Release version 1

.github/workflows/run-publish-maven.yml

@@ -30,11 +30,11 @@ jobs:
           token: ${{secrets.BIOKOTLINMAVEN}}
           fetch-depth: 0
 
-      - name: Set up JDK 17
+      - name: Set up JDK 21
         uses: actions/setup-java@v3
         with:
           distribution: temurin
-          java-version: '17'
+          java-version: '21'
           cache: 'gradle'
 
       - name: Make gradlew executable

.github/workflows/run-tests-on-pr.yml

@@ -22,7 +22,7 @@ jobs:
       - uses: actions/setup-java@v3
         with:
           distribution: temurin
-          java-version: 17
+          java-version: 21
       - name: Setup Gradle
         uses: gradle/[email protected]
         with:

README.md

@@ -1,54 +1,42 @@
 # README #
 
-BioKotlin is in the early stages of development, but we expect to support nucleotide and 
+[BioKotlin](https://www.biokotlin.org) supports nucleotide and 
 protein sequence manipulation, fast sequence IO, alignment, motif, pathway support.  
 
 BioKotlin leverages the performance and type safety of the JVM languages with ease of Python like scripting.
-Because the Kotlin language is compiled on the fly it can be thousands of times faster for
-certain applications than scripting languages.  Because it uses the JVM, we expect high interoperability with
+Because the Kotlin language is compiled, it can be many times faster for
+certain applications than scripting languages. Because it uses the JVM, we expect high interoperability with
 [GATK](https://gatk.broadinstitute.org/hc/en-us), SamTools [HTSJDK](https://samtools.github.io/htsjdk/), 
 BioJava, [TASSEL](https://www.maizegenetics.net/tassel) for GWAS and Genome Wide Prediction, and the PHG - the 
-pangenome representation.  Additionally, since we have mimicked the beautiful API of [BioPython](https://biopython.org), 
+pangenome representation. Additionally, since we have mimicked the beautiful API of [BioPython](https://biopython.org), 
 we expect fast and efficient interoperability with BioPython through GraalVM.
 
- We expect to have extensive cross language support with the use of GraalVM's support of JVM, Python, and R (FastR). 
+ You can follow our current progress at our [GitHub Page](https://github.com/maize-genetics/BioKotlin) 
 
- You can follow our current progress at our [Trello Board](https://bitbucket.org/bucklerlab/biokotlin/addon/trello/trello-board) 
-
-### What is this repository for? ###
+### BioKotlin Links ###
 
-* This is the main repository for BioKotlin development
-* We follow a Git-Flow branching structure
-* Since we are in early development, most of the code is in the 
-[develop](https://bitbucket.org/bucklerlab/biokotlin/branch/develop) and associated branches
+* Main website for [BioKotlin](https://www.biokotlin.org)
+* [Documentation (API)](https://javadoc.io/doc/org.biokotlin/biokotlin/latest/index.html)
 
-### How do I get set up? ###
+### How to Use ###
 
-* Configuration for a User
-    * JupyterLab with Kotlin
+* JupyterLab with Kotlin
+  * Install the Kotlin kernel for JupyterLab
+  * Add the following to your JupyterLab configuration file:
+  * %use biokotlin
 
-* Configuration for a Power User (or Developer)
-    * IntelliJ with Kotlin support  
-    * JupyterLab with Kotlin
-
-* Dependencies
-* 
+* Kotlin Script
+    * Add the following to your Kotlin script (.main.kts) file:
+    * @file:DependsOn("org.biokotlin:biokotlin:1.0.0")
 
-* How to run tests
-* Deployment instructions
+* Maven Central Dependency (i.e. pom.xml, build.gradle.kts)
+    * https://mvnrepository.com/artifact/org.biokotlin/biokotlin
 
-### Contribution guidelines ###
-
-* Writing tests
-* Code review
-* Other guidelines
+* Installable Tar File from Biokotlin Tools
+    * Download the latest tar file from (https://github.com/maize-genetics/biokotlin-tools/releases)
 
 ### Who do I talk to? ###
 
-* Edward Buckler - [email protected]
-* Terry Casstevens - [email protected]
-
-### ToDo ###
-1. Making the 
-8. Interop between languages using GraalVM
+* [Discussion Page](https://github.com/maize-genetics/BioKotlin/discussions)
+* [Issues Page](https://github.com/maize-genetics/BioKotlin/issues)
 

