binaries.yml

name: Binaries

on:
  push:
    branches:
      - main
      - main-release
    paths-ignore:
      - 'docs/**'
      - 'src/test/**'
      - 'README.md'
    tags:
      - '*'
  pull_request:
    types:
      - opened
      - synchronize
      - reopened
      - labeled
  merge_group:
  workflow_dispatch:
    inputs:
      jvmDistribution:
        description: "JDK distribution (setup-java)"
        type: choice
        default: corretto
        options:
          # These are the distributions listed at https://github.com/actions/setup-java/blob/main/README.md#supported-distributions
          - adopt
          - adopt-openj9
          - corretto
          - dragonwell
          - graalvm
          - jetbrains
          - liberica
          - microsoft
          - oracle
          - sapmachine
          - semeru
          - temurin
          - zulu
      jvmVendor:
        description: "JDK vendor (gradle toolchain)"
        type: choice
        default: AMAZON
        options:
          # These are the vendors listed at https://docs.gradle.org/current/javadoc/org/gradle/jvm/toolchain/JvmVendorSpec.html
          - ADOPTIUM
          - ADOPTOPENJDK
          - AMAZON
          - APPLE
          - AZUL
          - BELLSOFT
          - GRAAL_VM
          - HEWLETT_PACKARD
          - IBM
          - JETBRAINS
          - MICROSOFT
          - ORACLE
          - SAP
          - TENCENT
      useEaJdk:
        description: "Use early-access JDK and JavaFX"
        type: boolean
        required: false
        default: false
      jdkVersion:
        description: "JDK EA version (used for gradle)"
        type: number
        required: false
        default: 26
      jdkVersionFlavour:
        description: "JDK EA flavour (used for oracle-actions/setup-java)"
        type: choice
        required: false
        default: stable
        options:
          # use the next JDK
          - stable
          # use the next-next JDK
          - latest
      javafxVersion:
        description: "JavaFX EA"
        type: string
        required: false
        default: "26-ea+22"
      notarization:
        description: "Notarize macOS DMG and PKG"
        type: boolean
        required: false
        default: false
      upload:
        description: "Upload to builds.jabref.org"
        type: boolean
        required: false
        default: false
      upload-as-artifact:
        description: "Upload to GitHub artifacts store"
        type: boolean
        required: false
        default: true

permissions:
  actions: write
  contents: read
  pull-requests: write

env:
  GRADLE_OPTS: -Xmx4g -Dorg.gradle.vfs.watch=false
  JAVA_OPTS: -Xmx4g

  # API keys
  AstrophysicsDataSystemAPIKey: ${{ secrets.AstrophysicsDataSystemAPIKey }}
  BiodiversityHeritageApiKey: ${{ secrets.BiodiversityHeritageApiKey}}
  IEEEAPIKey: ${{ secrets.IEEEAPIKey }}
  SpringerNatureAPIKey: ${{ secrets.SpringerNatureAPIKey }}


concurrency:
  group: "${{ github.workflow }}-${{ github.head_ref || github.ref }}-${{ github.event_name }}-${{ github.event.inputs.useEaJdk }}-${{ github.event.inputs.jdkVersion }}-${{ github.event.inputs.jdkVersionFlavour }}-${{ github.event.inputs.javafxVersion }}"
  cancel-in-progress: true

jobs:
  conditions:
    # Dependency updates should only run in the main repo
    if: ${{ github.repository == 'JabRef/jabref' || github.actor != 'dependabot[bot]' || github.ref_name != 'main' }}
    runs-on: ubuntu-slim
    outputs:
      upload-to-builds-jabref-org: ${{ steps.binary.outputs.upload-to-builds-jabref-org }}
      secretspresent: ${{ steps.binary.outputs.secretspresent }}
      tagbuild: ${{ steps.binary.outputs.tagbuild }}
      # required to avoid obsolete builds in case of labels != "dev: binaries"
      should-build: ${{ steps.binary.outputs.should-build }}
      should-jbundle: ${{ steps.binary.outputs.should-jbundle }}
      should-notarize: ${{ steps.binary.outputs.should-notarize }}
      jvmDistribution:  ${{ steps.binary.outputs.jvmDistribution }}
      useEaJdk:  ${{ steps.binary.outputs.useEaJdk }}
      jdkVersion: ${{ steps.binary.outputs.jdkVersion }}
      jdkVersionFlavour: ${{ steps.binary.outputs.jdkVersionFlavour }}
      javafxVersion: ${{ steps.binary.outputs.javafxVersion }}
    steps:
      - uses: awalsh128/cache-apt-pkgs-action@latest
        with:
          packages: jq
          version: 1.0
      - name: Determine conditions
        id: binary
        shell: bash
        env:
          BUILDJABREFPRIVATEKEY: ${{ secrets.buildJabRefPrivateKey }}
          GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
          EVENT_NAME: ${{ github.event_name }}
          LABEL_NAME: ${{ github.event.label.name }}
          REPO_OWNER: ${{ github.repository_owner }}
        run: |
          set -euo pipefail
          set -x
          PS4='+ ${LINENO}: '

          if [[ "$EVENT_NAME" != "labeled" || "$LABEL_NAME" == "automerge"  || "$LABEL_NAME" == "dev: binaries" ]]; then
            echo "📦 build enabled"
            echo "📦 build enabled" >> $GITHUB_STEP_SUMMARY
            echo "should-build=true" >> "$GITHUB_OUTPUT"
          else
            echo "⊘ build should be skipped"
            echo "⊘ build should be skipped" >> $GITHUB_STEP_SUMMARY
            echo "should-build=false" >> "$GITHUB_OUTPUT"
            exit 0
          fi

          if [[ "${{ github.event.inputs.useEaJdk || 'false' }}" == "true" ]]; then
            echo "🚀 JDK EA build enabled"
            echo "🚀 JDK EA build enabled" >> "$GITHUB_STEP_SUMMARY"

