Refactor, remove unused files, remove BasicSampler

kmath-core/build.gradle.kts

@@ -1,3 +1,5 @@
+import ru.mipt.npm.gradle.Maturity
+
 plugins {
     id("ru.mipt.npm.mpp")
     id("ru.mipt.npm.native")
@@ -11,33 +13,39 @@ kotlin.sourceSets.commonMain {
 
 readme {
     description = "Core classes, algebra definitions, basic linear algebra"
-    maturity = ru.mipt.npm.gradle.Maturity.DEVELOPMENT
+    maturity = Maturity.DEVELOPMENT
     propertyByTemplate("artifact", rootProject.file("docs/templates/ARTIFACT-TEMPLATE.md"))
+
     feature(
         id = "algebras",
         description = "Algebraic structures: contexts and elements",
         ref = "src/commonMain/kotlin/kscience/kmath/operations/Algebra.kt"
     )
+
     feature(
         id = "nd",
         description = "Many-dimensional structures",
         ref = "src/commonMain/kotlin/kscience/kmath/structures/NDStructure.kt"
     )
+
     feature(
         id = "buffers",
         description = "One-dimensional structure",
         ref = "src/commonMain/kotlin/kscience/kmath/structures/Buffers.kt"
     )
+
     feature(
         id = "expressions",
         description = "Functional Expressions",
         ref = "src/commonMain/kotlin/kscience/kmath/expressions"
     )
+
     feature(
         id = "domains",
         description = "Domains",
         ref = "src/commonMain/kotlin/kscience/kmath/domains"
     )
+
     feature(
         id = "autodif",
         description = "Automatic differentiation",

kmath-core/src/commonMain/kotlin/kscience/kmath/operations/BigInt.kt

@@ -237,18 +237,18 @@ public class BigInt internal constructor(
         )
 
         private fun compareMagnitudes(mag1: Magnitude, mag2: Magnitude): Int {
-            when {
+            return when {
-                mag1.size > mag2.size -> return 1
+                mag1.size > mag2.size -> 1
-                mag1.size < mag2.size -> return -1
+                mag1.size < mag2.size -> -1
+
                 else -> {
-                    for (i in mag1.size - 1 downTo 0) {
+                    for (i in mag1.size - 1 downTo 0) return when {
-                        if (mag1[i] > mag2[i]) {
+                        mag1[i] > mag2[i] -> 1
-                            return 1
+                        mag1[i] < mag2[i] -> -1
-                        } else if (mag1[i] < mag2[i]) {
+                        else -> continue
-                            return -1
                     }
-                    }
+
-                    return 0
+                    0
                 }
             }
         }
@@ -298,10 +298,11 @@ public class BigInt internal constructor(
             var carry = 0uL
 
             for (i in mag.indices) {
-                val cur: ULong = carry + mag[i].toULong() * x.toULong()
+                val cur = carry + mag[i].toULong() * x.toULong()
                 result[i] = (cur and BASE).toUInt()
                 carry = cur shr BASE_SIZE
             }
+
             result[resultLength - 1] = (carry and BASE).toUInt()
 
             return stripLeadingZeros(result)

kmath-core/src/commonMain/kotlin/kscience/kmath/structures/Buffers.kt

@@ -71,7 +71,7 @@ public interface Buffer<T> {
         @Suppress("UNCHECKED_CAST")
         public inline fun <T : Any> auto(type: KClass<T>, size: Int, initializer: (Int) -> T): Buffer<T> =
             when (type) {
-                Double::class -> RealBuffer(size) { initializer(it) as Double } as Buffer<T>
+                Double::class -> real(size) { initializer(it) as Double } as Buffer<T>
                 Short::class -> ShortBuffer(size) { initializer(it) as Short } as Buffer<T>
                 Int::class -> IntBuffer(size) { initializer(it) as Int } as Buffer<T>
                 Long::class -> LongBuffer(size) { initializer(it) as Long } as Buffer<T>

kmath-core/src/commonMain/kotlin/kscience/kmath/structures/Structure2D.kt

@@ -22,7 +22,7 @@ public interface Structure2D<T> : NDStructure<T> {
 
     override fun elements(): Sequence<Pair<IntArray, T>> = sequence {
         for (i in (0 until rowNum))
-            for (j in (0 until colNum)) yield(intArrayOf(i, j) to get(i, j))
+            for (j in (0 until colNum)) yield(intArrayOf(i, j) to this@Structure2D[i, j])
     }
 
     public companion object
@@ -35,7 +35,6 @@ private inline class Structure2DWrapper<T>(val structure: NDStructure<T>) : Stru
     override val shape: IntArray get() = structure.shape
 
     override operator fun get(i: Int, j: Int): T = structure[i, j]
-
     override fun elements(): Sequence<Pair<IntArray, T>> = structure.elements()
 }
 

