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GHA: Modularize actions (apt dependencies, sonar tools) (#2197)
* GHA: Test composite actions * .. * sonar
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‎.github/actions/install-apt-dependencies/action.yml‎

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name: Install apt dependencies
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description: Install apt dependencies for the AMICI Python package
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runs:
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using: "composite"
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steps:
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- run: |
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sudo apt-get update \
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&& sudo apt-get install -y \
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g++ \
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libatlas-base-dev \
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libboost-chrono-dev \
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libboost-math-dev \
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libboost-serialization-dev \
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libhdf5-serial-dev \
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swig
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shell: bash

‎.github/actions/setup-sonar-tools/action.yml‎

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name: Set up Sonar tools
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description: Download and install sonar-scanner and build-wrapper
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runs:
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using: "composite"
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steps:
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- run: echo "SONAR_SCANNER_VERSION=5.0.1.3006" >> $GITHUB_ENV
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shell: bash
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- run: echo "SONAR_SCANNER_HOME=${HOME}/.sonar/sonar-scanner-$SONAR_SCANNER_VERSION-linux" >> $GITHUB_ENV
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shell: bash
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- run: echo "SONAR_SCANNER_OPTS=-server" >> $GITHUB_ENV
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shell: bash
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- run: echo "${SONAR_SCANNER_HOME}/bin" >> $GITHUB_PATH
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shell: bash
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- run: echo "${HOME}/.sonar/build-wrapper-linux-x86" >> $GITHUB_PATH
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shell: bash
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- name: Install sonarcloud tools
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run: |
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sudo apt-get install nodejs curl unzip \
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&& curl --create-dirs -sSLo $HOME/.sonar/sonar-scanner.zip \
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https://binaries.sonarsource.com/Distribution/sonar-scanner-cli/sonar-scanner-cli-$SONAR_SCANNER_VERSION-linux.zip \
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&& unzip -o $HOME/.sonar/sonar-scanner.zip -d $HOME/.sonar/ \
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&& curl --create-dirs -sSLo $HOME/.sonar/build-wrapper-linux-x86.zip \
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https://sonarcloud.io/static/cpp/build-wrapper-linux-x86.zip \
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&& unzip -o $HOME/.sonar/build-wrapper-linux-x86.zip -d $HOME/.sonar/ \
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shell: bash

‎.github/workflows/test_benchmark_collection_models.yml‎

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with:
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fetch-depth: 20
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# install dependencies
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- name: apt
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run: |
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sudo apt-get update \
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&& sudo apt-get install -y swig libatlas-base-dev
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- name: Install apt dependencies
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uses: ./.github/actions/install-apt-dependencies
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- run: echo "${HOME}/.local/bin/" >> $GITHUB_PATH
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‎.github/workflows/test_install.yml‎

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- run: echo "AMICI_DIR=$(pwd)" >> $GITHUB_ENV
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# install amici dependencies
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- name: Install apt dependencies
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uses: ./.github/actions/install-apt-dependencies
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- name: apt
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run: |
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sudo apt-get update \
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&& sudo apt-get install -y \
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cmake \
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g++ \
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libatlas-base-dev \
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libboost-serialization-dev \
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libhdf5-serial-dev \
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swig
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cmake
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- name: Build suitesparse
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run: |
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- run: echo "AMICI_DIR=$(pwd)" >> $GITHUB_ENV
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# install amici dependencies
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- name: apt
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run: |
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sudo apt-get update \
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&& sudo apt-get install -y \
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g++ \
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libatlas-base-dev \
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libboost-serialization-dev \
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libhdf5-serial-dev \
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swig
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- name: Install apt dependencies
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uses: ./.github/actions/install-apt-dependencies
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- name: Create AMICI sdist
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run: |

‎.github/workflows/test_performance.yml‎

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with:
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fetch-depth: 20
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# install dependencies
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- name: apt
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run: |
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sudo apt-get update \
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&& sudo apt-get install -y swig libatlas-base-dev
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- name: Install apt dependencies
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uses: ./.github/actions/install-apt-dependencies
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- run: pip3 install petab shyaml build
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- run: echo "${HOME}/.local/bin/" >> $GITHUB_PATH

‎.github/workflows/test_petab_test_suite.yml‎

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with:
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fetch-depth: 20
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- name: Install apt dependencies
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uses: ./.github/actions/install-apt-dependencies
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# install dependencies
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- name: apt
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run: |
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sudo apt-get update \
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&& sudo apt-get install -y \
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swig \
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libatlas-base-dev \
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python3-venv
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&& sudo apt-get install -y python3-venv
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- name: Build BNGL
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run: |