            echo "JDK EA version: ${{ github.event.inputs.jdkVersion }}"
            echo "JDK EA version: ${{ github.event.inputs.jdkVersion }}" >> "$GITHUB_STEP_SUMMARY"

            echo "JDK EA flavour: ${{ github.event.inputs.jdkVersionFlavour }}"
            echo "JDK EA flavour: ${{ github.event.inputs.jdkVersionFlavour }}" >> "$GITHUB_STEP_SUMMARY"

            echo "JavaFX version: ${{ github.event.inputs.javafxVersion }}"
            echo "JavaFX version: ${{ github.event.inputs.javafxVersion }}" >> "$GITHUB_STEP_SUMMARY"

            echo "useEaJdk=true" >> "$GITHUB_OUTPUT"
          else
            echo "🛡️ JDK stable version used"
            echo "🛡️ JDK stable version used" >> "$GITHUB_STEP_SUMMARY"
            echo "useEaJdk=false" >> "$GITHUB_OUTPUT"
            echo "JVM vendor: ${{ github.event.inputs.jvmVendor || '(unset)' }}"
            echo "JVM vendor: ${{ github.event.inputs.jvmVendor || '(unset)' }}" >> "$GITHUB_STEP_SUMMARY"
          fi

          # The distribution to use at setup-java
          echo "JVM distribution: ${{ github.event.inputs.jvmDistribution || 'corretto' }}"
          echo "jvmDistribution=${{ github.event.inputs.jvmDistribution || 'corretto' }}" >> "$GITHUB_OUTPUT"

          # Enable testing of EA JDKs later even if not triggered by workflow dispatch.
          # One needs to set "useEaJdk=true" above even at the stable case to enable this.
          echo "jdkVersion=${{ github.event.inputs.jdkVersion || '26' }}" >> "$GITHUB_OUTPUT"
          echo "jdkVersionFlavour=${{ github.event.inputs.jdkVersionFlavour || 'stable' }}" >> "$GITHUB_OUTPUT"
          echo "javafxVersion=${{ github.event.inputs.javafxVersion || '26-ea+22' }}" >> "$GITHUB_OUTPUT"

          if [ -z "$BUILDJABREFPRIVATEKEY" ]; then
            echo "⊘ Secret BUILDJABREFPRIVATEKEY not present – skipping upload"
            echo "⊘ Secret BUILDJABREFPRIVATEKEY not present – skipping upload"
            echo "upload-to-builds-jabref-org=false" >> "$GITHUB_OUTPUT"
            echo "secretspresent=false" >> "$GITHUB_OUTPUT"
            exit 0
          fi
          echo "secretspresent=true" >> "$GITHUB_OUTPUT"

          if [[ "$GITHUB_REF" == refs/heads/gh-readonly-queue* ]]; then
            echo "⊘ merge queue – skipping upload"
            echo "⊘ merge queue – skipping upload" >> $GITHUB_STEP_SUMMARY
            echo "upload-to-builds-jabref-org=false" >> "$GITHUB_OUTPUT"
            exit 0
          fi

          if [[ "${GITHUB_REF}" == refs/tags/* ]]; then
            echo "🏷️ tag build" >> $GITHUB_STEP_SUMMARY
            echo "tagbuild=true" >> "$GITHUB_OUTPUT"
            echo "🧰 jbundle build" >> $GITHUB_STEP_SUMMARY
            echo "should-jbundle=true" >> "$GITHUB_OUTPUT"
          else
            echo "⊘ no tag bulid" >> $GITHUB_STEP_SUMMARY
            echo "tagbuild=false" >> "$GITHUB_OUTPUT"
          fi

          if [[ "${GITHUB_REF}" == refs/tags/* ]] || [[ "${GITHUB_REF}" == "refs/heads/main-release" ]] || [[ "${{ inputs.notarization }}" == "true" ]]; then
            # This workflow runs on ubuntu-latest even for notarization for macOS; need to check later if really on macOS
            echo "🧾 macOS notarization"
            echo "🧾 macOS notarization" >> $GITHUB_STEP_SUMMARY
            echo "should-notarize=true" >> "$GITHUB_OUTPUT"
            if [[ "${GITHUB_REF}" == refs/tags/* || ( "${{ github.event_name }}" == "push" && ("${{ github.ref_name }}" == "main" || "${{ github.ref_name }}" == "main-release") ) ]]; then
              echo "☁️ will upload"
              echo "☁️ will upload" >> $GITHUB_STEP_SUMMARY
              echo "upload-to-builds-jabref-org=true" >> "$GITHUB_OUTPUT"
              exit 0;
            fi;
            echo "☁️ Non-PR event – will upload: ${{ github.event.inputs.upload || 'false' }}"
            echo "☁️ Non-PR event – will upload: ${{ github.event.inputs.upload || 'false' }}" >> $GITHUB_STEP_SUMMARY
            echo "upload-to-builds-jabref-org=${{ github.event.inputs.upload || 'false' }}" >> "$GITHUB_OUTPUT"
            exit 0
          fi

          echo "⊘ no macOS notarization"
          echo "⊘ no macOS notarization" >> $GITHUB_STEP_SUMMARY
          echo "should-notarize=false" >> "$GITHUB_OUTPUT"

          if [[ "${{ github.event_name }}" == "push" ]]; then
            if [[ "${{ github.ref_name }}" == "main" ]]; then
              echo "☁️ Push to \`main\` – will upload"
              echo "☁️ Push to \`main\` – will upload" >> $GITHUB_STEP_SUMMARY
              echo "upload-to-builds-jabref-org=true" >> "$GITHUB_OUTPUT"
              echo "🧰 jbundle build" >> $GITHUB_STEP_SUMMARY
              echo "should-jbundle=true" >> "$GITHUB_OUTPUT"
              exit 0
            fi;
            echo "⊘ Push to some branch not main – skipping upload"
            echo "⊘ Push to some branch not main – skipping upload" >> $GITHUB_STEP_SUMMARY
            echo "upload-to-builds-jabref-org=false" >> "$GITHUB_OUTPUT"
            echo "🚫🧰 no jbundle build" >> $GITHUB_STEP_SUMMARY
            echo "should-jbundle=false" >> "$GITHUB_OUTPUT"
            exit 0
          fi;