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

@@ -29,13 +29,12 @@ class NumberNDFieldTest {
 
         val array = real2D(3, 3) { i, j -> (i * 10 + j).toDouble() }
 
-        for (i in 0..2) {
+        for (i in 0..2)
             for (j in 0..2) {
                 val expected = (i * 10 + j).toDouble()
                 assertEquals(expected, array[i, j], "Error at index [$i, $j]")
             }
     }
-    }
 
     @Test
     fun testExternalFunction() {

kmath-coroutines/src/commonMain/kotlin/kscience/kmath/chains/Chain.kt

@@ -63,12 +63,10 @@ public class MarkovChain<out R : Any>(private val seed: suspend () -> R, private
 
     public fun value(): R? = value
 
-    public override suspend fun next(): R {
+    public override suspend fun next(): R = mutex.withLock {
-        mutex.withLock {
         val newValue = gen(value ?: seed())
         value = newValue
-            return newValue
+        newValue
-        }
     }
 
     public override fun fork(): Chain<R> = MarkovChain(seed = { value ?: seed() }, gen = gen)
@@ -90,12 +88,10 @@ public class StatefulChain<S, out R>(
 
     public fun value(): R? = value
 
-    public override suspend fun next(): R {
+    public override suspend fun next(): R = mutex.withLock {
-        mutex.withLock {
         val newValue = state.gen(value ?: state.seed())
         value = newValue
-            return newValue
+        newValue
-        }
     }
 
     public override fun fork(): Chain<R> = StatefulChain(forkState(state), seed, forkState, gen)

kmath-coroutines/src/commonMain/kotlin/kscience/kmath/streaming/BufferFlow.kt

@@ -28,7 +28,7 @@ public fun <T> Flow<T>.chunked(bufferSize: Int, bufferFactory: BufferFactory<T>)
     var counter = 0
 
     this@chunked.collect { element ->
-        list.add(element)
+        list += element
         counter++
 
         if (counter == bufferSize) {

kmath-coroutines/src/commonMain/kotlin/kscience/kmath/streaming/RingBuffer.kt

@@ -48,11 +48,9 @@ public class RingBuffer<T>(
     /**
      * A safe snapshot operation
      */
-    public suspend fun snapshot(): Buffer<T> {
+    public suspend fun snapshot(): Buffer<T> = mutex.withLock {
-        mutex.withLock {
         val copy = buffer.copy()
-            return VirtualBuffer(size) { i -> copy[startIndex.forward(i)] as T }
+        VirtualBuffer(size) { i -> copy[startIndex.forward(i)] as T }
-        }
     }
 
     public suspend fun push(element: T) {

kmath-functions/src/commonMain/kotlin/kscience/kmath/functions/Piecewise.kt

@@ -23,8 +23,8 @@ public class OrderedPiecewisePolynomial<T : Comparable<T>>(delimiter: T) :
      */
     public fun putRight(right: T, piece: Polynomial<T>) {
         require(right > delimiters.last()) { "New delimiter should be to the right of old one" }
-        delimiters.add(right)
+        delimiters += right
-        pieces.add(piece)
+        pieces += piece
     }
 
     public fun putLeft(left: T, piece: Polynomial<T>) {

kmath-prob/src/commonMain/kotlin/kscience/kmath/prob/Distribution.kt

@@ -5,8 +5,18 @@ import kscience.kmath.chains.Chain
 import kscience.kmath.chains.collect
 import kscience.kmath.structures.Buffer
 import kscience.kmath.structures.BufferFactory
+import kscience.kmath.structures.IntBuffer
 
