Code improvements / More schema (#13)

* more schema * schema updates * bump deps * code style * tweak input constraints * update deptree info * code style * test style
ogeagla · Feb 20, 2024 · c6f63a1 · c6f63a1
1 parent 382df97
commit c6f63a1
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diff --git a/doc/depstree.txt b/doc/depstree.txt
@@ -47,8 +47,8 @@
      [org.clojure/tools.analyzer "1.1.1"]
      [org.clojure/tools.reader "1.3.6"]
      [org.ow2.asm/asm "9.2"]
- [org.clojure/data.csv "1.0.1"]
- [org.clojure/tools.cli "1.0.219"]
+ [org.clojure/data.csv "1.1.0"]
+ [org.clojure/tools.cli "1.1.230"]
  [org.knowm.xchart/xchart "3.8.7"]
    [com.madgag/animated-gif-lib "1.4"]
    [de.erichseifert.vectorgraphics2d/VectorGraphics2D "0.13"]
@@ -65,7 +65,7 @@
          [org.junit.jupiter/junit-jupiter-engine "5.10.1" :scope "runtime"]
            [org.junit.platform/junit-platform-engine "1.10.1" :scope "runtime"]
          [org.junit.jupiter/junit-jupiter-params "5.10.1"]
- [org.matheclipse/matheclipse-core "3.1.0-20240215.072506-61" :exclusions [[org.slf4j/slf4j-api] [com.fasterxml.jackson.core/jackson-core]]]
+ [org.matheclipse/matheclipse-core "3.1.0-20240219.223701-64" :exclusions [[org.slf4j/slf4j-api] [com.fasterxml.jackson.core/jackson-core]]]
    [com.esotericsoftware/kryo "5.6.0"]
      [com.esotericsoftware/minlog "1.3.1"]
      [com.esotericsoftware/reflectasm "1.11.9"]
@@ -97,7 +97,7 @@
      [org.jgrapht/jgrapht-core "1.5.3-20240118.050300-19"]
        [org.jheaps/jheaps "0.14"]
    [org.logicng/logicng-j11 "2.4.3"]
-   [org.matheclipse/matheclipse-external "3.1.0-20240215.072506-61"]
+   [org.matheclipse/matheclipse-external "3.1.0-20240219.223701-64"]
      [com.fasterxml.jackson.core/jackson-databind "2.16.1"]
        [com.fasterxml.jackson.core/jackson-annotations "2.16.1"]
      [com.google.guava/guava "33.0.0-jre"]
@@ -109,10 +109,10 @@
        [org.checkerframework/checker-qual "3.41.0"]
      [io.pebbletemplates/pebble "3.2.2"]
        [org.unbescape/unbescape "1.1.6.RELEASE"]
-   [org.matheclipse/matheclipse-parser "3.1.0-20240215.072506-61"]
+   [org.matheclipse/matheclipse-parser "3.1.0-20240219.223701-64"]
    [org.organicdesign/Paguro "3.10.3"]
      [org.jetbrains/annotations "23.0.0"]
- [org.matheclipse/matheclipse-gpl "3.1.0-20240215.072506-61" :exclusions [[org.slf4j/slf4j-api] [com.fasterxml.jackson.core/jackson-core]]]
+ [org.matheclipse/matheclipse-gpl "3.1.0-20240219.223701-64" :exclusions [[org.slf4j/slf4j-api] [com.fasterxml.jackson.core/jackson-core]]]
    [org.apache.logging.log4j/log4j-1.2-api "2.22.1"]
  [org.slf4j/jcl-over-slf4j "2.0.12"]
  [org.slf4j/slf4j-api "2.0.12"]

diff --git a/project.clj b/project.clj
@@ -7,9 +7,9 @@
                  [org.clojure/core.async "1.6.681"]
                  [metosin/malli "0.14.0"]
 
-                 [org.clojure/tools.cli "1.0.219"]
+                 [org.clojure/tools.cli "1.1.230"]
 
-                 [org.clojure/data.csv "1.0.1"]
+                 [org.clojure/data.csv "1.1.0"]
 
                  [seesaw/seesaw "1.5.0"]
                  [flames "0.5.0"]

diff --git a/src/closyr/ops/common.clj b/src/closyr/ops/common.clj
@@ -146,7 +146,7 @@
                  (str expr) " / " (str variable) " : " (or (.getMessage e) e)))))
 
