Merge branch 'master' into track-selection-counts

project.clj

@@ -1,4 +1,4 @@
-(defproject clojush "2.0.27"
+(defproject clojush "2.0.28"
   :description "The Push programming language and the PushGP genetic programming
                 system implemented in Clojure.
                 See http://hampshire.edu/lspector/push.html"

src/clojush/instructions/genome.clj

@@ -21,7 +21,8 @@
     (if (and (not (empty? (:integer state)))
              (not (empty? (:genome state)))
              (not (empty? (stack-ref :genome 0 state)))
-             (< (count (first (:genome state))) @global-max-points)) ;; should really be max genome length
+             (< (count (first (:genome state)))
+                (/ @global-max-points 2)))
       (let [genome (stack-ref :genome 0 state)
             index (mod (stack-ref :integer 0 state) (count genome))]
         (->> (pop-item :integer state)

src/clojush/problems/boolean/digital_multiplier.clj

@@ -129,8 +129,8 @@
      :atom-generators (dm-atom-generators num-bits-n)
      :population-size 1000
      :max-generations 500
-     :max-points 400
-     :max-points-in-initial-program 200
+     :max-points 800
+     :max-genome-size-in-initial-program 200
      :evalpush-limit 400
      :epigenetic-markers []
      :genetic-operator-probabilities {[:alternation :uniform-mutation] 1}

src/clojush/problems/boolean/mux_11.clj

@@ -79,8 +79,8 @@
                               ;boolean_dup boolean_swap boolean_pop boolean_rot
                               )
    :population-size 100
-   :max-points 100
-   :max-points-in-initial-program 100
+   :max-points 200
+   :max-genome-size-in-initial-program 100
    :genetic-operator-probabilities {:uniform-close-mutation 0.1
                                     :alternation 0.45
                                     :uniform-mutation 0.45}

src/clojush/problems/boolean/mux_6.clj

@@ -73,8 +73,8 @@
                               d0 d1 d2 d3
                               ;boolean_dup boolean_swap boolean_pop boolean_rot
                               )
-   :max-points 200
-   :max-points-in-initial-program 200
+   :max-points 400
+   :max-genome-size-in-initial-program 200
    :genetic-operator-probabilities {:uniform-close-mutation 0.1
                                     :alternation 0.45
                                     :uniform-mutation 0.45}

src/clojush/problems/boolean/mux_indexed.clj

@@ -87,8 +87,8 @@
                           ;integer_add integer_sub integer_mult integer_div integer_mod
                           ;integer_dup integer_swap integer_pop integer_rot
                           ))
-   :max-points 200
-   :max-points-in-initial-program 200
+   :max-points 400
+   :max-genome-size-in-initial-program 200
    :genetic-operator-probabilities {:uniform-close-mutation 0.1
                                     :alternation 0.45
                                     :uniform-mutation 0.45}

src/clojush/problems/boolean/valiant.clj

@@ -97,8 +97,8 @@
 ;                                   (repeat 25 
 ;                                           '(boolean_and boolean_or boolean_not exec_if))))
 ;   :use-lexicase-selection true
-;   :max-points 10000
-;   :max-points-in-initial-program 10
+;   :max-points 20000
+;   :max-genome-size-in-initial-program 10
 ;   :population-size 100
 ;   :evalpush-limit 10000
 ;   :mutation-probability 0.4
@@ -121,8 +121,8 @@
                             (apply concat 
                                    (repeat 25 
                                            '(boolean_and boolean_or boolean_not exec_if))))
-   :max-points 1000
-   :max-points-in-initial-program 100
+   :max-points 2000
+   :max-genome-size-in-initial-program 100
    :population-size 100
    :evalpush-limit 2000
    :genetic-operator-probabilities {[:alternation :uniform-mutation] 1.0} ;Somewhat equivalent to normal Push's ULTRA operator

src/clojush/problems/control/dsoar.clj

@@ -293,7 +293,7 @@
    ;:simplification-probability 0.3
    ;:reproduction-probability 0.1
    ;:reproduction-simplifications 10
-   :max-points 200
-   :max-points-in-initial-program 200
+   :max-points 400
+   :max-genome-size-in-initial-program 200
    :evalpush-limit 1000
    })

