Merge branch 'develop' of https://github.com/mikera/core.matrix.git into

develop

Conflicts:
	src/test/clojure/clojure/core/matrix/test_double_array.clj

.gitignore

@@ -4,7 +4,7 @@
 /.settings
 /classes
 /doc
-
+/out
 .DS_Store
 .html
 bench

.travis.yml

@@ -1,6 +1,5 @@
 language: java
 jdk:
   - oraclejdk8
-  - oraclejdk7
   - openjdk7
-sudo: false
+sudo: true

CHANGELOG.md

@@ -2,6 +2,10 @@
 All notable changes to this project will be documented in this file, as of core.matrix 0.50.0
 This project adheres to [Semantic Versioning](http://semver.org/).
 
+## [0.61.0] - 2017-...
+### Added
+- add-emap! and set-emap! API functions
+
 ## [0.60.3] - 2017-05-18
 ### Fixed
 - New upload to Clojars attempting to resolve deployment issue (see: https://github.com/clojars/clojars-web/issues/640)

pom.xml

@@ -3,7 +3,7 @@
 	<modelVersion>4.0.0</modelVersion>
 	<artifactId>core.matrix</artifactId>
 	<description>N-dimensional array programming API for Clojure</description>
-	<version>0.60.4-SNAPSHOT</version>
+	<version>0.61.1-SNAPSHOT</version>
 	<packaging>jar</packaging>
 
 	<url>https://github.com/mikera/core.matrix</url>

project.clj

@@ -36,40 +36,36 @@
 
              :cljs
              {:dependencies [[org.clojure/clojurescript "1.7.228"]
-                             [thinktopic/aljabr "0.1.0-SNAPSHOT" :exclusions [net.mikera/core.matrix]]]
+                             [thinktopic/aljabr "0.1.0-SNAPSHOT" :exclusions [net.mikera/core.matrix]]
+                             ]
 
               :plugins [[lein-figwheel "0.5.0-6"]
-                        [lein-cljsbuild "1.1.2"]]
+                        [lein-doo "0.1.7"]
+                        [lein-cljsbuild "1.1.7"]
+                        ]
 
               :cljsbuild {:builds
-                          [{:id :dev
-                            :figwheel true
-                            :source-paths ["src/main/clojure" "src/test/cljs" "src/test/clojure"]
-                            :compiler {:output-to "resources/public/js/core.matrix.js"
-                                       :asset-path   "js/out"
-                                       :optimizations :none
-                                       :parallel-build true
-                                       :pretty-print true}}
-                           {:id :test
-                            :source-paths ["src/main/clojure" "src/test/cljs" "src/test/clojure"]
-                            :compiler {:output-to "resources/public/js/unit-test.js"
-                                       :asset-path   "js/out"
-                                       ;:main "clojure.core.matrix.test-basics"
-                                       :optimizations :advanced
-                                       :parallel-build true
-                                       :pretty-print false}}]
+                          {:dev {:figwheel true
+                                 :source-paths ["src/main/clojure" "src/test/cljs" "src/test/clojure"]
+                                 :compiler {:output-to "resources/public/js/core.matrix.js"
+                                            :asset-path   "js/out"
+                                            :optimizations :none
+                                            :parallel-build true
+                                            :pretty-print true}}
+                           :test {:source-paths ["src/main/clojure" "src/test/cljs" "src/test/clojure"]
+                                  :compiler {:output-to "resources/public/js/unit-test.js"
+                                             :asset-path   "out/"
+                                             :main clojure.core.matrix.cljs-runner
+                                             :optimizations :none 
+                                             :parallel-build true
+                                             :pretty-print false}}}
 
-                          ;:test-commands {"unit" ["phantomjs" "resources/public/js/unit-test.js"]}
+                                        :figwheel {:load-warninged-code true :css-dirs ["resources/public/css"] :server-port 8765}
                           }
-
-              :figwheel {:load-warninged-code true
-                         :css-dirs ["resources/public/css"]
-                         :server-port 8765}}
-             }
+             }}
 
   :marginalia {:javascript ["http://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"]}
 
-
   :codox {:namespaces [clojure.core.matrix
                        clojure.core.matrix.dataset
                        clojure.core.matrix.io

src/main/clojure/clojure/core/matrix.cljc

@@ -1463,6 +1463,9 @@ elements not-equal to the argument are 0.
 (defn mul
   "Performs element-wise multiplication with scalars and numerical arrays.
 
+   Examples: 
+     (mul [1 2] [3 4]) ;=> [3 8]
+
    Behaves like clojure.core/* for scalar values."
   ([] 1.0)
   ([a] a)
@@ -1483,10 +1486,7 @@ elements not-equal to the argument are 0.
 (defn mmul
   "Performs matrix multiplication on matrices or vectors. 
 
