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Merge branch 'release/9.2.0'
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‎.github/actions/setup-build-tools/action.yml‎

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# Orchestrates setup of all build tools based on project requirements.
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#
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# Author: John Grimes
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name: Setup Build Tools
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description: Orchestrates setup of Java, R, Python, and Bun build environments.
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inputs:
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java:
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description: Set up Java/Maven environment.
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required: false
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default: "true"
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java-version:
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description: Java version to install.
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required: false
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default: "21"
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r:
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description: Set up R environment.
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required: false
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default: "false"
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r-version:
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description: R version to install.
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required: false
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default: "4.1.3"
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r-pandoc:
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description: Install Pandoc for R documentation.
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required: false
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default: "false"
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python:
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description: Set up Python/uv environment.
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required: false
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default: "false"
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bun:
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description: Set up Bun runtime.
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required: false
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default: "false"
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sonar-cache:
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description: Enable SonarQube cache.
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required: false
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default: "false"
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runs:
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using: composite
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steps:
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- name: Set up Java and Maven
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if: inputs.java == 'true'
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uses: ./.github/actions/setup-java-maven
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with:
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java-version: ${{ inputs.java-version }}
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enable-sonar-cache: ${{ inputs.sonar-cache }}
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- name: Set up R
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if: inputs.r == 'true'
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uses: ./.github/actions/setup-r
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with:
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r-version: ${{ inputs.r-version }}
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install-pandoc: ${{ inputs.r-pandoc }}
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- name: Set up Python
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if: inputs.python == 'true'
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uses: ./.github/actions/setup-python
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- name: Set up Bun
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if: inputs.bun == 'true'
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uses: oven-sh/setup-bun@v2

‎.github/actions/setup-java-maven/action.yml‎

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# Sets up Java with Maven caching and required environment variables.
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#
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# Author: John Grimes
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name: Setup Java and Maven
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description: Sets up Java with Maven repository caching, SonarQube caching, and MAVEN_OPTS.
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inputs:
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java-version:
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description: Java version to install.
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required: false
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default: "21"
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distribution:
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description: JDK distribution to use.
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required: false
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default: zulu
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enable-sonar-cache:
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description: Enable SonarQube cache.
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required: false
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default: "true"
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runs:
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using: composite
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steps:
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- name: Set up JDK
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uses: actions/setup-java@v4
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with:
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java-version: ${{ inputs.java-version }}
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distribution: ${{ inputs.distribution }}
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- name: Cache local Maven repository
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uses: actions/cache@v4
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with:
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path: ~/.m2/repository
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key: ${{ runner.os }}-maven-${{ hashFiles('**/pom.xml') }}
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restore-keys: |-
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${{ runner.os }}-maven-
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- name: Cache SonarQube packages
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if: inputs.enable-sonar-cache == 'true'
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uses: actions/cache@v4
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with:
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path: ~/.sonar/cache
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key: ${{ runner.os }}-sonar
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restore-keys: ${{ runner.os }}-sonar
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# The add-exports and add-opens flags are required for Java 21.
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- name: Set MAVEN_OPTS
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shell: bash
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run: echo "MAVEN_OPTS=--add-exports=java.base/sun.nio.ch=ALL-UNNAMED --add-opens=java.base/java.net=ALL-UNNAMED" >> $GITHUB_ENV

‎.github/actions/setup-python/action.yml‎

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# Sets up Python environment using uv with caching.
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#
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# Author: John Grimes
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name: Setup Python
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description: Sets up Python using uv with caching enabled.
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inputs:
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enable-cache:
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description: Enable uv cache.
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required: false
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default: "true"
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runs:
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using: composite
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steps:
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- name: Install uv
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uses: astral-sh/setup-uv@v6
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with:
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enable-cache: ${{ inputs.enable-cache }}

‎.github/actions/setup-r/action.yml‎

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# Sets up R environment with package caching, TinyTeX, and libcurl.
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#
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# Author: John Grimes
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name: Setup R
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description: Sets up R with package caching, TinyTeX, libcurl, and optionally Pandoc.
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inputs:
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r-version:
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description: R version to install.
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required: false
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default: "4.1.3"
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install-pandoc:
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description: Install Pandoc for documentation generation.
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required: false
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default: "false"
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runs:
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using: composite
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steps:
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- name: Set up R
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uses: r-lib/actions/setup-r@v2
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with:
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r-version: ${{ inputs.r-version }}
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use-public-rspm: true
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- name: Set up Pandoc
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if: inputs.install-pandoc == 'true'
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uses: r-lib/actions/setup-pandoc@v2
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- name: Cache R packages
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uses: actions/cache@v4
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with:
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path: ${{ runner.temp }}/Library
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key: r-packages-${{ runner.os }}-${{ hashFiles('lib/R/DESCRIPTION.src') }}
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restore-keys: r-packages-${{ runner.os }}-
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# TinyTeX and libcurl are required for building the R package documentation.
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- name: Install TinyTeX and libcurl
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shell: bash
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run: |
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wget --max-redirect=0 -qO- "https://tinytex.yihui.org/install-bin-unix.sh" | sh
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echo "$HOME/bin" >> $GITHUB_PATH
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sudo apt-get install -y libcurl4-openssl-dev

