Merge pull request #77 from SciProgCentre/dev

0.6.2

.github/workflows/pages.yml

@@ -1,28 +1,31 @@
 name: Dokka publication
 
 on:
-  push:
+  workflow_dispatch:
-    branches: [ master ]
+  release:
+    types: [ created ]
 
 jobs:
   build:
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-latest
     timeout-minutes: 40
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3.0.0
-      - uses: DeLaGuardo/setup-graalvm@4.0
+      - uses: actions/setup-java@v3.0.0
         with:
-          graalvm: 21.2.0
+          java-version: 11
-          java: java11
+          distribution: liberica
-          arch: amd64
+      - name: Cache konan
-      - uses: actions/cache@v2
+        uses: actions/cache@v3.0.1
         with:
-          path: ~/.gradle/caches
+          path: ~/.konan
           key: ${{ runner.os }}-gradle-${{ hashFiles('*.gradle.kts') }}
           restore-keys: |
             ${{ runner.os }}-gradle-
-      - run: ./gradlew dokkaHtmlMultiModule --build-cache --no-daemon --no-parallel --stacktrace
+      - uses: gradle/gradle-build-action@v2.1.5
-      - uses: JamesIves/github-pages-deploy-action@4.1.0
+        with:
+          arguments: dokkaHtmlMultiModule --no-parallel
+      - uses: JamesIves/github-pages-deploy-action@v4.3.0
         with:
           branch: gh-pages
           folder: build/dokka/htmlMultiModule

.github/workflows/publish.yml

@@ -9,32 +9,18 @@ jobs:
   publish:
     environment:
       name: publish
-    env:
-      publishing.github: false
     strategy:
       matrix:
         os: [ macOS-latest, windows-latest ]
     runs-on: ${{matrix.os}}
     steps:
-      - name: Checkout the repo
+      - uses: actions/checkout@v3.0.0
-        uses: actions/checkout@v2
+      - uses: actions/setup-java@v3.10.0
-      - name: Set up JDK 11
-        uses: DeLaGuardo/setup-graalvm@4.0
         with:
-          graalvm: 21.2.0
+          java-version: 11
-          java: java11
+          distribution: liberica
-          arch: amd64
-      - name: Cache gradle
-        uses: actions/cache@v2
-        with:
-          path: |
-            ~/.gradle/caches
-            ~/.gradle/wrapper
-          key: ${{ runner.os }}-gradle-${{ hashFiles('*.gradle.kts') }}
-          restore-keys: |
-            ${{ runner.os }}-gradle-
       - name: Cache konan
-        uses: actions/cache@v2
+        uses: actions/cache@v3.0.1
         with:
           path: ~/.konan
           key: ${{ runner.os }}-gradle-${{ hashFiles('*.gradle.kts') }}
@@ -42,14 +28,23 @@ jobs:
             ${{ runner.os }}-gradle-
       - name: Publish Windows Artifacts
         if: matrix.os == 'windows-latest'
-        shell: cmd
+        uses: gradle/gradle-build-action@v2.4.0
-        run: >
+        with:
-          ./gradlew release --no-daemon --build-cache -Ppublishing.enabled=true
+          arguments: |
-          -Ppublishing.space.user=${{ secrets.SPACE_APP_ID }}
+            publishAllPublicationsToSpaceRepository
-          -Ppublishing.space.token=${{ secrets.SPACE_APP_SECRET }}
+            -Ppublishing.targets=all
+            -Ppublishing.space.user=${{ secrets.SPACE_APP_ID }}
+            -Ppublishing.space.token=${{ secrets.SPACE_APP_SECRET }}
       - name: Publish Mac Artifacts
         if: matrix.os == 'macOS-latest'
-        run: >
+        uses: gradle/gradle-build-action@v2.4.0
-          ./gradlew release --no-daemon --build-cache -Ppublishing.enabled=true
+        with:
-          -Ppublishing.space.user=${{ secrets.SPACE_APP_ID }}
+          arguments: |
-          -Ppublishing.space.token=${{ secrets.SPACE_APP_SECRET }}
+            publishMacosX64PublicationToSpaceRepository
+            publishMacosArm64PublicationToSpaceRepository
+            publishIosX64PublicationToSpaceRepository
+            publishIosArm64PublicationToSpaceRepository
+            publishIosSimulatorArm64PublicationToSpaceRepository
+            -Ppublishing.targets=all
+            -Ppublishing.space.user=${{ secrets.SPACE_APP_ID }}
+            -Ppublishing.space.token=${{ secrets.SPACE_APP_SECRET }}

