cormas · PrasannaPal21 · Mar 24, 2025 · Mar 24, 2025 · Mar 24, 2025 · Mar 26, 2025
diff --git a/README.md b/README.md
@@ -1,4 +1,4 @@
-<p align="center"><img alt="CORMAS" src="docs/_media/logo.png" style="width: 25%; height: 25%">
+<p align="center"><img alt="CORMAS" src="./img/CormasLogo.png" style="width: 25%; height: 25%">
 <h1 align="center">CORMAS</h1>
   <p align="center">
     <b>CO</b>mmon pool <b>R</b>essources and <b>M</b>ulti-<b>A</b>gent <b>S</b>imulations
@@ -57,7 +57,7 @@ Metacello new
 ```
 
 All packages load into the Cormas-* package names:
-<p><img alt="Loading..." src="assets/images/loadingCormas.jpg" style="width: 40%; height: 40%">
+<p><img alt="Loading..." src="./img/loadingCormas.jpg" style="width: 40%; height: 40%">
 
 ## CLI Installation
 
@@ -91,10 +91,10 @@ As you use Cormas, you should always save your image (the state of your environm
 For that, select `Save` from the Pharo menu.
 
 Alternatively, if you want to save your image in a custom location, select `Save As...`:
-<p><img alt="SaveAs" src="assets/images/saveAs.jpg" style="width: 12%; height: 12%">
+<p><img alt="SaveAs" src="./img/saveAs.jpg" style="width: 12%; height: 12%">
 
 Then write the name of your choice (e.g.: `CormasPharo.image`):
-<p><img alt="Loading..." src="assets/images/saveImage.jpg" style="width: 40%; height: 40%">
+<p><img alt="Loading..." src="./img/saveImage.jpg" style="width: 40%; height: 40%">
 
 # Contributors ✨
 

diff --git a/img/CormasLogo.png b/img/CormasLogo.png
diff --git a/img/loadingCormas.jpg b/img/loadingCormas.jpg
diff --git a/img/saveAs.jpg b/img/saveAs.jpg
diff --git a/img/saveImage.jpg b/img/saveImage.jpg
diff --git a/src/Cormas-Core/CMAbstractModel.class.st b/src/Cormas-Core/CMAbstractModel.class.st
@@ -173,14 +173,11 @@ CMAbstractModel >> allTheEntities [
 
 { #category : 'accessing - entities' }
 CMAbstractModel >> allTheEntities: aClass [
-	" Answer a <Collection> of all the instances of aClass (and sub classes) collected by cormasModel. 
-	Usefull for abstract classes
-
-	Example: (self allTheEntities: Forager) is returning all the instances of restrained and unrestrained foragers "
+	"Purpose: This method returns a collection of all instances of aClass and of the instances of all its subclasses"
 
 	| coll |
 	coll := OrderedCollection new.
-	aClass withAllSubclasses do: [:cl | cl isAbstract ifFalse: [coll addAll: (self entitiesOfClass: cl)]].
+	aClass withAllSubclasses do: [:cl | cl hasSubclasses ifFalse: [coll addAll: (self entitiesOfClass: cl)]].
 	^ coll
 ]
 
@@ -616,11 +613,9 @@ Example: self dominance: #groupNumber"
 
 { #category : 'accessing - entities' }
 CMAbstractModel >> entitiesOfClass: aClass [
-	"Returns a collection of all the instances of aClass"
-
 	| getter |
 
-	aClass isAbstract ifTrue: [ ^ OrderedCollection new ].
+	aClass hasSubclasses ifTrue: [ ^ OrderedCollection new ].
 
 	getter := self getterForEntityClass: aClass.
 
@@ -714,7 +709,7 @@ CMAbstractModel >> initialize [
 { #category : 'accessing' }
 CMAbstractModel >> initializeAgentsOfClass: aClass [
 
-	(aClass isAbstract not and: [ aClass isLocated ]) ifTrue: [ 
+	(aClass hasSubclasses not and: [ aClass isLocated ]) ifTrue: [ 
 		(self entitiesOfClass: aClass) do: [ :each | each leave ] ].
