Introduce PerformancePitfall annotation

CHANGELOG.md

@@ -12,6 +12,7 @@
 - Integration for any Field element
 - Extended operations for ND4J fields
 - Jupyter Notebook integration module (kmath-jupyter)
+- `@PerformancePitfall` annotation to mark possibly slow API
 
 ### Changed
 - Exponential operations merged with hyperbolic functions

LICENSE

@@ -1,201 +0,0 @@
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kmath-core/src/commonMain/kotlin/space/kscience/kmath/data/ColumnarData.kt

@@ -5,6 +5,7 @@
 
 package space.kscience.kmath.data
 
+import space.kscience.kmath.misc.PerformancePitfall
 import space.kscience.kmath.misc.Symbol
 import space.kscience.kmath.misc.UnstableKMathAPI
 import space.kscience.kmath.nd.Structure2D
@@ -25,6 +26,7 @@ public interface ColumnarData<out T> {
  * A zero-copy method to represent a [Structure2D] as a two-column x-y data.
  * There could more than two columns in the structure.
  */
+@OptIn(PerformancePitfall::class)
 @UnstableKMathAPI
 public fun <T> Structure2D<T>.asColumnarData(mapping: Map<Symbol, Int>): ColumnarData<T> {
     require(shape[1] >= mapping.maxOf { it.value }) { "Column index out of bounds" }

kmath-core/src/commonMain/kotlin/space/kscience/kmath/data/XYColumnarData.kt

@@ -5,6 +5,7 @@
 
 package space.kscience.kmath.data
 
+import space.kscience.kmath.misc.PerformancePitfall
 import space.kscience.kmath.misc.Symbol
 import space.kscience.kmath.misc.UnstableKMathAPI
 import space.kscience.kmath.nd.Structure2D
@@ -49,6 +50,7 @@ public fun <T, X : T, Y : T> XYColumnarData(x: Buffer<X>, y: Buffer<Y>): XYColum
  * A zero-copy method to represent a [Structure2D] as a two-column x-y data.
  * There could more than two columns in the structure.
  */
+@OptIn(PerformancePitfall::class)
 @UnstableKMathAPI
 public fun <T> Structure2D<T>.asXYData(xIndex: Int = 0, yIndex: Int = 1): XYColumnarData<T, T, T> {
     require(shape[1] >= max(xIndex, yIndex)) { "Column index out of bounds" }

kmath-core/src/commonMain/kotlin/space/kscience/kmath/linear/BufferedLinearSpace.kt

@@ -5,6 +5,7 @@
 
 package space.kscience.kmath.linear
 
+import space.kscience.kmath.misc.PerformancePitfall
 import space.kscience.kmath.nd.*
 import space.kscience.kmath.operations.Ring
 import space.kscience.kmath.operations.invoke
@@ -50,6 +51,7 @@ public class BufferedLinearSpace<T : Any, A : Ring<T>>(
         this
     }
 
+    @OptIn(PerformancePitfall::class)
     override fun Matrix<T>.dot(other: Matrix<T>): Matrix<T> {
         require(colNum == other.rowNum) { "Matrix dot operation dimension mismatch: ($rowNum, $colNum) x (${other.rowNum}, ${other.colNum})" }
         return elementAlgebra {
@@ -67,6 +69,7 @@ public class BufferedLinearSpace<T : Any, A : Ring<T>>(
         }
     }
 
+    @OptIn(PerformancePitfall::class)
     override fun Matrix<T>.dot(vector: Point<T>): Point<T> {
         require(colNum == vector.size) { "Matrix dot vector operation dimension mismatch: ($rowNum, $colNum) x (${vector.size})" }
         return elementAlgebra {

kmath-core/src/commonMain/kotlin/space/kscience/kmath/misc/annotations.kt

@@ -15,3 +15,15 @@ package space.kscience.kmath.misc
 @Retention(value = AnnotationRetention.BINARY)
 @RequiresOptIn("This API is unstable and could change in future", RequiresOptIn.Level.WARNING)
 public annotation class UnstableKMathAPI
+
+/**
+ * Marks API which could cause performance problems. The code, marked by this API is not necessary slow, but could cause
+ * slow-down in some cases. Refer to the documentation and benchmark it to be sure.
+ */
+@MustBeDocumented
+@Retention(value = AnnotationRetention.BINARY)
+@RequiresOptIn(
+    "Refer to the documentation to use this API in performance-critical code",
+    RequiresOptIn.Level.WARNING
+)
+public annotation class PerformancePitfall

