phypanda 1.0__tar.gz

phypanda-1.0/LICENSE

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+MIT License
+
+Copyright (c) 2025 N. 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.

phypanda-1.0/PKG-INFO

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+Metadata-Version: 2.4
+Name: phypanda
+Version: 1.0
+Summary: package containing the PaNDA framework for exploring, visualizing and maximizing phylogenetic diversity in phylogenetic networks
+Home-page: https://github.com/nholtgrefe/panda/tree/main/phypanda
+Author: N. Holtgrefe
+Author-email: "N. Holtgrefe" <n.a.l.holtgrefe@tudelft.nl>
+Classifier: License :: OSI Approved :: MIT License
+Requires-Python: >=3.7
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: physquirrel<=1.1
+Requires-Dist: numpy>=2.0
+Requires-Dist: networkx>=3.0
+Requires-Dist: matplotlib>=3.7
+Dynamic: license-file
+
+# `phypanda`
+`phypanda` is a Python package that contains PaNDA (Phylogenetic Network Diversity Algorithms): a software framework for exploring, visualizing and maximizing phylogenetic diversity in phylogenetic networks.
+
+
+## List of important features
+- Maximizing all-paths diversity in a rooted phylogenetic network
+- Computing the all-paths diversity for a given set of taxa in a rooted phylogenetic network
+- Greedily select a set of taxa with large all-paths diversity
+
+## Installation
+If you have an up-to-date version of [Python](https://www.python.org/downloads/) installed on your device, the standard package manager `pip` should come pre-installed. Then, you can install `phypanda` from [PyPI](https://pypi.org/project/phypanda/) by simply using the following command in a terminal:
+
+```
+python -m pip install phypanda
+```
+
+  
+## Example usage
+
+### Importing the package
+To get started with `phypanda`, open a Python shell and import the package with:
+
+```
+import phypanda as ppa
+```
+
+### Maximizing all-paths diversity
+To maximize the all-paths diversity of a rooted network (given in `eNewick` format) for a set of `k` taxa, use the function `solve_MAPPD`. For example, when finding a set of 10 taxa with maximum all-paths diversity in the [Xiphophorus network](https://github.com/nholtgrefe/panda/blob/main/data/exp2_xiphophorus_network.txt) from the PaNDA paper, run:
+
+```
+enewick = '((((((((((Xgordoni:1.3295084631587457,Xmeyeri:1.3295084631587457):0.0,Xcouchianus:1.329508093234352):6.999730834529853,Xvariatus:8.329238927764205):2.1769451514229345,Xevelynae:10.50618407918714):1.118605313770228,(Xxiphidium:7.2210504457107145,#H24:0.0):4.403738947246653):0.0,Xmilleri:11.624787067955268):4.296868586395352,Xandersi:15.92165565435062):0.9486610416497712,Xmaculatus:16.87031669600039):0.5723386247384958,((((Xmontezumae:7.221055986870681,(Xcortezi:5.485599585171238,((Xmalinche:5.485605240002155,Xbirchmanni:5.485605240002155):0.0)#H26:0.0):1.7354564016994427):0.0,((Xnigrensis:2.4303498026154564,Xmultilineatus:2.4303498026154564):0.19174715477323678,(Xpygmaeus:1.347820846400494,Xcontinens:1.347820846400494):1.2742761109881993):4.598960284156991):0.0,#H26:1.7354540549075645):0.0)#H24:10.2216024589192):2.1886232296055894,((Xclemenciae:11.254572014210282,Xmonticolus:11.254572014210282):6.4012991117391564,(#H25:1.6332001759073602,(Xsignum:10.266850863153604,((Xhellerii:8.633649976742058)#H25:1.6332013685506936,(Xalvarezi:8.362082334652573,Xmayae:8.362082334652573):1.9047690106401785):0.0):0.0):7.3890209733000205):1.975407424395037);'
+k = 10
+pd, taxa = ppa.solve_MAPPD(enewick, k)
+```
+
+To print the resulting maximum all-paths diversity and the selected taxa, run:
+
+```
+print(f"Maximum all-paths diversity for k = {k} is {pd}")
+print("Selected taxa:", taxa)
+```
+
+        
+For a complete overview of different methods and extra parameter options, please check the method descriptions in the [source code](https://github.com/nholtgrefe/panda/tree/main/phypanda/src/phypanda) of `phypanda`.
+
+
+## Citation
+If you use `phypanda`, please cite the corresponding paper:
+
+> **PaNDA: Efficient Optimization of Phylogenetic Diversity in Networks**.
+> *Niels Holtgrefe, Leo van Iersel, Ruben Meuwese, Yukihiro Murakami, Jannik Schestag.*
+> bioRxiv, 2025. doi: [10.1101/2025.11.14.688467](https://www.biorxiv.org/content/10.1101/2025.11.14.688467)

