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Merge tag 'sparse-array-0.1.0'

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Simon Brooke 2019-06-26 13:28:15 +01:00
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23
README.md
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@ -4,6 +4,8 @@ A Clojure library designed to manipulate sparse *arrays* - multi-dimensional spa
Arbitrary numbers of dimensions are supported, up to limits imposed by the JVM stack. Arbitrary numbers of dimensions are supported, up to limits imposed by the JVM stack.
[![Clojars Project](https://img.shields.io/clojars/v/sparse-array.svg)](https://clojars.org/sparse-array)
## Conventions: ## Conventions:
### Sparse arrays ### Sparse arrays
@ -32,7 +34,26 @@ Thus an array with a single value 'hello' at coordinates x = 3, y = 4, z = 5 wou
} }
``` ```
At the present stage of development, where the expectations of an operation are violated, `nil` is returned and no exception is thrown. However, it's probable that later there will be at least the option of thowing specific exceptions, as otherwise debugging could be tricky. ### Errors and error-reporting
A dynamic variable, `*safe-sparse-operations*`, is provided to handle behaviour in error conditions. If this is `false`, bad data will generally not cause an exception to be thrown, and corrupt structures may be returned, thus:
```clojure
(put (make-sparse-array :x :y :z) "hello" 3) ;; insufficient coordinates specified
=> {:dimensions 3, :coord :x, :content (:y :z), 3 {:dimensions 2, :coord :y, :content (:z), nil {:dimensions 1, :coord :z, :content :data, nil nil}}}
```
However, if `*safe-sparse-operations*` is bound to `true`, exceptions will be thrown instead:
```clojure
(binding [*safe-sparse-operations* true]
(put (make-sparse-array :x :y :z) "hello" 3))
ExceptionInfo Expected 3 coordinates; found 1 clojure.core/ex-info (core.clj:4617)
```
Sanity checking data is potentially expensive; for this reason `*safe-sparse-operations*` defaults to `false`, but you make wish to bind it to `true` especially while debugging.
### Dense arrays ### Dense arrays

25
project.clj
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@ -1,6 +1,27 @@
(defproject sparse-array "0.1.0-SNAPSHOT" (defproject sparse-array "0.1.0"
:description "A Clojure library designed to manipulate sparse *arrays* - multi-dimensional spaces accessed by indices, but containing arbitrary values rather than just numbers. For sparse spaces which contain numbers only, you're better to use a *sparse matrix* library, for example [clojure.core.matrix](https://mikera.github.io/core.matrix/)." :description "A Clojure library designed to manipulate sparse *arrays* - multi-dimensional spaces accessed by indices, but containing arbitrary values rather than just numbers. For sparse spaces which contain numbers only, you're better to use a *sparse matrix* library, for example [clojure.core.matrix](https://mikera.github.io/core.matrix/)."
:url "http://example.com/FIXME" :url "http://example.com/FIXME"
:license {:name "Eclipse Public License" :license {:name "Eclipse Public License"
:url "http://www.eclipse.org/legal/epl-v10.html"} :url "http://www.eclipse.org/legal/epl-v10.html"}
:dependencies [[org.clojure/clojure "1.8.0"]]) :dependencies [[org.clojure/clojure "1.8.0"]]
:plugins [[lein-codox "0.10.4"]
[lein-release "1.0.5"]]
;; `lein release` doesn't play nice with `git flow release`. Run `lein release` in the
;; `develop` branch, then merge the release tag into the `master` branch.
:release-tasks [["vcs" "assert-committed"]
["clean"]
["test"]
["codox"]
["change" "version" "leiningen.release/bump-version" "release"]
["vcs" "commit"]
;; ["vcs" "tag"] -- not working, problems with secret key
["uberjar"]
["install"]
["deploy" "clojars"]
["change" "version" "leiningen.release/bump-version"]
["vcs" "commit"]])

145
src/sparse_array/core.clj
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@ -1,5 +1,18 @@
(ns sparse-array.core) (ns sparse-array.core)
(declare put get)
(def ^:dynamic *safe-sparse-operations*
"Whether spase array operations should be conducted safely, with careful
checking of data conventions and exceptions thrown if expectations are not
met. Normally `false`."
false)
(defn- unsafe-sparse-operations?