src/clojush/problems/control/lawnmower.clj

@@ -237,7 +237,7 @@
    ;:simplification-probability 0.3
    ;:reproduction-probability 0.1
    ;:reproduction-simplifications 10
-   :max-points 200
-   :max-points-in-initial-program 200
+   :max-points 400
+   :max-genome-size-in-initial-program 200
    :evalpush-limit 1000
    })

src/clojush/problems/demos/autoconstructive_digital_multiplier.clj

@@ -210,13 +210,14 @@
 
 ;(defn dm-meta-error-fn
 ;  "Takes an individual and an argmap and returns a meta-error value."
-;  [ind {:keys [atom-generators max-points-in-initial-program] :as argmap}]
-;  (let [random-genome (random-plush-genome max-points-in-initial-program atom-generators argmap)
+;  [ind {:keys [atom-generators max-genome-size-in-initial-program] :as argmap}]
+;  (let [random-genome (random-plush-genome max-genome-size-in-initial-program atom-generators argmap)
 ;        semantics-fn (fn [g1 g2]
 ;                       (full-dm-error-function
 ;                         (translate-plush-genome-to-push-program
 ;                           {:genome
-;                            (produce-child-genome-by-autoconstruction g1 g2)})))
+;                            (produce-child-genome-by-autoconstruction g1 g2)}
+;                           argmap)))
 ;        e1 (semantics-fn (:genome ind) random-genome)]
 ;    (if (= (:errors ind) e1)
 ;      1
@@ -243,8 +244,8 @@
      :atom-generators (dm-atom-generators num-bits-n)
      :population-size 500
      :max-generations 10000
-     :max-points 2000
-     :max-points-in-initial-program 100
+     :max-points 4000
+     :max-genome-size-in-initial-program 100
      :evalpush-limit 10000
      :epigenetic-markers [:close :silent]
      :genetic-operator-probabilities {:autoconstruction 1.0}

src/clojush/problems/integer_regression/change.clj

@@ -76,8 +76,8 @@
 (def argmap
   {:error-function (change-error-function 150)
    :atom-generators change-atom-generators
-   :max-points 500
-   :max-points-in-initial-program 500
+   :max-points 1000
+   :max-genome-size-in-initial-program 500
    :evalpush-limit 800
    :population-size 2000
    :max-generations 1000

src/clojush/problems/integer_regression/factorial.clj

@@ -72,8 +72,8 @@
                        )
    :population-size 1000
    :max-generations 500
-   :max-points 500
-   :max-points-in-initial-program 100
+   :max-points 1000
+   :max-genome-size-in-initial-program 100
    :evalpush-limit 1000
    :genetic-operator-probabilities {[:alternation :uniform-mutation] 0.5
                                     [:alternation :uniform-mutation :uniform-close-mutation] 0.5}

src/clojush/problems/integer_regression/mackey_glass_int.clj

@@ -96,8 +96,8 @@
   {:error-function (partial error-function 200);; Use 200 random samples
    :atom-generators atom-generators
    :report-simplifications 0
-   :max-points 500
-   :max-points-in-initial-program 500
+   :max-points 1000
+   :max-genome-size-in-initial-program 500
    :evalpush-limit 500
    :population-size 1000
    :epigenetic-markers []

src/clojush/problems/integer_regression/tagged_tg8.clj

@@ -51,7 +51,7 @@
    :genetic-operator-probabilities {:alternation 0.5
                                     :uniform-mutation 0.4
                                     :uniform-close-mutation 0.1}
-   :max-points 100
-   :max-points-in-initial-program 100
+   :max-points 200
+   :max-genome-size-in-initial-program 100
    :population-size 5000
    })

src/clojush/problems/integer_regression/tg8.clj

@@ -51,7 +51,7 @@
    ;:crossover-probability 0.3
    ;:simplification-probability 0.3
    ;:reproduction-simplifications 10
-   :max-points 100
-   :max-points-in-initial-program 100
+   :max-points 200
+   :max-genome-size-in-initial-program 100
    :population-size 5000
    })