kmath-core/src/commonMain/kotlin/space/kscience/kmath/nd/BufferND.kt

@@ -5,6 +5,7 @@
 
 package space.kscience.kmath.nd
 
+import space.kscience.kmath.misc.PerformancePitfall
 import space.kscience.kmath.structures.Buffer
 import space.kscience.kmath.structures.BufferFactory
 import space.kscience.kmath.structures.MutableBuffer
@@ -32,6 +33,7 @@ public open class BufferND<T>(
 
     override val shape: IntArray get() = strides.shape
 
+    @PerformancePitfall
     override fun elements(): Sequence<Pair<IntArray, T>> = strides.indices().map {
         it to this[it]
     }

kmath-core/src/commonMain/kotlin/space/kscience/kmath/nd/Structure1D.kt

@@ -5,6 +5,7 @@
 
 package space.kscience.kmath.nd
 
+import space.kscience.kmath.misc.PerformancePitfall
 import space.kscience.kmath.structures.Buffer
 import space.kscience.kmath.structures.MutableBuffer
 import space.kscience.kmath.structures.asMutableBuffer
@@ -46,6 +47,8 @@ private value class Structure1DWrapper<T>(val structure: StructureND<T>) : Struc
     override val size: Int get() = structure.shape[0]
 
     override operator fun get(index: Int): T = structure[index]
+
+    @PerformancePitfall
     override fun elements(): Sequence<Pair<IntArray, T>> = structure.elements()
 }
 
@@ -55,6 +58,8 @@ private value class Structure1DWrapper<T>(val structure: StructureND<T>) : Struc
 private class MutableStructure1DWrapper<T>(val structure: MutableStructureND<T>) : MutableStructure1D<T> {
     override val shape: IntArray get() = structure.shape
     override val size: Int get() = structure.shape[0]
+
+    @PerformancePitfall
     override fun elements(): Sequence<Pair<IntArray, T>> = structure.elements()
 
     override fun get(index: Int): T = structure[index]
@@ -62,8 +67,8 @@ private class MutableStructure1DWrapper<T>(val structure: MutableStructureND<T>)
         structure[intArrayOf(index)] = value
     }
 
-    override fun copy(): MutableBuffer<T> =
+    @PerformancePitfall
-        structure.elements().map { it.second }.toMutableList().asMutableBuffer()
+    override fun copy(): MutableBuffer<T> = structure.elements().map { it.second }.toMutableList().asMutableBuffer()
 }
 
 
@@ -75,8 +80,10 @@ private value class Buffer1DWrapper<T>(val buffer: Buffer<T>) : Structure1D<T> {
     override val shape: IntArray get() = intArrayOf(buffer.size)
     override val size: Int get() = buffer.size
 
-    override fun elements(): Sequence<Pair<IntArray, T>> =
+    @PerformancePitfall
-        buffer.asSequence().mapIndexed { index, value -> intArrayOf(index) to value }
+    override fun elements(): Sequence<Pair<IntArray, T>> = buffer.asSequence().mapIndexed { index, value ->
+        intArrayOf(index) to value
+    }
 
     override operator fun get(index: Int): T = buffer[index]
 }
@@ -85,8 +92,10 @@ internal class MutableBuffer1DWrapper<T>(val buffer: MutableBuffer<T>) : Mutable
     override val shape: IntArray get() = intArrayOf(buffer.size)
     override val size: Int get() = buffer.size
 
-    override fun elements(): Sequence<Pair<IntArray, T>> =
+    @PerformancePitfall
-        buffer.asSequence().mapIndexed { index, value -> intArrayOf(index) to value }
+    override fun elements(): Sequence<Pair<IntArray, T>> = buffer.asSequence().mapIndexed { index, value ->
+        intArrayOf(index) to value
+    }
 
     override operator fun get(index: Int): T = buffer[index]
     override fun set(index: Int, value: T) {

kmath-core/src/commonMain/kotlin/space/kscience/kmath/nd/Structure2D.kt

@@ -5,10 +5,11 @@
 
 package space.kscience.kmath.nd
 
+import space.kscience.kmath.misc.PerformancePitfall
 import space.kscience.kmath.misc.UnstableKMathAPI
 import space.kscience.kmath.structures.Buffer
-import space.kscience.kmath.structures.VirtualBuffer
 import space.kscience.kmath.structures.MutableListBuffer
+import space.kscience.kmath.structures.VirtualBuffer
 import kotlin.jvm.JvmInline
 import kotlin.reflect.KClass
 