‎.github/actions/upload-test-artifacts/action.yml‎

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# Uploads test reports, coverage, and build artifacts.
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#
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# Author: John Grimes
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name: Upload Test Artifacts
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description: Uploads test reports, coverage reports, and optionally JARs and language packages.
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inputs:
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name-prefix:
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description: Prefix for artifact names (e.g., "server-").
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required: false
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default: ""
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path-prefix:
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description: Path prefix for finding files (e.g., "server/").
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required: false
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default: ""
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include-jars:
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description: Include built JAR files.
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required: false
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default: "false"
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include-python:
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description: Include Python wheel.
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required: false
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default: "false"
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include-r:
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description: Include R package.
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required: false
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default: "false"
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include-site:
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description: Include documentation site.
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required: false
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default: "false"
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runs:
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using: composite
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steps:
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- name: Save test reports
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uses: actions/upload-artifact@v4
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with:
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name: ${{ inputs.name-prefix }}surefire-reports
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path: ${{ inputs.path-prefix }}**/surefire-reports/
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- name: Save coverage reports
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uses: actions/upload-artifact@v4
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with:
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name: ${{ inputs.name-prefix }}coverage-reports
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path: |
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${{ inputs.path-prefix }}**/jacoco.exec
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${{ inputs.path-prefix }}**/jacoco.xml
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${{ inputs.path-prefix }}**/target/site/jacoco
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${{ inputs.path-prefix }}**/target/site/jacoco-aggregate
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${{ inputs.path-prefix }}lib/python/**/coverage.xml
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- name: Save built JARs
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if: inputs.include-jars == 'true'
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uses: actions/upload-artifact@v4
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with:
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name: jars
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path: |
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utilities/target/utilities-*.jar
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encoders/target/encoders-*.jar
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terminology/target/terminology-*.jar
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fhirpath/target/fhirpath-*.jar
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library-api/target/library-api-*.jar
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library-runtime/target/library-runtime-*.jar
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lib/python/target/python-*.jar
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lib/R/target/r-*.jar
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if-no-files-found: error
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- name: Save Python wheel
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if: inputs.include-python == 'true'
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uses: actions/upload-artifact@v4
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with:
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name: python-wheel
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path: lib/python/target/py-dist/pathling-*.whl
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- name: Save R package
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if: inputs.include-r == 'true'
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uses: actions/upload-artifact@v4
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with:
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name: r-package
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path: lib/R/target/pathling_*.tar.gz
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- name: Save site
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if: inputs.include-site == 'true'
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uses: actions/upload-artifact@v4
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with:
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name: site
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path: site/target/site/

‎.github/workflows/benchmark.yml‎

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- name: Get workflow run info
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id: get_run_info
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uses: actions/github-script@v7
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env:
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RUN_ID: ${{ github.event.inputs.run_id }}
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with:
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script: |
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const runId = parseInt(process.env.RUN_ID, 10);
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if (isNaN(runId) || runId <= 0) {
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core.setFailed('Invalid run_id: must be a positive integer');
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return;
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}
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const { data: run } = await github.rest.actions.getWorkflowRun({
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owner: context.repo.owner,
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repo: context.repo.repo,
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run_id: ${{ github.event.inputs.run_id }}
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run_id: runId
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});
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core.setOutput('commit_sha', run.head_sha);
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core.setOutput('run_id', runId);
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- name: Checkout code
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uses: actions/checkout@v4
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with:
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fetch-depth: 0
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ref: ${{ steps.get_run_info.outputs.commit_sha }}
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- name: Set up JDK
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uses: actions/setup-java@v4
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- name: Set up build environment
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uses: ./.github/actions/setup-build-tools
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with:
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java-version: 21
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distribution: "zulu"
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java: "true"
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sonar-cache: "false"
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- name: Download JARs from specified run
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uses: actions/download-artifact@v4
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with:
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name: jars
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run-id: ${{ github.event.inputs.run_id }}
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run-id: ${{ steps.get_run_info.outputs.run_id }}
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github-token: ${{ secrets.GITHUB_TOKEN }}
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path: jars/
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