dds/README.org

* dds: A Home-made Toolkit for Discrete Dynamical Systems in Racket
This is a toolkit for playing with various discrete dynamical systems
in [[https://racket-lang.org/][Racket]].  A discrete dynamical system is a system which evolves from
a discrete state to some other discrete states (many or one).  The
systems are discrete in the sense that we can identify successive
states with no other states in between.  Equivalently, the phase state
of the system is discrete (and is often called the state graph).
These constraints imply the possibility of associating discrete,
possibly branching timelines to any evolution of the system.

*DISCLAIMER:* I develop this toolkit as a support for my research on
discrete dynamical systems.  The primary objective for this framework
is to fit my approach to these systems.  Essentially, this framework
should fit to the "shape of my mind", which is not necessarily the
same as yours.

Currently, the toolkit includes the following files:

  - [[file:generic.rkt][generic.rkt]]: The generic interface for a discrete dynamical
    system, with functions for constructing state graphs.
  - [[file:utils.rkt][utils.rkt]]: Misc utility functions.
  - [[file:networks.rkt][networks.rkt]]: Implements network-based models, which generalise
    Boolean networks, threshold Boolean automata networks, multivalued
    networks, etc.
  - [[file:rs.rkt][rs.rkt]]: Implements reaction systems, a variant of set rewriting.

The toolkit is designed with Emacs [[https://orgmode.org/][Org-mode]] interoperability in mind.
The file [[file:example/example.org][example/example.org]] explains the features available for
interaction with Org-mode.

** Roadmap
   Here is my current roadmap for this toolkit, in order.  The first
   element is what I am currently working on.  The degree of certainty
   that I work on the subsequent items decreases with their position
   in the list.

*** TODO Convert =dds= to Typed Racket
    Rewriting =dds= with Typed Racket will be a major refactoring,
    consisting in the following 3 phases which will happen more or
    less in parallel:

    - define types, add type signatures, add types for functions
      I import from =graph=;
    - transfer the comments from the source files to Scribble
      documentation;
    - redefine the generic interface for dynamics, which is currently
      in =generics=.

    I plan to implement the new dynamics interface as a classes, since
    Typed Racket can now type classes.  I didn't really like generics:
    they are quite cumbersome, and I think I can do more with classes.

    People on Racket Users suggested using structures with fields
    containing functions, but it does not seem to get me to my goal of
    having type-level methods/functions.

    The order in which I will convert the modules:

    1. =utils=
    2. =functions=
    3. =dynamics= (currently =generics=)
    4. =networks=
    5. =rs=

    This is how I will convert a module =A=:

    1. Create a copy =A-untyped.rkt=.
    2. Empty =A.rkt=.
    3. Transfer the definitions from =A-untyped.rkt= to =A.rkt= one by
       one, adding the necessary types, signatures, and typed imports
       as I go.
    4. When done, remove =A-untyped.rkt=.

*** TODO Split =networks= into general networks and threshold Boolean networks
*** TODO Submit =update-graph= to =stchang=
*** TODO Implement the BN \to RS conversion
*** TODO Implement the minimisation of TBF/SBF
*** TODO Contribute to Racket
    - Make sequence-filter allow multivalued sequences, provided the
      arity of the predicate is consistent with the arity of
      the sequence.
    - Add a sequence->hash function that accepts a multivalued
      sequence of keys and values (exactly like what in-hash produces)
      and copies them into a hash table.
*** TODO Test network inference with [[https://docs.racket-lang.org/racklog/index.html][Racklog]]