From 1e70bebba6240410eac9a9bd3bad72749dee7ec1 Mon Sep 17 00:00:00 2001 From: Alexander Nozik Date: Wed, 20 Nov 2019 16:12:41 +0300 Subject: [PATCH] Version update + some useful extensions --- build.gradle.kts | 2 +- examples/build.gradle.kts | 6 +- .../kmath/commons/prob/DistributionDemo.kt | 6 +- .../scientifik/kmath/structures/ComplexND.kt | 31 ++++--- gradle/artifactory.gradle | 31 ------- gradle/bintray.gradle | 85 ------------------ gradle/wrapper/gradle-wrapper.jar | Bin 55616 -> 58702 bytes gradle/wrapper/gradle-wrapper.properties | 2 +- gradlew | 29 +++--- .../scientifik/kmath/operations/Algebra.kt | 2 + .../kmath/operations/NumberAlgebra.kt | 4 +- .../kmath/structures/BoxingNDField.kt | 9 ++ .../kmath/structures/ComplexNDField.kt | 9 +- .../kmath/structures/RealNDField.kt | 7 ++ .../kmath/operations/RealFieldTest.kt | 2 +- .../kotlin/scientifik/kmath/chains/Chain.kt | 18 ++-- .../scientifik/kmath/prob/Distribution.kt | 30 ++++--- .../kmath/prob/FactorizedDistribution.kt | 21 +++++ .../scientifik/kmath/prob/SamplerAlgebra.kt | 4 +- .../kotlin/scientifik/kmath/prob/Statistic.kt | 8 +- .../scientifik/kmath/prob/distributions.kt | 31 +++++++ settings.gradle.kts | 10 +-- 22 files changed, 157 insertions(+), 190 deletions(-) delete mode 100644 gradle/artifactory.gradle delete mode 100644 gradle/bintray.gradle create mode 100644 kmath-prob/src/commonMain/kotlin/scientifik/kmath/prob/distributions.kt diff --git a/build.gradle.kts b/build.gradle.kts index 4e55432ee..0b4171486 100644 --- a/build.gradle.kts +++ b/build.gradle.kts @@ -1,5 +1,5 @@ plugins { - id("scientifik.publish") version "0.1.6" apply false + id("scientifik.publish") version "0.2.5" apply false } val kmathVersion by extra("0.1.4-dev") diff --git a/examples/build.gradle.kts b/examples/build.gradle.kts index 98d8607e2..ad59afc5c 100644 --- a/examples/build.gradle.kts +++ b/examples/build.gradle.kts @@ -4,8 +4,8 @@ import org.jetbrains.kotlin.gradle.tasks.KotlinCompile plugins { java kotlin("jvm") - kotlin("plugin.allopen") version "1.3.41" - id("kotlinx.benchmark") version "0.2.0-dev-2" + kotlin("plugin.allopen") version "1.3.60" + id("kotlinx.benchmark") version "0.2.0-dev-5" } configure { @@ -59,6 +59,6 @@ benchmark { tasks.withType { kotlinOptions { - jvmTarget = "1.8" + jvmTarget = Scientifik.JVM_VERSION } } \ No newline at end of file diff --git a/examples/src/main/kotlin/scientifik/kmath/commons/prob/DistributionDemo.kt b/examples/src/main/kotlin/scientifik/kmath/commons/prob/DistributionDemo.kt index 401dde780..3c5f53e13 100644 --- a/examples/src/main/kotlin/scientifik/kmath/commons/prob/DistributionDemo.kt +++ b/examples/src/main/kotlin/scientifik/kmath/commons/prob/DistributionDemo.kt @@ -2,17 +2,17 @@ package scientifik.kmath.commons.prob import kotlinx.coroutines.runBlocking import scientifik.kmath.chains.Chain -import scientifik.kmath.chains.mapWithState +import scientifik.kmath.chains.collectWithState import scientifik.kmath.prob.Distribution import scientifik.kmath.prob.RandomGenerator data class AveragingChainState(var num: Int = 0, var value: Double = 0.0) -fun Chain.mean(): Chain = mapWithState(AveragingChainState(),{it.copy()}){chain-> +fun Chain.mean(): Chain = collectWithState(AveragingChainState(),{it.copy()}){ chain-> val next = chain.next() num++ value += next - return@mapWithState value / num + return@collectWithState value / num } diff --git a/examples/src/main/kotlin/scientifik/kmath/structures/ComplexND.kt b/examples/src/main/kotlin/scientifik/kmath/structures/ComplexND.kt index b57e9db79..cc8b68d85 