          if [[ "${{ github.event_name }}" == "workflow_dispatch" ]]; then
            echo "☁️? Dispatch event – will upload: ${{ github.event.inputs.upload || 'false' }}"
            echo "☁️= Dispatch event – will upload: ${{ github.event.inputs.upload || 'false' }}" >> $GITHUB_STEP_SUMMARY
            echo "upload-to-builds-jabref-org=${{ github.event.inputs.upload || 'false' }}" >> "$GITHUB_OUTPUT"
            echo "should-jbundle=${{ github.event.inputs.upload || 'false' }}" >> "$GITHUB_OUTPUT"
            exit 0
          fi

          LABELS=$(gh api repos/${{ github.repository }}/issues/${{ github.event.pull_request.number }}/labels --jq '.[].name')

          if echo "$LABELS" | grep -q "^dev: binaries$"; then
            echo "☁️ Label 'dev: binaries' found – will upload"
            echo "☁️ Label 'dev: binaries' found – will upload" >> $GITHUB_STEP_SUMMARY
            echo "upload-to-builds-jabref-org=true" >> "$GITHUB_OUTPUT"
            echo "🧰 jbundle build" >> $GITHUB_STEP_SUMMARY
            echo "should-jbundle=true" >> "$GITHUB_OUTPUT"
          else
            echo "⊘ Label 'dev: binaries' not found – skipping upload"
            echo "⊘ Label 'dev: binaries' not found – skipping upload" >> $GITHUB_STEP_SUMMARY
            echo "upload-to-builds-jabref-org=false" >> "$GITHUB_OUTPUT"
            echo "🚫🧰 no jbundle build" >> $GITHUB_STEP_SUMMARY
            echo "should-jbundle=false" >> "$GITHUB_OUTPUT"
          fi

  disk-space-check:
    needs: conditions
    runs-on: ubuntu-slim
    outputs:
      available: ${{ steps.diskspace.outputs.available }}
    steps:
      - name: No upload
        if: needs.conditions.outputs.upload-to-builds-jabref-org == 'false'
        shell: bash
        run: |
          echo "⊘ no upload – skipping upload"
          echo "⊘ no upload – skipping upload" >> $GITHUB_STEP_SUMMARY
          echo "available=false" >> "$GITHUB_OUTPUT"
      - name: Setup SSH key
        if: needs.conditions.outputs.upload-to-builds-jabref-org == 'true'
        run: |
          echo "${{ secrets.buildJabRefPrivateKey }}" > sshkey
          chmod 600 sshkey
      - name: Check disk space on builds.jabref.org
        if: needs.conditions.outputs.upload-to-builds-jabref-org == 'true'
        id: diskspace
        shell: bash
        run: |
          PR_NUMBER="${{ github.event.pull_request.number }}"
          if [[ -z "$PR_NUMBER" ]]; then
            echo "☁️ Not a pull request event – skipping disk space check – will upload"
            echo "☁️ Not a pull request event – skipping disk space check – will upload" >> $GITHUB_STEP_SUMMARY
            echo "available=true" >> "$GITHUB_OUTPUT"
            exit 0
          fi

          TARGET="/var/www/builds.jabref.org/www/pull-$PR_NUMBER"
          SSH_OPTS="-p 9922 -i sshkey -o StrictHostKeyChecking=no"
          HOST="jrrsync@build-upload.jabref.org"
          if ssh $SSH_OPTS "$HOST" "test -d '$TARGET'"; then
            echo "☁️ Target exists: $TARGET - will upload"
            echo "☁️ Target exists: $TARGET - will upload" >> $GITHUB_STEP_SUMMARY
            echo "available=true" >> "$GITHUB_OUTPUT"
            exit 0
          fi

          echo "🤔 Target does not exist: $TARGET"
          echo "🤔 Target does not exist: $TARGET" >> $GITHUB_STEP_SUMMARY

          USAGE=$(ssh -p 9922 -i sshkey -o StrictHostKeyChecking=no jrrsync@build-upload.jabref.org \
            "df --output=pcent /var/www/builds.jabref.org | tail -n1 | tr -dc '0-9'")
          echo "Remote usage: ${USAGE}%"
          echo "Remote usage: ${USAGE}%" >> $GITHUB_STEP_SUMMARY

          if [ "$USAGE" -lt 80 ]; then
            echo "☁️ enough disk space available – will upload"
            echo "☁️ enough disk space available – will upload" >> $GITHUB_STEP_SUMMARY
            echo "available=true" >> "$GITHUB_OUTPUT"
          else
            echo "⛔ not enough disk space – skipping upload"
            echo "⛔ not enough disk space – skipping upload" >> $GITHUB_STEP_SUMMARY
            echo "available=false" >> "$GITHUB_OUTPUT"
          fi

