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Merge pull request #1 from maize-genetics/init-clikt-commands
Initial biokotlin-tools repository
2 parents df73c58 + c2f0901 commit decd5f6

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‎.github/workflows/run_deploy_on_merge.yml

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name: Run Deployment When Pushing to Master
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on:
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workflow_dispatch:
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push:
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branches:
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- main
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paths:
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- 'src/**'
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jobs:
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check-app-changes:
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runs-on: ubuntu-latest
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outputs:
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app_changed: ${{ steps.check_app_changes.outputs.app_changed }}
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steps:
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- name: Checkout repo
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uses: actions/checkout@v3
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with:
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token: ${{secrets.BIOKOTLINTOOLSCD}}
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fetch-depth: 0
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- name: Check if app directory changed
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id: check_app_changes
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run: |
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LAST_RELEASE_TAG=$(git describe --tags $(git rev-list --tags --max-count=1))
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echo "LAST_RELEASE_TAG was $LAST_RELEASE_TAG"
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LAST_RELEASE_COMMIT=$(git rev-list -n 1 $LAST_RELEASE_TAG)
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echo "LAST_RELEASE_COMMIT was $LAST_RELEASE_COMMIT"
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changed_files=$(git diff-tree --no-commit-id --name-only $LAST_RELEASE_COMMIT $GITHUB_SHA | grep '^src' || echo "none")
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echo "Changed app files: $changed_files"
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if [ "$changed_files" != "none" ]; then
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echo "App directory has changed since the last release."
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echo "app_changed=true" >> "$GITHUB_OUTPUT"
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else
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echo "App directory hasn't changed since the last release."
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echo "app_changed=false" >> "$GITHUB_OUTPUT"
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fi
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build-and-release:
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runs-on: ubuntu-latest
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needs: check-app-changes
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if: ${{ needs.check-app-changes.outputs.app_changed == 'true' }}
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steps:
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- name: Checkout repo
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uses: actions/checkout@v3
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with:
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token: ${{secrets.BIOKOTLINTOOLSCD}}
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- name: Setup Miniconda
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uses: conda-incubator/setup-miniconda@v2
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with:
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auto-activate-base: true
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activate-environment: ""
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miniconda-version: "latest"
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# Uses semantic commits to automate version bumping.
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# No scope or "fix:" = PATCH, "feat:" or "minor:" = MINOR, "BREAKING CHANGE:", "major:", or fix/feat with appended "!" = MAJOR
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# Additional details: https://www.conventionalcommits.org/en/v1.0.0/
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- name: Increment version
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run: |
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#!/bin/bash
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COMMIT_MSG=$(git log -1 --pretty=format:"%b" || git log -1 --pretty=format:"%B")
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source version.properties
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BUMP_TYPE="patchVersion"
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if [[ $COMMIT_MSG == *"BREAKING CHANGE"* || $COMMIT_MSG == *"!"* || $COMMIT_MSG == *"major:"* ]]; then
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majorVersion=$((majorVersion + 1))
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minorVersion=0
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patchVersion=0
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BUMP_TYPE="majorVersion"
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elif [[ $COMMIT_MSG == *"feat:"* || $COMMIT_MSG == *"minor:"* ]]; then
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minorVersion=$((minorVersion + 1))
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patchVersion=0
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BUMP_TYPE="minorVersion"
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else
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patchVersion=$((patchVersion + 1))
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fi
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echo "majorVersion=$majorVersion" > version.properties
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echo "minorVersion=$minorVersion" >> version.properties
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echo "patchVersion=$patchVersion" >> version.properties
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VERSION=$majorVersion.$minorVersion.$patchVersion
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RELEASE=$majorVersion.$minorVersion
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echo "COMMIT_MSG=$COMMIT_MSG" >> $GITHUB_ENV
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echo "VERSION=$VERSION" >> $GITHUB_ENV
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echo "RELEASE=$RELEASE" >> $GITHUB_ENV
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echo "BUMP_TYPE=$BUMP_TYPE" >> $GITHUB_ENV
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- name: Commit version changes
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uses: EndBug/add-and-commit@v7
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with:
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add: 'version.properties'
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message: Bump ${{ env.BUMP_TYPE }}
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author_email: [email protected]
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author_name: Git Action Bot
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- name: Push changes
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uses: ad-m/github-push-action@master
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with:
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github_token: ${{ secrets.GITHUB_TOKEN }}
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branch: ${{ github.ref }}
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- name: Set up JDK 17
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uses: actions/setup-java@v3
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with:
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distribution: temurin
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java-version: '17'
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cache: 'gradle'
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- name: Update applications.conf
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run: src/scripts/update_applications_conf.sh
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- name: Make gradlew executable
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run: chmod +x ./gradlew
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- name: Build BioKotlin Tools
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run: ./gradlew clean build --no-daemon
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- name: Get matching release
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uses: cardinalby/[email protected]
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id: matching_release
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env:
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GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
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with:
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releaseName: v${{ env.RELEASE }}
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doNotFailIfNotFound: 'true'
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- name: Delete matching release if exists
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if: steps.matching_release.outputs.id != ''
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run: |
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curl -X DELETE -H "Authorization: token ${{ secrets.GITHUB_TOKEN }}" "https://api.github.com/repos/${{ github.repository }}/releases/${{ steps.matching_release.outputs.id}}"
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# Updates the latest release if just a new patch, drafts a new prerelease if major or minor version has changed
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- name: Make github release
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uses: svenstaro/upload-release-action@v2
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with:
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repo_token: ${{ secrets.GITHUB_TOKEN }}
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release_name: v${{ env.RELEASE }}
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tag: ${{ env.VERSION }}
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file: build/distributions/biokotlin-tools.tar
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asset_name: BioKotlinTools-v${{ env.RELEASE }}.tar
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overwrite: ${{ env.BUMP_TYPE == 'patchVersion' }}
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prerelease: ${{ env.BUMP_TYPE != 'patchVersion' }}
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body: |
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${{ steps.matching_release.outputs.body }}
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${{ env.COMMIT_MSG }}
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‎build.gradle.kts