CHANGELOG.md

@@ -14,6 +14,12 @@
 
 ### Security
 
+## 0.6.2 - 2023-07-29
+
+### Changed
+- Meta to Json serializer now serializes a single item with index as an array. It is important for plotly integration.
+- Meta to Json serializes Meta without children a value as literal or array instead of an object with `@value` field.
+
 ## 0.6.1 - 2023-03-31
 
 ### Added

README.md

@@ -3,47 +3,39 @@
 
 ![Gradle build](https://github.com/mipt-npm/dataforge-core/workflows/Gradle%20build/badge.svg)
 
-<hr/>
 
-* ### [dataforge-context](dataforge-context)
+### [dataforge-context](dataforge-context)
 > 
 >
 > **Maturity**: DEVELOPMENT
-<hr/>
 
-* ### [dataforge-data](dataforge-data)
+### [dataforge-data](dataforge-data)
 > 
 >
 > **Maturity**: EXPERIMENTAL
-<hr/>
 
-* ### [dataforge-io](dataforge-io)
+### [dataforge-io](dataforge-io)
 > 
 >
 > **Maturity**: PROTOTYPE
-<hr/>
 
-* ### [dataforge-meta](dataforge-meta)
+### [dataforge-meta](dataforge-meta)
 > 
 >
 > **Maturity**: DEVELOPMENT
-<hr/>
 
-* ### [dataforge-scripting](dataforge-scripting)
+### [dataforge-scripting](dataforge-scripting)
 > 
 >
 > **Maturity**: PROTOTYPE
-<hr/>
 
-* ### [dataforge-workspace](dataforge-workspace)
+### [dataforge-workspace](dataforge-workspace)
 > 
 >
 > **Maturity**: EXPERIMENTAL
-<hr/>
 
-* ### [dataforge-io-yaml](dataforge-io/dataforge-io-yaml)
+### [dataforge-io/dataforge-io-yaml](dataforge-io/dataforge-io-yaml)
 > YAML meta converters and Front Matter envelope format
 >
 > **Maturity**: PROTOTYPE
-<hr/>
 

build.gradle.kts

@@ -9,7 +9,7 @@ plugins {
 
 allprojects {
     group = "space.kscience"
-    version = "0.6.1"
+    version = "0.6.2"
 }
 
 subprojects {

dataforge-context/README.md

@@ -0,0 +1,32 @@
+# Module dataforge-context
+
+Context and provider definitions
+
+## Usage
+
+## Artifact:
+
+The Maven coordinates of this project are `space.kscience:dataforge-context:0.6.2-dev-2`.
+
+**Gradle Groovy:**
+```groovy
+repositories {
+    maven { url 'https://repo.kotlin.link' }
+    mavenCentral()
+}
+
+dependencies {
+    implementation 'space.kscience:dataforge-context:0.6.2-dev-2'
+}
+```
+**Gradle Kotlin DSL:**
+```kotlin
+repositories {
+    maven("https://repo.kotlin.link")
+    mavenCentral()
+}
+
+dependencies {
+    implementation("space.kscience:dataforge-context:0.6.2-dev-2")
+}
+```