  compute-matrix:
    needs: conditions
    runs-on: ubuntu-slim
    outputs:
      matrix: ${{ steps.set.outputs.matrix }}
    steps:
      - id: set
        name: Compute Matrix
        shell: bash
        env:
          SHOULD_NOTARIZE: ${{ needs.conditions.outputs.should-notarize }}
        run: |
          # if you change the os version rename all other occurrences
          # ./gradlew on Windows is because of https://github.com/gradle/gradle/pull/34227
          MATRIX_JSON='{
            "include": [
              {
                "os": "ubuntu-22.04",
                "displayName": "linux-amd64",
                "gradleCommand": "gradle",
                "archivePortable": "tar -c -C jabgui/build/packages/ubuntu-22.04 JabRef | pigz --rsyncable > jabgui/build/packages/ubuntu-22.04/JabRef-portable_linux.tar.gz && rm -R jabgui/build/packages/ubuntu-22.04/JabRef",
                "archivePortableJabKit": "tar -c -C jabkit/build/packages/ubuntu-22.04 jabkit | pigz --rsyncable > jabkit/build/packages/ubuntu-22.04/jabkit-portable_linux.tar.gz && rm -R jabkit/build/packages/ubuntu-22.04/jabkit",
                "archivePortableJabLS": "tar -c -C jabls-cli/build/packages/ubuntu-22.04 jabls | pigz --rsyncable > jabls-cli/build/packages/ubuntu-22.04/jabls-portable_linux.tar.gz && rm -R jabls-cli/build/packages/ubuntu-22.04/jabls",
                "suffix": "",
                "archForDebianRepack": "_amd64"
              },
              {
                "os": "ubuntu-22.04-arm",
                "displayName": "linux-arm",
                "gradleCommand": "gradle",
                "archivePortable": "tar -c -C jabgui/build/packages/ubuntu-22.04-arm JabRef | pigz --rsyncable > jabgui/build/packages/ubuntu-22.04-arm/JabRef-portable_linux_arm64.tar.gz && rm -R jabgui/build/packages/ubuntu-22.04-arm/JabRef",
                "archivePortableJabKit": "tar -c -C jabkit/build/packages/ubuntu-22.04-arm jabkit | pigz --rsyncable > jabkit/build/packages/ubuntu-22.04-arm/jabkit-portable_linux_arm64.tar.gz && rm -R jabkit/build/packages/ubuntu-22.04-arm/jabkit",
                "archivePortableJabLS": "tar -c -C jabls-cli/build/packages/ubuntu-22.04-arm jabls | pigz --rsyncable > jabls-cli/build/packages/ubuntu-22.04-arm/jabls-portable_linux_arm64.tar.gz && rm -R jabls-cli/build/packages/ubuntu-22.04-arm/jabls",
                "suffix": "_arm64",
                "archForDebianRepack": "_arm64"
              },
              {
                "os": "windows-latest",
                "displayName": "windows-amd64",
                "gradleCommand": "./gradlew",
                "archivePortable": "7z a -r jabgui/build/packages/windows-latest/JabRef-portable_windows.zip ./jabgui/build/packages/windows-latest/JabRef && rm -R jabgui/build/packages/windows-latest/JabRef",
                "archivePortableJabKit": "7z a -r jabkit/build/packages/windows-latest/jabkit-portable_windows.zip ./jabkit/build/packages/windows-latest/jabkit && rm -R jabkit/build/packages/windows-latest/jabkit",
                "archivePortableJabLS": "7z a -r jabls-cli/build/packages/windows-latest/jabls-portable_windows.zip ./jabls-cli/build/packages/windows-latest/jabls && rm -R jabls-cli/build/packages/windows-latest/jabls",
                "suffix": "",
                "archForDebianRepack": ""
              },
              {
                "os": "macos-15-intel",
                "displayName": "macOS-intel",
                "gradleCommand": "./gradlew",
                "archivePortable": "7z a -r jabgui/build/packages/macos-15-intel/JabRef-portable_macos-intel.zip ./jabgui/build/packages/macos-15-intel/JabRef.app && rm -R jabgui/build/packages/macos-15-intel/JabRef.app",
                "archivePortableJabKit": "7z a -r jabkit/build/packages/macos-15-intel/jabkit-portable_macos-intel.zip ./jabkit/build/packages/macos-15-intel/jabkit.app && rm -R jabkit/build/packages/macos-15-intel/jabkit.app",
                "archivePortableJabLS": "7z a -r jabls-cli/build/packages/macos-15-intel/jabls-portable_macos-intel.zip ./jabls-cli/build/packages/macos-15-intel/jabls.app && rm -R jabls-cli/build/packages/macos-15-intel/jabls.app",
                "suffix": "_intel",
                "archForDebianRepack": ""
              },
              {
                "os": "macos-15",
                "displayName": "macOS-silicon",
                "gradleCommand": "./gradlew",
                "archivePortable": "7z a -r jabgui/build/packages/macos-15/JabRef-portable_macos-silicon.zip ./jabgui/build/packages/macos-15/JabRef.app && rm -R jabgui/build/packages/macos-15/JabRef.app",
                "archivePortableJabKit": "7z a -r jabkit/build/packages/macos-15/jabkit-portable_macos-silicon.zip ./jabkit/build/packages/macos-15/jabkit.app && rm -R jabkit/build/packages/macos-15/jabkit.app",
                "archivePortableJabLS": "7z a -r jabls-cli/build/packages/macos-15/jabls-portable_macos-silicon.zip ./jabls-cli/build/packages/macos-15/jabls.app && rm -R jabls-cli/build/packages/macos-15/jabls.app",
                "suffix": "_silicon",
                "archForDebianRepack": ""
              }
            ]
          }'

          if [[ "$GITHUB_REF" != "refs/heads/main" && "$SHOULD_NOTARIZE" != "true" ]]; then
            # drop macos-15-intel
            MATRIX_JSON="$(jq -c ' .include |= map(select(.os != "macos-15-intel")) ' <<<"$MATRIX_JSON")"
          else
            # Format into one line for output, otherwise it cannot be used as matrix output
            MATRIX_JSON="$(jq -c . <<<"$MATRIX_JSON")"
          fi

          echo "matrix=$MATRIX_JSON" >> "$GITHUB_OUTPUT"

  build:
    needs: [ compute-matrix, conditions, disk-space-check ]
    if: ${{ needs.conditions.outputs.should-build == 'true' }}
    strategy:
      fail-fast: false
      matrix:
        ${{ fromJSON(needs.compute-matrix.outputs.matrix) }}
    runs-on: ${{ matrix.os }}
    outputs:
      major: ${{ steps.gitversion.outputs.Major }}
      minor: ${{ steps.gitversion.outputs.Minor }}
      branchname: ${{ steps.normalize.outputs.branch }}
      url: ${{ steps.url.outputs.url }}
    name: ${{ matrix.displayName }} installer and portable version
    steps:
      - name: Fetch all history for all tags and branches
        uses: actions/checkout@v6
        with:
          fetch-depth: 0
          submodules: 'true'
          show-progress: 'false'