100644 --- a/examples/src/main/kotlin/scientifik/kmath/structures/ComplexND.kt +++ b/examples/src/main/kotlin/scientifik/kmath/structures/ComplexND.kt @@ -2,7 +2,8 @@ package scientifik.kmath.structures import scientifik.kmath.linear.transpose import scientifik.kmath.operations.Complex -import scientifik.kmath.operations.toComplex +import scientifik.kmath.operations.ComplexField +import scientifik.kmath.operations.invoke import kotlin.system.measureTimeMillis fun main() { @@ -39,19 +40,21 @@ fun main() { fun complexExample() { //Create a context for 2-d structure with complex values - NDField.complex(4, 8).run { - //a constant real-valued structure - val x = one * 2.5 - operator fun Number.plus(other: Complex) = Complex(this.toDouble() + other.re, other.im) - //a structure generator specific to this context - val matrix = produce { (k, l) -> - k + l*i + ComplexField { + nd(4, 8) { + //a constant real-valued structure + val x = one * 2.5 + operator fun Number.plus(other: Complex) = Complex(this.toDouble() + other.re, other.im) + //a structure generator specific to this context + val matrix = produce { (k, l) -> + k + l * i + } + + //Perform sum + val sum = matrix + x + 1.0 + + //Represent the sum as 2d-structure and transpose + sum.as2D().transpose() } - - //Perform sum - val sum = matrix + x + 1.0 - - //Represent the sum as 2d-structure and transpose - sum.as2D().transpose() } } diff --git a/gradle/artifactory.gradle b/gradle/artifactory.gradle deleted file mode 100644 index 12e59642b..000000000 --- a/gradle/artifactory.gradle +++ /dev/null @@ -1,31 +0,0 @@ -apply plugin: "com.jfrog.artifactory" - -artifactory { - def artifactory_user = project.hasProperty('artifactoryUser') ? project.property('artifactoryUser') : "" - def artifactory_password = project.hasProperty('artifactoryPassword') ? project.property('artifactoryPassword') : "" - def artifactory_contextUrl = 'http://npm.mipt.ru:8081/artifactory' - - contextUrl = artifactory_contextUrl //The base Artifactory URL if not overridden by the publisher/resolver - publish { - repository { - repoKey = 'gradle-dev-local' - username = artifactory_user - password = artifactory_password - } - - defaults { - publications('jvm', 'js', 'kotlinMultiplatform', 'metadata') - publishBuildInfo = false - publishArtifacts = true - publishPom = true - publishIvy = false - } - } - resolve { - repository { - repoKey = 'gradle-dev' - username = artifactory_user - password = artifactory_password - } - } -} \ No newline at end of file diff --git a/gradle/bintray.gradle b/gradle/bintray.gradle deleted file mode 100644 index 8da83c860..000000000 --- a/gradle/bintray.gradle +++ /dev/null @@ -1,85 +0,0 @@ -apply plugin: 'com.jfrog.bintray' - -def vcs = "https://github.com/mipt-npm/kmath" - -def pomConfig = { - licenses { - license { - name "The Apache Software License, Version 2.0" - url "http://www.apache.org/licenses/LICENSE-2.0.txt" - distribution "repo" - } - } - developers { - developer { - id "MIPT-NPM" - name "MIPT nuclear physics methods laboratory" - organization "MIPT" - organizationUrl "http://npm.mipt.ru" - } - } - scm { - url vcs - } -} - -project.ext.configureMavenCentralMetadata = { pom -> - def root = asNode() - root.appendNode('name', project.name) - root.appendNode('description', project.description) - root.appendNode('url', vcs) - root.children().last() + pomConfig -} - -project.ext.configurePom = pomConfig - - -// Configure publishing -publishing { - repositories { - maven { - url = "https://bintray.com/mipt-npm/scientifik" - } - } - - // Process