+/**
+ * Sampler that generates chains of values of type [T].
+ */
 public fun interface Sampler<T : Any> {
+    /**
+     * Generates a chain of samples.
+     *
+     * @param generator the randomness provider.
+     * @return the new chain.
+     */
     public fun sample(generator: RandomGenerator): Chain<T>
 }
 
@@ -59,16 +69,25 @@ public fun <T : Any> Sampler<T>.sampleBuffer(
         //clear list from previous run
         tmp.clear()
         //Fill list
-        repeat(size) { tmp.add(chain.next()) }
+        repeat(size) { tmp += chain.next() }
         //return new buffer with elements from tmp
         bufferFactory(size) { tmp[it] }
     }
 }
 
+/**
+ * Samples one value from this [Sampler].
+ */
 public suspend fun <T : Any> Sampler<T>.next(generator: RandomGenerator): T = sample(generator).first()
 
 /**
- * Generate a bunch of samples from real distributions
+ * Generates [size] real samples and chunks them into some buffers.
  */
 public fun Sampler<Double>.sampleBuffer(generator: RandomGenerator, size: Int): Chain<Buffer<Double>> =
     sampleBuffer(generator, size, Buffer.Companion::real)
+
+/**
+ * Generates [size] integer samples and chunks them into some buffers.
+ */
+public fun Sampler<Int>.sampleBuffer(generator: RandomGenerator, size: Int): Chain<Buffer<Int>> =
+    sampleBuffer(generator, size, ::IntBuffer)

kmath-prob/src/commonMain/kotlin/kscience/kmath/prob/FactorizedDistribution.kt

@@ -38,6 +38,6 @@ public class DistributionBuilder<T : Any> {
     private val distributions = ArrayList<NamedDistribution<T>>()
 
     public infix fun String.to(distribution: Distribution<T>) {
-        distributions.add(NamedDistributionWrapper(this, distribution))
+        distributions += NamedDistributionWrapper(this, distribution)
     }
 }

kmath-prob/src/commonMain/kotlin/kscience/kmath/prob/RandomGenerator.kt

@@ -82,6 +82,8 @@ public interface RandomGenerator {
 
 /**
  * Implements [RandomGenerator] by delegating all operations to [Random].
+ *
+ * @property random the underlying [Random] object.
  */
 public inline class DefaultGenerator(public val random: Random = Random) : RandomGenerator {
     public override fun nextBoolean(): Boolean = random.nextBoolean()

kmath-prob/src/commonMain/kotlin/kscience/kmath/prob/SamplerAlgebra.kt

@@ -7,25 +7,28 @@ import kscience.kmath.chains.zip
 import kscience.kmath.operations.Space
 import kscience.kmath.operations.invoke
 
-public class BasicSampler<T : Any>(public val chainBuilder: (RandomGenerator) -> Chain<T>) : Sampler<T> {
+/**
-    public override fun sample(generator: RandomGenerator): Chain<T> = chainBuilder(generator)
+ * Implements [Sampler] by sampling only certain [value].
-}
+ *
-
+ * @property value the value to sample.
+ */
 public class ConstantSampler<T : Any>(public val value: T) : Sampler<T> {
     public override fun sample(generator: RandomGenerator): Chain<T> = ConstantChain(value)
 }
 
 /**
- * A space for samplers. Allows to perform simple operations on distributions
+ * A space of samplers. Allows to perform simple operations on distributions.
+ *
+ * @property space the space to provide addition and scalar multiplication for [T].
  */
 public class SamplerSpace<T : Any>(public val space: Space<T>) : Space<Sampler<T>> {
     public override val zero: Sampler<T> = ConstantSampler(space.zero)
 
-    public override fun add(a: Sampler<T>, b: Sampler<T>): Sampler<T> = BasicSampler { generator ->
+    public override fun add(a: Sampler<T>, b: Sampler<T>): Sampler<T> = Sampler { generator ->
         a.sample(generator).zip(b.sample(generator)) { aValue, bValue -> space { aValue + bValue } }
     }
 