      - name: Install GitVersion
        id: pre-gitversion
        # background: true
        uses: gittools/actions/gitversion/setup@v3.2.1
        with:
          versionSpec: "5.x"
      - name: Run GitVersion
        # wait: pre-gitversion
        # background: true
        id: gitversion
        uses: gittools/actions/gitversion/execute@v3.2.1

      - name: Setup SSH key
        if: ${{ needs.disk-space-check.outputs.available == 'true' }}
        run: |
          echo "${{ secrets.buildJabRefPrivateKey }}" > sshkey
          chmod 600 sshkey
      - name: Setup rsync (macOS)
        if: ${{ (needs.disk-space-check.outputs.available == 'true') && (startsWith(matrix.os, 'macos')) }}
        run: brew install rsync
      - name: Setup rsync (Windows)
        if: ${{ (needs.disk-space-check.outputs.available == 'true') && (matrix.os == 'windows-latest') }}
        # We want to have rsync available at this place to avoid uploading and downloading from GitHub artifact store (taking > 5 minutes in total)
        # We cannot use "action-rsyncer", because that requires Docker which is unavailable on Windows
        # We cannot use "setup-rsync", because that does not work on Windows
        # We do not use egor-tensin/setup-cygwin@v4, because it replaces the default shell
        # We need to use v6.4.4 as v6.4.5 misses "lib\rsync\tools\bin\ssh.exe"
        run: choco install rsync --version=6.4.4

      - name: Patch used JDK
        if: ${{ github.event_name == 'workflow_dispatch' && inputs.jvmVendor != 'AMAZON' }}
        shell: bash
        run: |
          set -ex
          PS4='+$LINENO: '
          SED_I=(-i)
          [[ '${{ startsWith(matrix.os, 'macos') }}' == 'true' ]] && SED_I=(-i '')
          sed "${SED_I[@]}" "s/AMAZON/${{ inputs.jvmVendor }}/" build-logic/src/main/kotlin/org.jabref.gradle.feature.compile.gradle.kts
          cat build-logic/src/main/kotlin/org.jabref.gradle.feature.compile.gradle.kts

      # Setup JDK EA and JavaFX EA
      - name: Set up latest JDK EA from jdk.java.net
        if: ${{ needs.conditions.outputs.useEaJdk == 'true' }}
        uses: oracle-actions/setup-java@v1
        with:
          website: jdk.java.net
          release: EA
          version: ${{ needs.conditions.outputs.jdkVersionFlavour }}
      - name: Tell gradle to use JDK EA and JavaFX EA
        if: ${{ needs.conditions.outputs.useEaJdk == 'true' }}
        shell: bash
        run: |
          set -ex
          PS4='+$LINENO: '
          SED_I=(-i)
          [[ '${{ startsWith(matrix.os, 'macos') }}' == 'true' ]] && SED_I=(-i '')

          sed "${SED_I[@]}" "s/JavaLanguageVersion.of(25)/JavaLanguageVersion.of(${{ needs.conditions.outputs.jdkVersion }})/" build-logic/src/main/kotlin/org.jabref.gradle.feature.compile.gradle.kts
          sed "${SED_I[@]}" "s/AMAZON/ORACLE/" build-logic/src/main/kotlin/org.jabref.gradle.feature.compile.gradle.kts
          sed "${SED_I[@]}" "s|val javafx = .*|val javafx = \"${{ needs.conditions.outputs.javafxVersion }}\"|" versions/build.gradle.kts

      - uses: ./.github/actions/setup-gradle
        with:
          distribution: ${{ needs.conditions.outputs.jvmDistribution }}
      - name: Output current Java environment
        shell: bash
        run: |
          set -x
          echo $PATH
          echo $JAVA_HOME
          java -version
          java -version >> $GITHUB_STEP_SUMMARY
          javac -version
          which jlink
          jlink --version

      - name: Normalize branch name
        id: normalize
        # wait: gitversion
        shell: bash
        run: |
          branch="${{ steps.gitversion.outputs.EscapedBranchName }}"
          branch="${branch%-merge}"   # removes suffix only if present

          if [[ "$branch" == tag* ]]; then
            # tag builds go into a sub folder
            branch="${{ steps.gitversion.outputs.BranchName }}"
          fi

          echo "branch=$branch" >> "$GITHUB_OUTPUT"
      - name: Output URL
        if: ${{ needs.disk-space-check.outputs.available == 'true' }}
        shell: bash
        id: url
        run: |
          echo "Link: https://builds.jabref.org/${{ steps.normalize.outputs.branch }}/"
          echo "Link: <https://builds.jabref.org/${{ steps.normalize.outputs.branch }}/>" >> $GITHUB_STEP_SUMMARY
          echo "url=https://builds.jabref.org/${{ steps.normalize.outputs.branch }}/" >> "$GITHUB_OUTPUT"
      - name: Create backlink to PR at builds.jabref.org
        # background: true
        if: ${{ (github.event_name == 'pull_request') && (needs.disk-space-check.outputs.available == 'true') && (matrix.os == 'ubuntu-22.04') }}
        run: |
          echo "Link to PR: ${{ github.event.pull_request.html_url }}" >> _h5ai.header.md
          rsync -rt --chmod=Du=rwx,Dg=rx,Do=rx,Fu=rw,Fg=r,Fo=r --itemize-changes --stats --rsync-path="mkdir -p /var/www/builds.jabref.org/www/${{ steps.normalize.outputs.branch }} && rsync" -e 'ssh -p 9922 -i sshkey -o StrictHostKeyChecking=no' _h5ai.header.md jrrsync@build-upload.jabref.org:/var/www/builds.jabref.org/www/${{ steps.normalize.outputs.branch }}/