each publication we have in this project - publications.all { publication -> - // apply changes to pom.xml files, see pom.gradle - pom.withXml(configureMavenCentralMetadata) - - - } -} - -bintray { - user = project.hasProperty('bintrayUser') ? project.property('bintrayUser') : System.getenv('BINTRAY_USER') - key = project.hasProperty('bintrayApiKey') ? project.property('bintrayApiKey') : System.getenv('BINTRAY_API_KEY') - publish = true - override = true // for multi-platform Kotlin/Native publishing - - pkg { - userOrg = "mipt-npm" - repo = "scientifik" - name = "scientifik.kmath" - issueTrackerUrl = "https://github.com/mipt-npm/kmath/issues" - licenses = ['Apache-2.0'] - vcsUrl = vcs - version { - name = project.version - vcsTag = project.version - released = new Date() - } - } -} - -bintrayUpload.dependsOn publishToMavenLocal - -// 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zpn+;DEMNw5|7gYv7Z{8paCXH43`6;^Ap`2JvVb{i{dKYdyH@GI0`!4_mdrr-RTLo2 z8Xnkpqra2@XtKrwwqOO!TvG<)um+y3X@dD%1I5<)!78nRfOSJKZaZL&8!qr^T?y>i z2^i={0EG6%{x?X}1|C>|%U_8eNWXvr-1$qlT!B0OH2=J~At(s{_tu4h6yJfWn;Kxq zK7S24aBNcotl9q`+=xH}wk)9lHMj7<%6 T.invoke(block: T.() -> R): R = run(block) + /** * Space-like operations without neutral element */ diff --git a/kmath-core/src/commonMain/kotlin/scientifik/kmath/operations/NumberAlgebra.kt b/kmath-core/src/commonMain/kotlin/scientifik/kmath/operations/NumberAlgebra.kt index a8c7f99fa..9639e4c28 100644 --- a/kmath-core/src/commonMain/kotlin/scientifik/kmath/operations/NumberAlgebra.kt +++ b/kmath-core/src/commonMain/kotlin/scientifik/kmath/operations/NumberAlgebra.kt @@ -1,7 +1,7 @@ package scientifik.kmath.operations import kotlin.math.abs -import kotlin.math.pow +import kotlin.math.pow as kpow /** * Advanced Number-like field that implements basic operations @@ -45,7 +45,7 @@ object RealField : ExtendedField, Norm { override inline fun sin(arg: Double) = kotlin.math.sin(arg) override inline fun cos(arg: Double) = kotlin.math.cos(arg) - override inline fun power(arg: Double, pow: Number) = arg.pow(pow.toDouble()) + override inline fun power(arg: Double, pow: Number) = arg.kpow(pow.toDouble()) override inline fun exp(arg: Double) = kotlin.math.exp(arg) override inline fun ln(arg: Double) = kotlin.math.ln(arg) diff --git a/kmath-core/src/commonMain/kotlin/scientifik/kmath/structures/BoxingNDField.kt b/kmath-core/src/commonMain/kotlin/scientifik/kmath/structures/BoxingNDField.kt index a73c58939..e6d4b226d 100644 --- a/kmath-core/src/commonMain/kotlin/scientifik/kmath/structures/BoxingNDField.kt +++ b/kmath-core/src/commonMain/kotlin/scientifik/kmath/structures/BoxingNDField.kt @@ -70,4 +70,13 @@ class BoxingNDField>( override fun NDBuffer.toElement(): FieldElement, *, out BufferedNDField> = BufferedNDFieldElement(this@BoxingNDField, buffer) +} + +inline fun , R> F.nd( + noinline bufferFactory: BufferFactory, + vararg shape: Int, + action: NDField.() -> R +): R { + val ndfield: BoxingNDField = NDField.boxing(this, *shape, bufferFactory = bufferFactory) + return ndfield.action() } \ No newline at end of file diff --git a/kmath-core/src/commonMain/kotlin/scientifik/kmath/structures/ComplexNDField.kt b/kmath-core/src/commonMain/kotlin/scientifik/kmath/structures/ComplexNDField.kt index e9d518bd5..a79366a99 100644 --- a/kmath-core/src/commonMain/kotlin/scientifik/kmath/structures/ComplexNDField.kt +++ b/kmath-core/src/commonMain/kotlin/scientifik/kmath/structures/ComplexNDField.kt @@ -134,4 +134,11 @@ operator fun ComplexNDElement.minus(arg: Double) = fun NDField.Companion.complex(vararg shape: Int): ComplexNDField = ComplexNDField(shape) fun NDElement.Companion.complex(vararg shape: Int, initializer: ComplexField.