 
 	self resetEntities: aClass

diff --git a/src/Cormas-Core/CMEntity.class.st b/src/Cormas-Core/CMEntity.class.st
@@ -132,12 +132,21 @@ CMEntity class >> initializeParameters [
 ]
 
 { #category : 'testing' }
-CMEntity class >> isAbstract [
+CMEntity class >> hasSubclasses [
 	"Purpose: to test the existence of subclasses"
 
 	^self subclasses notEmpty
 ]
 
+{ #category : 'testing' }
+CMEntity class >> isAbstract [
+	"This method is deprecated as it conflicts with Pharo's standard meaning of 'isAbstract'.
+	Please use #hasSubclasses instead."
+
+	self deprecated: 'Use #hasSubclasses instead' transformWith: '`@receiver isAbstract' -> '`@receiver hasSubclasses'.
+	^self hasSubclasses
+]
+
 { #category : 'testing' }
 CMEntity class >> isLocated [
 

diff --git a/src/Cormas-Core/CMSpaceModel.class.st b/src/Cormas-Core/CMSpaceModel.class.st
@@ -65,7 +65,7 @@ CMSpaceModel class >> forModel: aCormasModel [
 		yourself
 ]
 
-{ #category : 'ESE (regular) - special locations' }
+{ #category : 'accessing cell' }
 CMSpaceModel >> cellAt: aRowIndex at: aColumnIndex [
 
 	^ cormasModel cells at: ((aRowIndex - 1) * numberOfColumns + aColumnIndex)
@@ -77,7 +77,7 @@ CMSpaceModel >> cells [
 	^ cormasModel cells
 ]
 
-{ #category : 'ESE (regular) - special locations' }
+{ #category : 'accessing cell' }
 CMSpaceModel >> cellsBetweenColumn: colNumber1 andColumn: colNumber2 [
 	"Return the cells between the colNumber1 and the colNumber2 of the spatial grid.
 colNumber1   <Integer> lineNumber = Positive Integer
@@ -92,7 +92,7 @@ colNumber2   <Integer> colNumber = Positive Integer"
 	^ cells
 ]
 
-{ #category : 'ESE (regular) - special locations' }
+{ #category : 'accessing cell' }
 CMSpaceModel >> cellsBetweenRow: lineNumber1 andRow: lineNumber2 [
 	"Return the cells between the lineNumber1 and the lineNumber2 of the spatial grid.
 lineNumber1   <Integer> lineNumber = Positive Integer
@@ -107,7 +107,7 @@ lineNumber2   <Integer> colNumber = Positive Integer"
 	^ cells
 ]
 
-{ #category : 'ESE (regular) - special locations' }
+{ #category : 'accessing cell' }
 CMSpaceModel >> cellsBetweenRow: aRowNumber1 andRow: aRowNumber2 column: aColumnNumber1 andColumn: aColumnNumber2 [
 
 	| topRowNumber bottomRowNumber leftColumnNumber rightColumnNumber result |
@@ -124,7 +124,7 @@ CMSpaceModel >> cellsBetweenRow: aRowNumber1 andRow: aRowNumber2 column: aColumn
 		select: [ :cell | result includes: cell ]
 ]
 
-{ #category : 'ESE (regular) - special locations' }
+{ #category : 'accessing cell' }
 CMSpaceModel >> cellsInRectangleFrom: cell1 to: cell2 [
 	"Return the cells between the lineNumber and the colNumber of the spatial grid. The Cells are ordered from cell1 to cell2.
 cell1   <SpatialEntityElement>  
@@ -160,21 +160,21 @@ cell2   <SpatialEntityElement> "
 	^cells
 ]
 
-{ #category : 'ESE (regular) - special locations' }
+{ #category : 'accessing cell' }
 CMSpaceModel >> cellsOfColumn: colNumber [
 	"Return the cells in the colNumber of the spatial grid.
 colNumber   <Integer> colNumber = Positive Integer"
 
 	^ cormasModel cells select: [ :cell | cell columnNumber = colNumber ]
 ]
 
-{ #category : 'ESE (regular) - special locations' }
+{ #category : 'accessing cell' }
 CMSpaceModel >> cellsOfRow: aRowNumber [
 
 	^ cormasModel cells select: [ :cell | cell rowNumber = aRowNumber ]
 ]
 
-{ #category : 'ESE (regular) - special locations' }
+{ #category : 'accessing cell' }
 CMSpaceModel >> centralCell [
 	(numberOfRows even or: [ numberOfColumns even ])
 		ifTrue: [ ^ self error: 'Grid dimensions is not odd' ].