@@ -33,12 +34,14 @@ public interface Structure2D<T> : StructureND<T> {
     /**
      * The buffer of rows of this structure. It gets elements from the structure dynamically.
      */
+    @PerformancePitfall
     public val rows: List<Buffer<T>>
         get() = List(rowNum) { i -> VirtualBuffer(colNum) { j -> get(i, j) } }
 
     /**
      * The buffer of columns of this structure. It gets elements from the structure dynamically.
      */
+    @PerformancePitfall
     public val columns: List<Buffer<T>>
         get() = List(colNum) { j -> VirtualBuffer(rowNum) { i -> get(i, j) } }
 
@@ -80,12 +83,14 @@ public interface MutableStructure2D<T> : Structure2D<T>, MutableStructureND<T> {
     /**
      * The buffer of rows of this structure. It gets elements from the structure dynamically.
      */
+    @PerformancePitfall
     override val rows: List<MutableStructure1D<T>>
         get() = List(rowNum) { i -> MutableBuffer1DWrapper(MutableListBuffer(colNum) { j -> get(i, j) })}
 
     /**
      * The buffer of columns of this structure. It gets elements from the structure dynamically.
      */
+    @PerformancePitfall
     override val columns: List<MutableStructure1D<T>>
         get() = List(colNum) { j -> MutableBuffer1DWrapper(MutableListBuffer(rowNum) { i -> get(i, j) }) }
 }
@@ -105,6 +110,7 @@ private value class Structure2DWrapper<T>(val structure: StructureND<T>) : Struc
     @UnstableKMathAPI
     override fun <F : StructureFeature> getFeature(type: KClass<out F>): F? = structure.getFeature(type)
 
+    @PerformancePitfall
     override fun elements(): Sequence<Pair<IntArray, T>> = structure.elements()
 }
 

kmath-core/src/commonMain/kotlin/space/kscience/kmath/nd/StructureND.kt

@@ -5,6 +5,7 @@
 
 package space.kscience.kmath.nd
 
+import space.kscience.kmath.misc.PerformancePitfall
 import space.kscience.kmath.misc.UnstableKMathAPI
 import space.kscience.kmath.structures.Buffer
 import space.kscience.kmath.structures.BufferFactory
@@ -48,6 +49,7 @@ public interface StructureND<T> {
      *
      * @return the lazy sequence of pairs of indices to values.
      */
+    @PerformancePitfall
     public fun elements(): Sequence<Pair<IntArray, T>>
 
     /**
@@ -61,6 +63,7 @@ public interface StructureND<T> {
         /**
          * Indicates whether some [StructureND] is equal to another one.
          */
+        @PerformancePitfall
         public fun <T : Any> contentEquals(st1: StructureND<T>, st2: StructureND<T>): Boolean {
             if (st1 === st2) return true
 
@@ -169,6 +172,7 @@ public interface MutableStructureND<T> : StructureND<T> {
 /**
  * Transform a structure element-by element in place.
  */
+@OptIn(PerformancePitfall::class)
 public inline fun <T> MutableStructureND<T>.mapInPlace(action: (IntArray, T) -> T): Unit =
     elements().forEach { (index, oldValue) -> this[index] = action(index, oldValue) }
 

kmath-core/src/commonTest/kotlin/space/kscience/kmath/linear/DoubleLUSolverTest.kt

@@ -5,12 +5,14 @@
 
 package space.kscience.kmath.linear
 
+import space.kscience.kmath.misc.PerformancePitfall
 import space.kscience.kmath.misc.UnstableKMathAPI
 import space.kscience.kmath.nd.StructureND
 import kotlin.test.Test
 import kotlin.test.assertEquals
 import kotlin.test.assertTrue
 
