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ENH: Add GitHub actions (#1)
* CNF: add base workflows * CNF: use previous image * CNF: added tar based image build * CNF: pinned debian, changed pull request workflow * CNF: fixed env var referencing * CNF: updated os for runners * CNF: update upload version * CNF: added dev multistage * CNF: updated action versions * CNF: try new config * CNF: target dev stage * CNF: added coverage * CNF: only include source files for coverage * CNF: added source to the correct place * CNF: add PR comment and update coverage report toml settings * CNF: call with uv * CNF: enable caching * CNF: optimize docker cache and remove uid change * CNF: removed upload to artifact storage * CNF: add sticky comment to avoid spam
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‎.github/workflows/main.yml‎

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name: CI - Run Unit Tests in Docker with Coverage
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on:
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push:
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branches: [ main ]
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pull_request:
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branches: [ main ]
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jobs:
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test:
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runs-on: ubuntu-latest
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steps:
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- name: Checkout code
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uses: actions/checkout@v4
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- name: Set up Docker Buildx
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uses: docker/setup-buildx-action@v3
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- name: Build Docker image with Cache
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uses: docker/build-push-action@v5
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with:
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context: .
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file: ./Dockerfile # Assuming Dockerfile is at the root
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# Build the 'dev' target stage
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target: dev
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# Tag the image locally so subsequent steps can use it
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tags: my-test-image:latest
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# IMPORTANT: Load the image into the local Docker daemon
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load: true
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# Enable layer caching using GitHub Actions cache
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cache-from: type=gha
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cache-to: type=gha,mode=max
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- name: Run tests with dFBA extra
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run: |
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# Runs coverage collection via 'uv run' using --with pytest-cov.
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# Uses --parallel-mode for coverage data.
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# Generates uniquely named JUnit report.
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docker run --rm \
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-v "$(pwd):/app" \
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-w /app \
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my-test-image:latest \
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uv run --with dfba --with pytest --with pytest-cov coverage run --parallel-mode -m pytest ./tests/extras --junitxml=test-report-dfba.xml
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- name: Run tests without dFBA extra
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run: |
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# Runs coverage collection via 'uv run' using --with pytest-cov.
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# Uses --parallel-mode for coverage data.
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# Generates uniquely named JUnit report.
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docker run --rm \
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-v "$(pwd):/app" \
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-w /app \
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my-test-image:latest \
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uv run --with pytest --with pytest-cov coverage run --parallel-mode -m pytest ./tests/core --junitxml=test-report-core.xml
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# --- The step below only runs if BOTH test steps above succeeded ---
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- name: Combine and Report Coverage
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if: success()
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run: |
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# Runs combine, report, and html generation in a single container
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# Saves the console summary to /app/coverage_summary.txt within the container
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# which maps to coverage_summary.txt on the runner host via the volume mount.
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docker run --rm \
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-v "$(pwd):/app" \
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-w /app \
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my-test-image:latest \
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sh -c '\
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echo "Combining coverage data..." && \
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uv run --with pytest --with pytest-cov coverage combine && \
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echo "Generating coverage summary..." && \
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uv run --with pytest --with pytest-cov coverage report -m > /app/coverage_summary.txt && \
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echo "Generating HTML coverage report..." && \
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uv run --with pytest --with pytest-cov coverage html -d htmlcov \
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'
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# Also echo the summary to the main job log for easy viewing there
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echo "--- Coverage Summary ---"
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cat coverage_summary.txt
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echo "------------------------"
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- name: Format Coverage Comment Body
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# Prepare the content for the comment in a file
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# Only run on successful PR builds
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if: success() && github.event_name == 'pull_request'
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run: |
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echo '### :test_tube: Coverage Report' > coverage_comment.md
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echo '' >> coverage_comment.md
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echo '```text' >> coverage_comment.md
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cat coverage_summary.txt >> coverage_comment.md
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echo '' >> coverage_comment.md # Ensure newline before closing fence
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echo '```' >> coverage_comment.md
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# Optional: Add a hidden HTML comment marker for extra safety/identification
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# echo "<!-- coverage-report-marker -->" >> coverage_comment.md
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- name: Post or Update Coverage Comment
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# Use the sticky comment action
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# Only run on successful PR builds
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if: success() && github.event_name == 'pull_request'
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uses: marocchino/sticky-pull-request-comment@v2
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with:
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# Tell the action to read the comment body from the file we just created
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path: coverage_comment.md