‎.github/workflows/test_python_cplusplus.yml‎

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- run: echo "AMICI_DIR=$(pwd)" >> $GITHUB_ENV
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- run: echo "BNGPATH=${GITHUB_WORKSPACE}/ThirdParty/BioNetGen-2.7.0" >> $GITHUB_ENV
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# sonar cloud
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- run: echo "SONAR_SCANNER_VERSION=5.0.1.3006" >> $GITHUB_ENV
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- run: echo "SONAR_SCANNER_HOME=${HOME}/.sonar/sonar-scanner-$SONAR_SCANNER_VERSION-linux" >> $GITHUB_ENV
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- run: echo "SONAR_SCANNER_OPTS=-server" >> $GITHUB_ENV
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- run: echo "${SONAR_SCANNER_HOME}/bin" >> $GITHUB_PATH
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- run: echo "${HOME}/.sonar/build-wrapper-linux-x86" >> $GITHUB_PATH
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# TODO: add to ci image
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- name: Install sonarcloud tools
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run: |
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sudo apt-get install nodejs curl unzip \
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&& curl --create-dirs -sSLo $HOME/.sonar/sonar-scanner.zip \
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https://binaries.sonarsource.com/Distribution/sonar-scanner-cli/sonar-scanner-cli-$SONAR_SCANNER_VERSION-linux.zip \
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&& unzip -o $HOME/.sonar/sonar-scanner.zip -d $HOME/.sonar/ \
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&& curl --create-dirs -sSLo $HOME/.sonar/build-wrapper-linux-x86.zip \
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https://sonarcloud.io/static/cpp/build-wrapper-linux-x86.zip \
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&& unzip -o $HOME/.sonar/build-wrapper-linux-x86.zip -d $HOME/.sonar/ \
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- name: Set up Sonar tools
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uses: ./.github/actions/setup-sonar-tools
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- name: Install apt dependencies
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uses: ./.github/actions/install-apt-dependencies
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# install amici dependencies
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- name: apt
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&& sudo apt-get install -y \
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cmake \
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g++ \
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libatlas-base-dev \
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libboost-serialization-dev \
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libboost-chrono-dev \
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libhdf5-serial-dev \
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python3-venv \
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swig \
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lcov \
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libboost-math-dev
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‎.github/workflows/test_python_ver_matrix.yml‎

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with:
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fetch-depth: 20
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# install dependencies
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- name: apt
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run: |
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sudo apt-get update \
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&& sudo apt-get install -y \
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swig \
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libatlas-base-dev \
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libhdf5-serial-dev \
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libboost-math-dev
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- name: Install apt dependencies
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uses: ./.github/actions/install-apt-dependencies
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# install AMICI
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- name: Build BNGL

‎.github/workflows/test_sbml_semantic_test_suite.yml‎

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- uses: actions/checkout@v3
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with:
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fetch-depth: 1
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- name: apt
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run: |
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sudo apt-get update \
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&& sudo apt-get install -y swig4.0 libatlas-base-dev
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- name: Install apt dependencies
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uses: ./.github/actions/install-apt-dependencies
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- run: AMICI_PARALLEL_COMPILE=2 ./scripts/installAmiciSource.sh
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- run: AMICI_PARALLEL_COMPILE=2 ./scripts/run-SBMLTestsuite.sh ${{ matrix.cases }}
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‎.github/workflows/test_valgrind.yml‎

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- uses: actions/checkout@v3
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- run: git fetch --prune --unshallow
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- name: Install apt dependencies
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uses: ./.github/actions/install-apt-dependencies
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# install amici dependencies
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- name: apt
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run: |
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sudo apt-get update \
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&& sudo apt-get install -y \
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cmake \
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g++ \
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libatlas-base-dev \
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libboost-serialization-dev \
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libhdf5-serial-dev \
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python3-venv \
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swig \
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valgrind \
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libboost-math-dev
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valgrind
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- name: Build AMICI
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run: |
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- uses: actions/checkout@v3
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- run: git fetch --prune --unshallow
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- name: Install apt dependencies
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uses: ./.github/actions/install-apt-dependencies
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# install amici dependencies
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- name: apt
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run: |
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sudo apt-get update \
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&& sudo apt-get install -y \
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cmake \
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g++ \
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libatlas-base-dev \
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libboost-serialization-dev \
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libhdf5-serial-dev \
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python3-venv \
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swig \
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valgrind \
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libboost-math-dev
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valgrind
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- name: Build AMICI
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run: |

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