src/clojush/problems/regression/bioavailability.clj

@@ -138,8 +138,8 @@
 (def argmap
   {:error-function (partial bioavailability-error-function :train)
    :atom-generators bioavailability-atom-generators
-   :max-points 500
-   :max-points-in-initial-program 500
+   :max-points 1000
+   :max-genome-size-in-initial-program 500
    :evalpush-limit 500
    :population-size 500
    :max-generations 100

src/clojush/problems/regression/korns_regression_p12.clj

@@ -276,8 +276,8 @@
                       'float_cos
                       ;'float_tan
                       )
-   :max-points 30
-   :max-points-in-initial-program 30
+   :max-points 60
+   :max-genome-size-in-initial-program 30
    :evalpush-limit 50
    :population-size 500
    :epigenetic-markers []

src/clojush/problems/regression/pagie_hogeweg_with_erc.clj

@@ -87,8 +87,8 @@
   {:error-function (partial error-function (count data));; Use all samples
    :atom-generators atom-generators
    :report-simplifications 0
-   :max-points 500
-   :max-points-in-initial-program 500
+   :max-points 1000
+   :max-genome-size-in-initial-program 500
    :evalpush-limit 500
    :population-size 1000
    :max-generations 1000

src/clojush/problems/software/calc.clj

@@ -489,8 +489,8 @@
    :max-generations 100000
    :evalpush-limit 3000
    :tag-limit 10000
-   :max-points 3000
-   :max-points-in-initial-program 500 ;;100
+   :max-points 6000
+   :max-genome-size-in-initial-program 500 ;;100
    :mutation-probability 0.0
    :crossover-probability 0.0
    :simplification-probability 0

src/clojush/problems/software/checksum.clj

@@ -151,8 +151,8 @@
 (def argmap
   {:error-function (checksum-error-function checksum-data-domains)
    :atom-generators checksum-atom-generators
-   :max-points 800
-   :max-points-in-initial-program 400
+   :max-points 1600
+   :max-genome-size-in-initial-program 400
    :evalpush-limit 1500
    :population-size 1000
    :max-generations 300

src/clojush/problems/software/collatz_numbers.clj

@@ -138,8 +138,8 @@
 (def argmap
   {:error-function (collatz-numbers-error-function collatz-numbers-data-domains)
    :atom-generators collatz-numbers-atom-generators
-   :max-points 600
-   :max-points-in-initial-program 300
+   :max-points 1200
+   :max-genome-size-in-initial-program 300
    :evalpush-limit 15000
    :population-size 1000
    :max-generations 300

src/clojush/problems/software/compare_string_lengths.clj

@@ -138,8 +138,8 @@
 (def argmap
   {:error-function (csl-error-function csl-data-domains)
    :atom-generators csl-atom-generators
-   :max-points 400
-   :max-points-in-initial-program 200
+   :max-points 800
+   :max-genome-size-in-initial-program 200
    :evalpush-limit 600
    :population-size 1000
    :max-generations 300

src/clojush/problems/software/count_odds.clj

@@ -144,8 +144,8 @@
 (def argmap
   {:error-function (count-odds-error-function count-odds-data-domains)
    :atom-generators count-odds-atom-generators
-   :max-points 500
-   :max-points-in-initial-program 250
+   :max-points 1000
+   :max-genome-size-in-initial-program 250
    :evalpush-limit 1500
    :population-size 1000
    :max-generations 300

src/clojush/problems/software/digits.clj

@@ -132,8 +132,8 @@
 (def argmap
   {:error-function (digits-error-function digits-data-domains)
    :atom-generators digits-atom-generators
-   :max-points 300
-   :max-points-in-initial-program 150
+   :max-points 600
+   :max-genome-size-in-initial-program 150
    :evalpush-limit 600
    :population-size 1000
    :max-generations 300