‎Dockerfile‎

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FROM debian:bookworm-slim as builder
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ARG SUNDIALS_VERSION="5.0.0"
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ENV SUNDIALS="/opt/sundials"
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WORKDIR /
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# install debian essentials for building dependencies
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RUN apt-get update && apt-get install -y --no-install-recommends \
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gcc \
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cmake \
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build-essential \
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curl \
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gnupg2 \
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ca-certificates \
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&& update-ca-certificates \
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&& rm -rf /var/lib/apt/lists/*
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RUN curl -L -O "https://github.com/LLNL/sundials/releases/download/v${SUNDIALS_VERSION}/sundials-${SUNDIALS_VERSION}.tar.gz" && \
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tar -xzf sundials-${SUNDIALS_VERSION}.tar.gz && \
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mkdir ${SUNDIALS} && \
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mkdir ${SUNDIALS}/install && \
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mkdir ${SUNDIALS}/build && \
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cd ${SUNDIALS}/build && \
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cmake -DCMAKE_INSTALL_PREFIX=${SUNDIALS}/install \
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-DEXAMPLES_INSTALL_PATH=${SUNDIALS}/install/examples \
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/sundials-${SUNDIALS_VERSION} && \
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make && \
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make install
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# SUNDIALS container image
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FROM python:3.10-slim-bookworm as dev
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ARG GLPK_VERSION="4.65"
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ENV SUNDIALS="/opt/sundials"
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COPY --from=builder ${SUNDIALS}/install ${SUNDIALS}
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RUN apt-get update && apt-get install -y --no-install-recommends \
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curl \
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pybind11-dev \
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build-essential \
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gcc \
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gnupg2 \
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cmake \
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gfortran \
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libgmp-dev \
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python-dev-is-python3 \
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libglpk-dev && \
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rm -rf /var/lib/apt/lists/*
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# GLPK
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# Download the specified distribution, verify it and install
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RUN curl -L -O "ftp://ftp.gnu.org/gnu/glpk/glpk-${GLPK_VERSION}.tar.gz" && \
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curl -L -O "ftp://ftp.gnu.org/gnu/glpk/glpk-${GLPK_VERSION}.tar.gz.sig" && \
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gpg --keyserver keyserver.ubuntu.com --recv-keys 5981E818 && \
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gpg --verify "glpk-${GLPK_VERSION}.tar.gz.sig" && \
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tar -xzf "glpk-${GLPK_VERSION}.tar.gz" && \
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cd "glpk-${GLPK_VERSION}" && \
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./configure --with-gmp && \
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make && \
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make install && \
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cd .. && \
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rm -rf "glpk-${GLPK_VERSION}"*
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ARG SUNDIALS_VERSION=5.1.0
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ARG GLPK_VERSION=4.65
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ARG EXTRAS="dfba"
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FROM ghcr.io/amyris/sundials-glpk-pybind:sundials-${SUNDIALS_VERSION}-glpk-${GLPK_VERSION} as dev
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COPY --from=ghcr.io/astral-sh/uv:0.6.11 /uv /uvx /bin/
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ENV UV_COMPILE_BYTECODE=1
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COPY pyproject.toml ./
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ARG EXTRAS="dfba"
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RUN EXTRA_NAMES=$(echo $EXTRAS | sed 's/,/ --extra /g' | sed 's/^/--extra /')
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RUN echo ${EXTRA_NAMES}
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‎pyproject.toml‎

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]
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build-backend = "setuptools.build_meta"
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[tool.coverage.run]
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source = ["src"] # List format often used here
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parallel = true
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branch = true
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# omit = ["src/__init__.py", "src/config/*"] # Optional
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[tool.coverage.report]
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show_missing = true
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# fail_under = 90 # Optional
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# exclude_lines = [ # Optional
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# "pragma: no cover",
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# "raise NotImplementedError",
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# "if __name__ == .__main__.:",
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# ]
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[tool.coverage.html]
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directory = "htmlcov"
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[tool.coverage.xml]
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# output = "coverage.xml" # Optional

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