+@OptIn(PerformancePitfall::class)
 fun <T : Any> assertMatrixEquals(expected: StructureND<T>, actual: StructureND<T>) {
     assertTrue { StructureND.contentEquals(expected, actual) }
 }

kmath-core/src/commonTest/kotlin/space/kscience/kmath/linear/MatrixTest.kt

@@ -5,6 +5,7 @@
 
 package space.kscience.kmath.linear
 
+import space.kscience.kmath.misc.PerformancePitfall
 import space.kscience.kmath.misc.UnstableKMathAPI
 import space.kscience.kmath.nd.StructureND
 import space.kscience.kmath.nd.as2D
@@ -13,6 +14,7 @@ import kotlin.test.assertEquals
 import kotlin.test.assertTrue
 
 @UnstableKMathAPI
+@OptIn(PerformancePitfall::class)
 @Suppress("UNUSED_VARIABLE")
 class MatrixTest {
     @Test

kmath-core/src/commonTest/kotlin/space/kscience/kmath/structures/NumberNDFieldTest.kt

@@ -6,6 +6,7 @@
 package space.kscience.kmath.structures
 
 import space.kscience.kmath.linear.LinearSpace
+import space.kscience.kmath.misc.PerformancePitfall
 import space.kscience.kmath.nd.*
 import space.kscience.kmath.operations.Norm
 import space.kscience.kmath.operations.invoke
@@ -74,6 +75,7 @@ class NumberNDFieldTest {
     }
 
     object L2Norm : Norm<StructureND<out Number>, Double> {
+        @OptIn(PerformancePitfall::class)
         override fun norm(arg: StructureND<out Number>): Double =
             kotlin.math.sqrt(arg.elements().sumOf { it.second.toDouble() })
     }

kmath-coroutines/src/jvmMain/kotlin/space/kscience/kmath/structures/LazyStructureND.kt

@@ -7,6 +7,7 @@ package space.kscience.kmath.structures
 
 import kotlinx.coroutines.*
 import space.kscience.kmath.coroutines.Math
+import space.kscience.kmath.misc.PerformancePitfall
 import space.kscience.kmath.nd.DefaultStrides
 import space.kscience.kmath.nd.StructureND
 
@@ -24,6 +25,7 @@ public class LazyStructureND<T>(
     public suspend fun await(index: IntArray): T = deferred(index).await()
     public override operator fun get(index: IntArray): T = runBlocking { deferred(index).await() }
 
+    @OptIn(PerformancePitfall::class)
     public override fun elements(): Sequence<Pair<IntArray, T>> {
         val strides = DefaultStrides(shape)
         val res = runBlocking { strides.indices().toList().map { index -> index to await(index) } }

kmath-ejml/src/test/kotlin/space/kscience/kmath/ejml/EjmlMatrixTest.kt

@@ -12,12 +12,14 @@ import org.ejml.dense.row.factory.DecompositionFactory_DDRM
 import space.kscience.kmath.linear.DeterminantFeature
 import space.kscience.kmath.linear.LupDecompositionFeature
 import space.kscience.kmath.linear.getFeature
+import space.kscience.kmath.misc.PerformancePitfall
 import space.kscience.kmath.misc.UnstableKMathAPI
 import space.kscience.kmath.nd.StructureND
 import kotlin.random.Random
 import kotlin.random.asJavaRandom
 import kotlin.test.*
 
+@OptIn(PerformancePitfall::class)
 fun <T : Any> assertMatrixEquals(expected: StructureND<T>, actual: StructureND<T>) {
     assertTrue { StructureND.contentEquals(expected, actual) }
 }

kmath-for-real/src/commonMain/kotlin/space/kscience/kmath/real/RealMatrix.kt

@@ -3,9 +3,13 @@
  * 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(PerformancePitfall::class)
+@file:Suppress("unused")
+
 package space.kscience.kmath.real
 
 import space.kscience.kmath.linear.*
+import space.kscience.kmath.misc.PerformancePitfall
 import space.kscience.kmath.misc.UnstableKMathAPI
 import space.kscience.kmath.operations.DoubleField
 import space.kscience.kmath.structures.Buffer

kmath-for-real/src/commonTest/kotlin/kaceince/kmath/real/DoubleMatrixTest.kt

@@ -7,6 +7,7 @@ package kaceince.kmath.real
 
 import space.kscience.kmath.linear.LinearSpace
 import space.kscience.kmath.linear.matrix
+import space.kscience.kmath.misc.PerformancePitfall
 import space.kscience.kmath.misc.UnstableKMathAPI
 import space.kscience.kmath.nd.StructureND
 import space.kscience.kmath.real.*
@@ -15,6 +16,7 @@ import kotlin.test.Test
 import kotlin.test.assertEquals
 import kotlin.test.assertTrue
 