dataforge-data/README.md

@@ -0,0 +1,32 @@
+# Module dataforge-data
+
+
+
+## Usage
+
+## Artifact:
+
+The Maven coordinates of this project are `space.kscience:dataforge-data:0.6.2-dev-2`.
+
+**Gradle Groovy:**
+```groovy
+repositories {
+    maven { url 'https://repo.kotlin.link' }
+    mavenCentral()
+}
+
+dependencies {
+    implementation 'space.kscience:dataforge-data:0.6.2-dev-2'
+}
+```
+**Gradle Kotlin DSL:**
+```kotlin
+repositories {
+    maven("https://repo.kotlin.link")
+    mavenCentral()
+}
+
+dependencies {
+    implementation("space.kscience:dataforge-data:0.6.2-dev-2")
+}
+```

dataforge-data/src/commonMain/kotlin/space/kscience/dataforge/actions/ReduceAction.kt

@@ -112,7 +112,6 @@ internal class ReduceAction<T : Any, R : Any>(
  * A one-to-one mapping action
  */
 @DFExperimental
-@Suppress("FunctionName")
 public inline fun <reified T : Any, reified R : Any> Action.Companion.reduce(
     noinline builder: ReduceGroupBuilder<T, R>.() -> Unit,
 ): Action<T, R> = ReduceAction(typeOf<R>(), builder)

dataforge-data/src/commonMain/kotlin/space/kscience/dataforge/actions/SplitAction.kt

@@ -87,7 +87,6 @@ internal class SplitAction<T : Any, R : Any>(
  * Action that splits each incoming element into a number of fragments defined in builder
  */
 @DFExperimental
-@Suppress("FunctionName")
 public inline fun <T : Any, reified R : Any> Action.Companion.split(
     noinline builder: SplitBuilder<T, R>.() -> Unit,
 ): Action<T, R> = SplitAction(typeOf<R>(), builder)

dataforge-io/README.md

@@ -0,0 +1,32 @@
+# Module dataforge-io
+
+IO module
+
+## Usage
+
+## Artifact:
+
+The Maven coordinates of this project are `space.kscience:dataforge-io:0.6.2-dev-2`.
+
+**Gradle Groovy:**
+```groovy
+repositories {
+    maven { url 'https://repo.kotlin.link' }
+    mavenCentral()
+}
+
+dependencies {
+    implementation 'space.kscience:dataforge-io:0.6.2-dev-2'
+}
+```
+**Gradle Kotlin DSL:**
+```kotlin
+repositories {
+    maven("https://repo.kotlin.link")
+    mavenCentral()
+}
+
+dependencies {
+    implementation("space.kscience:dataforge-io:0.6.2-dev-2")
+}
+```

dataforge-io/build.gradle.kts

@@ -10,8 +10,8 @@ kscience {
     jvm()
     js()
     native()
-    useSerialization("1.4.1")
+    useSerialization()
-    useSerialization("1.4.1", sourceSet = space.kscience.gradle.DependencySourceSet.TEST) {
+    useSerialization(sourceSet = space.kscience.gradle.DependencySourceSet.TEST) {
         cbor()
     }
     dependencies {
@@ -20,6 +20,6 @@ kscience {
     }
 }
 
-readme{
+readme {
     maturity = space.kscience.gradle.Maturity.PROTOTYPE
 }

dataforge-io/dataforge-io-yaml/README.md

@@ -0,0 +1,32 @@
+# Module dataforge-io-yaml
+
+YAML meta IO
+
+## Usage
+
+## Artifact:
+
+The Maven coordinates of this project are `space.kscience:dataforge-io-yaml:0.6.2-dev-2`.
+
+**Gradle Groovy:**
+```groovy
+repositories {
+    maven { url 'https://repo.kotlin.link' }
+    mavenCentral()
+}
+
+dependencies {
+    implementation 'space.kscience:dataforge-io-yaml:0.6.2-dev-2'
+}
+```
+**Gradle Kotlin DSL:**
+```kotlin
+repositories {
+    maven("https://repo.kotlin.link")
+    mavenCentral()
+}
+
+dependencies {
+    implementation("space.kscience:dataforge-io-yaml:0.6.2-dev-2")
+}
+```

dataforge-io/dataforge-io-yaml/build.gradle.kts

@@ -4,10 +4,6 @@ plugins {
 
 description = "YAML meta IO"
 
