script to generate docs

Generating_Documentation.md

@@ -1,4 +1,8 @@
-To generate documentation with codox, run "lein codox" on command line to generate first batch of HTMl files.
+# Generating Documentation for Propeller
-Then, run FunctionsToMD to take Push instructions generated by `def-instruction` and spit it out to a Markdown file.
+
-Then, run HTMLFix to fix the ordered lists in `Adding_Genetic_Operators.md`, `Adding_Problem.md`, and 
+To generate documentation with [codox](https://github.com/weavejester/codox), run `GenerateDocs.sh` in the command line. 
+This will run "lein codox" on the command line to generate first batch of HTMl files.
+Then, it runs FunctionsToMD to take Push instructions generated by `def-instruction` and spit it out to a Markdown file.
+Then, it runs HTMLFix to fix the ordered lists in `Adding_Genetic_Operators.md`, `Adding_Problem.md`, and 
 `Adding_Selection_Method.md`. 
+

deps.edn

@@ -7,5 +7,7 @@
  :mvn/repos {}
  :codox {:extra-deps {codox/codox {:mvn/version "0.10.8"}}
          :exec-fn codox.main/generate-docs
-         :exec-args {:source-paths ["path/to/src"]}
+         :exec-args {:doc-paths ["src/docs_src"]
+                     :output-path "docs"
+                     :metadata {:doc "FIXME: write docs" :doc/format :markdown}}
          }}

docs/Adding_Problem.html

@@ -25,6 +25,7 @@
 <li>Define the possible Push instructions to be used to create plushys. It should be a non-lazy list of instructions from <code>push/instructions</code></li>
 <li>Define an error function that will evaluate plushys and add <code>:behaviors parsed-outputs</code>, <code>:errors</code>, and <code>:total-error</code> to the individual</li>
 <li>Define the function <code>-main</code> with a map of default arguments.</li>
+</ol>
 <h2><a href="#example-of-a-problem" id="example-of-a-problem"></a>Example of a Problem</h2>
 <pre><code class="language-clojure">(ns propeller.problems.PSB2.solve-boolean
   (:require [psb2.core :as psb2]

docs/Adding_Selection_Method.html

@@ -14,4 +14,5 @@
 <pre><code>lein run -m propeller.problems.simple-regression :parent-selection :new-selection-method"
 </code></pre>
 </li>
+</ol>
 </div></div></div></body></html>

