Merge branch 'PolyMathOrg:master' into least-squares

Author: jordanmontt

CONTRIBUTING.md

@@ -2,7 +2,7 @@
 
 *This file is currently not complete but will be improve step by step.*
 
-You need to download Pharo 8.0 first.
+You need to download Pharo 9.0 or 10 first.
 
 ## Setup Iceberg
 You need an ssh key in order to commit on github. Open Iceberg tool, and then click on the settings. Check the box : "Use custom SSH keys".
@@ -14,7 +14,7 @@ All changes you'll do will be versionned in your own fork of the [PolyMath repos
 Go to PolyMath github's repository and click on the fork button on the top right. Yes, this means that you'll need a github account to contribute to PolyMath.
 
 ## Load last dev version of PolyMath
-In a fresh Pharo 8.0 image, load last development version of Polymath : 
+In a fresh Pharo 9.0 or 10 image, load last development version of Polymath : 
 
 ```Smalltalk
 Metacello new

README.md

@@ -21,11 +21,11 @@
 <img width="1675" alt="Screenshot 2019-04-24 at 11 12 57" src="https://user-images.githubusercontent.com/327334/56652094-66eb7780-6682-11e9-9753-101be18df67c.png">
 
 
-You can load PolyMath 1.0.3 into a fresh Pharo 9.0 or 10 image with:
+You can load PolyMath 1.0.4 into a fresh Pharo 9.0 or 10 image with:
 
 ```Smalltalk
 Metacello new
-        repository: 'github://PolyMathOrg/PolyMath:v1.0.3';
+        repository: 'github://PolyMathOrg/PolyMath:v1.0.4';
         baseline: 'PolyMath';
         load
 ```
@@ -39,7 +39,7 @@ Metacello new
         load
 ```
 
-We have **872** green tests ! At the moment, all the development happens in the master branch (we are using [trunk-based development](https://trunkbaseddevelopment.com/)).
+We have **900** green tests ! At the moment, all the development happens in the master branch (we are using [trunk-based development](https://trunkbaseddevelopment.com/)).
 
 PolyMath is a Pharo project, similar to existing scientific libraries like NumPy, SciPy for Python or SciRuby for Ruby. PolyMath already provides the following basic functionalities:
 - complex and quaternions extensions,

src/Math-AutomaticDifferenciation/PMDualNumber.class.st

@@ -133,11 +133,19 @@ PMDualNumber >> asInteger [
 	^ value asInteger
 ]
 
+{ #category : #comparing }
+PMDualNumber >> closeTo: aDualNumber [
+
+	^ (value closeTo: aDualNumber value) and: [ 
+		  eps closeTo: aDualNumber eps ]
+]
+
 { #category : #'mathematical functions' }
 PMDualNumber >> conjugated [
+
 	^ self class
-		value: self value conjugated
-		eps: self eps asComplex complexConjugate
+		  value: self value complexConjugate
+		  eps: self eps asComplex complexConjugate
 ]
 
 { #category : #'mathematical functions' }
@@ -157,7 +165,12 @@ PMDualNumber >> eps: aNumber [
 
 { #category : #comparing }
 PMDualNumber >> equalsTo: aDualNumber [
-	^ (value equalsTo: aDualNumber value) and: [ eps equalsTo: aDualNumber eps ]
+
+	self
+		deprecated: 'Use closeTo: instead'
+		transformWith: '`@rec equalsTo: `@arg' -> '`@rec closeTo: `@arg'.
+
+	^ self closeTo: aDualNumber 
 ]
 
 { #category : #testing }

src/Math-AutomaticDifferenciation/PMHyperDualNumber.class.st

@@ -96,6 +96,14 @@ PMHyperDualNumber >> arcTan [
 		yourself
 ]
 
+{ #category : #comparing }
+PMHyperDualNumber >> closeTo: aHyperDualNumber [
+
+	^ (super closeTo: aHyperDualNumber) and: [ 
+		  (eps2 closeTo: aHyperDualNumber eps2) and: [ 
+			  eps1eps2 closeTo: aHyperDualNumber eps1eps2 ] ]
+]
+
 { #category : #'mathematical functions' }
 PMHyperDualNumber >> cos [
 	^ super cos
@@ -126,9 +134,12 @@ PMHyperDualNumber >> eps2: anEps2 [
 
 { #category : #comparing }
 PMHyperDualNumber >> equalsTo: aHyperDualNumber [
-	^ (super equalsTo: aHyperDualNumber)
-		and: [ (eps2 equalsTo: aHyperDualNumber eps2)
-				and: [ eps1eps2 equalsTo: aHyperDualNumber eps1eps2 ] ] 
+
+	self
+		deprecated: 'Use closeTo: instead'
+		transformWith: '`@rec equalsTo: `@arg' -> '`@rec closeTo: `@arg'.
+
+	^ self closeTo: aHyperDualNumber
 ]
 