 
-(defn- inversely-proportional-to-leaf-size
+(defn- probability-inversely-proportional-to-leaf-size
   [leaf-count scalar]
   (let [leaf-scalar (min 1.0
                          (max 0.005
@@ -159,19 +159,22 @@
 (defn should-modify-leaf
   "Based on probability, check if should modify leaf"
   [leaf-count {^IAST expr :expr ^ISymbol x-sym :sym :as pheno}]
-  (inversely-proportional-to-leaf-size leaf-count 1.5))
+  (probability-inversely-proportional-to-leaf-size
+    leaf-count 1.5))
 
 
 (defn should-modify-branch
   "Based on probability, check if should modify branch"
   [leaf-count {^IAST expr :expr ^ISymbol x-sym :sym :as pheno}]
-  (inversely-proportional-to-leaf-size leaf-count 0.5))
+  (probability-inversely-proportional-to-leaf-size
+    leaf-count 0.5))
 
 
 (defn should-modify-ast-head
   "Based on probability, check if should modify AST head"
   [leaf-count {^IAST expr :expr ^ISymbol x-sym :sym :as pheno}]
-  (inversely-proportional-to-leaf-size leaf-count 0.25))
+  (probability-inversely-proportional-to-leaf-size
+    leaf-count 0.25))
 
 
 (def do-not-simplify-fns*
@@ -186,20 +189,20 @@
 
 (defn- check-simplify-timing
   [^IAST expr done?*]
-  (let [report-done?* (atom false)]
+  (let [report-slow-operation?* (atom false)]
     (go-loop [c 0]
       (when-not @done?*
         ;; wait sequence in ms looks like: 100, 316, 1000, ...
         (<! (timeout (int (Math/pow (max 2.0 (/ *long-simplify-thresh-ms* 200))
                                     (+ 1.5 (/ c 4))))))
         (when (> c 6)
-          (reset! report-done?* true)
+          (reset! report-slow-operation?* true)
           (swap! do-not-simplify-fns* assoc (str expr) 1)
           (log/warn "Warning: simplify taking a long time: " c
                     " " (.leafCount expr) " : " (str expr)
                     " total slow fns: " (count @do-not-simplify-fns*)))
         (recur (inc c))))
-    (when @report-done?*
+    (when @report-slow-operation?*
       (log/warn "Warning: simplify took a long time: "
                 " : " (str expr)
                 " total slow fns: " (count @do-not-simplify-fns*)))))
@@ -243,8 +246,8 @@
 (defn ^IAST maybe-simplify
   "Maybe simplify pheno expr"
   [{^IAST expr :expr ^ISymbol x-sym :sym ^ExprEvaluator util :util p-id :id simple? :simple? :as pheno}]
-  (if (and (<= (.leafCount expr) *simplify-max-leafs*)
-           (not simple?)
+  (if (and (not simple?)
+           (<= (.leafCount expr) *simplify-max-leafs*)
            (< (rand) *simplify-probability-sampler*))
     (let [start              (Date.)
           done?*             (atom false)

diff --git a/src/closyr/symbolic_regression.clj b/src/closyr/symbolic_regression.clj
@@ -44,7 +44,7 @@
   (chan))
 
 
-(def ^:private sim-input-args*
+(def sim-input-args*
   "Data from GUI to use in the iterations"
   (atom nil))
 
@@ -158,7 +158,7 @@
         true))))
 
 
-(defn- repaint-gui
+(defn- update-gui-with-solver-data
   [chart-iter
    {:keys [^XYChart best-fn-chart
            ^XYChart scores-chart
@@ -256,7 +256,7 @@
     (when-let [sim-msg (<! sim->gui-chan)]
       (try
 
-        (repaint-gui chart-iter ui-elements conf sim-msg)
+        (update-gui-with-solver-data chart-iter ui-elements conf sim-msg)
 
         (catch Exception e
           (log/error "Err in redrawing GUI: " (.getMessage e))
@@ -354,7 +354,7 @@
 
 (defn ->run-args
   "Generate one-time computed args for solver"
-  {:malli/schema [:=> [:cat map?] #'specs/SolverRunArgs]}
+  {:malli/schema [:=> [:cat #'specs/SolverInputArgs] #'specs/SolverRunArgs]}
   [{input-xs-exprs     :input-xs-exprs
     input-xs-vec       :input-xs-vec
     input-ys-vec       :input-ys-vec

diff --git a/src/closyr/util/spec.clj b/src/closyr/util/spec.clj
@@ -142,7 +142,7 @@
 
 
 (def ^:private PopulationCount
-  [:int {:min 1 :max 10000}])
+  [:int {:min 1 :max 100000}])
 
