Merge branch 'master' into plot_pca

PolyMathOrg · May 25, 2023 · ab0a10a · ab0a10a
2 parents b8ffb91 + d9a495e
commit ab0a10a
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diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml
@@ -0,0 +1,27 @@
+name: Release
+
+env:
+  GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+
+on:
+  release:
+    types: [created, edited]
+
+jobs:
+  build:
+    strategy:
+      matrix:
+        smalltalk: [ Pharo64-9.0, Pharo64-10, Pharo64-11 ]
+        os: [ macos-latest, windows-latest, ubuntu-latest]
+    runs-on: ${{ matrix.os }}
+    name: ${{ matrix.smalltalk }} on ${{ matrix.os }}
+    env:
+      PROJECT_NAME: PolyMath-${{ matrix.smalltalk }}
+    steps:
+      - uses: actions/checkout@v3
+      - uses: hpi-swa/setup-smalltalkCI@v1
+        with:
+          smalltalk-image: ${{ matrix.smalltalk }}
+      - run: smalltalkci -s ${{ matrix.smalltalk }}
+        shell: bash
+        timeout-minutes: 15
diff --git a/.github/workflows/smalltalk-ci.yml b/.github/workflows/smalltalk-ci.yml
@@ -1,31 +1,24 @@
-name: CI matrix
+name: CI
 
-on:
-  push:
-    branches: [ master ]
-  pull_request:
-    branches: [ master ]
+env:
+  GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
 
-  # Allows you to run this workflow manually from the Actions tab
-  workflow_dispatch:
+on: [ push, pull_request ]
 
-# A workflow run is made up of one or more jobs that can run sequentially or in parallel
 jobs:
   build:
+    runs-on: ubuntu-latest
+    env:
+      PROJECT_NAME: PolyMath-${{ matrix.smalltalk }}
     strategy:
       matrix:
-        os: [ macos-latest, windows-latest, ubuntu-latest]
-        smalltalk: [ Pharo64-9.0, Pharo64-10]
-    runs-on: ${{ matrix.os }}
-    name: ${{ matrix.smalltalk }} on ${{ matrix.os }}
+        smalltalk: [ Pharo64-9.0, Pharo64-10, Pharo64-11 ]
+    name: ${{ matrix.smalltalk }}
     steps:
-      - uses: actions/checkout@v2
-      - name: Setup smalltalkCI
-        uses: hpi-swa/setup-smalltalkCI@v1
+      - uses: actions/checkout@v3
+      - uses: hpi-swa/setup-smalltalkCI@v1
         with:
           smalltalk-image: ${{ matrix.smalltalk }}
-      - name: Load Image and Run Tests
-        run: smalltalkci -s ${{ matrix.smalltalk }}
-        env:
-          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+      - run: smalltalkci -s ${{ matrix.smalltalk }}
+        shell: bash
         timeout-minutes: 15
diff --git a/.gitignore b/.gitignore
@@ -0,0 +1 @@
+**/.DS_STORE
diff --git a/.smalltalk.ston b/.smalltalk.ston
@@ -7,21 +7,11 @@ SmalltalkCISpec {
     }
   ],
   #testing : {
+    #include : {
+      #packages : [ 'Math-.*' ]
+    },
     #coverage : {
-      #packages : [
-        'Math-A*',
-	'Math-B*',
-	'Math-C*',
-	'Math-D*',
-	'Math-FunctionFit',
-	'Math-K*',
-	'Math-M*',
-	'Math-N*',
-	'Math-ODE',
-	'Math-P*',
-	'Math-Q*',
-	'Math-R*',
-	'Math-TNSE' ]
+      #packages : [ 'Math-*' ]
     }
   }
 }
diff --git a/README.md b/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 1.0.4 into a fresh Pharo 9.0 or 10 image with:
+You can load PolyMath 1.0.5 into a fresh Pharo 9.0 or 10 image with:
 
 ```Smalltalk
 Metacello new
-        repository: 'github://PolyMathOrg/PolyMath:v1.0.4';
+        repository: 'github://PolyMathOrg/PolyMath:v1.0.5';
         baseline: 'PolyMath';
         load
 ```

diff --git a/src/BaselineOfPolyMath/BaselineOfPolyMath.class.st b/src/BaselineOfPolyMath/BaselineOfPolyMath.class.st
@@ -17,157 +17,94 @@ Class {
 
 { #category : #baseline }
 BaselineOfPolyMath >> baseline: spec [
+
 	<baseline>
-	spec
-		for: #common
-		do: [
-			spec blessing: #baseline.
