crinklywrappr/wolframatte

This is a small, zero-dependency library that allows you to call mathematica.

Coordinates

com.github.crinklywrappr/wolframatte {:mvn/version "1.0.7"}

Why?

clojuratica isn't actively maintained and has been forked lots of times. wolframite is the successor, but it's unfinished and based on clojuratica like everything else. I wanted a simpler, fresh approach.

Usage

Connecting to mathematica

(require '[crinklywrappr.wolframatte.core :refer :all])
(def ml (link "/path/to/jlink.jar"))

Encoding expression

Mathematica/Wolfram One/Wolfram Player are all distributed with JLink.jar. Be sure to include it in your project.

Use the following functions for encoding mathematica expressions.

(li 1 2 3)
;=> Expr "{1, 2, 3}"

(call :Plus 1 2)
;=> Expr "Plus[1, 2]"

(prop {:a 1 :b 2} :a)
;=> Expr "Association[Rule[a, 1], Rule[b, 2]][1]"

;; general purpose encode
(encode {:a 1 :b 2})
;=> Expr "Association[Rule[a, 1], Rule[b, 2]]"

Nest expressions.

(call :Divide (call :Plus 'a 1) (call :Plus 'b 1))
;=> Expr "Divide[Plus[a, 1], Plus[b, 1]]"

The arithmetic operations have special handling

(li '(+ 1 2) '(- 1 2) '(* 1 2) '(/ 1 2) (list pow 1 2))
;=> Expr "{Plus[1, 2], Subtract[1, 2], Times[1, 2], Divide[1, 2], Power[1, 2]}"

Decoding expressions

Use decode:

((juxt #(mapv type %) identity)
 (decode
  (li
   []
   1
   (BigInteger. "1")
   0.01
   (BigDecimal. "0.01")
   3/2
   true false
   "True" "False" "hello, world"
   nil
   {:a 1 :b 2} (first {:a 1 :b 2})
   '(+ 1 2) '(- 1 2) '(* 1 2) '(/ 1 2) (list pow 1 2))))
;=>
[[clojure.lang.PersistentVector
  java.lang.Long
  java.math.BigInteger
  java.lang.Double
  java.math.BigDecimal
  clojure.lang.Ratio
  clojure.lang.Symbol
  clojure.lang.Symbol
  java.lang.String
  java.lang.String
  java.lang.String
  clojure.lang.Symbol
  clojure.lang.PersistentArrayMap
  clojure.lang.MapEntry
  clojure.lang.PersistentList
  clojure.lang.PersistentList
  clojure.lang.PersistentList
  clojure.lang.PersistentList
  clojure.lang.PersistentList]
 [[]
  1
  1
  0.01
  0.01M
  3/2
  True
  False
  "True"
  "False"
  "hello, world"
  Null
  {a 1, b 2}
  [a 1]
  (+ 1 2)
  (- 1 2)
  (* 1 2)
  (/ 1 2)
  (^ 1 2)]]

Querying mathematica

Use answer

(decode (answer ml (call :FactorInteger 12345)))
;=> [[3 1] [5 1] [823 1]]

Less boilerplate

I added some simple boilerplate reduction w/ the following functions and macros:

• wrap-fn: wrap a mathematica expression in a clojure function
• intern-fns: intern mathematica functions in your namespace by name
• with-link: provide the mathlink object for all encapsulated queries
• math: remove (decode (answer ...)) boilerplate

(intern-fns :Solve :Equal :Plus :Power :Times :Function :Take :Sort :Map :GenomeData)

(def genome-fn
    (wrap-fn
     (Function ['n]
               (Take
                (Sort
                 (Map
                  (Function ['gene]
                            [(GenomeData 'gene "SequenceLength") 'gene])
                  (GenomeData)))
                'n))))

 (with-link ml
    (math
     (genome-fn 4)
     (Solve (Equal (Plus (Power 'x 2) (Times 'a 'x) 1) 0) 'x)))               
;=>
[[[11 "IGHD727"] [16 "IGHD411"] [16 "IGHD417"] [16 "IGHD44"]]
 [[[x (* 1/2 (+ (* -1 a) (* -1 (^ (+ -4 (^ a 2)) 1/2))))]]
  [[x (* 1/2 (+ (* -1 a) (^ (+ -4 (^ a 2)) 1/2)))]]]]

Custom encoders/decoders

The following atoms can be modified to include custom encoders/decoders:

• arithmetic: a map of keywords to mathematica functions e.g. (swap arithmetic assoc :fi "FactorInteger")
• encoders: a list of vectors which are [predicate transform]
• decoders: a list of vectors which are [predicate transform]

In addition, you can call add-encoder and add-decoder to place your custom encoders and decoders at the front of the list.

TODO

• Add specific instructions for different systems and build tools
• Add example repository
• Add encoding/decoding examples

License

Copyright © 2023 crinklywrappr

Distributed under the Eclipse Public License version 1.0.