(IntArray) -> Complex): ComplexNDElement = - NDField.complex(*shape).produce(initializer) \ No newline at end of file + NDField.complex(*shape).produce(initializer) + +/** + * Produce a context for n-dimensional operations inside this real field + */ +inline fun ComplexField.nd(vararg shape: Int, action: ComplexNDField.() -> R): R { + return NDField.complex(*shape).run(action) +} \ No newline at end of file diff --git a/kmath-core/src/commonMain/kotlin/scientifik/kmath/structures/RealNDField.kt b/kmath-core/src/commonMain/kotlin/scientifik/kmath/structures/RealNDField.kt index 82a237817..8c1bd4239 100644 --- a/kmath-core/src/commonMain/kotlin/scientifik/kmath/structures/RealNDField.kt +++ b/kmath-core/src/commonMain/kotlin/scientifik/kmath/structures/RealNDField.kt @@ -119,3 +119,10 @@ operator fun RealNDElement.plus(arg: Double) = */ operator fun RealNDElement.minus(arg: Double) = map { it - arg } + +/** + * Produce a context for n-dimensional operations inside this real field + */ +inline fun RealField.nd(vararg shape: Int, action: RealNDField.() -> R): R { + return NDField.real(*shape).run(action) +} \ No newline at end of file diff --git a/kmath-core/src/commonTest/kotlin/scientifik/kmath/operations/RealFieldTest.kt b/kmath-core/src/commonTest/kotlin/scientifik/kmath/operations/RealFieldTest.kt index aedbf6655..779cfc4b8 100644 --- a/kmath-core/src/commonTest/kotlin/scientifik/kmath/operations/RealFieldTest.kt +++ b/kmath-core/src/commonTest/kotlin/scientifik/kmath/operations/RealFieldTest.kt @@ -6,7 +6,7 @@ import kotlin.test.assertEquals class RealFieldTest { @Test fun testSqrt() { - val sqrt = with(RealField) { + val sqrt = RealField { sqrt(25 * one) } assertEquals(5.0, sqrt) diff --git a/kmath-coroutines/src/commonMain/kotlin/scientifik/kmath/chains/Chain.kt b/kmath-coroutines/src/commonMain/kotlin/scientifik/kmath/chains/Chain.kt index 161dc3b7f..8dba9e215 100644 --- a/kmath-coroutines/src/commonMain/kotlin/scientifik/kmath/chains/Chain.kt +++ b/kmath-coroutines/src/commonMain/kotlin/scientifik/kmath/chains/Chain.kt @@ -122,23 +122,23 @@ class ConstantChain(val value: T) : Chain { * Map the chain result using suspended transformation. Initial chain result can no longer be safely consumed * since mapped chain consumes tokens. Accepts regular transformation function */ -fun Chain.pipe(func: suspend (T) -> R): Chain = object : Chain { - override suspend fun next(): R = func(this@pipe.next()) - override fun fork(): Chain = this@pipe.fork().pipe(func) +fun Chain.map(func: suspend (T) -> R): Chain = object : Chain { + override suspend fun next(): R = func(this@map.next()) + override fun fork(): Chain = this@map.fork().map(func) } /** * Map the whole chain */ -fun Chain.map(mapper: suspend (Chain) -> R): Chain = object : Chain { - override suspend fun next(): R = mapper(this@map) - override fun fork(): Chain = this@map.fork().map(mapper) +fun Chain.collect(mapper: suspend (Chain) -> R): Chain = object : Chain { + override suspend fun next(): R = mapper(this@collect) + override fun fork(): Chain = this@collect.fork().collect(mapper) } -fun Chain.mapWithState(state: S, stateFork: (S) -> S, mapper: suspend S.(Chain) -> R): Chain = +fun Chain.collectWithState(state: S, stateFork: (S) -> S, mapper: suspend S.