Adapted requirements: now boring code but no warning

src/main/clojure/conexp/api/namespace.clj

@@ -12,7 +12,8 @@
         conexp.layouts.freese
         conexp.layouts.layered
         conexp.layouts.dim-draw
-        conexp.api.shorthands))
+        conexp.api.shorthands
+        clojure.set))
 
 ;;;
 
@@ -24,7 +25,8 @@
                  conexp.layouts.freese
                  conexp.layouts.layered
                  conexp.layouts.dim-draw
-                 conexp.api.shorthands]))
+                 conexp.api.shorthands
+                 clojure.set])) ;; basic set operations
 
 (def functions
   (concat

src/main/clojure/conexp/base.clj

@@ -9,7 +9,9 @@
 (ns conexp.base
   "Basic definitions for conexp-clj."
   (:require [clojure.math.combinatorics :as comb]
-            [clojure.java.io            :as io]))
+            [clojure.java.io            :as io]
+            [clojure.set :refer [difference union subset? intersection]]
+            [clojure.math.numeric-tower :as nt]))
 
 ;;; def macros, inspired and partially copied from clojure.contrib.def
 
@@ -77,24 +79,24 @@ metadata (as provided by def) merged into the metadata of the original."
           (last dforms)))))
 ;;; Namespace tools
 
-(defn immigrate
-  "Create a public var in this namespace for each public var in the
-  namespaces named by ns-names. The created vars have the same name, root
-  binding, and metadata as the original except that their :ns metadata
-  value is this namespace.
-
-  This function is literally copied from the clojure.contrib.ns-utils library."
-  [& ns-names]
-  (doseq [ns ns-names]
-    (require ns)
-    (doseq [[sym, ^clojure.lang.Var var] (ns-publics ns)]
-      (let [sym (with-meta sym (assoc (meta var) :ns *ns*))]
-        (if (.hasRoot var)
-          (intern *ns* sym (.getRawRoot var))
-          (intern *ns* sym))))))
-
-(immigrate 'clojure.set
-           'clojure.math.numeric-tower)
+;; (defn immigrate
+;;   "Create a public var in this namespace for each public var in the
+;;   namespaces named by ns-names. The created vars have the same name, root
+;;   binding, and metadata as the original except that their :ns metadata
+;;   value is this namespace.
+
+;;   This function is literally copied from the clojure.contrib.ns-utils library."
+;;   [& ns-names]
+;;   (doseq [ns ns-names]
+;;     (require ns)
+;;     (doseq [[sym, ^clojure.lang.Var var] (ns-publics ns)]
+;;       (let [sym (with-meta sym (assoc (meta var) :ns *ns*))]
+;;         (if (.hasRoot var)
+;;           (intern *ns* sym (.getRawRoot var))
+;;           (intern *ns* sym))))))
+
+;; (immigrate 'clojure.set
+;;            'clojure.math.numeric-tower)
 
 ;;; Version
 
@@ -586,7 +588,7 @@ metadata (as provided by def) merged into the metadata of the original."
   and returns double otherwise."
   [a b]
   (if (not (and (integer? a) (integer? b)))
-    (clojure.math.numeric-tower/expt a b)
+    (nt/expt a b)
     (let [^clojure.lang.BigInt a (bigint a),
           b (long b)]
       (if (< b 0)

src/main/clojure/conexp/fca/causal_implications.clj

@@ -5,7 +5,7 @@
    [conexp.io.contexts :refer :all]
    [conexp.fca.contexts :refer :all]
    [conexp.fca.implications :refer :all]
-   [clojure.set :as set]))
+   [clojure.set :refer [difference union subset? intersection]]))
 
 ;For a full Explanation of the Concepts refer to *Mining Causal Association Rules*
 ;https://www.researchgate.net/publication/262240022_Mining_Causal_Association_Rules
@@ -26,9 +26,9 @@
              (and (subset? premise b-attributes) (not (subset? premise a-attributes))))
          ;check whether controlled variables have same realizations in both objects
          (subset? controlled-variables
-                  (set/union (set/intersection a-attributes b-attributes)
-                             (set/intersection (set/difference controlled-variables a-attributes) 
-                                               (set/difference controlled-variables b-attributes)))))))
+                  (union (intersection a-attributes b-attributes)
+                             (intersection (difference controlled-variables a-attributes) 
+                                               (difference controlled-variables b-attributes)))))))
 
 (defn find-matched-record-pair [ctx impl controlled-variables objs-considered a]
   "Searches objs-considered for an object that forms a matched record pair with a,
@@ -47,13 +47,13 @@
   (let [objs (objects ctx)]
     (filter seq 
             (reduce (fn [present-objs new-obj]
-              (if (contains? (reduce set/union present-objs) new-obj)
+              (if (contains? (reduce union present-objs) new-obj)
                 present-objs
                 (conj present-objs (find-matched-record-pair 
                                            ctx 
                                            impl 
                                            controlled-variables 
-                                           (set/difference objs (reduce set/union present-objs)) 
+                                           (difference objs (reduce union present-objs)) 
                                            new-obj))))
               #{} objs))))
 