 
 (def ^:private GAPhenotype
@@ -265,6 +265,23 @@
    [:max-leafs [:maybe #'MaxLeafs]]])
 
 
+(def ^:private SolverInputArgs
+  [:map
+   {:closed true}
+   [:use-flamechart {:optional true} [:maybe :boolean]]
+   [:use-gui? {:optional true} [:maybe :boolean]]
+   [:initial-muts {:optional true} [:sequential #'GAMutation]]
+   [:initial-phenos {:optional true} [:maybe #'GAPopulationPhenotypes]]
+   [:input-xs-exprs {:optional true} [:vector #'SymbolicExpr]]
+   [:input-ys-exprs {:optional true} [:vector #'SymbolicExpr]]
+   [:input-xs-vec #'NumberVector]
+   [:input-ys-vec #'NumberVector]
+   [:input-iters {:optional true} #'Iterations]
+   [:iters {:optional true} #'Iterations]
+   [:input-phenos-count {:optional true} #'PopulationCount]
+   [:max-leafs {:optional true} [:maybe #'MaxLeafs]]])
+
+
 (def ^:private SolverGUIMessage
   [:map
    {:closed true}

diff --git a/test/closyr/symbolic_regression_test.clj b/test/closyr/symbolic_regression_test.clj
@@ -153,7 +153,7 @@
                    :initial-muts       (ops-init/initial-mutations)
                    :iters              5
                    :use-gui?           false
-                   :use-flamechart     true
+                   :use-flamechart     false
                    :input-xs-exprs     (->> (range 50)
                                             (map (fn [i] (* Math/PI (/ i 15.0))))
                                             ops-common/doubles->exprs)
@@ -167,7 +167,14 @@
                    100))
 
             (is (= iters-done
-                   5))))))
+                   5))
+
+            (is (= (set (keys @symreg/sim-input-args*))
+                   #{:input-xs-exprs
+                     :input-xs-vec
+                     :input-ys-vec}))
+
+            (reset! symreg/sim-input-args* {})))))
 
     (testing "with provided data using record"
       (with-redefs-fn {#'symreg/config->log-steps (fn [_ _] 10)}
@@ -192,7 +199,14 @@
                    100))
 
             (is (= iters-done
-                   5))))))))
+                   5))
+
+            (is (= (set (keys @symreg/sim-input-args*))
+                   #{:input-xs-exprs
+                     :input-xs-vec
+                     :input-ys-vec}))
+
+            (reset! symreg/sim-input-args* {})))))))
 
 
 #_(deftest can-run-experiment-gui:start-stop
@@ -242,6 +256,9 @@
                                :input-iters        200
                                :input-phenos-count 500}))
 
+                    (is (= (set (keys @symreg/sim-input-args*))
+                           #{:input-xs-vec :input-ys-vec}))
+
                     (<! (timeout 100))
                     (is (put! symreg/*sim-stop-start-chan*
                               {:new-state :pause}))
@@ -280,6 +297,14 @@
 
                     (<! (timeout 100))
 
+                    (is (= (set (keys @symreg/sim-input-args*))
+                           #{:input-iters
+                             :input-phenos-count
+                             :input-xs-exprs
+                             :input-xs-vec
+                             :input-ys-vec
+                             :max-leafs}))
+
                     (is (put! symreg/*sim-stop-start-chan*
                               {:new-state :stop}))
 

diff --git a/test/closyr/util_spec_test.clj b/test/closyr/util_spec_test.clj
@@ -19,6 +19,39 @@
       ISymbol)))
 
 
+(deftest inputs-from-gui-spec
+  (testing "GUI input data"
+    (is (= (me/humanize
+             (m/explain #'specs/SolverGUIMessage
+                        {:max-leafs          20,
+                         :input-iters        10000,
+                         :input-phenos-count 50000,
+                         :new-state          :start,
+                         :input-data-x
+                         [0.0
+                          1.6331994645247656
+                          3.2931726907630523
+                          4.953145917001338
+                          6.613119143239625
+                          8.273092369477911
+                          9.933065595716197
+                          11.593038821954485
+                          13.25301204819277
+                          14.912985274431056],
+                         :input-data-y
+                         [2.3704663212435237
+                          3.2253886010362693
+                          3.7694300518134716
+                          3.9248704663212437
+                          1.1269430051813476
+                          -5.090673575129534
+                          1.204663212435233
+                          2.215025906735751
+                          1.5155440414507773
+                          6.955958549222798]}))
+           nil))))
+
+
 (deftest generates-custom-types
   (testing "valid Expr"
     (is (instance?