"returns `true` if `*safe-sparse-operations*` is `false`, and vice versa."
[]
(not (true? *safe-sparse-operations*)))
(defn make-sparse-array (defn make-sparse-array
"Make a sparse array with these `dimensions`. Every member of `dimensions` "Make a sparse array with these `dimensions`. Every member of `dimensions`
must be a keyword; otherwise, `nil` will be returned." must be a keyword; otherwise, `nil` will be returned."
@ -14,26 +27,63 @@
:data :data
(rest dimensions))})) (rest dimensions))}))
(defn- safe-test-or-throw
"If `v` is truthy or `*safe-sparse-operations*` is false, return `v`;
otherwise, throw an `ExceptionInfo` with this `message` and the map `m`."
[v message m]
(if-not
v
(if
*safe-sparse-operations*
(throw (ex-info message m))
v)
v))
(defn sparse-array? (defn sparse-array?
"`true` if `x` is a sparse array conforming to the conventions established "`true` if `x` is a sparse array conforming to the conventions established
by this library, else `false`." by this library, else `false`."
([x] ([x]
(and (apply
(map? x) sparse-array?
(pos? (:dimensions x)) (cons
(keyword? (:coord x)) x
(cons
(:coord x)
(if (if
(coll? (:content x)) (coll? (:content x))
(:content x))))))
([x & axes]
(and
(safe-test-or-throw
(map? x)
"Array must be a map" {:array x})
(safe-test-or-throw
(and (integer? (:dimensions x)) (pos? (:dimensions x)))
(str "The value of `:dimensions` must be a positive integer, not " (:dimensions x))
{:array x})
(safe-test-or-throw
(keyword? (:coord x))
(str "The value of `:coord` must be a keyword, not " (:coord x))
{:array x})
(safe-test-or-throw
(= (:coord x) (first axes))
(str "The value of `:coord` must be " (first axes) ", not " (:coord x))
{:array x})
(if
(empty? (rest axes))
(safe-test-or-throw
(= (:content x) :data)
"If there are no further axes the value of `:content` must be `:data`"
{:array x})
(and
(= (:content x) (rest axes))
(every? (every?
sparse-array? sparse-array?
(map #(x %) (filter integer? (keys x)))) (map #(x %) (filter integer? (keys x)))))))))
(= (:content x) :data)))))
(defn put (defn- unsafe-put
"Return a sparse array like this `array` but with this `value` at these [array value coordinates]
`coordinates`. Returns `nil` if any coordinate is invalid." (cond
[array value & coordinates]
(if
(every? (every?
#(and (integer? %) (or (zero? %) (pos? %))) #(and (integer? %) (or (zero? %) (pos? %)))
coordinates) coordinates)
@ -51,14 +101,75 @@
(apply make-sparse-array (:content array))) (apply make-sparse-array (:content array)))
(cons value (rest coordinates)))))))) (cons value (rest coordinates))))))))
(defn put
"Return a sparse array like this `array` but with this `value` at these
`coordinates`. Returns `nil` if any coordinate is invalid."
[array value & coordinates]
(cond
(nil? value)
nil
(unsafe-sparse-operations?)
(unsafe-put array value coordinates)
(not (sparse-array? array))
(throw (ex-info "Sparse array expected" {:array array}))
(not= (:dimensions array) (count coordinates))
(throw
(ex-info
(str "Expected " (:dimensions array) " coordinates; found " (count coordinates))
{:array array
:coordinates coordinates}))
(not
(every?
#(and (integer? %) (or (zero? %) (pos? %)))
coordinates))
(throw
(ex-info
"Coordinates must be zero or positive integers"
{:array array
:coordinates coordinates
:invalid (remove #(and (pos? %) (integer? %)) coordinates)}))
:else
(unsafe-put array value coordinates)
value
*safe-sparse-operations*))
(defn- unsafe-get
;; TODO: I am CERTAIN there is a more elegant solution to this.
[array coordinates]
(let [v (array (first coordinates))]
(cond
(= :data (:content array))
v
(nil? v)
nil
:else
(apply get (cons v (rest coordinates))))))
(defn get (defn get
"Return the value in this sparse `array` at these `coordinates`." "Return the value in this sparse `array` at these `coordinates`."