      # jablib is used by all components - thus, compile it first
      - name: jablib jar
        id: jablib-jar
        # wait: gitversion
        # background: true
        run: ${{ matrix.gradleCommand }} :jablib:jar
        env:
          VERSION: ${{ steps.gitversion.outputs.AssemblySemVer }}
          VERSION_INFO: ${{ steps.gitversion.outputs.InformationalVersion }}

      # Save disk space
      # Hint by https://dev.to/mathio/squeezing-disk-space-from-github-actions-runners-an-engineers-guide-3pjg
      - run: sudo rm -rf /usr/local/lib/android/sdk
        # background: true
        if: startsWith(matrix.os, 'ubuntu')
      - run: sudo rm -rf /usr/local/.ghcup
        # background: true
        if: startsWith(matrix.os, 'ubuntu')
      - run: sudo rm -rf /usr/share/swift
        # background: true
        if: startsWith(matrix.os, 'ubuntu')

      # Both JabRef Language Server and JabRef HTTP Server are required by the GUI
      # They are independent from each other and could be build in parallel.
      # - wait: jablib-jar # plus "normalize"
      - name: jabls jar
        # background: true
        id: jabls-jar
        run: ${{ matrix.gradleCommand }} :jabls:jar
        env:
          VERSION: ${{ steps.gitversion.outputs.AssemblySemVer }}
          VERSION_INFO: ${{ steps.gitversion.outputs.InformationalVersion }}
      - name: jabsrv jar
        # background: true
        id: jabsrv-jar
        run: ${{ matrix.gradleCommand }} :jabsrv:jar
        env:
          VERSION: ${{ steps.gitversion.outputs.AssemblySemVer }}
          VERSION_INFO: ${{ steps.gitversion.outputs.InformationalVersion }}

      - name: Setup macOS key chain
        if: (startsWith(matrix.os, 'macos')) && (needs.conditions.outputs.secretspresent == 'true')
        uses: slidoapp/import-codesign-certs@1923310662e8682dd05b76b612b53301f431cd5d
        with:
          p12-file-base64: ${{ secrets.OSX_SIGNING_CERT }}
          p12-password: ${{ secrets.OSX_CERT_PWD }}
          keychain-password: tEmPoRaRY-PaeSWD
      - name: Setup macOS key chain for app id cert
        if: (startsWith(matrix.os, 'macos')) && (needs.conditions.outputs.secretspresent == 'true')
        uses: slidoapp/import-codesign-certs@1923310662e8682dd05b76b612b53301f431cd5d
        with:
          p12-file-base64: ${{ secrets.OSX_SIGNING_CERT_APPLICATION }}
          p12-password: ${{ secrets.OSX_CERT_PWD }}
          create-keychain: false
          keychain-password: tEmPoRaRY-PaeSWD

      - name: Install jbundle
        if: ${{ (matrix.os == 'ubuntu-22.04') && (needs.conditions.outputs.should-jbundle == 'true') }}
        uses: baptiste0928/cargo-install@v3
        with:
          crate: jbundle
          git: https://github.com/avelino/jbundle/
          branch: main
      - name: Install pigz and cache (Linux)
        if: startsWith(matrix.os, 'ubuntu')
        uses: awalsh128/cache-apt-pkgs-action@latest
        with:
          packages: pigz
          version: 1.0

      - name: Workaround for jpackage issue
        run: |
          cd jabgui
          cp buildres/linux/JabRef.png .   # Linux
          cp buildres/windows/JabRef.ico . # Windows

      - name: Check WiX Version
        run: candle -?
        if: startsWith(matrix.os, 'windows')

      # jars already exists - thus, these calls will build on the jar result (hopefully).
      # - wait: [ jabls-jar, jabsrv-jar ]