(Chain) -> R): Chain = object : Chain { - override suspend fun next(): R = state.mapper(this@mapWithState) - override fun fork(): Chain = this@mapWithState.fork().mapWithState(stateFork(state), stateFork, mapper) + override suspend fun next(): R = state.mapper(this@collectWithState) + override fun fork(): Chain = this@collectWithState.fork().collectWithState(stateFork(state), stateFork, mapper) } /** diff --git a/kmath-prob/src/commonMain/kotlin/scientifik/kmath/prob/Distribution.kt b/kmath-prob/src/commonMain/kotlin/scientifik/kmath/prob/Distribution.kt index a11799517..44af84d5d 100644 --- a/kmath-prob/src/commonMain/kotlin/scientifik/kmath/prob/Distribution.kt +++ b/kmath-prob/src/commonMain/kotlin/scientifik/kmath/prob/Distribution.kt @@ -1,8 +1,9 @@ package scientifik.kmath.prob import scientifik.kmath.chains.Chain -import scientifik.kmath.chains.map -import kotlin.jvm.JvmName +import scientifik.kmath.chains.collect +import scientifik.kmath.structures.Buffer +import scientifik.kmath.structures.BufferFactory interface Sampler { fun sample(generator: RandomGenerator): Chain @@ -45,24 +46,27 @@ fun > UnivariateDistribution.integral(from: T, to: T): Doub return cumulative(to) - cumulative(from) } - /** * Sample a bunch of values */ -fun Sampler.sampleBunch(generator: RandomGenerator, size: Int): Chain> { +fun Sampler.sampleBuffer( + generator: RandomGenerator, + size: Int, + bufferFactory: BufferFactory = Buffer.Companion::boxing +): Chain> { require(size > 1) - return sample(generator).map{chain -> - List(size){chain.next()} + //creating temporary storage once + val tmp = ArrayList(size) + return sample(generator).collect { chain -> + for (i in tmp.indices) { + tmp[i] = chain.next() + } + bufferFactory(size) { tmp[it] } } } /** * Generate a bunch of samples from real distributions */ -@JvmName("realSampleBunch") -fun Sampler.sampleBunch(generator: RandomGenerator, size: Int): Chain { - require(size > 1) - return sample(generator).map{chain -> - DoubleArray(size){chain.next()} - } -} \ No newline at end of file +fun Sampler.sampleBuffer(generator: RandomGenerator, size: Int) = + sampleBuffer(generator, size, Buffer.Companion::real) \ No newline at end of file diff --git a/kmath-prob/src/commonMain/kotlin/scientifik/kmath/prob/FactorizedDistribution.kt b/kmath-prob/src/commonMain/kotlin/scientifik/kmath/prob/FactorizedDistribution.kt index d70db4f83..ea526c058 100644 --- a/kmath-prob/src/commonMain/kotlin/scientifik/kmath/prob/FactorizedDistribution.kt +++ b/kmath-prob/src/commonMain/kotlin/scientifik/kmath/prob/FactorizedDistribution.kt @@ -23,4 +23,25 @@ class FactorizedDistribution(val distributions: Collection acc + chain.next() } } } +} + +class NamedDistributionWrapper(val name: String, val distribution: Distribution) : NamedDistribution { + override fun probability(arg: Map): Double = distribution.probability( + arg[name] ?: error("Argument with name $name not found in input parameters") + ) + + override fun sample(generator: RandomGenerator): Chain> { + val chain = distribution.sample(generator) + return SimpleChain { + mapOf(name to chain.next()) + } + } +} + +class DistributionBuilder{ + private val distributions = ArrayList>() + + infix fun String.to(distribution: Distribution){ + distributions.add(NamedDistributionWrapper(this,distribution)) + } } \ No newline at end of file diff --git a/kmath-prob/src/commonMain/kotlin/scientifik/kmath/prob/SamplerAlgebra.kt b/kmath-prob/src/commonMain/kotlin/scientifik/kmath/prob/SamplerAlgebra.kt index ca9d74aab..3a60c0bda 100644 --- a/kmath-prob/src/commonMain/kotlin/scientifik/kmath/prob/SamplerAlgebra.kt +++ b/kmath-prob/src/commonMain/kotlin/scientifik/kmath/prob/SamplerAlgebra.kt @@ -2,7 +2,7 @@ package scientifik.kmath.prob import scientifik.kmath.chains.Chain import scientifik.kmath.chains.ConstantChain -import scientifik.kmath.chains.pipe +import scientifik.kmath.chains.map import scientifik.kmath.chains.zip import scientifik.kmath.operations.Space @@ -26,6 +26,6 @@ class SamplerSpace(val space: Space) : Space> { } override fun multiply(a: Sampler, k: Number): Sampler = BasicSampler { generator -> - a.sample(generator).pipe { space.run { it * k.toDouble() } } + a.sample(generator).map { space.run { it * k.toDouble() } } } } \ No newline at end of file diff --git a/kmath-prob/src/commonMain/kotlin/scientifik/kmath/prob/Statistic.kt b/kmath-prob/src/commonMain/kotlin/scientifik/kmath/prob/Statistic.kt index b02eb598b..1af2570b0 100644 --- a/kmath-prob/src/commonMain/kotlin/scientifik/kmath/prob/Statistic.kt +++ b/kmath-prob/src/commonMain/kotlin/scientifik/kmath/prob/Statistic.kt @@ -21,10 +21,16 @@ interface Statistic { /** * A statistic tha could be computed separately on different blocks of data and then composed + * @param T - source type + * @param I - intermediate block type + * @param R - result type */ interface ComposableStatistic : Statistic { + //compute statistic on a single block suspend fun computeIntermediate(data: Buffer): I + //Compose two blocks suspend fun composeIntermediate(first: I, second: I): I + //Transform block to result suspend fun toResult(intermediate: I): R override suspend fun invoke(data: Buffer): R = toResult(computeIntermediate(data)) @@ -32,7 +38,7 @@ interface ComposableStatistic : Statistic { @FlowPreview @ExperimentalCoroutinesApi -fun ComposableStatistic.flowIntermediate( +private fun ComposableStatistic.flowIntermediate( flow: Flow>, dispatcher: CoroutineDispatcher = Dispatchers.Default ): Flow = flow diff --git a/kmath-prob/src/commonMain/kotlin/scientifik/kmath/prob/distributions.kt b/kmath-prob/src/commonMain/kotlin/scientifik/kmath/prob/distributions.kt new file mode 100644 index 000000000..ff6e2a551 --- /dev/null +++ b/kmath-prob/src/commonMain/kotlin/scientifik/kmath/prob/distributions.kt @@ -0,0 +1,31 @@ +package scientifik.kmath.prob + +import scientifik.kmath.chains.Chain +import scientifik.kmath.chains.SimpleChain + +class UniformDistribution(val range: ClosedFloatingPointRange) : UnivariateDistribution { + + private val length = range.endInclusive - range.start + + override fun probability(arg: Double): Double { + return if (arg in range) { + return 1.0 / length + } else { + 0.0 + } + } + + override fun sample(generator: RandomGenerator): Chain { + return SimpleChain { + range.start + generator.nextDouble() * length + } + } + + override fun cumulative(arg: Double): Double { + return when { + arg < range.start -> 0.0 + arg >= range.endInclusive -> 1.0 + else -> (arg - range.start) / length + } + } +} \ No newline at end of file diff --git a/settings.gradle.kts b/settings.gradle.kts index 042558d25..f52edfac5 100644 --- a/settings.gradle.kts +++ b/settings.gradle.kts @@ -1,10 +1,10 @@ pluginManagement { plugins { - id("scientifik.mpp") version "0.1.6" - id("scientifik.jvm") version "0.1.6" - id("scientifik.atomic") version "0.1.6" - id("scientifik.publish") version "0.1.6" + id("scientifik.mpp") version "0.2.5" + id("scientifik.jvm") version "0.2.5" + id("scientifik.atomic") version "0.2.5" + id("scientifik.publish") version "0.2.5" } repositories { @@ -25,8 +25,6 @@ pluginManagement { } } -enableFeaturePreview("GRADLE_METADATA") - rootProject.name = "kmath" include( ":kmath-memory",