-  Equivalent to inner-product when applied to vectors.  Will treat a 1D vector roughly as a
-  1xN matrix (row vector) when it's the first argument, or as an Nx1 matrix
-  (column vector) when it's the second argument--except that the dimensionality
-  of the result will be different from what it would be with matrix arguments."
+   Equivalent to inner-product, but may be more efficient for matrices."
   ([] 1.0)
   ([a] a)
   ([a b]
@@ -1581,7 +1581,9 @@ elements not-equal to the argument are 0.
     v))
 
 (defn add
-  "Performs element-wise addition on one or more numerical arrays."
+  "Performs element-wise addition on one or more numerical arrays.
+
+   Will broadcast to the smallest shape compatible will addition of all input arrays."
   ([] 0.0)
   ([a] a)
   ([a b]
@@ -1610,12 +1612,15 @@ elements not-equal to the argument are 0.
 
 (defn add-product
   "Adds the element-wise product of two numerical arrays to the first array.
-   Arrays should be the same shape."
+   
+   Arrays should be the same shape, some implementations may support broadcasting."
   ([m a b]
     (mp/add-product m a b)))
 
 (defn add-product!
-  "Adds the product of two numerical arrays to the first array. Returns the mutated array."
+  "Adds the product of two numerical arrays to the first array. Returns the mutated array.
+
+   Arrays should be the same shape, some implementations may support broadcasting."
   ([m a b]
     (mp/add-product! m a b)
     m))
@@ -1717,46 +1722,6 @@ elements not-equal to the argument are 0.
     (mp/set-inner-product! m a b factor)
     m))
 
-(defn op 
-  "Computes the specified operation on the array a and returns a new array.
-
-   The operation is implementation specific. Throws an error if the operator is not recognised by the implementation of a, or
-   if the operation is invalid for the given parameters."
-  ([operation a]
-    (TODO))
-  ([operation a & args]
-    (TODO)))
-
-(defn op! 
-  "Computes the specified operation on the array a and mutates the array a.
-
-   The operation is implementation specific. Throws an error if the operator is not recognised by the implementation of a, or
-   if the operation is invalid for the given parameters."
-  ([operation a]
-    (TODO))
-  ([operation a & args]
-    (TODO)))
-
-(defn set-op! 
-  "Computes the specified operation on the array a and stores the result in the destination array, which must be mutable.
-
-   The operation is implementation specific. Throws an error if the operator is not recognised by the implementation of a, or
-   if the operation is invalid for the given parameters."
-  ([operation dest a]
-    (TODO))
-  ([operation dest a & args]
-    (TODO)))
-
-(defn add-op! 
-  "Computes the specified operation on the array a and adds the result to the destination array, which must be mutable.
-
-   The operation is implementation specific. Throws an error if the operator is not recognised by the implementation of a, or
-   if the operation is invalid for the given parameters."
-  ([operation dest a]
-    (TODO))
-  ([operation dest a & args]
-    (TODO)))
-
 (defn sub
   "Performs element-wise subtraction on one or more numerical arrays.
 
@@ -1815,7 +1780,9 @@ elements not-equal to the argument are 0.
     (mp/square m)))
 
 (defn normalise
-  "Normalises a numerical vector (scales to unit length). Returns a new normalised vector.
+  "Normalises a numerical vector (scales to unit length, i.e. the L2 norm). 
+
+   Returns a new normalised vector.
 
    The result is undefined if the initial length of the vector is zero (it is possible the
    implementation may return NaNs or zeros). If this is a concern, it is recommended to check
@@ -1832,7 +1799,7 @@ elements not-equal to the argument are 0.
 
 (defn dot
   "Efficiently computes the scalar dot product (1Dx1D inner product) of two numerical vectors. Prefer this API
-   function if you are performing a dot product on 1D vectors and want a scalar result.
+   function if you are performing a dot product on 1D vectors and require a scalar result.
 
    If either argument is not a vector, will compute and return a higher dimensional inner-product."
   ([a b]
@@ -2153,6 +2120,9 @@ elements not-equal to the argument are 0.
      (emap (fn [x] (str x)) (double-array [1 2 3]))             ;; Throws an error
      (emap (fn [x] (str x)) (coerce [] (double-array [1 2 3]))) ;; OK!
 
