Update Gradle, Kotlin, KMath; fix build problems; drop PSI in code generation

Author: CommanderTvis

.github/workflows/build.yml

@@ -1,18 +1,20 @@
-# Based on https://github.com/touchlab/Stately/blob/main/.github/workflows/build.yml
+name: Gradle build
 
-name: build
 on: [ push ]
 
 jobs:
   build:
     runs-on: ubuntu-20.04
+    timeout-minutes: 30
     steps:
       - name: Checkout the repo
         uses: actions/checkout@v2
       - name: Set up JDK 11
-        uses: actions/setup-java@v1
+        uses: DeLaGuardo/setup-graalvm@4.0
         with:
-          java-version: 11
+          graalvm: 21.1.0
+          java: java11
+          arch: amd64
       - name: Cache gradle
         uses: actions/cache@v2
         with:

.github/workflows/pages.yml

@@ -12,9 +12,25 @@ jobs:
       - name: Checkout the repo
         uses: actions/checkout@v2
       - name: Set up JDK 11
-        uses: actions/setup-java@v1
+        uses: DeLaGuardo/setup-graalvm@4.0
         with:
-          java-version: 11
+          graalvm: 21.1.0
+          java: java11
+          arch: amd64
+      - name: Cache gradle
+        uses: actions/cache@v2
+        with:
+          path: ~/.gradle/caches
+          key: ubuntu-20.04-gradle-${{ hashFiles('*.gradle.kts') }}
+          restore-keys: |
+            ubuntu-20.04-gradle-
+      - name: Cache konan
+        uses: actions/cache@v2
+        with:
+          path: ~/.konan
+          key: ${{ runner.os }}-gradle-${{ hashFiles('*.gradle.kts') }}
+          restore-keys: |
+            ${{ runner.os }}-gradle-
       - name: Build
         run: ./gradlew dokkaHtml --no-daemon --no-parallel --stacktrace
       - name: Deploy to GitHub Pages

.github/workflows/publish.yml

@@ -10,14 +10,16 @@ jobs:
   publish:
     environment:
       name: publish
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-20.04
     steps:
       - name: Checkout the repo
         uses: actions/checkout@v2
       - name: Set up JDK 11
-        uses: actions/setup-java@v1
+        uses: DeLaGuardo/setup-graalvm@4.0
         with:
-          java-version: 11
+          graalvm: 21.1.0
+          java: java11
+          arch: amd64
       - name: Cache gradle
         uses: actions/cache@v2
         with:

README.md

@@ -6,12 +6,12 @@
 [![Gradle build](https://github.com/mipt-npm/kmath-gsl/workflows/build/badge.svg)](https://github.com/mipt-npm/kmath-gsl/actions/workflows/build.yml)
 [![Space](https://img.shields.io/maven-metadata/v?label=Space&metadataUrl=https://maven.pkg.jetbrains.space/mipt-npm/p/sci/maven/space/kscience/kmath-gsl/maven-metadata.xml)](https://maven.pkg.jetbrains.space/mipt-npm/p/sci/maven/space/kscience/kmath-gsl/0.2.1-dev-1/)
 
- - [matrix-contexts](src/nativeMain/kotlin/GslMatrixContext.kt) : Matrix Contexts over Double, Float, and Complex implemented with GSL
+ - [matrix-contexts](src/nativeMain/kotlin/GslLinearSpace.kt) : LinearSpace implementations for Double, Float, and Complex matrices and vectors implemented with GSL
 
 
 ## Artifact:
 
-The Maven coordinates of this project are `space.kscience:kmath-gsl:0.2.1-dev-1`.
+The Maven coordinates of this project are `space.kscience:kmath-gsl:0.3.0-dev-1`.
 
