Merge remote-tracking branch 'spc/dev' into dev

examples/src/main/kotlin/space/kscience/kmath/fit/chiSquared.kt

@@ -9,6 +9,7 @@ import kotlinx.html.br
 import kotlinx.html.h3
 import space.kscience.kmath.commons.optimization.CMOptimizer
 import space.kscience.kmath.distributions.NormalDistribution
+import space.kscience.kmath.expressions.DifferentiableExpression
 import space.kscience.kmath.expressions.autodiff
 import space.kscience.kmath.expressions.symbol
 import space.kscience.kmath.operations.asIterable
@@ -19,6 +20,7 @@ import space.kscience.kmath.real.DoubleVector
 import space.kscience.kmath.real.map
 import space.kscience.kmath.real.step
 import space.kscience.kmath.stat.chiSquaredExpression
+import space.kscience.kmath.structures.Float64
 import space.kscience.plotly.*
 import space.kscience.plotly.models.ScatterMode
 import space.kscience.plotly.models.TraceValues
@@ -64,7 +66,7 @@ suspend fun main() {
     val yErr = y.map { sqrt(it) }//RealVector.same(x.size, sigma)
 
     // compute differentiable chi^2 sum for given model ax^2 + bx + c
-    val chi2 = Double.autodiff.chiSquaredExpression(x, y, yErr) { arg ->
+    val chi2: DifferentiableExpression<Float64> = Double.autodiff.chiSquaredExpression(x, y, yErr) { arg ->
         //bind variables to autodiff context
         val a = bindSymbol(a)
         val b = bindSymbol(b)

kmath-ast/src/jsMain/kotlin/space/kscience/kmath/wasm/internal/WasmBuilder.kt

@@ -7,9 +7,13 @@ package space.kscience.kmath.wasm.internal
 
 import space.kscience.kmath.UnstableKMathAPI
 import space.kscience.kmath.ast.TypedMst
-import space.kscience.kmath.expressions.*
+import space.kscience.kmath.expressions.DoubleExpression
+import space.kscience.kmath.expressions.Expression
+import space.kscience.kmath.expressions.IntExpression
+import space.kscience.kmath.expressions.Symbol
 import space.kscience.kmath.internal.binaryen.*
 import space.kscience.kmath.internal.webassembly.Instance
+import space.kscience.kmath.named.SimpleSymbolIndexer
 import space.kscience.kmath.operations.*
 import space.kscience.kmath.structures.Float64
 import space.kscience.kmath.internal.binaryen.Module as BinaryenModule

kmath-ast/src/jsMain/kotlin/space/kscience/kmath/wasm/wasm.kt

@@ -11,6 +11,7 @@ import space.kscience.kmath.UnstableKMathAPI
 import space.kscience.kmath.ast.TypedMst
 import space.kscience.kmath.ast.evaluateConstants
 import space.kscience.kmath.expressions.*
+import space.kscience.kmath.named.SimpleSymbolIndexer
 import space.kscience.kmath.operations.Float64Field
 import space.kscience.kmath.operations.Int32Ring
 import space.kscience.kmath.structures.Float64

kmath-ast/src/jvmMain/kotlin/space/kscience/kmath/asm/asm.kt

@@ -12,6 +12,7 @@ import space.kscience.kmath.asm.internal.*
 import space.kscience.kmath.ast.TypedMst
 import space.kscience.kmath.ast.evaluateConstants
 import space.kscience.kmath.expressions.*
+import space.kscience.kmath.named.SimpleSymbolIndexer
 import space.kscience.kmath.operations.Algebra
 import space.kscience.kmath.operations.Float64Field
 import space.kscience.kmath.operations.Int32Ring

kmath-ast/src/jvmMain/kotlin/space/kscience/kmath/asm/internal/PrimitiveAsmBuilder.kt

