Deploy configuration

.gitignore

@@ -8,5 +8,4 @@
 # Cache of project
 .gradletasknamecache
 
-gradle/artifactory.gradle
+gradle.properties
-gradle/bintray.gradle

README.md

@@ -1,27 +1,48 @@
+Bintray: [ ![Download](https://api.bintray.com/packages/mipt-npm/scientifik/scientifik.kmath/images/download.svg) ](https://bintray.com/mipt-npm/scientifik/scientifik.kmath/_latestVersion)
+
 # KMath
 The Kotlin MATHematics library is intended as a Kotlin-based analog to Python's `numpy` library. In contrast to `numpy` and `scipy` it is modular and has a lightweight core.
 
 ## Features
 
+Actual feature list is [here](doc/features.md)
+
 * **Algebra**
     * Algebraic structures like rings, spaces and field (**TODO** add example to wiki)
     * Basic linear algebra operations (sums, products, etc.), backed by the `Space` API.
     * Complex numbers backed by the `Field` API (meaning that they will be usable in any structure like vectors and N-dimensional arrays).
-    * [In progress] advanced linear algebra operations like matrix inversion and LU decomposition.
+    * Advanced linear algebra operations like matrix inversion and LU decomposition.
-* **Array-like structures** Full support of [numpy-like ndarrays](https://docs.scipy.org/doc/numpy-1.13.0/reference/generated/numpy.ndarray.html) including mixed arithmetic operations and function operations over arrays and numbers just like in Python (with the added benefit of static type checking).
 
-* **Expressions** Expressions are one of the ultimate goals of KMath. By writing a single mathematical expression
+* **Array-like structures** Full support of many-dimenstional array-like structures 
+including mixed arithmetic operations and function operations over arrays and numbers (with the added benefit of static type checking).
+
+* **Expressions** By writing a single mathematical expression
 once, users will be able to apply different types of objects to the expression by providing a context. Exceptions
 can be used for a wide variety of purposes from high performance calculations to code generation.
 
-## Planned features
+* **Histograms** Fast multi-dimensional histograms.
 
-* **Common mathematics** It is planned to gradually wrap most parts of [Apache commons-math](http://commons.apache.org/proper/commons-math/) 
+* **Streaming** Streaming operations on mathematica objects and objects buffers.
+
+* **Commons-math wrapper** It is planned to gradually wrap most parts of [Apache commons-math](http://commons.apache.org/proper/commons-math/)
                            library in Kotlin code and maybe rewrite some parts to better suit the Kotlin programming paradigm, however there is no fixed roadmap for that. Feel free
                            to submit a feature request if you want something to be done first.
                            
+* **Koma wrapper** [Koma](https://github.com/kyonifer/koma) is a well established numerics library in kotlin, specifically linear algebra.
+The plan is to have wrappers for koma implementations for compatibility with kmath API.
+
+## Planned features
+
 * **Messaging** A mathematical notation to support multi-language and multi-node communication for mathematical tasks.
 
+* **Array statistics** 
+
+* **Integration** Univariate and multivariate integration framework.
+
+* **Probability and distributions**
+
+* **Fitting** Non-linear curve fitting facilities
+
 ## Multi-platform support
 
 KMath is developed as a multi-platform library, which means that most of interfaces are declared in the [common module](kmath-core/src/commonMain).
@@ -39,6 +60,10 @@ of optimized parts should be better than SciPy.
 
 ## Releases
 
+Working builds can be obtained here: [![](https://jitpack.io/v/altavir/kmath.svg)](https://jitpack.io/#altavir/kmath).
+
+### Development
+
 The project is currently in pre-release stage. Nightly builds can be used by adding an additional repository to the Gradle config like so:
 
 ```groovy
@@ -69,7 +94,19 @@ or in the Gradle Kotlin DSL:
 api("scientifik:kmath-core-jvm:0.1.0-dev")
 ```
 
-Working builds can be obtained here: [![](https://jitpack.io/v/altavir/kmath.svg)](https://jitpack.io/#altavir/kmath).
+### Release
+
+Release artifacts are accessible from bintray with following configuration:
+
+```kotlin
+repositories{
+    maven("https://dl.bintray.com/mipt-npm/scientifik")
+}
+
+dependencies{
+    api("scientifik:kmath-core-jvm:0.1.0")
+}
+```
 
 ## Contributing
 

build.gradle.kts

@@ -5,6 +5,7 @@ buildscript {
     val ioVersion: String by rootProject.extra("0.1.5")
     val coroutinesVersion: String by rootProject.extra("1.1.1")
     val atomicfuVersion: String by rootProject.extra("0.12.1")
+    val dokkaVersion: String by rootProject.extra("0.9.17")
 
     repositories {
         //maven("https://dl.bintray.com/kotlin/kotlin-eap")
@@ -15,6 +16,7 @@ buildscript {
         classpath("org.jetbrains.kotlin:kotlin-gradle-plugin:$kotlinVersion")
         classpath("org.jfrog.buildinfo:build-info-extractor-gradle:4+")
         classpath("com.jfrog.bintray.gradle:gradle-bintray-plugin:1.8.4")
+        classpath("org.jetbrains.dokka:dokka-gradle-plugin:$dokkaVersion")
     }
 }
 
@@ -22,20 +24,31 @@ plugins {
     id("com.jfrog.artifactory") version "4.9.1" apply false
 }
 
-allprojects {
+val kmathVersion by extra("0.1.0")
-    if (project.name.startsWith("kmath")) {
-        apply(plugin = "maven-publish")
-        apply(plugin = "com.jfrog.artifactory")
-    }
 