-repositories {
-    mavenCentral()
-}
-
 kscience {
     jvm()
     js()
@@ -20,10 +16,6 @@ kscience {
     }
 }
 
-repositories{
-    maven("https://dl.bintray.com/mamoe/yamlkt")
-}
-
 readme{
     maturity = space.kscience.gradle.Maturity.PROTOTYPE
     description ="""

dataforge-io/src/commonMain/kotlin/space/kscience/dataforge/io/JsonMetaFormat.kt

@@ -6,7 +6,7 @@ package space.kscience.dataforge.io
 import io.ktor.utils.io.core.Input
 import io.ktor.utils.io.core.Output
 import kotlinx.serialization.json.Json
-import kotlinx.serialization.json.JsonObject
+import kotlinx.serialization.json.JsonElement
 import space.kscience.dataforge.context.Context
 import space.kscience.dataforge.meta.Meta
 import space.kscience.dataforge.meta.descriptors.MetaDescriptor
@@ -19,8 +19,8 @@ import space.kscience.dataforge.meta.toMeta
 public class JsonMetaFormat(private val json: Json = DEFAULT_JSON) : MetaFormat {
 
     override fun writeMeta(output: Output, meta: Meta, descriptor: MetaDescriptor?) {
-        val jsonObject = meta.toJson(descriptor)
+        val jsonElement = meta.toJson(descriptor)
-        output.writeUtf8String(json.encodeToString(JsonObject.serializer(), jsonObject))
+        output.writeUtf8String(json.encodeToString(JsonElement.serializer(), jsonElement))
     }
 
     override fun readMeta(input: Input, descriptor: MetaDescriptor?): Meta {

dataforge-meta/README.md

@@ -0,0 +1,32 @@
+# Module dataforge-meta
+
+Meta definition and basic operations on meta
+
+## Usage
+
+## Artifact:
+
+The Maven coordinates of this project are `space.kscience:dataforge-meta:0.6.2-dev-2`.
+
+**Gradle Groovy:**
+```groovy
+repositories {
+    maven { url 'https://repo.kotlin.link' }
+    mavenCentral()
+}
+
+dependencies {
+    implementation 'space.kscience:dataforge-meta:0.6.2-dev-2'
+}
+```
+**Gradle Kotlin DSL:**
+```kotlin
+repositories {
+    maven("https://repo.kotlin.link")
+    mavenCentral()
+}
+
+dependencies {
+    implementation("space.kscience:dataforge-meta:0.6.2-dev-2")
+}
+```

dataforge-meta/build.gradle.kts

@@ -6,7 +6,7 @@ kscience {
     jvm()
     js()
     native()
-    useSerialization("1.4.1"){
+    useSerialization{
         json()
     }
 }

dataforge-meta/src/commonMain/kotlin/space/kscience/dataforge/meta/JsonMeta.kt

@@ -23,7 +23,6 @@ public fun Value.toJson(descriptor: MetaDescriptor? = null): JsonElement = when
 }
 
