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 utilities.
  - [[file:functions.rkt][functions.rkt]]: Definitions for working with functions: tabulating,
    constructing from tables, generating random functions, etc.
  - [[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 as a structure, from which
    all the concrete dynamics of the objects will inherit.  This will
    hopefully work like interface inheritance.  The current plan is to
    start converting =networks= to Typed Racket, then starting the new
    module =dynamics= to fill in the blanks progressively by moving
    over bits of code from =generics=.  The goal is to have an empty
    =generics= module at the end.

    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. =networks= and =dynamics= (currently =generics=) at the same
       time,
    4. =networks=,
    5. =rs=.

    I will convert the modules one by one by first creating a typed
    section (a submodule) and re-exporting its functions together with
    the untyped functions.  I will then move the functions one by one
    from the untyped section to the typed section.  When the untyped
    section is empty, I will convert the language of the entire module
    to Typed Racket and remove the submodule.

*** TODO Remove the artifacts of conversion to Typed Racket
    Since I am converting =dds= to Typed Racket gradually, I need to
    leave a couple artifacts to ensure that older code compiles with
    newer code.  These artifacts are marked with the keywords =TODO:=
    in the source.

*** TODO Fix =ob-racket= to work with Typed Racket
Currently, the =ob-racket= backend for running Racket code blocks in
Org-mode assumes the code is written in =#lang racket=, which breaks
the output for tables for example.  This makes the typed version of
=dds= essentially useless with tables.

*** TODO Fix [[file:example/example.org][example.org]]
I changed quite a number of things while converting =dds= to Typed
Racket, which should break a lot of things in [[file:example/example.org][example.org]].

*** TODO Think about splitting the library into lib and doc

*** TODO Consider splitting =dds/utils= into a separate package
*** TODO Implement [[https://en.wikipedia.org/wiki/P_system][P systems]]
*** TODO Implement a shorter syntax for defining Boolean functions
    Right now, this is how one defines the Boolean function:

    #+BEGIN_SRC racket :results output silent
(define (update-go st)
  (auto-hash-ref/:
   st
   (or (and (not :Go) :new-x) (and :Go :old-x))))
    #+END_SRC

    It would be nice and probably not too difficult to implement
    a macro allowing for a syntax like the following one:
    #+BEGIN_SRC racket :results output silent
(define-pbf my-pbf (or (and (not :Go) :new-x) (and :Go :old-x)))
    #+END_SRC

*** TODO Implement =monotone?=
    =monotone?= would verify whether a given Boolean function is
    monotone according to the definition in the book /Boolean
    Functions: Theory, Algorithms, and Applications/ by Crama
    and Hammer.

*** TODO Submit =update-graph= to =stchang=
*** DONE Split =networks= into general networks and threshold Boolean networks
*** TODO Consider optimizing the algorithms in =networks= and =dynamics=
*** 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]]