-			spec repository: 'github://PolyMathOrg/PolyMath/src'.
-			spec
-				baseline: 'SMark'
-					with: [ spec repository: 'github://smarr/SMark:v1.0.4' ];
-				baseline: 'XMLWriter'
-					with: [ spec
-						repository: 'github://pharo-contributions/XML-XMLWriter:2.9.x/src' ].
-			spec
-				package: 'ExtendedNumberParser';
-				package: 'Math-Accuracy-Core';
-				package: 'Math-Accuracy-ODE'
-					with: [ spec requires: #('Math-ODE' 'XMLWriter') ];
-				package: 'Math-ArbitraryPrecisionFloat'
-					with: [ spec requires: #('ExtendedNumberParser') ];
-				package: 'Math-AutomaticDifferenciation'
-					with: [ spec requires: #('Math-Numerical' 'Math-Matrix') ];
-				package: 'Math-Benchmarks-KDTree'
-					with: [ spec requires: #('Math-KDTree' 'SMark') ];
-				package: 'Math-Benchmarks-ODE'
-					with: [ spec requires: #('Math-ODE' 'SMark' 'XMLWriter') ];
-				package: 'Math-Chromosome'
-					with: [ spec requires: #('Math-Core') ];
-				package: 'Math-Clustering'
-					with:
-						[ spec requires: #('Math-Numerical' 'Math-Core-Process' 'Math-Matrix') ];
-				package: 'Math-Complex'
-					with: [ spec requires: #('Math-Numerical' 'Math-Polynomials') ];
-				package: 'Math-Core';
-				package: 'Math-Core-Distribution'
-					with: [ spec requires: #('Math-Core') ];
-				package: 'Math-Core-Process';
-				package: 'Math-Numerical'
-					with: [ spec
-						requires:
-							#('Math-Core' 'Math-Core-Process' 'Math-Core-Distribution' 'Math-DistributionGamma' 'Math-DistributionBeta' 'Math-DistributionForHistogram' 'Math-StatisticalMoments' 'Math-Series') ];
-				package: 'Math-Polynomials'
-					with: [ spec
-						requires:
-							#('Math-Core' 'Math-Core-Process' 'Math-Core-Distribution' 'Math-DistributionGamma' 'Math-DistributionBeta' 'Math-DistributionForHistogram' 'Math-StatisticalMoments' 'Math-Series') ];
-				package: 'Math-DistributionBeta'
-					with: [ spec requires: #('Math-DistributionGamma') ];
-				package: 'Math-DistributionForHistogram'
-					with: [ spec requires: #('Math-Core-Distribution') ];
-				package: 'Math-DistributionGamma'
-					with: [ spec requires: #('Math-Core-Distribution') ];
-				package: 'Math-FastFourierTransform'
-					with: [ spec requires: #('Math-Complex') ];
-				package: 'Math-FunctionFit'
-					with: [ spec
-						requires:
-							#('Math-Numerical' 'Math-Chromosome' 'Math-Accuracy-Core' 'Math-Core' 'Math-Matrix' 'Math-Polynomials') ];
-				package: 'Math-KDTree';
-				package: 'Math-KernelSmoothing'
-					with: [ spec
-						requires: #('Math-Quantile' 'Math-Numerical' 'Math-Polynomials') ];
-				package: 'Math-KolmogorovSmirnov'
-					with: [ spec requires: #('Math-Numerical' 'Math-Polynomials') ];
-				package: 'Math-Matrix';
-				package: 'Math-Number-Extensions';
-				package: 'Math-ODE'
-					with:
-						[ spec requires: #('Math-Numerical' 'Math-Matrix' 'Math-Polynomials') ];
-				package: 'Math-Permutation'
-					with: [ spec requires: #('Math-Core' 'Math-Matrix' 'Math-Core-Process') ];
-				package: 'Math-Physics-Constants';