@@ -14,6 +14,8 @@ import org.objectweb.asm.commons.InstructionAdapter
 import space.kscience.kmath.UnstableKMathAPI
 import space.kscience.kmath.ast.TypedMst
 import space.kscience.kmath.expressions.*
+import space.kscience.kmath.named.SimpleSymbolIndexer
+import space.kscience.kmath.named.SymbolIndexer
 import space.kscience.kmath.operations.*
 import space.kscience.kmath.structures.Float64
 import java.lang.invoke.MethodHandles

kmath-commons/src/jvmMain/kotlin/space/kscience/kmath/commons/optimization/CMOptimizer.kt

@@ -18,9 +18,9 @@ import space.kscience.attributes.AttributesBuilder
 import space.kscience.attributes.SetAttribute
 import space.kscience.kmath.UnstableKMathAPI
 import space.kscience.kmath.expressions.Symbol
-import space.kscience.kmath.expressions.SymbolIndexer
 import space.kscience.kmath.expressions.derivative
-import space.kscience.kmath.expressions.withSymbols
+import space.kscience.kmath.named.SymbolIndexer
+import space.kscience.kmath.named.withSymbols
 import space.kscience.kmath.optimization.*
 import space.kscience.kmath.structures.Float64
 import kotlin.collections.set

kmath-core/src/commonMain/kotlin/space/kscience/kmath/domains/Domain1D.kt

@@ -23,7 +23,7 @@ public abstract class Domain1D<T : Comparable<T>>(public val range: ClosedRange<
 
 @UnstableKMathAPI
 public class DoubleDomain1D(
-    @Suppress("CanBeParameter") public val doubleRange: ClosedFloatingPointRange<Float64>,
+    public val doubleRange: ClosedFloatingPointRange<Float64>,
 ) : Domain1D<Float64>(doubleRange), Float64Domain {
     override fun getLowerBound(num: Int): Double {
         require(num == 0)

kmath-core/src/commonMain/kotlin/space/kscience/kmath/expressions/DSAlgebra.kt

@@ -7,6 +7,7 @@ package space.kscience.kmath.expressions
 
 import space.kscience.attributes.SafeType
 import space.kscience.kmath.UnstableKMathAPI
+import space.kscience.kmath.named.SymbolIndexer
 import space.kscience.kmath.operations.*
 import space.kscience.kmath.structures.Buffer
 import space.kscience.kmath.structures.MutableBuffer

kmath-core/src/commonMain/kotlin/space/kscience/kmath/expressions/DSCompiler.kt

@@ -126,7 +126,7 @@ public class DSCompiler<T, out A : Algebra<T>> internal constructor(
      * If all orders are set to 0, then the 0<sup>th</sup> order derivative is returned, which is the value of the
      * function.
      *
-     * The indices of derivatives are between 0 and [size] &minus; 1. Their specific order is fixed for a given compiler, but
+     * The indices of derivatives are between 0 and [getSize] &minus; 1. Their specific order is fixed for a given compiler, but
      * otherwise not publicly specified. There are however some simple cases which have guaranteed indices:
      *
      *  * the index of 0<sup>th</sup> order derivative is always 0

kmath-core/src/commonMain/kotlin/space/kscience/kmath/expressions/Expression.kt

@@ -9,6 +9,7 @@ import space.kscience.attributes.SafeType
 import space.kscience.attributes.WithType
 import space.kscience.attributes.safeTypeOf
 import space.kscience.kmath.UnstableKMathAPI
+import space.kscience.kmath.named.SymbolIndexer
 import space.kscience.kmath.operations.Algebra
 import space.kscience.kmath.operations.DoubleField
 import space.kscience.kmath.operations.IntRing