;; TODO: I am CERTAIN there is a more elegant solution to this.
[array & coordinates] [array & coordinates]
(if (cond
(= :data (:content array)) (unsafe-sparse-operations?)
(array (first coordinates)) (unsafe-get array coordinates)
(apply get (cons (array (first coordinates)) (rest coordinates))))) (not (sparse-array? array))
(throw (ex-info "Sparse array expected" {:array array}))
(not (every?
#(and (integer? %) (or (zero? %) (pos? %)))
coordinates))
(throw
(ex-info
"Coordinates must be zero or positive integers"
{:array array
:coordinates coordinates
:invalid (remove #(and (pos? %) (integer? %)) coordinates)}))
(not (= (:dimensions array) (count coordinates)))
(throw
(ex-info
(str "Expected " (:dimensions array) " coordinates; found " (count coordinates))
{:array array
:coordinates coordinates}))
:else
(unsafe-get array coordinates)))
(defn merge-sparse-arrays (defn merge-sparse-arrays
"Return a sparse array taking values from sparse arrays `a1` and `a2`, "Return a sparse array taking values from sparse arrays `a1` and `a2`,
@ -74,7 +185,7 @@
nil nil
(= :data (:content a1)) (= :data (:content a1))
(merge a1 a2) (merge a1 a2)
:else (or (unsafe-sparse-operations?) (and (sparse-array? a1) (sparse-array? a2)))
(reduce (reduce
merge merge
a2 a2

154
test/sparse_array/core_test.clj
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@ -4,7 +4,94 @@
(deftest creation-and-testing (deftest creation-and-testing
(testing "Creation and testing." (testing "Creation and testing."
(is (sparse-array? (make-sparse-array :x :y :z))))) (is (sparse-array? (make-sparse-array :x :y :z)))
(is (sparse-array? {:dimensions 2,
:coord :x,
:content '(:y),
3 {:dimensions 1,
:coord :y,
:content :data,
4 "hello"},
4 {:dimensions 1,
:coord :y,
:content :data,
3 "goodbye"}}))
(is (= (sparse-array? []) false))
(is (= (sparse-array? "hello") false))
(is (=
(sparse-array?
(dissoc (make-sparse-array :x :y :z) :dimensions))
false)
"All mandatory keywords must be present: dimensions")
(is (=
(sparse-array?
(dissoc (make-sparse-array :x :y :z) :coord))
false)
"All mandatory keywords must be present: coord")
(is (=
(sparse-array?
(dissoc (make-sparse-array :x :y :z) :content))
false)
"All mandatory keywords must be present: content")
(is (=
(sparse-array? {:dimensions 2,
:coord :x,
:content '(:y),
3 {:dimensions 1,
:coord :y,
:content :data,
4 "hello"},
4 {:dimensions 1,
:coord :y,
:content :data,
3 "goodbye"}
5 :foo})
false)
"Can't have data in a non-data layer")
))
(deftest testing-safe
(testing "Checking that correct exceptions are thrown when `*safe-sparse-operations*` is true"
(binding [*safe-sparse-operations* true]
(is
(thrown-with-msg?
clojure.lang.ExceptionInfo
#"Array must be a map"
(sparse-array? [])))
(is
(thrown-with-msg?
clojure.lang.ExceptionInfo
#"The value of `:dimensions` must be a positive integer, not .*"
(sparse-array?
(dissoc (make-sparse-array :x :y :z) :dimensions)))
"All mandatory keywords must be present: dimensions")
(is (thrown-with-msg?
clojure.lang.ExceptionInfo
#"The value of `:coord` must be a keyword, not .*"
(sparse-array?
(dissoc (make-sparse-array :x :y :z) :coord))))
(is (thrown-with-msg?
clojure.lang.ExceptionInfo
#"If there are no further axes the value of `:content` must be `:data`"
(sparse-array?