@@ -103,10 +103,10 @@
   "Used to compute the bounds of the confidence interval within the confidence-interval method.
    Computes the upper bound if + is supplied as op, lower bound if - is supplied."
   (Math/exp (op (Math/log odds-ratio)
-               (* zconf (Math/sqrt (+ (/ 1 (absolute-support ctx [(set/union premise conclusion) #{}]))
+               (* zconf (Math/sqrt (+ (/ 1 (absolute-support ctx [(union premise conclusion) #{}]))
                                       (/ 1 (absolute-support ctx [premise conclusion]))
                                       (/ 1 (absolute-support ctx [conclusion premise])) 
-                                      (/ 1 (absolute-support ctx [#{} (set/union premise conclusion)]))))))))
+                                      (/ 1 (absolute-support ctx [#{} (union premise conclusion)]))))))))
 
 (defn confidence-interval [ctx impl odds-ratio zconf]
   "Computes the confidence interval of the implication. odds-ratio is the regular odds ratio of
@@ -180,9 +180,9 @@
    confidence interval is greather than 1." 
   (let [premise (premise impl) 
         conclusion (conclusion impl)
-        E (reduce set/union (exclusive-variables ctx premise thresh)) 
-        controlled-variables (set/difference (attributes ctx)  
-                                             (set/union conclusion irrelevant-vars E premise))
+        E (reduce union (exclusive-variables ctx premise thresh)) 
+        controlled-variables (difference (attributes ctx)  
+                                             (union conclusion irrelevant-vars E premise))
         fair-data (fair-data-set ctx impl controlled-variables)
         fair-odds (fair-odds-ratio ctx impl fair-data)]
 
@@ -217,8 +217,8 @@
       (causal-association-rule-discovery 
          ctx ;context
          #{} ;current causal rules
-         (set/difference frequent-vars #{response-var})  ;frequent single variables
-         (for [x (set/difference frequent-vars #{response-var})] #{x}) ;itemsets of the current iteration
+         (difference frequent-vars #{response-var})  ;frequent single variables
+         (for [x (difference frequent-vars #{response-var})] #{x}) ;itemsets of the current iteration
          ivars ;irrelevant variables in respect to response-var
          min-lsupp ;minimum local support
          0 ;counter, counts up to max-length
@@ -237,9 +237,9 @@
 
       (causal-association-rule-discovery 
          ctx
-         (set/union rule-set new-causal-rules)
+         (union rule-set new-causal-rules)
          variables
-         (set/difference (filter #(> (local-support ctx (->Implication #{%} #{response-var})) min-lsupp) new-item-sets) 
+         (difference (filter #(> (local-support ctx (->Implication #{%} #{response-var})) min-lsupp) new-item-sets) 
                          (find-redundant ctx current new-item-sets response-var));filter item sets
          ivars
          min-lsupp

src/main/clojure/conexp/fca/concept_transform.clj

@@ -9,7 +9,8 @@
 (ns conexp.fca.concept-transform
   (:require [conexp.base :refer :all] 
             [conexp.fca.contexts :refer :all] 
-            [conexp.fca.cover :refer :all]))
+            [conexp.fca.cover :refer :all]
+            [clojure.set :refer [difference union subset? intersection]]))
 
 
 

src/main/clojure/conexp/fca/contexts.clj

@@ -9,7 +9,9 @@
 (ns conexp.fca.contexts
   "Provides the implementation of formal contexts and functions on them."
   (:require [clojure.core.reducers :as r]
-            [conexp.base :refer :all]))
+            [clojure.set :refer [difference intersection union subset?]]
+            [conexp.base :refer :all]
+            ))
 
 ;;;
 

src/main/clojure/conexp/fca/cover.clj

@@ -19,7 +19,8 @@
               to-binary-matrix
               bitwise-context-attribute-closure]]
              [clojure.core.reducers :as r]
-             [clojure.core.async :refer [<!!]])
+             [clojure.core.async :refer [<!!]]
+             [clojure.set :refer [difference union subset? intersection]])
   (:import [java.util BitSet]))
 