@@ -250,7 +250,7 @@ The aggregates will  occupy the whole grid.
 
 ]
 
-{ #category : 'ESE initialize-release' }
+{ #category : 'initialization' }
 CMSpaceModel >> createCells [
 
 	1 to: self gridSize do: [ :i |
@@ -393,7 +393,7 @@ CMSpaceModel >> initialize [
 	isClosedEnvironment := true
 ]
 
-{ #category : 'ESE initialize-release' }
+{ #category : 'initialization' }
 CMSpaceModel >> initializeRegularNumberOfRows: aNumberOfRows numberOfColumns: aNumberOfColumns neighbourhood: aNumber closed: aBoolean [
 	" Private - Create a grid of regular cells."
 
@@ -426,12 +426,12 @@ CMSpaceModel >> isIrregular [
 	^gridCellShape = #irregular
 ]
 
-{ #category : 'ESE (regular) - special locations' }
+{ #category : 'accessing cell' }
 CMSpaceModel >> lowerLeftCell [
 	^ cormasModel cells at: numberOfColumns * (numberOfRows - 1) + 1
 ]
 
-{ #category : 'ESE (regular) - special locations' }
+{ #category : 'accessing cell' }
 CMSpaceModel >> lowerRightCell [
 	^ cormasModel cells at: numberOfColumns * numberOfRows
 ]
@@ -488,7 +488,7 @@ CMSpaceModel >> numberOfNeighbours [
 	^ self neighbourhoodConfiguration numberOfNeighbours
 ]
 
-{ #category : 'ESE initialize-release' }
+{ #category : 'initialization' }
 CMSpaceModel >> numberOfNeighbours: anIntegerOrSymbol [
 	" Create the grid.
 	Set the receiver's neighbourhood configuration to contain anIntegerOrSymbol neighbours "
@@ -532,19 +532,19 @@ CMSpaceModel >> printOn: aStream [
 
 ]
 
-{ #category : 'ESE (regular) - special locations' }
+{ #category : 'accessing cell' }
 CMSpaceModel >> randomCell [
 	"Return a spatialEntityElement (aCell) picked randomly from the spatial grid."
 
 	^ self selectRandomlyFrom: cormasModel cells
 ]
 
-{ #category : 'ESE (regular) - special locations' }
+{ #category : 'accessing cell' }
 CMSpaceModel >> upperLeftCell [
 	^ cormasModel cells first
 ]
 
-{ #category : 'ESE (regular) - special locations' }
+{ #category : 'accessing cell' }
 CMSpaceModel >> upperRightCell [
 	^ cormasModel cells at: numberOfColumns
 ]

diff --git a/src/Cormas-SensitivityAnalysis/CMAverage150to500ValueCollector.class.st b/src/Cormas-SensitivityAnalysis/CMAverage150to500ValueCollector.class.st
diff --git a/src/Cormas-Tests/CMEntityTest.class.st b/src/Cormas-Tests/CMEntityTest.class.st
@@ -23,8 +23,14 @@ CMEntityTest >> testColorOfNumber [
 	self assert: (CMEntity colorOfNumber: 65) equals: Color purple
 ]
 
+{ #category : 'tests' }
+CMEntityTest >> testCormasEntityHasSubclasses [
+	self assert: CMEntity hasSubclasses
+]
+
 { #category : 'tests' }
 CMEntityTest >> testCormasEntityIsAbstract [
+	"This test is deprecated, use testCormasEntityHasSubclasses instead"
 	self assert: CMEntity isAbstract
 ]