-				package: 'Math-PrincipalComponentAnalysis'
-					with:
-						[ spec requires: #('Math-Numerical' 'Math-Matrix' 'Math-Polynomials') ];
-				package: 'Math-Quantile';
-				package: 'Math-Quaternion'
-					with:
-						[ spec requires: #('Math-Complex' 'Math-Numerical' 'Math-Polynomials') ];
-				package: 'Math-Random';
-				package: 'Math-Series';
-				package: 'Math-StatisticalMoments'
-					with: [ spec requires: #('Math-Core' 'Math-DistributionForHistogram') ];
-				package: 'Math-TSNE';
-				package: 'Math-Tests-Accuracy'
-					with: [ spec requires: #('Math-Accuracy-Core') ];
-				package: 'Math-Tests-ArbitraryPrecisionFloat'
-					with: [ spec requires: #('Math-ArbitraryPrecisionFloat') ];
-				package: 'Math-Tests-AutomaticDifferenciation'
-					with: [ spec requires: #('Math-AutomaticDifferenciation' 'Math-Matrix') ];
-				package: 'Math-Tests-Clustering'
-					with: [ spec
-						requires:
-							#('Math-Clustering' 'Math-Core' 'Math-Core-Distribution' 'Math-UtilsDataServer') ];
-				package: 'Math-Tests-Complex'
-					with: [ spec requires: #('Math-Complex') ];
-				package: 'Math-Tests-Core'
-					with: [ spec requires: #('Math-Core') ];
-				package: 'Math-Tests-Core-Distribution'
-					with: [ spec requires: #('Math-Core-Distribution') ];
-				package: 'Math-Tests-Core-Process'
-					with: [ spec requires: #('Math-Core-Process') ];
-				package: 'Math-Tests-Numerical'
-					with: [ spec requires: #('Math-Numerical' 'Math-UtilsDataServer') ];
-				package: 'Math-Tests-FastFourierTransform'
-					with: [ spec
-						requires: #('Math-FastFourierTransform' 'Math-Numerical' 'Math-Polynomials') ];
-				package: 'Math-Tests-FunctionFit';
-				package: 'Math-Tests-KDTree'
-					with: [ spec requires: #('Math-KDTree') ];
-				package: 'Math-Tests-KernelSmoothing'
-					with: [ spec requires: #('Math-KernelSmoothing') ];
-				package: 'Math-Tests-KolmogorovSmirnov'
-					with: [ spec
-						requires: #('Math-Numerical' 'Math-KolmogorovSmirnov' 'Math-Polynomials') ];
-				package: 'Math-Tests-Matrix'
-					with: [ spec
-						requires:
-							#('Math-Core' 'Math-Numerical' 'Math-StatisticalMoments' 'Math-Matrix' 'Math-Polynomials') ];
-				package: 'Math-Tests-Number-Extensions'
-					with: [ spec requires: #('Math-Number-Extensions') ];
-				package: 'Math-Tests-ODE' with: [ spec requires: #('Math-ODE') ];
-				package: 'Math-Tests-Permutation'
-					with: [ spec requires: #('Math-Permutation') ];
-				package: 'Math-Tests-PrincipalComponentAnalysis'
-					with: [ spec requires: #('Math-PrincipalComponentAnalysis') ];
-				package: 'Math-Tests-Quantile'
-					with: [ spec requires: #('Math-Quantile') ];
-				package: 'Math-Tests-Polynomials'
-					with: [ spec requires: #('Math-Polynomials') ];
-				package: 'Math-Tests-Quaternion'
-					with: [ spec requires: #('Math-Quaternion') ];
-				package: 'Math-Tests-Random'
-					with: [ spec requires: #('Math-Random') ];
-				package: 'Math-Tests-TSNE'
-					with: [ spec requires: #('Math-TSNE') ];
-				package: 'Math-UtilsDataServer'.