-    public override fun multiply(a: Sampler<T>, k: Number): Sampler<T> = BasicSampler { generator ->
+    public override fun multiply(a: Sampler<T>, k: Number): Sampler<T> = Sampler { generator ->
         a.sample(generator).map { space { it * k.toDouble() } }
     }
 }

kmath-prob/src/commonMain/kotlin/kscience/kmath/prob/internal/InternalGamma.kt

@@ -98,30 +98,23 @@ internal object InternalGamma {
     private const val INV_GAMMA1P_M1_C12 = .113302723198169588237412962033074E-05
     private const val INV_GAMMA1P_M1_C13 = -.205633841697760710345015413002057E-06
 
-    fun logGamma(x: Double): Double {
+    fun logGamma(x: Double): Double = when {
-        val ret: Double
+        x.isNaN() || x <= 0.0 -> Double.NaN
-
+        x < 0.5 -> logGamma1p(x) - ln(x)
-        when {
+        x <= 2.5 -> logGamma1p(x - 0.5 - 0.5)
-            x.isNaN() || x <= 0.0 -> ret = Double.NaN
-            x < 0.5 -> return logGamma1p(x) - ln(x)
-            x <= 2.5 -> return logGamma1p(x - 0.5 - 0.5)
 
         x <= 8.0 -> {
             val n = floor(x - 1.5).toInt()
-                var prod = 1.0
+            val prod = (1..n).fold(1.0, { prod, i -> prod * (x - i) })
-                (1..n).forEach { i -> prod *= x - i }
+            logGamma1p(x - (n + 1)) + ln(prod)
-                return logGamma1p(x - (n + 1)) + ln(prod)
         }
 
         else -> {
             val tmp = x + LANCZOS_G + .5
-                ret = (x + .5) * ln(tmp) - tmp + HALF_LOG_2_PI + ln(lanczos(x) / x)
+            (x + .5) * ln(tmp) - tmp + HALF_LOG_2_PI + ln(lanczos(x) / x)
         }
     }
 
-        return ret
-    }
-
     private fun regularizedGammaP(
         a: Double,
         x: Double,

kmath-prob/src/commonMain/kotlin/kscience/kmath/prob/internal/InternalUtils.kt

@@ -20,24 +20,17 @@ internal object InternalUtils {
 
     fun validateProbabilities(probabilities: DoubleArray?): Double {
         require(!(probabilities == null || probabilities.isEmpty())) { "Probabilities must not be empty." }
-        var sumProb = 0.0
 
-        probabilities.forEach { prob ->
+        val sumProb = probabilities.sumByDouble { prob ->
-            validateProbability(prob)
+            require(!(prob < 0 || prob.isInfinite() || prob.isNaN())) { "Invalid probability: $prob" }
-            sumProb += prob
+            prob
         }
 
         require(!(sumProb.isInfinite() || sumProb <= 0)) { "Invalid sum of probabilities: $sumProb" }
         return sumProb
     }
 
-    private fun validateProbability(probability: Double): Unit =
+    class FactorialLog private constructor(numValues: Int, cache: DoubleArray?) {
-        require(!(probability < 0 || probability.isInfinite() || probability.isNaN())) { "Invalid probability: $probability" }
-
-    class FactorialLog private constructor(
-        numValues: Int,
-        cache: DoubleArray?
-    ) {
         private val logFactorials: DoubleArray = DoubleArray(numValues)
 
         init {
@@ -46,14 +39,15 @@ internal object InternalUtils {
             if (cache != null && cache.size > BEGIN_LOG_FACTORIALS) {
                 // Copy available values.
                 endCopy = min(cache.size, numValues)
+
                 cache.copyInto(
                     logFactorials,
                     BEGIN_LOG_FACTORIALS,
                     BEGIN_LOG_FACTORIALS, endCopy
                 )
-            }
+            } else
             // All values to be computed
-            else endCopy = BEGIN_LOG_FACTORIALS
+                endCopy = BEGIN_LOG_FACTORIALS
 
             // Compute remaining values.
             (endCopy until numValues).forEach { i ->
@@ -65,9 +59,7 @@ internal object InternalUtils {
         }
 
         fun value(n: Int): Double {
-            if (n < logFactorials.size)
+            if (n < logFactorials.size) return logFactorials[n]
-                return logFactorials[n]
-
             return if (n < FACTORIALS.size) ln(FACTORIALS[n].toDouble()) else InternalGamma.logGamma(n + 1.0)
         }
 

kmath-prob/src/commonMain/kotlin/kscience/kmath/prob/samplers/AliasMethodDiscreteSampler.kt