build.gradle.kts

@@ -1,6 +1,6 @@
+import org.jetbrains.kotlin.gradle.dsl.JvmTarget
 import org.jetbrains.kotlin.gradle.tasks.KotlinCompile
 import org.jreleaser.model.Active
-import java.io.ByteArrayOutputStream
 import java.nio.file.Files
 import java.nio.file.Paths
 import kotlin.io.path.isRegularFile
@@ -10,20 +10,24 @@ import kotlin.jvm.optionals.getOrNull
 // The version is expected to be in the format X.Y.Z
 // JReleaser will use this version to create the release
 fun getVersionName(): String {
-    val stdout = ByteArrayOutputStream()
-    exec {
-        commandLine = listOf("git", "describe", "--tags", "--abbrev=0")
-        standardOutput = stdout
-    }
-    val versionStr = stdout.toString().trim().removePrefix("v").removePrefix("V")
+
+    val process = ProcessBuilder("git", "describe", "--tags", "--abbrev=0")
+        .redirectErrorStream(true)
+        .start()
+    val versionStr = process.inputStream.bufferedReader().readText().trim()
+        .removePrefix("v")
+        .removePrefix("V")
+
     val parts = versionStr.split('.')
     val normalizedStr = when (parts.size) {
         0 -> throw IllegalArgumentException("Version string is empty")
         1 -> "${parts[0]}.0.0"
         2 -> "${parts[0]}.${parts[1]}.0"
         else -> versionStr
     }
+
     return normalizedStr
+
 }
 
 group = "org.biokotlin"
@@ -33,11 +37,15 @@ version = getVersionName()
 This build script is need to use the early access
  */
 buildscript {
-    val kotlinVersion by extra("1.9.24")
+    val kotlinVersion by extra("2.1.21")
+}
+
+kotlin {
+    jvmToolchain(21)
 }
 
 plugins {
-    val kotlinVersion = "1.9.24"
+    val kotlinVersion = "2.1.21"
     java
     kotlin("jvm") version kotlinVersion
     kotlin("plugin.serialization") version kotlinVersion
@@ -49,7 +57,7 @@ plugins {
     //id("org.jetbrains.kotlinx.dataframe") version "1.0-SNAPSHOT"
 
     application
-    id("org.jetbrains.dokka") version "1.9.20"
+    id("org.jetbrains.dokka") version "2.0.0"
     `java-library`
     `maven-publish`
     signing
@@ -74,8 +82,8 @@ dependencies {
 
     implementation("org.jetbrains.kotlin:kotlin-reflect:${kotlinVersion}")
     implementation("org.jetbrains.kotlin:kotlin-script-runtime:${kotlinVersion}")
-    implementation("org.jetbrains.kotlinx:kotlinx-coroutines-core:1.8.1")
-    implementation("org.jetbrains.kotlinx:kotlinx-serialization-json:1.2.2")
+    implementation("org.jetbrains.kotlinx:kotlinx-coroutines-core:1.10.2")
+    implementation("org.jetbrains.kotlinx:kotlinx-serialization-json:1.8.1")
 
     implementation("org.nield:kotlin-statistics:1.2.1")
     implementation("org.jetbrains.kotlinx:dataframe:0.8.0-rc-7")
@@ -91,18 +99,10 @@ dependencies {
     // https://kotlinlang.org/docs/reference/evolution/compatibility-modes.html
     // implementation("net.maizegenetics:tassel:5.2.60")
 
-    // Wide range of sequence tools in Java - API is dated
-    // implementation("org.biojava:biojava:5.3.0")
-    // implementation("org.biojava:biojava-genome:5.3.0")
-
-    implementation("org.graalvm.sdk:graal-sdk:21.2.0")
     implementation("org.apache.commons:commons-csv:1.8")
 
     implementation("com.google.guava:guava:33.1.0-jre")
-    implementation("org.apache.tinkerpop:gremlin-core:3.5.1")
-
 
-    implementation(group = "ch.qos.logback", name = "logback-classic", version = "1.2.6")
     implementation("it.unimi.dsi:fastutil:8.5.12")
     implementation("org.lz4:lz4-java:1.8.0")
 
@@ -120,12 +120,11 @@ dependencies {
 // kotlin.sourceSets.getByName("main").kotlin.srcDir("build/generated/ksp/main/kotlin/")
 
 java {
-    // withJavadocJar()
     withSourcesJar()
 }
 
 tasks.withType<KotlinCompile>().configureEach {
-    kotlinOptions.jvmTarget = "17"
+    compilerOptions.jvmTarget.set(JvmTarget.JVM_21)
 }
 
 tasks {
@@ -197,9 +196,7 @@ fun tutorialInjector() {
         .filter { it.toString().endsWith("package-list") }
         .findFirst()
 
-    val packageList = optionalPackageList.getOrNull()?.let {
-        it.toFile().readText()
-    } ?: ""
+    val packageList = optionalPackageList.getOrNull()?.toFile()?.readText() ?: ""
 
     //Replaces shorthand links with accurate ones and inserts links into code
     val linkFinder = Regex("<a href=\"\\..*?>")
@@ -359,7 +356,7 @@ fun recursivelyInjectImages(file: File, depth: Int) {
     }
 }
 