+   Implemenations may *optionally* support custom function types. If this is the case, the
+   parameter m must be a valid array from the given implementation.
+
    Returns a new array of the same element-type and shape as the array m."
   ([f m]
     (mp/element-map m f))
@@ -2162,7 +2132,8 @@ elements not-equal to the argument are 0.
     (mp/element-map m f a more)))
 
 (defn emap-indexed
-  "Element-wise map-indexed over all elements of one or more arrays.
+  "Element-wise map-indexed over all elements of one or more arrays. Like
+   emap, but provides an index as the second argument to the mapping function.
 
    f must accept as first argument the index vector of the current element,
    and return a result compatible with the element-type of the array m
@@ -2242,6 +2213,28 @@ elements not-equal to the argument are 0.
   ([f m a & more]
     (mp/element-map! m f a more) m))
 
+(defn add-emap!
+  "Adds the result of emap to a destination array.
+
+   dest must be a mutable numerical array. Returns dest."
+  ([dest f a]
+    (mp/add-emap! dest f a) dest)
+  ([dest f a b]
+    (mp/add-emap! dest f a b) dest)
+  ([dest f a b & more]
+    (mp/add-emap! dest f a b more) dest))
+
+(defn set-emap!
+  "Sets the destination array to the result of an emap operation.
+
+   dest must be a mutable array. Returns dest."
+  ([dest f a]
+    (mp/set-emap! dest f a) dest)
+  ([dest f a b]
+    (mp/set-emap! dest f a b) dest)
+  ([dest f a b & more]
+    (mp/set-emap! dest f a b more) dest))
+
 (defn emap-indexed!
   "Element-wise map-indexed over all elements of one or more arrays.
 

src/main/clojure/clojure/core/matrix/impl/defaults.cljc

@@ -1438,6 +1438,26 @@
       ;; check for no slices, in which case we must return nil
       (if (seq slcs) slcs nil))))
 
+(extend-protocol mp/PAddEmap
+  #?(:clj Object :cljs object)
+  (add-emap!
+    ([dest f a]
+      (mp/matrix-add! dest (mp/element-map a f)))
+    ([dest f a b]
+      (mp/matrix-add! dest (mp/element-map a f b)))
+    ([dest f a b more]
+      (mp/matrix-add! dest (mp/element-map a f b more)))))
+
+(extend-protocol mp/PSetEmap
+  #?(:clj Object :cljs object)
+  (set-emap!
+    ([dest f a]
+      (mp/assign! dest (mp/element-map a f)))
+    ([dest f a b]
+      (mp/assign! dest (mp/element-map a f b)))
+    ([dest f a b more]
+      (mp/assign! dest (mp/element-map a f b more)))))
+
 ;; functional operations
 (extend-protocol mp/PFunctionalOperations
   #?(:clj Number :cljs number)

src/main/clojure/clojure/core/matrix/protocols.cljc

@@ -1051,14 +1051,14 @@ would often be a numeric base type)."
     [m f]
     [m f a]
     [m f a more]
-    "Maps f over all elements of m (and optionally other matrices), returning a new matrix.
+    "Maps f over all elements of m (and optionally other arrays), returning a new matrix.
      f is expected to produce elements of a type supported by the implementation of m - failure
      to do so may cause an error.")
   (element-map!
     [m f]
     [m f a]
     [m f a more]
-    "Maps f over all elements of m (and optionally other matrices), mutating the elements of m in place.
+    "Maps f over all elements of m (and optionally other arrays), mutating the elements of m in place.
      Must throw an exception if m is not mutable.
      f is expected to produce elements of a type supported by the implementation of m - failure
      to do so may cause an error.")
@@ -1068,6 +1068,29 @@ would often be a numeric base type)."
     "Reduces with the function f over all elements of m.
      Implementations do not need to support clojure.core/reduced"))
 
+(defprotocol PAddEmap
+  "Protocol to support the add-emap! API function."
+  (add-emap!
+    [dest f a]
+    [dest f a b]
+    [dest f a b more]
+    "Maps f over all elements of a (and optionally other arrays), adding the result to dest.
+     Must throw an exception if dest is not mutable.
+     f is expected to produce elements of a type supported by the implementation of dest - failure
+     to do so may cause an error."))
+
+(defprotocol PSetEmap
+  "Protocol to support the set-emap! API function."
+  (set-emap!
+    [dest f a]
+    [dest f a b]
+    [dest f a b more]
+    "Maps f over all elements of a (and optionally other arrays), storing the result in dest.
+     Must throw an exception if dest is not mutable.
+     f is expected to produce elements of a type supported by the implementation of dest - failure
+     to do so may cause an error."))
+
+
 (defprotocol PMapIndexed
   "Protocol for map-indexed operation on matrices"
   ;; This protocol is created instead of adding element-map-indexed to PFunctionalOperations to

src/test/cljs/clojure/core/matrix/cljs_runner.cljs

@@ -0,0 +1,5 @@
+(ns clojure.core.matrix.cljs-runner
+  (:require [doo.runner :refer-macros [doo-tests]]
+            [clojure.core.matrix.test-api]))
+
+(doo-tests 'clojure.core.matrix.test-api)