TODO.md

TODO Items and Project Planning for TDA4j

Project Startup

• Set up basic project
• Set up GitHub
• Set up continuous integration testing
• Set up documentation building framework
• Example code org.appliedtopology.tda4j.Simplex
• Example test code org.appliedtopology.tda4j.SimplexSpec

JavaPlex in Scala

• Sketch out class hierarchy to duplicate JavaPlex with particular attention to simple calling interfaces

  • Create a FilteredSimplex class that implements an implicit ordering
  • Rename type variables in Simplex.scala for better understanding
    • [ x] Create an implicit Ordering[FilteredSimplex] that orders by filtration value first, by dimension second, and finally by lexicographic ordering
    • Explore how to create a Stream[FilteredSimplex] from a selection of "maximal" simplices, or an incomplete selection of simplices (this will involve figuring out which additional simplices to add)
    • Add Chain (needs to access Numeric to get + , - , *). SortedMap could work for this, but looking for alternatives. Want Chain[C <: Cell,F] to extend (ie inherit from) C => F(so that it contains an apply(queryCell : C) : F that returns the coefficient at queryCell

• Do what is noted in this link : https://github.com/appliedtopology/tda4j/commit/6fe9b275f1f9af2c598b7bc904494a799abc1c0f#commitcomment-101549463

• Write Perisitent Homology Algos

• Write relevant tests to specify required behaviour

• Write code to duplicate JavaPlex's computations and analyses of persistent homology

• [x ] Write up Test Suite for Chain class

• [x ] Write up ScalaDocs for Chain

• implicit conversion from Cell to Chain

• work on extends Equals to implement canEquals and equals

• FUTURE NOTE - Micheal Robinson to ask for TDA Mathlab api implementation Ex. question: "What can you envision using this library for?"

• END OF LIBRARY IMPLEMENTATION TASK: Look to do a pull-request for RedBlackTree.scala for merging 2 red-black trees (which are the under the hood algorithms for TreeMap, which SortedMap (which is used by chainMap)) (Noted important links :https://github.com/scala/scala/blob/4905801fc161300ba20bae4f7adf045b1698e831/src/library/scala/collection/immutable/RedBlackTree.scala#L1201 and https://github.com/scala/scala/blob/4905801fc161300ba20bae4f7adf045b1698e831/src/library/scala/collection/immutable/RedBlackTree.scala#L943)

Ripser on the JRE

• Sketch out class hierarchy to duplicate Ripser with ability to enlarge for duplicating JavaPlex
• Write relevant tests to specify required behaviour
• Write code to duplicate Ripser's computation of Persistent Homology of Vietoris-Rips complexes

Document

• Port Henry Adams' tutorials to TDA4j.