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import org.jetbrains.kotlin.gradle.tasks.KotlinCompile
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// Note Kotlin version needs to be updated in both the buildscript and plugins.
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// Dependencies will follow the buildscript
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group = "org.biokotlin"
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// This build script is need to use the early access
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buildscript {
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val kotlinVersion by extra("1.9.24")
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repositories {
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mavenCentral()
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gradlePluginPortal()
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}
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dependencies {
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classpath("org.jetbrains.kotlin:kotlin-gradle-plugin:$kotlinVersion")
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classpath(kotlin("serialization", version = kotlinVersion))
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}
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}
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plugins {
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val kotlinVersion = "1.9.24"
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java
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kotlin("jvm") version kotlinVersion
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kotlin("plugin.serialization") version kotlinVersion
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// Shadow allows for the creation of fat jars (all dependencies)
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id("com.github.johnrengelman.shadow") version "8.1.1"
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application
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`java-library`
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}
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apply {
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plugin("kotlinx-serialization")
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}
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repositories {
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mavenCentral()
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gradlePluginPortal()
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maven("https://maven.imagej.net/content/groups/public/")
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maven("https://jitpack.io")
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maven("https://dl.bintray.com/kotlin/kotlin-eap")
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maven("https://kotlin.bintray.com/kotlinx")
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}
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dependencies {
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val kotlinVersion = rootProject.extra["kotlinVersion"]
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implementation("org.biokotlin:biokotlin:0.18")
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implementation("org.apache.logging.log4j:log4j-core:2.23.1")
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implementation("org.apache.logging.log4j:log4j-api:2.23.1")
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implementation("com.github.ajalt.clikt:clikt:4.2.2")
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implementation("org.jetbrains.kotlin:kotlin-reflect:${kotlinVersion}")
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implementation("org.jetbrains.kotlin:kotlin-script-runtime:${kotlinVersion}")
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implementation("org.jetbrains.kotlinx:kotlinx-coroutines-core:1.8.1")
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implementation("org.jetbrains.kotlinx:kotlinx-serialization-json:1.2.2")
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implementation("org.nield:kotlin-statistics:1.2.1")
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implementation("com.github.holgerbrandl:krangl:0.18")
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implementation("org.jetbrains.kotlinx:dataframe:0.8.0-rc-7")
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// Biology possible dependencies
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// Support fasta, bam, sam, vcf, bcf support
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implementation("com.github.samtools:htsjdk:4.0.1")
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implementation("org.graalvm.sdk:graal-sdk:21.2.0")
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implementation("org.apache.commons:commons-csv:1.8")
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implementation("com.google.guava:guava:33.1.0-jre")
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implementation("org.apache.tinkerpop:gremlin-core:3.5.1")
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implementation("org.jgrapht:jgrapht-core:1.5.1")
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implementation("io.github.oshai:kotlin-logging-jvm:5.0.0")
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implementation(group = "ch.qos.logback", name = "logback-classic", version = "1.2.6")
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implementation("it.unimi.dsi:fastutil:8.5.12")
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implementation("org.lz4:lz4-java:1.8.0")
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testImplementation("org.junit.jupiter:junit-jupiter:5.8.0")
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val kotestVersion = "5.6.2"
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listOf("runner-junit5", "assertions-core", "property", "framework-datatest").forEach {
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testImplementation("io.kotest:kotest-$it-jvm:$kotestVersion")
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}
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}
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// include versions.properties file in jar file
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tasks.jar {
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from(sourceSets.main.get().output)
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from(projectDir) {
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include("version.properties")
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}
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}
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java {
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withSourcesJar()
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}
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tasks.withType<KotlinCompile>().configureEach {
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kotlinOptions.jvmTarget = "17"
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}
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tasks {
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println("Source directories: ${sourceSets["main"].allSource.srcDirs}")
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}
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application {
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mainClass.set("biokotlin.cli.BiokotlinToolsKt")
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// Set name of generated scripts in bin/
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applicationName = "biokotlin-tools"
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}
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tasks.test {
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useJUnitPlatform()
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testLogging {
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events("passed", "skipped", "failed")
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}
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}
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tasks.jar {
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from(sourceSets.main.get().output)
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}

‎gradle/wrapper/gradle-wrapper.jar

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‎gradle/wrapper/gradle-wrapper.properties

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distributionBase=GRADLE_USER_HOME
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distributionPath=wrapper/dists
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distributionUrl=https\://services.gradle.org/distributions/gradle-8.9-bin.zip
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networkTimeout=10000
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validateDistributionUrl=true
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zipStoreBase=GRADLE_USER_HOME
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zipStorePath=wrapper/dists

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