      - uses: ./.github/actions/package
        name: Package JabRef Language Server
        id: jabls-cli
        # background: true
        with:
          gradleCommand: ${{ matrix.gradleCommand }}
          component: jabls-cli
          componentShort: jabls
          branchName: ${{ steps.normalize.outputs.branch }}
          AssemblySemVer: ${{ steps.gitversion.outputs.AssemblySemVer }}
          Major: ${{ steps.gitversion.outputs.Major }}
          Minor: ${{ steps.gitversion.outputs.Minor }}
          InformationalVersion: ${{ steps.gitversion.outputs.InformationalVersion }}
          diskSpaceAvailable: ${{ needs.disk-space-check.outputs.available }}
          os: ${{ matrix.os }}
          displayName: ${{ matrix.displayName }}
          archivePortable: ${{ matrix.archivePortableJabLS }}
          archForDebianRepack: ${{ matrix.archForDebianRepack }}
          suffix: ${{ matrix.suffix }}
          shouldJbundle: ${{ needs.conditions.outputs.should-jbundle }}
          uploadAsArtifact: "${{ github.event.inputs.upload-as-artifact }}"
          secretsPresent: "${{ needs.conditions.outputs.secretspresent }}"
          astrophysicsDataSystemApiKey: ${{ secrets.AstrophysicsDataSystemAPIKey }}
          biodiversityHeritageApiKey: ${{ secrets.BiodiversityHeritageApiKey }}
          ieeeApiKey: ${{ secrets.IEEEAPIKey }}
          springerNatureApiKey: ${{ secrets.SpringerNatureAPIKey }}
      - uses: ./.github/actions/package
        name: Package JabRef HTTP Server
        # background: true
        with:
          gradleCommand: ${{ matrix.gradleCommand }}
          component: jabsrv-cli
          componentShort: jabsrv
          branchName: ${{ steps.normalize.outputs.branch }}
          AssemblySemVer: ${{ steps.gitversion.outputs.AssemblySemVer }}
          Major: ${{ steps.gitversion.outputs.Major }}
          Minor: ${{ steps.gitversion.outputs.Minor }}
          InformationalVersion: ${{ steps.gitversion.outputs.InformationalVersion }}
          diskSpaceAvailable: ${{ needs.disk-space-check.outputs.available }}
          os: ${{ matrix.os }}
          displayName: ${{ matrix.displayName }}
          archivePortable: 'NONE'
          archForDebianRepack: ${{ matrix.archForDebianRepack }}
          suffix: ${{ matrix.suffix }}
          shouldJbundle: ${{ needs.conditions.outputs.should-jbundle }}
          uploadAsArtifact: "${{ github.event.inputs.upload-as-artifact }}"
          secretsPresent: "${{ needs.conditions.outputs.secretspresent }}"
          astrophysicsDataSystemApiKey: ${{ secrets.AstrophysicsDataSystemAPIKey }}
          biodiversityHeritageApiKey: ${{ secrets.BiodiversityHeritageApiKey }}
          ieeeApiKey: ${{ secrets.IEEEAPIKey }}
          springerNatureApiKey: ${{ secrets.SpringerNatureAPIKey }}
      - uses: ./.github/actions/package
        name: Package JabGUI
        id: jabgui
        # background: true
        with:
          gradleCommand: ${{ matrix.gradleCommand }}
          component: jabgui
          componentShort: jabgui
          branchName: ${{ steps.normalize.outputs.branch }}
          AssemblySemVer: ${{ steps.gitversion.outputs.AssemblySemVer }}
          Major: ${{ steps.gitversion.outputs.Major }}
          Minor: ${{ steps.gitversion.outputs.Minor }}
          InformationalVersion: ${{ steps.gitversion.outputs.InformationalVersion }}
          diskSpaceAvailable: ${{ needs.disk-space-check.outputs.available }}
          os: ${{ matrix.os }}
          displayName: ${{ matrix.displayName }}
          archivePortable: ${{ matrix.archivePortable }}
          archForDebianRepack: ${{ matrix.archForDebianRepack }}
          suffix: ${{ matrix.suffix }}
          shouldJbundle: ${{ needs.conditions.outputs.should-jbundle }}
          uploadAsArtifact: "${{ github.event.inputs.upload-as-artifact }}"
          secretsPresent: "${{ needs.conditions.outputs.secretspresent }}"
          astrophysicsDataSystemApiKey: ${{ secrets.AstrophysicsDataSystemAPIKey }}
          biodiversityHeritageApiKey: ${{ secrets.BiodiversityHeritageApiKey }}
          ieeeApiKey: ${{ secrets.IEEEAPIKey }}
          springerNatureApiKey: ${{ secrets.SpringerNatureAPIKey }}
      - uses: ./.github/actions/package
        name: Package JabKit
        # background: true
        with:
          gradleCommand: ${{ matrix.gradleCommand }}
          component: jabkit
          componentShort: jabkit
          branchName: ${{ steps.normalize.outputs.branch }}
          AssemblySemVer: ${{ steps.gitversion.outputs.AssemblySemVer }}
          Major: ${{ steps.gitversion.outputs.Major }}
          Minor: ${{ steps.gitversion.outputs.Minor }}
          InformationalVersion: ${{ steps.gitversion.outputs.InformationalVersion }}
          diskSpaceAvailable: ${{ needs.disk-space-check.outputs.available }}
          os: ${{ matrix.os }}
          displayName: ${{ matrix.displayName }}
          archivePortable: ${{ matrix.archivePortableJabKit }}
          archForDebianRepack: ${{ matrix.archForDebianRepack }}
          suffix: ${{ matrix.suffix }}
          shouldJbundle: ${{ needs.conditions.outputs.should-jbundle }}
          uploadAsArtifact: "${{ github.event.inputs.upload-as-artifact }}"
          secretsPresent: "${{ needs.conditions.outputs.secretspresent }}"
          astrophysicsDataSystemApiKey: ${{ secrets.AstrophysicsDataSystemAPIKey }}
          biodiversityHeritageApiKey: ${{ secrets.BiodiversityHeritageApiKey }}
          ieeeApiKey: ${{ secrets.IEEEAPIKey }}
          springerNatureApiKey: ${{ secrets.SpringerNatureAPIKey }}

      - name: Upload jabgui and jabls-cli to GitHub workflow artifacts store for notarization (macOS)
        if: ${{ (startsWith(matrix.os, 'macos')) && (needs.conditions.outputs.should-notarize == 'true') }}
        # wait: [ jabgui, jabls-cli ]
        uses: actions/upload-artifact@v7
        with:
          # tbn = to-be-notarized
          name: JabRef-${{ matrix.os }}-tbn
          path: |
            jabgui/build/packages/${{ matrix.os }}
            jabls-cli/build/packages/${{ matrix.os }}
          compression-level: 0 # no compression

