Home-Page" metadata field:
+    # https://packaging.python.org/specifications/core-metadata/#home-page-optional
+    url="https://github.com/NakhlehLab/PhyNetPy",  # Optional
+    # This should be your name or the name of the organization which owns the
+    # project.
+    author="Mark Kessler",  # Optional
+    # This should be a valid email address corresponding to the author listed
+    # above.
+    author_email="mak17@rice.edu",  # Optional
+    # Classifiers help users find your project by categorizing it.
+    #
+    # For a list of valid classifiers, see https://pypi.org/classifiers/
+    classifiers=[  # Optional
+        # How mature is this project? Common values are
+        #   3 - Alpha
+        #   4 - Beta
+        #   5 - Production/Stable
+        "Development Status :: 3 - Alpha",
+        # Indicate who your project is intended for
+        "Intended Audience :: Developers",
+        "Intended Audience :: Science/Research",
+        "Topic :: Software Development :: Build Tools",
+        # Pick your license as you wish
+        "License :: OSI Approved :: MIT License",
+        # Specify the Python versions you support here. In particular, ensure
+        # that you indicate you support Python 3. These classifiers are *not*
+        # checked by 'pip install'. See instead 'python_requires' below.
+        
+        "Programming Language :: Python :: 3.8",
+        "Programming Language :: Python :: 3.9",
+        "Programming Language :: Python :: 3.10"
+    ],
+    # This field adds keywords for your project which will appear on the
+    # project page. What does your project relate to?
+    #
+    # Note that this is a list of additional keywords, separated
+    # by commas, to be used to assist searching for the distribution in a
+    # larger catalog.
+    keywords="phylogenetics, networks, data, biology, graphical modeling, development, methods, statistics, bayesian, python",  # Optional
+    # When your source code is in a subdirectory under the project root, e.g.
+    # `src/`, it is necessary to specify the `package_dir` argument.
+    package_dir={"phynetpy": "src/PhyNetPy"},  # Optional
+    # You can just specify package directories manually here if your project is
+    # simple. Or you can use find_packages().
+    #
+    # Alternatively, if you just want to distribute a single Python file, use
+    # the `py_modules` argument instead as follows, which will expect a file
+    # called `my_module.py` to exist:
+    #
+    #   py_modules=["my_module"],
+    #
+    packages= ["phynetpy"], #find_packages(where="src"),  # Required
+    # Specify which Python versions you support. In contrast to the
+    # 'Programming Language' classifiers above, 'pip install' will check this
+    # and refuse to install the project if the version does not match. See
+    # https://packaging.python.org/guides/distributing-packages-using-setuptools/#python-requires
+    python_requires=">=3.8, <4",
+    # This field lists other packages that your project depends on to run.
+    # Any package you put here will be installed by pip when your project is
+    # installed, so they must be valid existing projects.
+    #
+    # For an analysis of "install_requires" vs pip's requirements files see:
+    # https://packaging.python.org/discussions/install-requires-vs-requirements/
+    install_requires=[
+        "numpy>=1.19.0",        # Works with Python 3.7+
+        "scikit-learn>=0.24.0", 
+        "matplotlib>=3.3.0",    
+        "networkx>=2.5",        
+        "biopython>=1.78",      
+        "python-nexus",         # No version constraint
+        "newick",               # No version constraint
+        "scipy>=1.5.0",         
+        "pulp",
+        ],  # Optional
+    # List additional groups of dependencies here (e.g. development
+    # dependencies). Users will be able to install these using the "extras"
+    # syntax, for example:
+    #
+    #   $ pip install sampleproject[dev]
+    #
+    # Similar to `install_requires` above, these must be valid existing
+    # projects.
+    extras_require={  # Optional
+        "dev": ["check-manifest"],
+        "test": ["coverage"],
+    },
+    # If there are data files included in your packages that need to be
+    # installed, specify them here.
+    # package_data={  # Optional
+    #     "sample": ["package_data.dat"],
+    # },
+    # Entry points. The following would provide a command called `sample` which
+    # executes the function `main` from this package when invoked:
+    # entry_points={  # Optional
+    #     "console_scripts": [
+    #         "sample=sample:main",
+    #     ],
+    # },
+    # List additional URLs that are relevant to your project as a dict.
+    #
+    # This field corresponds to the "Project-URL" metadata fields:
+    # https://packaging.python.org/specifications/core-metadata/#project-url-multiple-use
+    #
+    # Examples listed include a pattern for specifying where the package tracks
+    # issues, where the source is hosted, where to say thanks to the package
+    # maintainers, and where to support the project financially. The key is
+    # what's used to render the link text on PyPI.
+    project_urls={  # Optional
+        "Bug Reports": "https://github.com/NakhlehLab/PhyNetPy/issues",
+        "Source": "https://github.com/NakhlehLab/PhyNetPy"
+    },
+)