 //Use these methods to customize JSON key mapping
-@Suppress("NULLABLE_EXTENSION_OPERATOR_WITH_SAFE_CALL_RECEIVER")
 private fun String.toJsonKey(descriptor: MetaDescriptor?) = descriptor?.attributes?.get("jsonName").string ?: toString()
 
 private fun Meta.toJsonWithIndex(descriptor: MetaDescriptor?, index: String?): JsonElement = if (items.isEmpty()) {
@@ -35,9 +34,13 @@ private fun Meta.toJsonWithIndex(descriptor: MetaDescriptor?, index: String?): J
         val childDescriptor = descriptor?.children?.get(body)
         if (list.size == 1) {
             val (token, element) = list.first()
-            //do not add empty element
+                //do not add an empty element
-            val child: JsonElement = element.toJsonWithIndex(childDescriptor, token.index)
+                val child: JsonElement = element.toJsonWithIndex(childDescriptor, token.index)
-            body to child
+            if(token.index == null) {
+                body to child
+            } else {
+                body to JsonArray(listOf(child))
+            }
         } else {
             val elements: List<JsonElement> = list.sortedBy { it.key.index }.mapIndexed { index, entry ->
                 //Use index if it is not equal to the item order
@@ -61,30 +64,24 @@ private fun Meta.toJsonWithIndex(descriptor: MetaDescriptor?, index: String?): J
     JsonObject(pairs.toMap())
 }
 
-public fun Meta.toJson(descriptor: MetaDescriptor? = null): JsonObject {
+/**
-    val element = toJsonWithIndex(descriptor, null)
+ * Convert Meta to [JsonElement]. Meta with children is converted to [JsonObject].
-    return if (element is JsonObject) {
+ * Meta without children is converted to either [JsonPrimitive] or [JsonArray] depending on the value type.
-        element
+ * An empty Meta is converted to an empty JsonObject.
-    } else {
+ */
-        buildJsonObject {
+public fun Meta.toJson(descriptor: MetaDescriptor? = null): JsonElement = toJsonWithIndex(descriptor, null)
-            put("@value", element)
-        }
-    }
-}
 
 /**
  * Convert a Json primitive to a [Value]
  */
-public fun JsonPrimitive.toValue(descriptor: MetaDescriptor?): Value {
+public fun JsonPrimitive.toValue(descriptor: MetaDescriptor?): Value = when (this) {
-    return when (this) {
+    JsonNull -> Null
-        JsonNull -> Null
+    else -> {
-        else -> {
+        if (isString) {
-            if (isString) {
+            content.asValue()
-                StringValue(content)
+        } else {
-            } else {
+            //consider using LazyParse
-                //consider using LazyParse
+            content.parseValue()
-                content.parseValue()
-            }
         }
     }
 }

dataforge-meta/src/commonMain/kotlin/space/kscience/dataforge/meta/Value.kt

@@ -226,7 +226,7 @@ public fun <E : Enum<E>> E.asValue(): Value = EnumValue(this)
 
 
 /**
- * Create Value from String using closest match conversion
+ * Create Value from String using the closest match conversion
  */
 public fun String.parseValue(): Value {
 

dataforge-meta/src/commonTest/kotlin/space/kscience/dataforge/meta/MetaSerializationTest.kt

@@ -1,15 +1,45 @@
 package space.kscience.dataforge.meta
 
 import kotlinx.serialization.json.Json
+import space.kscience.dataforge.names.asName
 import kotlin.test.Test
 import kotlin.test.assertEquals
 
 class MetaSerializationTest {
 
     @Test
-    fun singleValueDeserialization(){
+    fun singleValueDeserialization() {
         val string = "ddd"
         val meta = Json.decodeFromString(MetaSerializer, string)
         assertEquals(string, meta.value?.string)
     }
+
+    @Test
+    fun complexMeta() {
+        val meta = Meta {
+            "a" put 28.3
+            "b" put doubleArrayOf(1.0, 2.0, 3.2)
+            "child" put Meta {
+                "a" put "aString"
+                "sns[0]" put Meta {
+                    "d" put 0
+                }
+                "sns[1]" put Meta {
+                    "d" put 1
+                }
+                setIndexed(
+                    "sns2".asName(),
+                    listOf(
+                        Meta { "d" put "first" },
+                        Meta("53")
+                    )
+                )
+            }
+        }
+
+        val string = Json.encodeToString(MetaSerializer, meta)
+        println(string)
+        val reconstructed = Json.decodeFromString(MetaSerializer, string)
+        assertEquals(meta, reconstructed)
+    }
 }