-val dokkaJar by tasks.creating(Jar::class) {
+val dokkaJar by tasks.registering(Jar::class) {
     dependsOn(dokkaHtml)
     mustRunAfter(dokkaHtml)
     group = JavaBasePlugin.DOCUMENTATION_GROUP

gradle/wrapper/gradle-wrapper.properties

@@ -1,6 +1,6 @@
 distributionBase=GRADLE_USER_HOME
 distributionPath=wrapper/dists
-distributionUrl=https\://services.gradle.org/distributions/gradle-8.7-bin.zip
+distributionUrl=https\://services.gradle.org/distributions/gradle-8.14.1-bin.zip
 networkTimeout=10000
 validateDistributionUrl=true
 zipStoreBase=GRADLE_USER_HOME

gradlew

@@ -15,6 +15,8 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 #
+# SPDX-License-Identifier: Apache-2.0
+#
 
 ##############################################################################
 #
@@ -55,7 +57,7 @@
 #       Darwin, MinGW, and NonStop.
 #
 #   (3) This script is generated from the Groovy template
-#       https://github.com/gradle/gradle/blob/HEAD/subprojects/plugins/src/main/resources/org/gradle/api/internal/plugins/unixStartScript.txt
+#       https://github.com/gradle/gradle/blob/HEAD/platforms/jvm/plugins-application/src/main/resources/org/gradle/api/internal/plugins/unixStartScript.txt
 #       within the Gradle project.
 #
 #       You can find Gradle at https://github.com/gradle/gradle/.
@@ -84,7 +86,7 @@ done
 # shellcheck disable=SC2034
 APP_BASE_NAME=${0##*/}
 # Discard cd standard output in case $CDPATH is set (https://github.com/gradle/gradle/issues/25036)
-APP_HOME=$( cd "${APP_HOME:-./}" > /dev/null && pwd -P ) || exit
+APP_HOME=$( cd -P "${APP_HOME:-./}" > /dev/null && printf '%s\n' "$PWD" ) || exit
 
 # Use the maximum available, or set MAX_FD != -1 to use that value.
 MAX_FD=maximum
@@ -112,7 +114,7 @@ case "$( uname )" in                #(
   NONSTOP* )        nonstop=true ;;
 esac
 
-CLASSPATH=$APP_HOME/gradle/wrapper/gradle-wrapper.jar
+CLASSPATH="\\\"\\\""
 
 
 # Determine the Java command to use to start the JVM.
@@ -203,15 +205,15 @@ fi
 DEFAULT_JVM_OPTS='"-Xmx64m" "-Xms64m"'
 
 # Collect all arguments for the java command:
-#   * DEFAULT_JVM_OPTS, JAVA_OPTS, JAVA_OPTS, and optsEnvironmentVar are not allowed to contain shell fragments,
+#   * DEFAULT_JVM_OPTS, JAVA_OPTS, and optsEnvironmentVar are not allowed to contain shell fragments,
 #     and any embedded shellness will be escaped.
 #   * For example: A user cannot expect ${Hostname} to be expanded, as it is an environment variable and will be
 #     treated as '${Hostname}' itself on the command line.
 
 set -- \
         "-Dorg.gradle.appname=$APP_BASE_NAME" \
         -classpath "$CLASSPATH" \
-        org.gradle.wrapper.GradleWrapperMain \
+        -jar "$APP_HOME/gradle/wrapper/gradle-wrapper.jar" \
         "$@"
 
 # Stop when "xargs" is not available.

gradlew.bat

@@ -13,6 +13,8 @@
 @rem See the License for the specific language governing permissions and
 @rem limitations under the License.
 @rem
+@rem SPDX-License-Identifier: Apache-2.0
+@rem
 
 @if "%DEBUG%"=="" @echo off
 @rem ##########################################################################
@@ -68,11 +70,11 @@ goto fail
 :execute
 @rem Setup the command line
 
-set CLASSPATH=%APP_HOME%\gradle\wrapper\gradle-wrapper.jar
+set CLASSPATH=
 
 
 @rem Execute Gradle
-"%JAVA_EXE%" %DEFAULT_JVM_OPTS% %JAVA_OPTS% %GRADLE_OPTS% "-Dorg.gradle.appname=%APP_BASE_NAME%" -classpath "%CLASSPATH%" org.gradle.wrapper.GradleWrapperMain %*
+"%JAVA_EXE%" %DEFAULT_JVM_OPTS% %JAVA_OPTS% %GRADLE_OPTS% "-Dorg.gradle.appname=%APP_BASE_NAME%" -classpath "%CLASSPATH%" -jar "%APP_HOME%\gradle\wrapper\gradle-wrapper.jar" %*
 
 :end
 @rem End local scope for the variables with windows NT shell