@@ -42,7 +42,7 @@ public open class AliasMethodDiscreteSampler private constructor(
     protected val alias: IntArray
 ) : Sampler<Int> {
 
-    private class SmallTableAliasMethodDiscreteSampler internal constructor(
+    private class SmallTableAliasMethodDiscreteSampler(
         probability: LongArray,
         alias: IntArray
     ) : AliasMethodDiscreteSampler(probability, alias) {
@@ -71,7 +71,7 @@ public open class AliasMethodDiscreteSampler private constructor(
         }
     }
 
-    override fun sample(generator: RandomGenerator): Chain<Int> = generator.chain {
+    public override fun sample(generator: RandomGenerator): Chain<Int> = generator.chain {
         // This implements the algorithm as per Vose (1991):
         // v = uniform()  in [0, 1)
         // j = uniform(n) in [0, n)

kmath-prob/src/commonMain/kotlin/kscience/kmath/prob/samplers/InternalGamma.kt

@@ -1,2 +0,0 @@
-package kscience.kmath.prob.samplers
-

kmath-prob/src/commonMain/kotlin/kscience/kmath/prob/samplers/InternalUtils.kt

@@ -1,2 +0,0 @@
-package kscience.kmath.prob.samplers
-

kmath-prob/src/commonMain/kotlin/kscience/kmath/prob/samplers/ZigguratNormalizedGaussianSampler.kt

@@ -26,18 +26,13 @@ public class ZigguratNormalizedGaussianSampler private constructor() :
     public override fun sample(generator: RandomGenerator): Chain<Double> = generator.chain { sampleOne(this) }
     public override fun toString(): String = "Ziggurat normalized Gaussian deviate"
 
-    private fun fix(
+    private fun fix(generator: RandomGenerator, hz: Long, iz: Int): Double {
-        generator: RandomGenerator,
+        var x = hz * W[iz]
-        hz: Long,
+
-        iz: Int
+        return when {
-    ): Double {
+            iz == 0 -> {
-        var x: Double
+                var y: Double
-        var y: Double
-        x = hz * W[iz]
 
-        return if (iz == 0) {
-            // Base strip.
-            // This branch is called about 5.7624515E-4 times per sample.
                 do {
                     y = -ln(generator.nextDouble())
                     x = -ln(generator.nextDouble()) * ONE_OVER_R
@@ -45,16 +40,10 @@ public class ZigguratNormalizedGaussianSampler private constructor() :
 
                 val out = R + x
                 if (hz > 0) out else -out
-        } else {
+            }
-            // Wedge of other strips.
+
-            // This branch is called about 0.027323 times per sample.
+            F[iz] + generator.nextDouble() * (F[iz - 1] - F[iz]) < gauss(x) -> x
-            // else
+            else -> sampleOne(generator)
-            // Try again.
-            // This branch is called about 0.012362 times per sample.
-            if (F[iz] + generator.nextDouble() * (F[iz - 1] - F[iz]) < gauss(
-                    x
-                )
-            ) x else sampleOne(generator)
         }
     }
 

kmath-prob/src/jvmMain/kotlin/kscience/kmath/prob/RandomSourceGenerator.kt

@@ -3,10 +3,14 @@ package kscience.kmath.prob
 import org.apache.commons.rng.UniformRandomProvider
 import org.apache.commons.rng.simple.RandomSource
 
-public class RandomSourceGenerator(public val source: RandomSource, seed: Long?) : RandomGenerator {
+/**
-    internal val random: UniformRandomProvider = seed?.let {
+ * Implements [RandomGenerator] by delegating all operations to [RandomSource].
-        RandomSource.create(source, seed)
+ *
-    } ?: RandomSource.create(source)
+ * @property source the underlying [RandomSource] object.
+ */
+public class RandomSourceGenerator internal constructor(public val source: RandomSource, seed: Long?) : RandomGenerator {
+    internal val random: UniformRandomProvider = seed?.let { RandomSource.create(source, seed) }
+        ?: RandomSource.create(source)
 
     public override fun nextBoolean(): Boolean = random.nextBoolean()
     public override fun nextDouble(): Double = random.nextDouble()
@@ -23,19 +27,84 @@ public class RandomSourceGenerator(public val source: RandomSource, seed: Long?)
     public override fun fork(): RandomGenerator = RandomSourceGenerator(source, nextLong())
 }
 