 **Gradle:**
 ```gradle
@@ -21,7 +21,7 @@ repositories {
 }
 
 dependencies {
-    implementation 'space.kscience:kmath-gsl:0.2.1-dev-1'
+    implementation 'space.kscience:kmath-gsl:0.3.0-dev-1'
 }
 ```
 **Gradle Kotlin DSL:**
@@ -32,6 +32,6 @@ repositories {
 }
 
 dependencies {
-    implementation("space.kscience:kmath-gsl:0.2.1-dev-1")
+    implementation("space.kscience:kmath-gsl:0.3.0-dev-1")
 }
 ```

build.gradle.kts

@@ -14,7 +14,7 @@ plugins {
 }
 
 group = "space.kscience"
-version = "0.2.1-dev-1"
+version = "0.3.0-dev-1"
 
 repositories.mavenCentral()
 
@@ -23,10 +23,8 @@ kotlin {
     data class DownloadLinks(val gsl: String)
 
     val (nativeTarget, downloadLinks) = when (System.getProperty("os.name")) {
-//        "Mac OS X" -> macosX64()
-
         "Linux" -> linuxX64() to DownloadLinks(
-            gsl = "https://anaconda.org/conda-forge/gsl/2.6/download/linux-64/gsl-2.6-he838d99_2.tar.bz2"
+            gsl = "https://anaconda.org/conda-forge/gsl/2.6/download/linux-64/gsl-2.6-he838d99_2.tar.bz2",
         )
 
         else -> {
@@ -38,14 +36,12 @@ kotlin {
     val thirdPartyDir =
         File("${System.getProperty("user.home")}/.konan/third-party/kmath-gsl-${project.property("version")}")
 
-    val main by nativeTarget.compilations.getting {
-        cinterops {
-            val libgsl by creating
-        }
-    }
 
+    val main by nativeTarget.compilations.getting
     val test by nativeTarget.compilations.getting
 
+    val libgsl by main.cinterops.creating
+
     val nativeMain by sourceSets.creating {
         val codegen by tasks.creating {
             matricesCodegen(kotlin.srcDirs.first().absolutePath + "/_Matrices.kt")
@@ -55,7 +51,7 @@ kotlin {
         kotlin.srcDirs(files().builtBy(codegen))
 
         dependencies {
-            api("space.kscience:kmath-complex:0.2.1")
+            api("space.kscience:kmath-complex:0.3.0-dev-12")
         }
     }
 
@@ -67,8 +63,7 @@ kotlin {
     test.defaultSourceSet.dependsOn(nativeTest)
 
     val downloadGsl by tasks.creating(Download::class) {
-        val url = downloadLinks.gsl
-        src(url)
+        src(downloadLinks.gsl)
         dest(File(thirdPartyDir, "libgsl.tar.bz2"))
         overwrite(false)
     }
@@ -80,13 +75,14 @@ kotlin {
     }
 
     val writeDefFile by tasks.creating {
-        val file = main.cinterops["libgsl"].defFile
+        val file = libgsl.defFile
         file.parentFile.mkdirs()
-        file.createNewFile()
+        if (!file.exists()) file.createNewFile()
 
         file.writeText("""
                     package=org.gnu.gsl
                     headers=gsl/gsl_blas.h gsl/gsl_linalg.h gsl/gsl_permute_matrix.h gsl/gsl_matrix.h gsl/gsl_vector.h gsl/gsl_errno.h
+                    linkerOpts = -L/usr/lib64 -L/usr/lib/x86_64-linux-gnu -lblas
                     staticLibraries=libgsl.a libgslcblas.a
                     compilerOpts=-I${thirdPartyDir}/include/
                     libraryPaths=${thirdPartyDir}/lib/
@@ -114,8 +110,9 @@ readme {
 
     feature(
         id = "matrix-contexts",
-        description = "Matrix Contexts over Double, Float, and Complex implemented with GSL",
-        ref = "src/nativeMain/kotlin/GslMatrixContext.kt"
+        description =
+        "LinearSpace implementations for Double, Float, and Complex matrices and vectors implemented with GSL",
+        ref = "src/nativeMain/kotlin/GslLinearSpace.kt"
     )
 }
 

buildSrc/build.gradle.kts

@@ -3,7 +3,3 @@ plugins {
 }
 
 repositories.mavenCentral()
-
-dependencies {
-    implementation(kotlin("compiler-embeddable", "1.4.32"))
-}

buildSrc/src/main/kotlin/codegenUtilities.kt

@@ -1,64 +1,5 @@
 package space.kscience.kmath.gsl.codegen
 