  comment-on-issue-and-pr:
    # separate job, because it should wait until all binaries are available
    needs: [ conditions, disk-space-check, build ]
    if: ${{ (github.event_name == 'pull_request') }}
    permissions:
      issues: write
      pull-requests: write
    runs-on: ubuntu-slim
    steps:
      - name: Comment PR
        if: ${{ needs.disk-space-check.outputs.available == 'true' }}
        uses: thollander/actions-comment-pull-request@v3
        with:
          message: |
            The build of this PR is available at <${{ needs.build.outputs.url }}>.
          comment-tag: download-link
          mode: recreate
      - name: Create GitHub Summary
        if: ${{ needs.disk-space-check.outputs.available == 'true' }}
        run: echo "The build of this PR is available at <${{ needs.build.outputs.url }}>." >> "$GITHUB_STEP_SUMMARY"
      - name: echo PR data
        env:
          PR_NUMBER: ${{ github.event.pull_request.number }}
          PR_URL:    ${{ github.event.pull_request.html_url }}
          PR_BODY:   ${{ github.event.pull_request.body }}
        run: |
          echo "PR Number: $PR_NUMBER"
          echo "PR URL: $PR_URL"
          printf 'PR Body:\n%s\n' "$PR_BODY"
      - name: Determine issue number
        id: get_issue_number
        uses: koppor/ticket-check-action@add-output
        with:
          token: ${{ secrets.GITHUB_TOKEN }}
          ticketLink: 'https://github.com/JabRef/jabref/issues/%ticketNumber%'
          ticketPrefix: '#'
          titleRegex: '^#(?<ticketNumber>\d+)'
          branchRegex: '^(?<ticketNumber>\d+)'
          # Matches GitHub's closes/fixes/resolves #{number}, but does not match our example `Closes #13109` in PULL_REQUEST_TEMPLATE
          bodyRegex: '(?<action>fixes|closes|resolves)\s+(?:https?:\/\/github\.com\/JabRef\/jabref\/issues\/)?#?(?<ticketNumber>(?!13109\b)\d+)'
          bodyRegexFlags: 'i'
          outputOnly: true
      - name: Comment on issue (build available)
        if: ${{ (steps.get_issue_number.outputs.ticketNumber != '-1') && (needs.disk-space-check.outputs.available == 'true') }}
        uses: thollander/actions-comment-pull-request@v3
        with:
          pr-number: ${{ steps.get_issue_number.outputs.ticketNumber }}
          message: >
            A pull request addressing the issue has been created.
            The build of this PR is available at <${{ needs.build.outputs.url }}>.


            For any feedback, add a comment to the pull request at ${{ github.event.pull_request.html_url }}.
          comment-tag: download-link

  notarize:
    # Outsourced in a separate job to be able to rerun if this fails for timeouts
    name: macOS notarization - ${{ matrix.displayName }}
    needs: [ conditions, build ]
    if: ${{ needs.conditions.outputs.should-notarize == 'true' }}
    strategy:
      # Ensure that calls to Apple are sequentially made
      max-parallel: 1
      matrix:
        include:
          - os: macos-15
            displayName: JabGui (macOS-silicon, notarized)
            path: 'jabgui'
            prefix: 'JabRef'
            suffix: '_silicon'
          - os: macos-15-intel
            displayName: JabGui (macOS-intel, notarized)
            path: 'jabgui'
            prefix: 'JabRef'
            suffix: '_intel'
          # - os: macos-15
          #   displayName: jabls (macOS-silicon, notarized)
          #   path: 'jabls-cli'
          #   prefix: 'jabls'
          #   suffix: '_silicon'
          # - os: macos-15-intel
          #   displayName: jabls (macOS-intel, notarized)
          #   path: 'jabls-cli'
          #   prefix: 'jabls'
          #   suffix: '_intel'
    runs-on: ${{ matrix.os }}
    steps:
      - name: Download from GitHub workflow artifacts store (macOS)
        uses: actions/download-artifact@v8
        with:
          name: JabRef-${{ matrix.os }}-tbn
      - name: Notarize dmg
        shell: bash
        run: |
          cd ${{ matrix.path }}
          find . -type f
          xcrun notarytool store-credentials "notarytool-profile" --apple-id "vorstand@jabref.org" --team-id "6792V39SK3" --password "${{ secrets.OSX_NOTARIZATION_APP_PWD }}"
          xcrun notarytool submit build/packages/${{ matrix.os }}/${{ matrix.prefix }}-${{ needs.build.outputs.major }}.${{ needs.build.outputs.minor }}${{ matrix.suffix}}.dmg --keychain-profile "notarytool-profile" --wait
          xcrun stapler staple build/packages/${{ matrix.os }}/${{ matrix.prefix }}-${{ needs.build.outputs.major }}.${{ needs.build.outputs.minor }}${{ matrix.suffix}}.dmg
      - name: Notarize pkg
        shell: bash
        run: |
          cd ${{ matrix.path }}
          xcrun notarytool store-credentials "notarytool-profile" --apple-id "vorstand@jabref.org" --team-id "6792V39SK3" --password "${{ secrets.OSX_NOTARIZATION_APP_PWD }}"
          xcrun notarytool submit build/packages/${{ matrix.os }}/${{ matrix.prefix }}-${{ needs.build.outputs.major }}.${{ needs.build.outputs.minor }}${{ matrix.suffix}}.pkg --keychain-profile "notarytool-profile" --wait
          xcrun stapler staple build/packages/${{ matrix.os }}/${{ matrix.prefix }}-${{ needs.build.outputs.major }}.${{ needs.build.outputs.minor }}${{ matrix.suffix}}.pkg
      - name: Upload to builds.jabref.org
        if: needs.conditions.outputs.upload-to-builds-jabref-org == 'true'
        shell: bash
        run: |
          echo "${{ secrets.buildJabRefPrivateKey }}" > sshkey
          chmod 600 sshkey
          rsync -rt --chmod=Du=rwx,Dg=rx,Do=rx,Fu=rw,Fg=r,Fo=r --itemize-changes --stats --rsync-path="mkdir -p /var/www/builds.jabref.org/www/${{ needs.build.outputs.branchname }} && rsync" -e 'ssh -p 9922 -i sshkey -o StrictHostKeyChecking=no' ${{ matrix.path }}/build/packages/${{ matrix.os }}/ jrrsync@build-upload.jabref.org:/var/www/builds.jabref.org/www/${{ needs.build.outputs.branchname }}/
      - name: Upload artifacts
        if: ${{ github.event.inputs.upload-as-artifact || 'false' == 'true' }}
        uses: actions/upload-artifact@v7
        with:
          name: ${{ matrix.displayName }}
          path: |
            ${{ matrix.path }}/build/packages/${{ matrix.os }}

  upload-pr-nnumber:
    runs-on: ubuntu-slim
    permissions:
      contents: read
      actions: write
    steps:
      - name: Create pr_number.txt
        run: echo "${{ github.event.pull_request.number }}" > pr_number.txt
      - uses: actions/upload-artifact@v7
        with:
          name: pr_number
          path: pr_number.txt