+allprojects {
     group = "scientifik"
-    version = "0.1.0-dev"
+    version = kmathVersion
 
     repositories {
         //maven("https://dl.bintray.com/kotlin/kotlin-eap")
         jcenter()
     }
 
+    apply(plugin = "maven")
+    apply(plugin = "maven-publish")
+
+    // apply bintray configuration
+    apply(from = "${rootProject.rootDir}/gradle/bintray.gradle")
+
+    //apply artifactory configuration
+    apply(from = "${rootProject.rootDir}/gradle/artifactory.gradle")
+}
+
+subprojects {
+    if (!name.startsWith("kmath")) return@subprojects
+
+
     extensions.findByType<KotlinMultiplatformExtension>()?.apply {
         jvm {
             compilations.all {
@@ -49,29 +62,49 @@ allprojects {
                 languageSettings.progressiveMode = true
             }
         }
-    }
+
 
         extensions.findByType<PublishingExtension>()?.apply {
-        val javadocJar by tasks.creating(Jar::class) {
+            publications.filterIsInstance<MavenPublication>().forEach { publication ->
-            archiveClassifier.value("javadoc")
+                if (publication.name == "kotlinMultiplatform") {
-            // TODO: instead of a single empty Javadoc JAR, generate real documentation for each module
+                    // for our root metadata publication, set artifactId with a package and project name
-        }
+                    publication.artifactId = project.name
-
+                } else {
-        val sourcesJar by tasks.creating(Jar::class) {
+                    // for targets, set artifactId with a package, project name and target name (e.g. iosX64)
-            archiveClassifier.value("sources")
+                    publication.artifactId = "${project.name}-${publication.name}"
-        }
-
-        repositories {
-            maven(uri("$buildDir/repo"))
-        }
-        publications.withType<MavenPublication>().all {
-            artifact(javadocJar)
-            artifact(sourcesJar)
-        }
-        //apply(from = "${rootProject.rootDir}/gradle/bintray.gradle")
                 }
             }
 
-if (file("gradle/artifactory.gradle").exists()) {
+            // Create empty jar for sources classifier to satisfy maven requirements
-    apply(from = "gradle/artifactory.gradle")
+            val stubSources by tasks.registering(Jar::class) {
+                archiveClassifier.set("sources")
+                //from(sourceSets.main.get().allSource)
             }
+
+            // Create empty jar for javadoc classifier to satisfy maven requirements
+            val stubJavadoc by tasks.registering(Jar::class) {
+                archiveClassifier.set("javadoc")
+            }
+
+            extensions.findByType<KotlinMultiplatformExtension>()?.apply {
+
+                targets.forEach { target ->
+                    val publication = publications.findByName(target.name) as MavenPublication
+
+                    // Patch publications with fake javadoc
+                    publication.artifact(stubJavadoc)
+
+                    // Remove gradle metadata publishing from all targets which are not native
+//                if (target.platformType.name != "native") {
+//                    publication.gradleModuleMetadataFile = null
+//                    tasks.matching { it.name == "generateMetadataFileFor${name.capitalize()}Publication" }.all {
+//                        onlyIf { false }
+//                    }
+//                }
+                }
+            }
+        }
+    }
+}
+
+

gradle/artifactory.gradle

@@ -0,0 +1,31 @@
+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
+        }
+    }
+}

gradle/bintray.gradle

@@ -0,0 +1,85 @@
+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
+
+// This is for easier debugging of bintray uploading problems
+bintrayUpload.doFirst {
+    publications = project.publishing.publications.findAll {
+        !it.name.contains('-test') && it.name != 'kotlinMultiplatform'
+    }.collect {
+        println("Uploading artifact '$it.groupId:$it.artifactId:$it.version' from publication '$it.name'")
+        it.name//https://github.com/bintray/gradle-bintray-plugin/issues/256
+    }
+}

kmath-commons/build.gradle.kts

@@ -1,5 +1,6 @@
 plugins {
     kotlin("jvm")
+    `maven-publish`
 }
 
 description = "Commons math binding for kmath"
@@ -11,3 +12,18 @@ dependencies {
     testImplementation("org.jetbrains.kotlin:kotlin-test")
     testImplementation("org.jetbrains.kotlin:kotlin-test-junit")
 }
+
+
+val sourcesJar by tasks.registering(Jar::class) {
+    classifier = "sources"
+    from(sourceSets.main.get().allSource)
+}
+
+publishing {
+    publications {
+        register("jvm", MavenPublication::class) {
+            from(components["java"])
+            artifact(sourcesJar.get())
+        }
+    }
+}

kmath-core/src/commonMain/kotlin/scientifik/kmath/linear/BufferMatrix.kt

@@ -2,6 +2,7 @@ package scientifik.kmath.linear
 
 import scientifik.kmath.operations.Ring
 import scientifik.kmath.structures.*
+import kotlin.jvm.JvmSynthetic
 
 /**
  * Basic implementation of Matrix space based on [NDStructure]
@@ -32,7 +33,6 @@ class BufferMatrix<T : Any>(
         }
     }
 
-
     override val shape: IntArray get() = intArrayOf(rowNum, colNum)
 
     override fun suggestFeature(vararg features: MatrixFeature) =

settings.gradle.kts

@@ -15,7 +15,7 @@ pluginManagement {
     }
 }
 
-//enableFeaturePreview("GRADLE_METADATA")
+enableFeaturePreview("GRADLE_METADATA")
 
 rootProject.name = "kmath"
 include(