-			spec
-				group: 'Accuracy'
-					with: #('Math-Accuracy-ODE' 'Math-Accuracy-Core');
-				group: 'Benchmarks'
-					with: #('Math-Benchmarks-ODE' 'Math-Benchmarks-KDTree');
-				group: 'Core'
-					with:
-					#('Math-Complex' 'Math-Quaternion' 'Math-Numerical' 'Math-Random' 'Math-KDTree' 'Math-ODE' 'Math-ArbitraryPrecisionFloat' 'Math-FastFourierTransform' 'ExtendedNumberParser' 'Math-Quantile' 'Math-Physics-Constants' 'Math-Polynomials' 'Math-TSNE' 'Math-Core-Process' 'Math-Core' 'Math-Core-Distribution');
-				group: 'Extensions'
-					with:
-					#('Math-Clustering' 'Math-Number-Extensions' 'Math-Chromosome' 'Math-PrincipalComponentAnalysis' 'Math-FunctionFit' 'Math-AutomaticDifferenciation' 'Math-KernelSmoothing' 'Math-Permutation' 'Math-KolmogorovSmirnov');
-				group: 'Tests'
-					with:
-					#('Math-Tests-Matrix' 'Math-Tests-Clustering' 'Math-Tests-Numerical' 'Math-Tests-Complex' 'Math-Tests-Quaternion' 'Math-Tests-Random' 'Math-Tests-ODE' 'Math-Tests-KDTree' 'Math-Tests-FunctionFit' 'Math-Tests-AutomaticDifferenciation' 'Math-Tests-FastFourierTransform' 'Math-Tests-Accuracy' 'Math-Tests-ArbitraryPrecisionFloat' 'Math-Tests-KolmogorovSmirnov' 'Math-Tests-Quantile' 'Math-Tests-Polynomials' 'Math-Tests-PrincipalComponentAnalysis' 'Math-Tests-KernelSmoothing' 'Math-Tests-Number-Extensions' 'Math-Tests-Permutation' 'Math-Tests-TSNE' 'Math-Tests-Core-Process' 'Math-Tests-Core-Distribution' 'Math-Tests-Core');
-				group: 'default'
-					with: #('Core' 'Extensions' 'Tests' 'Benchmarks' 'Accuracy') ]
+	spec for: #common do: [ "External dependencies"
+		self
+			sMark: spec;
+			xmlWriter: spec;
+			vectorMatrix: spec;
+			randomNumbers: spec.
+
+		spec
+			package: 'ExtendedNumberParser';
+			package: 'Math-Accuracy-Core';
+			package: 'Math-Accuracy-ODE' with: [ spec requires: #( 'Math-ODE' 'XMLWriter' ) ];
+			package: 'Math-ArbitraryPrecisionFloat' with: [ spec requires: #( 'ExtendedNumberParser' ) ];
+			package: 'Math-AutomaticDifferenciation' with: [ spec requires: #( 'Math-Numerical' 'MathVectorMatrix' ) ];
+			package: 'Math-Benchmarks-KDTree' with: [ spec requires: #( 'Math-KDTree' 'SMark' ) ];
+			package: 'Math-Benchmarks-ODE' with: [ spec requires: #( 'Math-ODE' 'SMark' 'XMLWriter' ) ];
+			package: 'Math-Chromosome' with: [ spec requires: #( 'MathVectorMatrix' ) ];
+			package: 'Math-Clustering' with: [ spec requires: #( 'Math-Numerical' 'Math-Core-Process' 'MathVectorMatrix' ) ];
+			package: 'Math-Complex' with: [ spec requires: #( 'Math-Numerical' 'Math-Polynomials' ) ];
+			package: 'Math-Helpers';
+			package: 'Math-Distributions' with: [ spec requires: #( 'MathVectorMatrix' 'Math-Quantile' 'Math-Core-Process' ) ];
+			package: 'Math-Core-Process';
+			package: 'Math-Numerical'
+			with: [ spec requires: #( 'MathVectorMatrix' 'Math-Core-Process' 'Math-Distributions' 'Math-StatisticalMoments'
+					   'Math-Series' ) ];
+			package: 'Math-Polynomials'