-import org.jetbrains.kotlin.cli.common.CLIConfigurationKeys
-import org.jetbrains.kotlin.cli.common.messages.MessageCollector
-import org.jetbrains.kotlin.cli.jvm.compiler.EnvironmentConfigFiles
-import org.jetbrains.kotlin.cli.jvm.compiler.KotlinCoreEnvironment
-import org.jetbrains.kotlin.com.intellij.mock.MockProject
-import org.jetbrains.kotlin.com.intellij.openapi.extensions.ExtensionPoint
-import org.jetbrains.kotlin.com.intellij.openapi.extensions.Extensions
-import org.jetbrains.kotlin.com.intellij.openapi.util.UserDataHolderBase
-import org.jetbrains.kotlin.com.intellij.pom.PomModel
-import org.jetbrains.kotlin.com.intellij.pom.PomModelAspect
-import org.jetbrains.kotlin.com.intellij.pom.PomTransaction
-import org.jetbrains.kotlin.com.intellij.pom.impl.PomTransactionBase
-import org.jetbrains.kotlin.com.intellij.pom.tree.TreeAspect
-import org.jetbrains.kotlin.com.intellij.psi.PsiElement
-import org.jetbrains.kotlin.com.intellij.psi.impl.source.tree.TreeCopyHandler
-import org.jetbrains.kotlin.config.CompilerConfiguration
-import sun.reflect.ReflectionFactory
-
-internal fun createProject(): MockProject {
-    val project = KotlinCoreEnvironment.createForProduction(
-        {},
-        CompilerConfiguration().apply { put(CLIConfigurationKeys.MESSAGE_COLLECTOR_KEY, MessageCollector.NONE) },
-        EnvironmentConfigFiles.JVM_CONFIG_FILES
-    ).project as MockProject
-
-    val extensionPoint = "org.jetbrains.kotlin.com.intellij.treeCopyHandler"
-
-    arrayOf(project.extensionArea, Extensions.getRootArea())
-        .asSequence()
-        .filterNot { it.hasExtensionPoint(extensionPoint) }
-        .forEach {
-            it.registerExtensionPoint(extensionPoint, TreeCopyHandler::class.java.name, ExtensionPoint.Kind.INTERFACE)
-        }
-
-    project.registerService(PomModel::class.java, object : UserDataHolderBase(), PomModel {
-        override fun runTransaction(transaction: PomTransaction) = (transaction as PomTransactionBase).run()
-
-        @Suppress("UNCHECKED_CAST")
-        override fun <T : PomModelAspect> getModelAspect(aspect: Class<T>): T? {
-            if (aspect == TreeAspect::class.java) {
-                val constructor = ReflectionFactory.getReflectionFactory().newConstructorForSerialization(
-                    aspect,
-                    Any::class.java.getDeclaredConstructor(*arrayOfNulls(0))
-                )
-
-                return constructor.newInstance() as T
-            }
-
-            return null
-        }
-    })
-
-    return project
-}
-
-internal operator fun PsiElement.plusAssign(e: PsiElement) {
-    add(e)
-}
-
 internal fun fn(pattern: String, type: String): String {
     if (type == "double") return pattern.replace("R", "_")
     return pattern.replace("R", "_${type}_")

buildSrc/src/main/kotlin/matricesCodegen.kt

@@ -1,21 +1,14 @@
 package space.kscience.kmath.gsl.codegen
 
 import org.intellij.lang.annotations.Language
-import org.jetbrains.kotlin.com.intellij.openapi.project.Project
-import org.jetbrains.kotlin.name.FqName
-import org.jetbrains.kotlin.psi.KtFile
-import org.jetbrains.kotlin.psi.KtPsiFactory
-import org.jetbrains.kotlin.resolve.ImportPath
 import java.io.File
 
-private fun KtPsiFactory.createMatrixClass(
-    f: KtFile,
+private fun Appendable.createMatrixClass(
     cTypeName: String,
     kotlinTypeName: String,
-    kotlinTypeAlias: String = kotlinTypeName
 ) {
     fun fn(pattern: String) = fn(pattern, cTypeName)
-    val className = "Gsl${kotlinTypeAlias}Matrix"
+    val className = "Gsl${kotlinTypeName}Matrix"
     val structName = sn("gsl_matrixR", cTypeName)
 
     @Language("kotlin") val text = """internal class $className(