 ;;;;;;;;;;;;;;;;;;;;; General Cover Methods ;;;;;;;;;;;;;;;;;;;;;;;;;;;;;

src/main/clojure/conexp/fca/dependencies.clj

@@ -11,6 +11,7 @@
    'Dependencies of many-valued attributes', 1987, Rudolf Wille
    http://www.opengrey.eu/item/display/10068/148205 "
   (:require [clojure.core.reducers :as r]
+            [clojure.set :refer [intersection subset?]]
             [conexp.base :refer :all]
             [conexp.fca.implications :refer [premise conclusion
                                              stem-base-from-base

src/main/clojure/conexp/fca/exploration.clj

@@ -11,7 +11,8 @@
   (:use conexp.base
         conexp.fca.contexts
         conexp.fca.implications)
-  (:require [clojure.core.reducers :as r]))
+  (:require [clojure.core.reducers :as r]
+            [clojure.set :refer [difference union intersection subset? ]]))
 
 
 (defn exploration-step

src/main/clojure/conexp/fca/graph.clj

@@ -3,7 +3,8 @@
             [conexp.math.algebra :as alg]
             [conexp.fca.lattices :as lat]
             [conexp.util.graph :refer :all]
-            [conexp.base :exclude [transitive-closure] :refer :all]))
+            [conexp.base :exclude [transitive-closure] :refer :all]
+            [clojure.set :refer [difference union subset? intersection]]))
 
 
 ;;; graph <-> lattice

src/main/clojure/conexp/fca/implications.clj

@@ -12,7 +12,9 @@
             [conexp.base :refer :all]
             [conexp.math.algebra :refer :all]
             [conexp.fca.contexts :refer :all]
-            [clojure.set :as set]))
+            [clojure.set :refer [difference union subset? intersection]]
+            [clojure.math.numeric-tower :as nt]
+            ))
 
 ;;;
 
@@ -604,15 +606,15 @@
   "Computes the confidence of an implication using the absolute-support method."
   [ctx impl]
   (let [premise (premise impl) conclusion (conclusion impl)]
-    (/ (absolute-support ctx [(set/union premise conclusion) #{}]) 
+    (/ (absolute-support ctx [(union premise conclusion) #{}]) 
        (absolute-support ctx [premise #{}]))))
 
 (defn odds-ratio 
   "Computes the odds ratio of an implication using the asupp method."
   [ctx impl]
   (let [premise (premise impl) conclusion (conclusion impl)]
-    (/ (* (absolute-support ctx [(set/union premise conclusion) #{}]) 
-          (absolute-support ctx [#{} (set/union premise conclusion)]))
+    (/ (* (absolute-support ctx [(union premise conclusion) #{}]) 
+          (absolute-support ctx [#{} (union premise conclusion)]))
        (* (absolute-support ctx [premise conclusion]) 
           (absolute-support ctx [conclusion premise]))
        )))
@@ -621,7 +623,7 @@
   "Computes the local support of an implication by dividing the support of the implication
    by the support of its conclusion. Uses the absolute-support function."
   (let [premise (premise impl) conclusion (conclusion impl)]
-    (/ (absolute-support ctx [(set/union premise conclusion) #{}])
+    (/ (absolute-support ctx [(union premise conclusion) #{}])
        (absolute-support ctx [conclusion #{}]))))
 
 (defn- frequent-itemsets
@@ -812,7 +814,7 @@
     (learn-implications-by-queries (attributes ctx)
                                    intent?
                                    (fn [implications]
-                                     (let [nr-iter (ceil (* (/ ε) (+ (swap! iter-counter inc)
+                                     (let [nr-iter (nt/ceil (* (/ ε) (+ (swap! iter-counter inc)
                                                                      (/ (Math/log (/ δ))
                                                                         (Math/log 2)))))]
                                        (or (some (fn [test-set]

src/main/clojure/conexp/fca/incremental_ganter.clj

@@ -13,7 +13,8 @@
    https://link.springer.com/article/10.1007/s10472-007-9057-2 "
   (:require [conexp.base :refer :all]
             [conexp.fca.implications :refer :all]
-            [conexp.fca.contexts :refer :all]))
+            [conexp.fca.contexts :refer :all]
+                        [clojure.set :refer [difference union subset? intersection]]))
 
 ;;;
 

src/main/clojure/conexp/fca/lattices.clj

@@ -12,6 +12,7 @@
         conexp.math.algebra
         conexp.fca.contexts
         conexp.fca.posets)
+  (:require [clojure.set :refer [difference union subset? intersection]])
   (:gen-class))
 
 ;;; Datastructure
@@ -466,7 +467,7 @@
   (let [lat-join (sup lat)
         lat-meet (inf lat)]
     (loop [X generators]
-      (let [X-new (clojure.set/union (into #{} (for [a X b X] (lat-join a b)))
+      (let [X-new (union (into #{} (for [a X b X] (lat-join a b)))
                                      (into #{} (for [a X b X] (lat-meet a b))))]
         (if (= X X-new) (make-lattice X lat-meet lat-join)
                         (recur X-new)))))

src/main/clojure/conexp/fca/many_valued_contexts.clj

@@ -8,7 +8,8 @@
 
 (ns conexp.fca.many-valued-contexts
   "Many-Valued-Contexts and some functions for scaling."
-  (:require [conexp.base :refer :all]
+  (:require [clojure.set :refer [difference union subset? intersection]]
+            [conexp.base :refer :all]
             [conexp.fca.contexts :refer :all]))
 