+			with: [ spec requires: #( 'MathVectorMatrix' 'Math-Core-Process' 'Math-Distributions' 'Math-StatisticalMoments'
+					   'Math-Series' ) ];
+			package: 'Math-FastFourierTransform' with: [ spec requires: #( 'Math-Complex' ) ];
+			package: 'Math-FunctionFit'
+			with: [ spec requires: #( 'Math-Numerical' 'Math-Chromosome' 'Math-Accuracy-Core' 'MathVectorMatrix' 'Math-Helpers' 'Math-Polynomials' ) ];
+			package: 'Math-KDTree';
+			package: 'Math-Number-Extensions';
+			package: 'Math-ODE' with: [ spec requires: #( 'Math-Numerical' 'MathVectorMatrix' 'Math-Polynomials' ) ];
+			package: 'Math-Permutation' with: [ spec requires: #( 'MathVectorMatrix' 'Math-Core-Process' ) ];
+			package: 'Math-Physics-Constants';
+			package: 'Math-PrincipalComponentAnalysis' with: [ spec requires: #( 'Math-Numerical' 'MathVectorMatrix' 'Math-Polynomials' ) ];
+			package: 'Math-Quantile';
+			package: 'Math-Quaternion' with: [ spec requires: #( 'Math-Complex' 'Math-Numerical' 'Math-Polynomials' ) ];
+			package: 'Math-Series';
+			package: 'Math-StatisticalMoments' with: [ spec requires: #( 'Math-Helpers' 'Math-Distributions' ) ];
+			package: 'Math-TSNE';
+			package: 'Math-Tests-Accuracy' with: [ spec requires: #( 'Math-Accuracy-Core' ) ];
+			package: 'Math-Tests-ArbitraryPrecisionFloat' with: [ spec requires: #( 'Math-ArbitraryPrecisionFloat' ) ];
+			package: 'Math-Tests-AutomaticDifferenciation' with: [ spec requires: #( 'Math-AutomaticDifferenciation' 'MathVectorMatrix' ) ];
+			package: 'Math-Tests-Clustering' with: [ spec requires: #( 'Math-Clustering' 'Math-Distributions' 'Math-UtilsDataServer' ) ];
+			package: 'Math-Tests-Complex' with: [ spec requires: #( 'Math-Complex' ) ];
+			package: 'Math-Tests-Distributions' with: [ spec requires: #( 'Math-Distributions' ) ];
+			package: 'Math-Tests-Core-Process' with: [ spec requires: #( 'Math-Core-Process' ) ];
+			package: 'Math-Tests-Numerical' with: [ spec requires: #( 'Math-Numerical' 'Math-UtilsDataServer' ) ];
+			package: 'Math-Tests-FastFourierTransform' with: [ spec requires: #( 'Math-FastFourierTransform' 'Math-Numerical' 'Math-Polynomials' ) ];
+			package: 'Math-Tests-FunctionFit';
+			package: 'Math-Tests-KDTree' with: [ spec requires: #( 'Math-KDTree' ) ];
+			package: 'Math-Tests-Number-Extensions' with: [ spec requires: #( 'Math-Number-Extensions' ) ];
+			package: 'Math-Tests-ODE' with: [ spec requires: #( 'Math-ODE' ) ];
+			package: 'Math-Tests-Permutation' with: [ spec requires: #( 'Math-Permutation' ) ];
+			package: 'Math-Tests-PrincipalComponentAnalysis' with: [ spec requires: #( 'Math-PrincipalComponentAnalysis' ) ];
+			package: 'Math-Tests-Quantile' with: [ spec requires: #( 'Math-Quantile' ) ];
+			package: 'Math-Tests-Polynomials' with: [ spec requires: #( 'Math-Polynomials' ) ];
+			package: 'Math-Tests-Quaternion' with: [ spec requires: #( 'Math-Quaternion' ) ];
+			package: 'Math-Tests-TSNE' with: [ spec requires: #( 'Math-TSNE' ) ];
+			package: 'Math-UtilsDataServer'.