kmath-core/src/commonMain/kotlin/space/kscience/kmath/named/NamedBuffer.kt

@@ -0,0 +1,22 @@
+/*
+ * Copyright 2018-2024 KMath contributors.
+ * Use of this source code is governed by the Apache 2.0 license that can be found in the license/LICENSE.txt file.
+ */
+
+@file:OptIn(UnstableKMathAPI::class)
+
+package space.kscience.kmath.named
+
+import space.kscience.kmath.UnstableKMathAPI
+import space.kscience.kmath.expressions.Symbol
+import space.kscience.kmath.structures.Buffer
+import space.kscience.kmath.structures.MutableBuffer
+
+public class NamedBuffer<T>(public val values: Buffer<T>, public val indexer: SymbolIndexer): Buffer<T> by values{
+    public operator fun get(symbol: Symbol): T = values[indexer.indexOf(symbol)]
+}
+
+public class NamedMutableBuffer<T>(public val values: MutableBuffer<T>, public val indexer: SymbolIndexer): MutableBuffer<T> by values{
+    public operator fun get(symbol: Symbol): T = values[indexer.indexOf(symbol)]
+    public operator fun set(symbol: Symbol, value: T) { values[indexer.indexOf(symbol)] = value }
+}

kmath-core/src/commonMain/kotlin/space/kscience/kmath/expressions/NamedMatrix.kt → kmath-core/src/commonMain/kotlin/space/kscience/kmath/named/NamedMatrix.kt

@@ -5,14 +5,24 @@
 
 @file:OptIn(UnstableKMathAPI::class)
 
-package space.kscience.kmath.expressions
+package space.kscience.kmath.named
 
 import space.kscience.kmath.PerformancePitfall
 import space.kscience.kmath.UnstableKMathAPI
+import space.kscience.kmath.expressions.Symbol
 import space.kscience.kmath.linear.Matrix
 import space.kscience.kmath.structures.getOrNull
 
+/**
+ * A square matrix that could be accessed via column and row names.
+ *
+ * Multiple symbols could in theory reference the same columns or rows. Some columns could be not references at all.
+ */
 public class NamedMatrix<T>(public val values: Matrix<T>, public val indexer: SymbolIndexer) : Matrix<T> by values {
+    init {
+        require(values.rows.size == values.columns.size) { "Only square matrices could be named" }
+    }
+
     public operator fun get(i: Symbol, j: Symbol): T = get(indexer.indexOf(i), indexer.indexOf(j))
 
     public companion object {

kmath-core/src/commonMain/kotlin/space/kscience/kmath/expressions/SymbolIndexer.kt → kmath-core/src/commonMain/kotlin/space/kscience/kmath/named/SymbolIndexer.kt

@@ -3,9 +3,10 @@
  * Use of this source code is governed by the Apache 2.0 license that can be found in the license/LICENSE.txt file.
  */
 
-package space.kscience.kmath.expressions
+package space.kscience.kmath.named
 
 import space.kscience.kmath.UnstableKMathAPI
+import space.kscience.kmath.expressions.Symbol
 import space.kscience.kmath.linear.Point
 import space.kscience.kmath.nd.Structure2D
 import space.kscience.kmath.structures.BufferFactory
@@ -69,6 +70,9 @@ public interface SymbolIndexer {
     public fun Map<Symbol, Double>.toDoubleArray(): DoubleArray = DoubleArray(symbols.size) { getValue(symbols[it]) }
 }
 
+@UnstableKMathAPI
+public val SymbolIndexer.size: Int get() = symbols.size
+
 @UnstableKMathAPI
 @JvmInline
 public value class SimpleSymbolIndexer(override val symbols: List<Symbol>) : SymbolIndexer

kmath-optimization/src/commonMain/kotlin/space/kscience/kmath/optimization/OptimizationProblem.kt

@@ -6,9 +6,9 @@
 package space.kscience.kmath.optimization
 
 import space.kscience.attributes.*
-import space.kscience.kmath.expressions.NamedMatrix
 import space.kscience.kmath.expressions.Symbol
 import space.kscience.kmath.misc.Loggable
+import space.kscience.kmath.named.NamedMatrix
 
 public interface OptimizationAttribute<T> : Attribute<T>
 

kmath-optimization/src/commonMain/kotlin/space/kscience/kmath/optimization/QowOptimizer.kt