@@ -29,18 +22,20 @@ private fun KtPsiFactory.createMatrixClass(
     override val colNum: Int
         get() = nativeHandle.pointed.size2.toInt()
 
-    override val rows: Buffer<Buffer<$kotlinTypeName>>
-        get() = VirtualBuffer(rowNum) { r ->
-            Gsl${kotlinTypeAlias}Vector(
+    @PerformancePitfall
+    override val rows: List<Buffer<$kotlinTypeName>>
+        get() = List(rowNum) { r ->
+            Gsl${kotlinTypeName}Vector(
                 ${fn("gsl_matrixRrow")}(nativeHandle, r.toULong()).placeTo(scope).pointed.vector.ptr,
                 scope,
                 false,
             )
         }
 
-    override val columns: Buffer<Buffer<$kotlinTypeName>>
-        get() = VirtualBuffer(rowNum) { c ->
-            Gsl${kotlinTypeAlias}Vector(
+    @PerformancePitfall
+    override val columns: List<Buffer<$kotlinTypeName>>
+        get() = List(rowNum) { c ->
+            Gsl${kotlinTypeName}Vector(
                 ${fn("gsl_matrixRcolumn")}(nativeHandle, c.toULong()).placeTo(scope).pointed.vector.ptr,
                 scope,
                 false,
@@ -60,45 +55,31 @@ private fun KtPsiFactory.createMatrixClass(
     }
 
     override fun close(): Unit = ${fn("gsl_matrixRfree")}(nativeHandle)
-
-    override fun equals(other: Any?): Boolean {
-        if (other is $className)
-            return ${fn("gsl_matrixRequal")}(nativeHandle, other.nativeHandle) == 1
-
-        return super.equals(other)
-    }
 }"""
-    f += createClass(text)
-    f += createNewLine(2)
+    appendLine(text)
+    appendLine()
 }
 
 /**
  * Generates matrices source code for kmath-gsl.
  */
-fun matricesCodegen(outputFile: String, project: Project = createProject()) {
-    val f = KtPsiFactory(project, true).run {
-        createFile("").also { f ->
-            f += createPackageDirective(FqName("space.kscience.kmath.gsl"))
-            f += createNewLine(2)
-            f += createImportDirective(ImportPath.fromString("kotlinx.cinterop.*"))
-            f += createNewLine(1)
-            f += createImportDirective(ImportPath.fromString("space.kscience.kmath.structures.*"))
-            f += createNewLine(1)
-            f += createImportDirective(ImportPath.fromString("org.gnu.gsl.*"))
-            f += createNewLine(2)
-            createMatrixClass(f, "double", "Double", "Real")
-            createMatrixClass(f, "float", "Float")
-            createMatrixClass(f, "short", "Short")
-            createMatrixClass(f, "ushort", "UShort")
-            createMatrixClass(f, "long", "Long")
-            createMatrixClass(f, "ulong", "ULong")
-            createMatrixClass(f, "int", "Int")
-            createMatrixClass(f, "uint", "UInt")
-        }
-    }
-
-    File(outputFile).apply {
-        parentFile.mkdirs()
-        writeText(f.text)
+fun matricesCodegen(outputFile: String): Unit = File(outputFile).run {
+    parentFile.mkdirs()
+    writer().use {
+        it.appendLine("package space.kscience.kmath.gsl")
+        it.appendLine()
+        it.appendLine("import kotlinx.cinterop.*")
+        it.appendLine("import org.gnu.gsl.*")
+        it.appendLine("import space.kscience.kmath.misc.PerformancePitfall")
+        it.appendLine("import space.kscience.kmath.structures.*")
+        it.appendLine()
+        it.createMatrixClass("double", "Double")
+        it.createMatrixClass("float", "Float")
+        it.createMatrixClass("short", "Short")
+        it.createMatrixClass("ushort", "UShort")
+        it.createMatrixClass("long", "Long")
+        it.createMatrixClass("ulong", "ULong")
+        it.createMatrixClass("int", "Int")
+        it.createMatrixClass("uint", "UInt")
     }
 }