src/clojush/problems/software/double_letters.clj

@@ -148,8 +148,8 @@
 (def argmap
   {:error-function (double-letters-error-function double-letters-data-domains)
    :atom-generators double-letters-atom-generators
-   :max-points 800
-   :max-points-in-initial-program 400
+   :max-points 1600
+   :max-genome-size-in-initial-program 400
    :evalpush-limit 1600
    :population-size 1000
    :max-generations 300

src/clojush/problems/software/even_squares.clj

@@ -150,8 +150,8 @@
 (def argmap
   {:error-function (even-squares-error-function even-squares-data-domains)
    :atom-generators even-squares-atom-generators
-   :max-points 400
-   :max-points-in-initial-program 200
+   :max-points 800
+   :max-genome-size-in-initial-program 200
    :evalpush-limit 2000
    :population-size 1000
    :max-generations 300

src/clojush/problems/software/for_loop_index.clj

@@ -141,8 +141,8 @@
 (def argmap
   {:error-function (loop-error-function loop-data-domains)
    :atom-generators loop-atom-generators
-   :max-points 300
-   :max-points-in-initial-program 150
+   :max-points 600
+   :max-genome-size-in-initial-program 150
    :evalpush-limit 600
    :population-size 1000
    :max-generations 300

src/clojush/problems/software/grade.clj

@@ -198,8 +198,8 @@
 (def argmap
   {:error-function (grade-error-function grade-data-domains)
    :atom-generators grade-atom-generators
-   :max-points 400
-   :max-points-in-initial-program 200
+   :max-points 800
+   :max-genome-size-in-initial-program 200
    :evalpush-limit 800
    :population-size 1000
    :max-generations 300

src/clojush/problems/software/last_index_of_zero.clj

@@ -148,8 +148,8 @@
 (def argmap
   {:error-function (last-index-of-zero-error-function last-index-of-zero-data-domains)
    :atom-generators last-index-of-zero-atom-generators
-   :max-points 300
-   :max-points-in-initial-program 150
+   :max-points 600
+   :max-genome-size-in-initial-program 150
    :evalpush-limit 600
    :population-size 1000
    :max-generations 300

src/clojush/problems/software/median.clj

@@ -127,8 +127,8 @@
 (def argmap
   {:error-function (median-error-function median-data-domains)
    :atom-generators median-atom-generators
-   :max-points 200
-   :max-points-in-initial-program 100
+   :max-points 400
+   :max-genome-size-in-initial-program 100
    :evalpush-limit 200
    :population-size 1000
    :max-generations 200

src/clojush/problems/software/mirror_image.clj

@@ -164,8 +164,8 @@
 (def argmap
   {:error-function (mirror-image-error-function mirror-image-data-domains)
    :atom-generators mirror-image-atom-generators
-   :max-points 300
-   :max-points-in-initial-program 150
+   :max-points 600
+   :max-genome-size-in-initial-program 150
    :evalpush-limit 600
    :population-size 1000
    :max-generations 300

src/clojush/problems/software/negative_to_zero.clj

@@ -148,8 +148,8 @@
 (def argmap
   {:error-function (negative-to-zero-error-function negative-to-zero-data-domains)
    :atom-generators negative-to-zero-atom-generators
-   :max-points 500
-   :max-points-in-initial-program 250
+   :max-points 1000
+   :max-genome-size-in-initial-program 250
    :evalpush-limit 1500
    :population-size 1000
    :max-generations 300

src/clojush/problems/software/number_io.clj

@@ -130,8 +130,8 @@
 (def argmap
   {:error-function (num-io-error-function num-io-data-domains)
    :atom-generators num-io-atom-generators
-   :max-points 200
-   :max-points-in-initial-program 100
+   :max-points 400
+   :max-genome-size-in-initial-program 100
    :evalpush-limit 200
    :population-size 1000
    :max-generations 200

src/clojush/problems/software/pig_latin.clj

@@ -159,8 +159,8 @@
 (def argmap
   {:error-function (pig-latin-error-function pig-latin-data-domains)
    :atom-generators pig-latin-atom-generators
-   :max-points 1000
-   :max-points-in-initial-program 500
+   :max-points 2000
+   :max-genome-size-in-initial-program 500
    :evalpush-limit 2000
    :population-size 1000
    :max-generations 300