+		spec
+			group: 'Accuracy' with: #( 'Math-Accuracy-ODE' 'Math-Accuracy-Core' );
+			group: 'Benchmarks' with: #( 'Math-Benchmarks-ODE' 'Math-Benchmarks-KDTree' );
+			group: 'Core'
+			with:
+				#( 'Math-Complex' 'Math-Quaternion' 'Math-Numerical' 'MathRandomNumbers' 'Math-KDTree' 'Math-ODE' 'Math-ArbitraryPrecisionFloat'
+				   'Math-FastFourierTransform' 'ExtendedNumberParser' 'Math-Quantile' 'Math-Physics-Constants' 'Math-Polynomials' 'Math-TSNE' 'Math-Core-Process'
+				   'Math-Helpers' 'MathVectorMatrix' 'Math-Distributions' );
+			group: 'Extensions'
+			with: #( 'Math-Clustering' 'Math-Number-Extensions' 'Math-Chromosome' 'Math-PrincipalComponentAnalysis' 'Math-FunctionFit' 'Math-AutomaticDifferenciation'
+				   'Math-Permutation' );
+			group: 'Tests'
+			with:
+				#( 'Math-Tests-Clustering' 'Math-Tests-Numerical' 'Math-Tests-Complex' 'Math-Tests-Quaternion' 'Math-Tests-ODE' 'Math-Tests-KDTree' 'Math-Tests-FunctionFit'
+				   'Math-Tests-AutomaticDifferenciation' 'Math-Tests-FastFourierTransform' 'Math-Tests-Accuracy' 'Math-Tests-ArbitraryPrecisionFloat'
+				   'Math-Tests-Quantile' 'Math-Tests-Polynomials' 'Math-Tests-PrincipalComponentAnalysis' 'Math-Tests-Number-Extensions' 'Math-Tests-Permutation'
+				   'Math-Tests-TSNE' 'Math-Tests-Core-Process' 'Math-Tests-Distributions' );
+			group: 'default' with: #( 'Core' 'Extensions' 'Tests' 'Benchmarks' 'Accuracy' ) ].
+
+	spec for: #( #'pharo6.x' #'pharo7.x' #'pharo8.x' #'pharo9.x' #'pharo10.x' ) do: [
+		spec
+			package: 'Math-Numerical' with: [ spec requires: #( 'Math-CompatibilityUpToPharo11' ) ];
+			package: 'Math-Benchmarks-KDTree' with: [ spec requires: #( 'Math-CompatibilityUpToPharo11' ) ];
+			package: 'Math-Tests-KDTree' with: [ spec requires: #( 'Math-CompatibilityUpToPharo11' ) ];
+			package: 'Math-CompatibilityUpToPharo11' ]
 ]
 
 { #category : #accessing }
@@ -176,3 +113,27 @@ BaselineOfPolyMath >> projectClass [
 		on: NotFound
 		do: [ super projectClass ]
 ]
+
+{ #category : #dependencies }
+BaselineOfPolyMath >> randomNumbers: spec [
+
+	spec baseline: 'MathRandomNumbers' with: [ spec repository: 'github://PolyMathOrg/random-numbers:v1.x.x/src' ]
+]
+
+{ #category : #dependencies }
+BaselineOfPolyMath >> sMark: spec [
+
+	spec baseline: 'SMark' with: [ spec repository: 'github://smarr/SMark:v1.0.4' ]
+]
+
+{ #category : #dependencies }
+BaselineOfPolyMath >> vectorMatrix: spec [
+
+	spec baseline: 'MathVectorMatrix' with: [ spec repository: 'github://PolyMathOrg/vector-matrix:v1.x.x/src' ]
+]
+
+{ #category : #dependencies }
+BaselineOfPolyMath >> xmlWriter: spec [
+
+	spec baseline: 'XMLWriter' with: [ spec repository: 'github://pharo-contributions/XML-XMLWriter:2.9.x/src' ]
+]