@@ -6,9 +6,15 @@
 package space.kscience.kmath.optimization
 
 import space.kscience.kmath.UnstableKMathAPI
-import space.kscience.kmath.expressions.*
+import space.kscience.kmath.expressions.DifferentiableExpression
+import space.kscience.kmath.expressions.Symbol
+import space.kscience.kmath.expressions.derivative
+import space.kscience.kmath.expressions.withDefaultArgs
 import space.kscience.kmath.linear.*
 import space.kscience.kmath.misc.log
+import space.kscience.kmath.named.NamedMatrix
+import space.kscience.kmath.named.SymbolIndexer
+import space.kscience.kmath.named.named
 import space.kscience.kmath.operations.Float64Field
 import space.kscience.kmath.operations.Float64L2Norm
 import space.kscience.kmath.operations.algebra

kmath-stat/src/commonMain/kotlin/space/kscience/kmath/distributions/MultivariateNormalDistribution.kt

@@ -0,0 +1,12 @@
+/*
+ * Copyright 2018-2024 KMath contributors.
+ * Use of this source code is governed by the Apache 2.0 license that can be found in the license/LICENSE.txt file.
+ */
+
+package space.kscience.kmath.distributions
+
+public interface MultivariateNormalDistribution: NamedDistribution<Double> {
+    public companion object{
+
+    }
+}

kmath-stat/src/commonMain/kotlin/space/kscience/kmath/stat/Mean.kt

@@ -6,9 +6,7 @@
 package space.kscience.kmath.stat
 
 import space.kscience.kmath.operations.*
-import space.kscience.kmath.structures.Buffer
-import space.kscience.kmath.structures.Float64
-import space.kscience.kmath.structures.indices
+import space.kscience.kmath.structures.*
 
 /**
  * Arithmetic mean
@@ -44,8 +42,8 @@ public class Mean<T>(
 
     public companion object {
         public fun evaluate(buffer: Buffer<Float64>): Double = Float64Field.mean.evaluateBlocking(buffer)
-        public fun evaluate(buffer: Buffer<Int>): Int = Int32Ring.mean.evaluateBlocking(buffer)
-        public fun evaluate(buffer: Buffer<Long>): Long = Int64Ring.mean.evaluateBlocking(buffer)
+        public fun evaluate(buffer: Buffer<Int32>): Int = Int32Ring.mean.evaluateBlocking(buffer)
+        public fun evaluate(buffer: Buffer<Int64>): Long = Int64Ring.mean.evaluateBlocking(buffer)
     }
 }
 

kmath-stat/src/jvmTest/kotlin/space/kscience/kmath/stat/StatisticTest.kt

@@ -9,6 +9,7 @@ import kotlinx.coroutines.flow.first
 import kotlinx.coroutines.flow.last
 import kotlinx.coroutines.flow.take
 import kotlinx.coroutines.runBlocking
+import kotlinx.coroutines.test.runTest
 import space.kscience.kmath.operations.Float64Field
 import space.kscience.kmath.random.RandomGenerator
 import space.kscience.kmath.random.chain
@@ -27,21 +28,21 @@ internal class StatisticTest {
     val chunked = data.chunked(1000)
 
     @Test
-    fun singleBlockingMean() {
-        val first = runBlocking { chunked.first() }
+    fun singleBlockingMean() = runTest {
+        val first = chunked.first()
         val res = Float64Field.mean(first)
         assertEquals(0.5, res, 1e-1)
     }
 
     @Test
-    fun singleSuspendMean() = runBlocking {
+    fun singleSuspendMean() = runTest {
         val first = runBlocking { chunked.first() }
         val res = Float64Field.mean(first)
         assertEquals(0.5, res, 1e-1)
     }
 
     @Test
-    fun parallelMean() = runBlocking {
+    fun parallelMean() = runTest {
         val average = Float64Field.mean
             .flow(chunked) //create a flow from evaluated results
             .take(100) // Take 100 data chunks from the source and accumulate them