 { #category : #'mathematical functions' }

src/Math-Chromosome/PMChromosomeManager.class.st

@@ -5,9 +5,10 @@ Class {
 		'population',
 		'populationSize',
 		'rateOfMutation',
-		'rateOfCrossover'
+		'rateOfCrossover',
+		'randomNumberGenerator'
 	],
-	#category : 'Math-Chromosome'
+	#category : #'Math-Chromosome'
 }
 
 { #category : #creation }
@@ -28,6 +29,12 @@ PMChromosomeManager >> crossover: aChromosome1 and: aChromosome2 [
 	^self subclassResponsibility
 ]
 
+{ #category : #initialization }
+PMChromosomeManager >> initialize [ 
+	super initialize.
+	randomNumberGenerator := Random new.
+]
+
 { #category : #information }
 PMChromosomeManager >> isFullyPopulated [
 
@@ -56,7 +63,7 @@ PMChromosomeManager >> populationSize: anInteger [
 PMChromosomeManager >> process: aChromosome1 and: aChromosome2 [ 
 
 	| roll |
-	roll := Number random.
+	roll := randomNumberGenerator next.
 	roll < rateOfCrossover 
 		ifTrue: [population addAll: (self crossover: aChromosome1 and: aChromosome2)]
 		ifFalse: 

src/Math-Chromosome/PMVectorChromosomeManager.class.st

@@ -5,28 +5,33 @@ Class {
 		'origin',
 		'range'
 	],
-	#category : 'Math-Chromosome'
+	#category : #'Math-Chromosome'
 }
 
 { #category : #operation }
 PMVectorChromosomeManager >> crossover: aChromosome1 and: aChromosome2 [
 
-	| index new1 new2|
-	index := ( aChromosome1 size - 1) random + 2.
+	| index new1 new2 |
+
+	index := randomNumberGenerator nextIntegerBetween: 2 and: aChromosome1 size.
+
 	new1 := self clone: aChromosome1.
 	new1 replaceFrom: index to: new1 size with: aChromosome2 startingAt: index.
+	
 	new2 := self clone: aChromosome2.
 	new2 replaceFrom: index to: new2 size with: aChromosome1 startingAt: index.
-	^Array with: new1 with: new2
+	
+	^ Array with: new1 with: new2
 ]
 
 { #category : #operation }
 PMVectorChromosomeManager >> mutate: aVector [
 
 	| index |
-	index := aVector size random + 1.
+	index := randomNumberGenerator nextIntegerBetween: 1 and: aVector size.
+
 	^( aVector copy)
-			at: index put: ( self randomComponent: index);
+			at: index put: (self randomComponent: index);
 			yourself
 ]
 
@@ -39,13 +44,13 @@ PMVectorChromosomeManager >> origin: aVector [
 { #category : #creation }
 PMVectorChromosomeManager >> randomChromosome [
 
-	^( ( 1 to: origin size) collect: [ :n | self randomComponent: n]) asPMVector
+	^ ((1 to: origin size) collect: [ :n | self randomComponent: n ]) asPMVector
 ]
 
 { #category : #information }
 PMVectorChromosomeManager >> randomComponent: anInteger [
 
-	^( range at: anInteger) asFloat random + ( origin at: anInteger)
+	^ (randomNumberGenerator nextBetween: 0 and: (range at: anInteger)) + (origin at: anInteger)
 ]
 
 { #category : #initialization }

src/Math-Complex/Number.extension.st

@@ -10,7 +10,7 @@ Number >> adaptToComplex: rcvr andSend: selector [
 Number >> asComplex [
 	"Answer a Complex number that represents value of the receiver."
 
-	^ PMComplex real: self imaginary: 0
+	^ PMComplexNumber real: self imaginary: 0
 ]
 
 { #category : #'*Math-Complex' }
@@ -25,7 +25,7 @@ Number >> complexConjugate [
 
 { #category : #'*Math-Complex' }
 Number >> i [
-	^ PMComplex real: 0 imaginary: self
+	^ PMComplexNumber real: 0 imaginary: self
 ]
 
 { #category : #'*Math-Complex' }
@@ -36,7 +36,7 @@ Number >> i: aNumber [
 	this is the same as (self + aNumber i) but a little bit more efficient."
 
 	aNumber isNumber ifFalse: [self error: 'Badly formed complex number'].
-	^PMComplex real: self imaginary: aNumber
+	^PMComplexNumber real: self imaginary: aNumber
 ]
 
 { #category : #'*Math-Complex' }