+@OptIn(PerformancePitfall::class)
 fun <T : Any> assertMatrixEquals(expected: StructureND<T>, actual: StructureND<T>) {
     assertTrue { StructureND.contentEquals(expected, actual) }
 }

kmath-jupyter/src/main/kotlin/space/kscience/kmath/jupyter/KMathJupyter.kt

@@ -8,11 +8,12 @@ import org.jetbrains.kotlinx.jupyter.api.DisplayResult
 import org.jetbrains.kotlinx.jupyter.api.HTML
 import org.jetbrains.kotlinx.jupyter.api.annotations.JupyterLibrary
 import org.jetbrains.kotlinx.jupyter.api.libraries.JupyterIntegration
-import space.kscience.kmath.expressions.MST
 import space.kscience.kmath.ast.rendering.FeaturedMathRendererWithPostProcess
 import space.kscience.kmath.ast.rendering.MathMLSyntaxRenderer
 import space.kscience.kmath.ast.rendering.renderWithStringBuilder
 import space.kscience.kmath.complex.Complex
+import space.kscience.kmath.expressions.MST
+import space.kscience.kmath.misc.PerformancePitfall
 import space.kscience.kmath.nd.Structure2D
 import space.kscience.kmath.operations.GroupOperations
 import space.kscience.kmath.operations.RingOperations
@@ -55,6 +56,7 @@ internal class KMathJupyter : JupyterIntegration() {
         }
     }
 
+    @OptIn(PerformancePitfall::class)
     override fun Builder.onLoaded() {
         import(
             "space.kscience.kmath.ast.*",

kmath-nd4j/src/main/kotlin/space/kscience/kmath/nd4j/Nd4jArrayStructure.kt

@@ -6,6 +6,7 @@
 package space.kscience.kmath.nd4j
 
 import org.nd4j.linalg.api.ndarray.INDArray
+import space.kscience.kmath.misc.PerformancePitfall
 import space.kscience.kmath.nd.MutableStructureND
 import space.kscience.kmath.nd.StructureND
 
@@ -24,6 +25,7 @@ public sealed class Nd4jArrayStructure<T> : MutableStructureND<T> {
 
     internal abstract fun elementsIterator(): Iterator<Pair<IntArray, T>>
     internal fun indicesIterator(): Iterator<IntArray> = ndArray.indicesIterator()
+    @PerformancePitfall
     public override fun elements(): Sequence<Pair<IntArray, T>> = Sequence(::elementsIterator)
 }
 

kmath-tensors/src/commonMain/kotlin/space/kscience/kmath/tensors/core/BufferedTensor.kt

@@ -1,7 +1,8 @@
 package space.kscience.kmath.tensors.core
 
+import space.kscience.kmath.misc.PerformancePitfall
 import space.kscience.kmath.nd.Strides
-import space.kscience.kmath.structures.*
+import space.kscience.kmath.structures.MutableBuffer
 import space.kscience.kmath.tensors.api.Tensor
 import space.kscience.kmath.tensors.core.internal.TensorLinearStructure
 
@@ -32,7 +33,8 @@ public open class BufferedTensor<T> internal constructor(
         mutableBuffer[bufferStart + linearStructure.offset(index)] = value
     }
 
+    @PerformancePitfall
     override fun elements(): Sequence<Pair<IntArray, T>> = linearStructure.indices().map {
-        it to this[it]
+        it to get(it)
     }
 }

kmath-viktor/src/main/kotlin/space/kscience/kmath/viktor/ViktorStructureND.kt

@@ -6,6 +6,7 @@
 package space.kscience.kmath.viktor
 
 import org.jetbrains.bio.viktor.F64Array
+import space.kscience.kmath.misc.PerformancePitfall
 import space.kscience.kmath.misc.UnstableKMathAPI
 import space.kscience.kmath.nd.*
 import space.kscience.kmath.operations.DoubleField
@@ -23,6 +24,7 @@ public class ViktorStructureND(public val f64Buffer: F64Array) : MutableStructur
         f64Buffer.set(*index, value = value)
     }
 
+    @PerformancePitfall
     public override fun elements(): Sequence<Pair<IntArray, Double>> =
         DefaultStrides(shape).indices().map { it to get(it) }
 }