PyTree
A fast implementation of trees from the mathematical theory of graphs
Inspired and applied in condensed matter physics,
cellular biology and the World Wide Web.
Mathematical Introduction
Graphs
Mathematical objects of the theory of graphs have one-to-one matrix
representations, as described by the theory of linear algebra.
In general, a graph is a network structure, whose off-diagonal terms
in the matrix representation are known to Condensed Matter Physicists
as hopping or interaction terms.
Trees
A particular graph, known as a tree, is a network with a
hierarchical structure, which we use to index
objects in their matrix representation.
Python implementation
The Tree is a Python subclass of a List, which adds the following attributes and methods:
Attributes
- parent : Tree or none (default)
children : Tree or none (default)
- ancestors : list of Trees lineage upwards
- root: root of the tree (parent without parent)
- descendants : lists lineage downwards (list of list of Trees)
- buds : lists descendants without descendants
Methods
- set_ids : add an index (id) to the buds of this Tree
- get_ids : get the indices (ids) of the buds of this Tree
.attribute : attributes are inherited down the linage
Summary
A graph structure defines a matrix; a tree structure
indexes the matrix.
The tree structure adds parents,
children, ancestors, descendants and inheritance of attributes.
Installation
Development environment
pip install --editable . --break-system-packages
Build and upload
python3 -m build
twine upload dist/*