(dissoc (make-sparse-array :x :y :z) :content)))
"All mandatory keywords must be present: content")
(is (thrown-with-msg?
clojure.lang.ExceptionInfo
#"Array must be a map"
(sparse-array? {:dimensions 2,
:coord :x,
:content '(:y),
3 {:dimensions 1,
:coord :y,
:content :data,
4 "hello"},
4 {:dimensions 1,
:coord :y,
:content :data,
3 "goodbye"}
5 :foo}))
"Can't have data in a non-data layer"))))
(deftest put-and-get (deftest put-and-get
(testing "get" (testing "get"
@ -14,6 +101,13 @@
:content '(:y) :content '(:y)
3 {:dimensions 1 :coord :y :content :data 4 "hello"}} 3 {:dimensions 1 :coord :y :content :data 4 "hello"}}
actual (get array 3 4)] actual (get array 3 4)]
(is (= actual expected)))
(let [expected nil
array {:dimensions 2,
:coord :x,
:content '(:y)
3 {:dimensions 1 :coord :y :content :data 4 "hello"}}
actual (get array 4 3)]
(is (= actual expected)))) (is (= actual expected))))
(testing "put" (testing "put"
(let [expected "hello" (let [expected "hello"
@ -26,12 +120,24 @@
(let (let
[expected "hello" [expected "hello"
actual (get (put (make-sparse-array :x) expected 3) 3)] actual (get (put (make-sparse-array :x) expected 3) 3)]
(is (= actual expected)))) (is (= actual expected)))
(binding [*safe-sparse-operations* true]
;; enabling error handling shouldn't make any difference
(let
[expected "hello"
actual (get (put (make-sparse-array :x) expected 3) 3)]
(is (= actual expected)))))
(testing "round trip, two dimensions" (testing "round trip, two dimensions"
(let (let
[expected "hello" [expected "hello"
actual (get (put (make-sparse-array :x :y) expected 3 4) 3 4)] actual (get (put (make-sparse-array :x :y) expected 3 4) 3 4)]
(is (= actual expected)))) (is (= actual expected)))
(binding [*safe-sparse-operations* true]
;; enabling error handling shouldn't make any difference
(let
[expected "hello"
actual (get (put (make-sparse-array :x :y) expected 3 4) 3 4)]
(is (= actual expected)))))
(testing "round trip, three dimensions" (testing "round trip, three dimensions"
(let (let
[expected "hello" [expected "hello"
@ -41,7 +147,29 @@
(let (let
[expected "hello" [expected "hello"
actual (get (put (make-sparse-array :p :q :r :s) expected 3 4 5 6) 3 4 5 6)] actual (get (put (make-sparse-array :p :q :r :s) expected 3 4 5 6) 3 4 5 6)]
(is (= actual expected))))) (is (= actual expected))))
(testing "Error handling, number of dimensions"
(binding [*safe-sparse-operations* true]
(is
(thrown-with-msg?
clojure.lang.ExceptionInfo
#"Expected 3 coordinates; found 2"
(put (make-sparse-array :x :y :z) "hello" 3 4)))
(is
(thrown-with-msg?
clojure.lang.ExceptionInfo
#"Expected 3 coordinates; found 4"
(put (make-sparse-array :x :y :z) "hello" 3 4 5 6)))
(is
(thrown-with-msg?
clojure.lang.ExceptionInfo
#"Expected 3 coordinates; found 2"
(get (make-sparse-array :x :y :z) 3 4)))
(is
(thrown-with-msg?
clojure.lang.ExceptionInfo
#"Expected 3 coordinates; found 4"
(get (make-sparse-array :x :y :z) 3 4 5 6))))))
(deftest merge-test (deftest merge-test
(testing "merge, one dimension" (testing "merge, one dimension"
@ -84,9 +212,17 @@
[nil nil nil nil nil] [nil nil nil nil nil]
[nil nil nil nil "hello"] [nil nil nil nil "hello"]
[nil nil nil "goodbye" nil]] [nil nil nil "goodbye" nil]]
actual (sparse-to-dense (put actual (sparse-to-dense {:dimensions 2,
(put :coord :x,
(make-sparse-array :x :y) :content '(:y),
"hello" 3 4) 3 {:dimensions 1,
"goodbye" 4 3))] :coord :y,
:content :data,
4 "hello"},
4 {:dimensions 1,
:coord :y,
:content :data,
3 "goodbye"}})]
(is (= actual expected))))) (is (= actual expected)))))