+/**
+ * Implements [UniformRandomProvider] by delegating all operations to [RandomGenerator].
+ *
+ * @property generator the underlying [RandomGenerator] object.
+ */
 public inline class RandomGeneratorProvider(public val generator: RandomGenerator) : UniformRandomProvider {
+    /**
+     * Generates a [Boolean] value.
+     *
+     * @return the next random value.
+     */
     public override fun nextBoolean(): Boolean = generator.nextBoolean()
+
+    /**
+     * Generates a [Float] value between 0 and 1.
+     *
+     * @return the next random value between 0 and 1.
+     */
     public override fun nextFloat(): Float = generator.nextDouble().toFloat()
+
+    /**
+     * Generates [Byte] values and places them into a user-supplied array.
+     *
+     * The number of random bytes produced is equal to the length of the the byte array.
+     *
+     * @param bytes byte array in which to put the random bytes.
+     */
     public override fun nextBytes(bytes: ByteArray): Unit = generator.fillBytes(bytes)
 
+    /**
+     * Generates [Byte] values and places them into a user-supplied array.
+     *
+     * The array is filled with bytes extracted from random integers. This implies that the number of random bytes
+     * generated may be larger than the length of the byte array.
+     *
+     * @param bytes the array in which to put the generated bytes.
+     * @param start the index at which to start inserting the generated bytes.
+     * @param len the number of bytes to insert.
+     */
     public override fun nextBytes(bytes: ByteArray, start: Int, len: Int) {
         generator.fillBytes(bytes, start, start + len)
     }
 
+    /**
+     * Generates an [Int] value.
+     *
+     * @return the next random value.
+     */
     public override fun nextInt(): Int = generator.nextInt()
+
+    /**
+     * Generates an [Int] value between 0 (inclusive) and the specified value (exclusive).
+     *
+     * @param n the bound on the random number to be returned. Must be positive.
+     * @return a random integer between 0 (inclusive) and [n] (exclusive).
+     */
     public override fun nextInt(n: Int): Int = generator.nextInt(n)
+
+    /**
+     * Generates a [Double] value between 0 and 1.
+     *
+     * @return the next random value between 0 and 1.
+     */
     public override fun nextDouble(): Double = generator.nextDouble()
+
+    /**
+     * Generates a [Long] value.
+     *
+     * @return the next random value.
+     */
     public override fun nextLong(): Long = generator.nextLong()
+
+    /**
+     * Generates a [Long] value between 0 (inclusive) and the specified value (exclusive).
+     *
+     * @param n Bound on the random number to be returned.  Must be positive.
+     * @return a random long value between 0 (inclusive) and [n] (exclusive).
+     */
     public override fun nextLong(n: Long): Long = generator.nextLong(n)
 }
 
@@ -48,8 +117,14 @@ public fun RandomGenerator.asUniformRandomProvider(): UniformRandomProvider = if
 else
     RandomGeneratorProvider(this)
 
+/**
+ * Returns [RandomSourceGenerator] with given [RandomSource] and [seed].
+ */
 public fun RandomGenerator.Companion.fromSource(source: RandomSource, seed: Long? = null): RandomSourceGenerator =
     RandomSourceGenerator(source, seed)
 
+/**
+ * Returns [RandomSourceGenerator] with [RandomSource.MT] algorithm and given [seed].
+ */
 public fun RandomGenerator.Companion.mersenneTwister(seed: Long? = null): RandomSourceGenerator =
     fromSource(RandomSource.MT, seed)

kmath-prob/src/jvmTest/kotlin/kscience/kmath/prob/SamplerTest.kt

@@ -7,11 +7,8 @@ class SamplerTest {
 
     @Test
     fun bufferSamplerTest() {
-        val sampler: Sampler<Double> =
+        val sampler = Sampler { it.chain { nextDouble() } }
-            BasicSampler { it.chain { nextDouble() } }
         val data = sampler.sampleBuffer(RandomGenerator.default, 100)
-        runBlocking {
+        runBlocking { println(data.next()) }
-            println(data.next())
-        }
     }
 }