docs/index.html

@@ -25,7 +25,7 @@
 </div></div><div class="index"><p>Public variables and functions:</p><ul><li> <a href="propeller.problems.software.number-io.html#var--main">-main</a> </li><li> <a href="propeller.problems.software.number-io.html#var-error-function">error-function</a> </li><li> <a href="propeller.problems.software.number-io.html#var-instructions">instructions</a> </li><li> <a href="propeller.problems.software.number-io.html#var-random-float">random-float</a> </li><li> <a href="propeller.problems.software.number-io.html#var-random-int">random-int</a> </li><li> <a href="propeller.problems.software.number-io.html#var-train-and-test-data">train-and-test-data</a> </li></ul></div></div><div class="namespace"><h3><a href="propeller.problems.software.smallest.html">propeller.problems.software.smallest</a></h3><div class="doc"><div class="markdown"><p>SMALLEST PROBLEM from C. Le Goues et al., "The ManyBugs and IntroClass Benchmarks</p>
 </div></div><div class="index"><p>Public variables and functions:</p><ul><li> <a href="propeller.problems.software.smallest.html#var--main">-main</a> </li><li> <a href="propeller.problems.software.smallest.html#var-error-function">error-function</a> </li><li> <a href="propeller.problems.software.smallest.html#var-instructions">instructions</a> </li><li> <a href="propeller.problems.software.smallest.html#var-random-int">random-int</a> </li><li> <a href="propeller.problems.software.smallest.html#var-train-and-test-data">train-and-test-data</a> </li></ul></div></div><div class="namespace"><h3><a href="propeller.problems.string-classification.html">propeller.problems.string-classification</a></h3><div class="doc"><div class="markdown"><p>String Classification:</p>
 </div></div><div class="index"><p>Public variables and functions:</p><ul><li> <a href="propeller.problems.string-classification.html#var--main">-main</a> </li><li> <a href="propeller.problems.string-classification.html#var-error-function">error-function</a> </li><li> <a href="propeller.problems.string-classification.html#var-instructions">instructions</a> </li><li> <a href="propeller.problems.string-classification.html#var-train-and-test-data">train-and-test-data</a> </li></ul></div></div><div class="namespace"><h3><a href="propeller.problems.valiant.html">propeller.problems.valiant</a></h3><div class="doc"><div class="markdown"><p>Possibly impossible to solve with genetic programming. Stems from the work of Leslie Valiant and involves determining the parity of an unknown subsequence of a larger sequence of bits.</p>
-</div></div><div class="index"><p>Public variables and functions:</p><ul><li> <a href="propeller.problems.valiant.html#var--main">-main</a> </li><li> <a href="propeller.problems.valiant.html#var-error-function">error-function</a> </li><li> <a href="propeller.problems.valiant.html#var-instructions">instructions</a> </li><li> <a href="propeller.problems.valiant.html#var-num-inputs">num-inputs</a> </li><li> <a href="propeller.problems.valiant.html#var-num-test">num-test</a> </li><li> <a href="propeller.problems.valiant.html#var-num-train">num-train</a> </li><li> <a href="propeller.problems.valiant.html#var-num-vars">num-vars</a> </li><li> <a href="propeller.problems.valiant.html#var-train-and-test-data">train-and-test-data</a> </li></ul></div></div><div class="namespace"><h3><a href="propeller.push.instructions.html">propeller.push.instructions</a></h3><div class="doc"><div class="markdown"><p>Push Instructions</p>
+</div></div><div class="index"><p>Public variables and functions:</p><ul><li> <a href="propeller.problems.valiant.html#var--main">-main</a> </li><li> <a href="propeller.problems.valiant.html#var-error-function">error-function</a> </li><li> <a href="propeller.problems.valiant.html#var-instructions">instructions</a> </li><li> <a href="propeller.problems.valiant.html#var-train-and-test-data">train-and-test-data</a> </li></ul></div></div><div class="namespace"><h3><a href="propeller.push.instructions.html">propeller.push.instructions</a></h3><div class="doc"><div class="markdown"><p>Push Instructions</p>
 </div></div><div class="index"><p>Public variables and functions:</p><ul><li> <a href="propeller.push.instructions.html#var-def-instruction">def-instruction</a> </li><li> <a href="propeller.push.instructions.html#var-generate-instructions">generate-instructions</a> </li><li> <a href="propeller.push.instructions.html#var-get-literal-type">get-literal-type</a> </li><li> <a href="propeller.push.instructions.html#var-get-stack-instructions">get-stack-instructions</a> </li><li> <a href="propeller.push.instructions.html#var-get-vector-literal-type">get-vector-literal-type</a> </li><li> <a href="propeller.push.instructions.html#var-instruction-table">instruction-table</a> </li><li> <a href="propeller.push.instructions.html#var-make-instruction">make-instruction</a> </li><li> <a href="propeller.push.instructions.html#var-make-metadata">make-metadata</a> </li><li> <a href="propeller.push.instructions.html#var-opens">opens</a> </li></ul></div></div><div class="namespace"><h3><a href="propeller.push.instructions.bool.html">propeller.push.instructions.bool</a></h3><div class="doc"><div class="markdown"><p>BOOLEAN Instructions, created with <code>propeller.push.instructions/def-instruction</code>. List of instructions can be found at <a href="Additional_Instructions.html">Additional Instructions</a>.</p>
 </div></div><div class="index"><p>Public variables and functions:</p><ul></ul></div></div><div class="namespace"><h3><a href="propeller.push.instructions.character.html">propeller.push.instructions.character</a></h3><div class="doc"><div class="markdown"><p>CHAR Instructions, created with <code>propeller.push.instructions/def-instruction</code>. List of instructions can be found at <a href="Additional_Instructions.html">Additional Instructions</a>.</p>
 </div></div><div class="index"><p>Public variables and functions:</p><ul></ul></div></div><div class="namespace"><h3><a href="propeller.push.instructions.code.html">propeller.push.instructions.code</a></h3><div class="doc"><div class="markdown"><p>CODE Instructions, created with <code>propeller.push.instructions/def-instruction</code>. List of instructions can be found at <a href="Additional_Instructions.html">Additional Instructions</a>.</p>

scripts/GenerateDocs.sh

@@ -0,0 +1,5 @@
+#!/bin/sh
+
+lein codox
+python3 FunctionsToMD.py
+python3 HTMLFix.py

src/propeller/problems/valiant.cljc

@@ -8,10 +8,10 @@
             [propeller.gp :as gp]
             #?(:cljs [cljs.reader :refer [read-string]])))
 
-(def num-vars 100)                                          ;10) ;100)                                          ;1000)
+(def ^:no-doc num-vars 100)                                          ;10) ;100)                                          ;1000)
-(def num-inputs 50)                                         ;5) ; 50)                                         ;500)
+(def ^:no-doc num-inputs 50)                                         ;5) ; 50)                                         ;500)
-(def num-train 500)                                         ;5000)
+(def ^:no-doc num-train 500)                                         ;5000)
-(def num-test 200)
+(def ^:no-doc num-test 200)
 
 (def train-and-test-data
   "Inputs are `num-train` random boolean values and outputs are the

src/propeller/push/instructions/numeric.cljc

@@ -167,6 +167,7 @@ Otherwise, acts as a NOOP"
 
 ;; Pushes the decrement (i.e. -1) of the top item of the stack
 (def _dec
+  "Pushes the decrement (i.e. -1) of the top item of the stack"
   ^{:stacks #{}
     :name "_dec"}
   (fn [stack state]

src/propeller/push/state.cljc

@@ -39,7 +39,7 @@
                         :vector_integer #(mapv (fn [i] (int (l/limit-number i))) (l/limit-vector %))
                         :vector_string  #(mapv (fn [s] (l/limit-string s)) (l/limit-vector %))})
 
-(def example-state {:exec    '()
+(def example-state "Example of a Push state." {:exec    '()
                     :integer '(1 2 3 4 5 6 7)
                     :string  '("abc")
                     :input   {:in1 4}})