phypanda-1.0/README.md

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+# `phypanda`
+`phypanda` is a Python package that contains PaNDA (Phylogenetic Network Diversity Algorithms): a software framework for exploring, visualizing and maximizing phylogenetic diversity in phylogenetic networks.
+
+
+## List of important features
+- Maximizing all-paths diversity in a rooted phylogenetic network
+- Computing the all-paths diversity for a given set of taxa in a rooted phylogenetic network
+- Greedily select a set of taxa with large all-paths diversity
+
+## Installation
+If you have an up-to-date version of [Python](https://www.python.org/downloads/) installed on your device, the standard package manager `pip` should come pre-installed. Then, you can install `phypanda` from [PyPI](https://pypi.org/project/phypanda/) by simply using the following command in a terminal:
+
+```
+python -m pip install phypanda
+```
+
+  
+## Example usage
+
+### Importing the package
+To get started with `phypanda`, open a Python shell and import the package with:
+
+```
+import phypanda as ppa
+```
+
+### Maximizing all-paths diversity
+To maximize the all-paths diversity of a rooted network (given in `eNewick` format) for a set of `k` taxa, use the function `solve_MAPPD`. For example, when finding a set of 10 taxa with maximum all-paths diversity in the [Xiphophorus network](https://github.com/nholtgrefe/panda/blob/main/data/exp2_xiphophorus_network.txt) from the PaNDA paper, run:
+
+```
+enewick = '((((((((((Xgordoni:1.3295084631587457,Xmeyeri:1.3295084631587457):0.0,Xcouchianus:1.329508093234352):6.999730834529853,Xvariatus:8.329238927764205):2.1769451514229345,Xevelynae:10.50618407918714):1.118605313770228,(Xxiphidium:7.2210504457107145,#H24:0.0):4.403738947246653):0.0,Xmilleri:11.624787067955268):4.296868586395352,Xandersi:15.92165565435062):0.9486610416497712,Xmaculatus:16.87031669600039):0.5723386247384958,((((Xmontezumae:7.221055986870681,(Xcortezi:5.485599585171238,((Xmalinche:5.485605240002155,Xbirchmanni:5.485605240002155):0.0)#H26:0.0):1.7354564016994427):0.0,((Xnigrensis:2.4303498026154564,Xmultilineatus:2.4303498026154564):0.19174715477323678,(Xpygmaeus:1.347820846400494,Xcontinens:1.347820846400494):1.2742761109881993):4.598960284156991):0.0,#H26:1.7354540549075645):0.0)#H24:10.2216024589192):2.1886232296055894,((Xclemenciae:11.254572014210282,Xmonticolus:11.254572014210282):6.4012991117391564,(#H25:1.6332001759073602,(Xsignum:10.266850863153604,((Xhellerii:8.633649976742058)#H25:1.6332013685506936,(Xalvarezi:8.362082334652573,Xmayae:8.362082334652573):1.9047690106401785):0.0):0.0):7.3890209733000205):1.975407424395037);'
+k = 10
+pd, taxa = ppa.solve_MAPPD(enewick, k)
+```
+
+To print the resulting maximum all-paths diversity and the selected taxa, run:
+
+```
+print(f"Maximum all-paths diversity for k = {k} is {pd}")
+print("Selected taxa:", taxa)
+```
+
+        
+For a complete overview of different methods and extra parameter options, please check the method descriptions in the [source code](https://github.com/nholtgrefe/panda/tree/main/phypanda/src/phypanda) of `phypanda`.
+
+
+## Citation
+If you use `phypanda`, please cite the corresponding paper:
+
+> **PaNDA: Efficient Optimization of Phylogenetic Diversity in Networks**.
+> *Niels Holtgrefe, Leo van Iersel, Ruben Meuwese, Yukihiro Murakami, Jannik Schestag.*
+> bioRxiv, 2025. doi: [10.1101/2025.11.14.688467](https://www.biorxiv.org/content/10.1101/2025.11.14.688467)

phypanda-1.0/pyproject.toml

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+[build-system]
+requires = ["setuptools>=61"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "phypanda"
+version = "1.0"
+description = "package containing the PaNDA framework for exploring, visualizing and maximizing phylogenetic diversity in phylogenetic networks"
+authors = [
+    { name = "N. Holtgrefe", email = "n.a.l.holtgrefe@tudelft.nl" }
+]
+readme = "README.md"
+requires-python = ">=3.7"
+classifiers = ["License :: OSI Approved :: MIT License"]
+
+dependencies = [
+    "physquirrel <= 1.1",
+    "numpy >= 2.0",
+    "networkx >= 3.0",
+    "matplotlib >= 3.7",
+]
+
+[tool.setuptools.packages.find]
+where = ["src"]

phypanda-1.0/setup.cfg

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+[metadata]
+name = phypanda
+version = 1.0
+author = N. Holtgrefe
+author_email = n.a.l.holtgrefe@tudelft.nl
+description = package containing the PaNDA framework for exploring, visualizing and maximizing phylogenetic diversity in phylogenetic networks
+long_description = file: README.md
+long_description_content_type = text/markdown
+url = https://github.com/nholtgrefe/panda/tree/main/phypanda
+classifiers = 
+	Programming Language :: Python :: 3
+	License :: OSI Approved :: MIT License
+	Operating System :: OS Independent
+
+[options]
+package_dir = 
+	= src
+packages = find:
+python_requires = >=3.6
+install_requires = 
+	physquirrel <= 1.1
+	numpy >= 1.20
+	networkx >= 3.0
+	matplotlib >= 3.7
+
+[options.packages.find]
+where = src
+
+[egg_info]
+tag_build = 
+tag_date = 0
+

phypanda-1.0/src/phypanda/__init__.py

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+from .mappd import DirectedNetwork, DP_instance, solve_MAPPD 
+from .scanwidth import TreeExtension, DAG