dataforge-scripting/README.md

@@ -0,0 +1,32 @@
+# Module dataforge-scripting
+
+
+
+## Usage
+
+## Artifact:
+
+The Maven coordinates of this project are `space.kscience:dataforge-scripting:0.6.2-dev-2`.
+
+**Gradle Groovy:**
+```groovy
+repositories {
+    maven { url 'https://repo.kotlin.link' }
+    mavenCentral()
+}
+
+dependencies {
+    implementation 'space.kscience:dataforge-scripting:0.6.2-dev-2'
+}
+```
+**Gradle Kotlin DSL:**
+```kotlin
+repositories {
+    maven("https://repo.kotlin.link")
+    mavenCentral()
+}
+
+dependencies {
+    implementation("space.kscience:dataforge-scripting:0.6.2-dev-2")
+}
+```

dataforge-workspace/README.md

@@ -0,0 +1,32 @@
+# Module dataforge-workspace
+
+
+
+## Usage
+
+## Artifact:
+
+The Maven coordinates of this project are `space.kscience:dataforge-workspace:0.6.2-dev-2`.
+
+**Gradle Groovy:**
+```groovy
+repositories {
+    maven { url 'https://repo.kotlin.link' }
+    mavenCentral()
+}
+
+dependencies {
+    implementation 'space.kscience:dataforge-workspace:0.6.2-dev-2'
+}
+```
+**Gradle Kotlin DSL:**
+```kotlin
+repositories {
+    maven("https://repo.kotlin.link")
+    mavenCentral()
+}
+
+dependencies {
+    implementation("space.kscience:dataforge-workspace:0.6.2-dev-2")
+}
+```

docs/templates/ARTIFACT-TEMPLATE.md

@@ -1,29 +0,0 @@
-> #### Artifact:
->
-> This module artifact: `${group}:${name}:${version}`.
->
->
-> [![Maven Central](https://img.shields.io/maven-central/v/space.kscience/${name}.svg?label=Maven%20Central)](https://search.maven.org/search?q=g:%22space.kscience%22%20AND%20a:%22${name}%22)
->
-> **Gradle:**
->
-> ```gradle
-> repositories {
->     maven { url 'https://repo.kotlin.link' }
-> }
-> 
-> dependencies {
->     implementation '${group}:${name}:${version}'
-> }
-> ```
-> **Gradle Kotlin DSL:**
->
-> ```kotlin
-> repositories {
->     maven("https://https://repo.kotlin.link")
-> }
-> 
-> dependencies {
->     implementation("${group}:${name}:${version}")
-> }
-> ```

docs/templates/README-TEMPLATE.md

@@ -3,4 +3,4 @@
 
 ![Gradle build](https://github.com/mipt-npm/dataforge-core/workflows/Gradle%20build/badge.svg)
 
-$modules
+${modules}

gradle.properties

@@ -6,4 +6,4 @@ kotlin.mpp.stability.nowarn=true
 kotlin.incremental.js.ir=true
 kotlin.native.ignoreDisabledTargets=true
 
-toolsVersion=0.14.5-kotlin-1.8.20-RC
+toolsVersion=0.14.9-kotlin-1.8.20

gradle/wrapper/gradle-wrapper.properties

@@ -1,5 +1,5 @@
 distributionBase=GRADLE_USER_HOME
 distributionPath=wrapper/dists
-distributionUrl=https\://services.gradle.org/distributions/gradle-8.0.2-bin.zip
+distributionUrl=https\://services.gradle.org/distributions/gradle-8.2-bin.zip
 zipStoreBase=GRADLE_USER_HOME
 zipStorePath=wrapper/dists