 ;;;

src/main/clojure/conexp/fca/metrics.clj

@@ -28,7 +28,8 @@
                            bitwise-attribute-derivation concepts]]
              [implications :refer :all]
              [lattices :refer [inf sup lattice-base-set make-lattice concept-lattice lattice-order]]]
-            [conexp.math.util :refer [eval-polynomial binomial-coefficient]])
+            [conexp.math.util :refer [eval-polynomial binomial-coefficient]]
+            [clojure.set :refer [difference union subset? intersection]])
   (:import [conexp.fca.lattices Lattice]
            [java.util ArrayList BitSet]))
 

src/main/clojure/conexp/fca/more.clj

@@ -10,6 +10,7 @@
   "More on FCA."
   (:require [conexp.base :refer :all]
             [clojure.core.reducers :as r]
+            [clojure.set :refer [difference union subset? intersection]]
             [conexp.fca
              [contexts :refer :all]
              [exploration :refer :all]

src/main/clojure/conexp/fca/posets.clj

@@ -7,7 +7,8 @@
 ;; You must not remove this notice, or any other, from this software.
 
 (ns conexp.fca.posets
-  (:require [conexp.base :refer :all]
+  (:require [clojure.set :refer [union difference subset?]]
+            [conexp.base :refer :all]
             [conexp.math.algebra :refer :all]
             [conexp.fca.contexts :refer :all]))
 

src/main/clojure/conexp/fca/protoconcepts.clj

@@ -13,7 +13,9 @@
             [conexp.math.algebra :refer :all]
             [conexp.fca.contexts :refer :all]
             [conexp.fca.lattices :refer :all]
-            [conexp.fca.posets :refer :all]))
+            [conexp.fca.posets :refer :all]
+            [clojure.set :refer [difference union subset? intersection]]
+            ))
 
 (deftype Protoconcepts [base-set order-function]
   Object

src/main/clojure/conexp/fca/random_contexts.clj

@@ -4,7 +4,7 @@
             [conexp.base :refer [set-of exists forall => defalias]]
             [conexp.fca.contexts :as contexts]
             [clojure.set :refer [subset? difference union intersection select]]
-            [clojure.math.numeric-tower :refer :all]
+            [clojure.math.numeric-tower :refer [expt]]
             [clojure.math.combinatorics :refer [cartesian-product]]
             )
   (:import [org.apache.commons.math3.distribution

src/main/clojure/conexp/fca/smeasure.clj

@@ -16,6 +16,7 @@
             [clojure.math.combinatorics :as comb]
             [loom.graph :as lg] [loom.alg :as la]
             [clojure.core.reducers :as r]
+            [clojure.set :refer [difference union subset? intersection]]
             [conexp.fca.implications :refer :all]))
 
 (defprotocol Smeasure

src/main/clojure/conexp/gui/editors/context_editor/context_editor.clj

@@ -16,7 +16,8 @@
             [conexp.gui.editors.context-editor.table-control :refer :all]
             [conexp.gui.editors.context-editor.widgets :refer :all]
             [conexp.gui.util :refer :all]
-            [seesaw.core :refer [button toolbar top-bottom-split]])
+            [seesaw.core :refer [button toolbar top-bottom-split]]
+            [clojure.set :refer [difference union subset? intersection]])
   (:import [java.awt.event ActionEvent KeyEvent]
            [javax.swing Box JTable KeyStroke]))
 

src/main/clojure/conexp/gui/editors/context_editor/table_control.clj

@@ -12,7 +12,8 @@
   (:require [clojure.string :refer [split split-lines]]
             [conexp.base :refer :all]
             [conexp.gui.editors.context-editor.widgets :refer :all]
-            [conexp.gui.util :refer :all])
+            [conexp.gui.util :refer :all]
+            [clojure.set :refer [difference union subset? intersection join map-invert]])
   (:import [java.awt.event ActionEvent ActionListener InputEvent KeyEvent MouseEvent]
            java.awt.Point
            [javax.swing AbstractAction DefaultCellEditor JComponent JScrollPane JTable JTextField KeyStroke]

src/main/clojure/conexp/io/contexts.clj

@@ -18,7 +18,8 @@
             [clojure.data.json               :as json]
             [json-schema.core                :as json-schema]
             [clojure.data.csv                :as csv]
-            [clojure.java.io                 :as io])
+            [clojure.java.io                 :as io]
+            [clojure.set :refer [difference union]])
   (:import [java.io PushbackReader]))