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Merge branch 'develop' into check_grad_sbml_test_suite
2 parents cf34778 + 32730f0 commit 22722e7

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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-doxygen/action.yml‎

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name: Set up doxygen
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description: |
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Download, build, and install doxygen.
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runs:
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using: "composite"
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steps:
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- name: Install apt dependencies for doxygen
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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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bison \
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ragel \
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graphviz \
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texlive-latex-extra
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shell: bash
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- name: Download and build doxygen
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run: sudo scripts/downloadAndBuildDoxygen.sh
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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/actions/setup-swig/action.yml‎

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name: Set up SWIG
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description: |
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Download and build SWIG and set the SWIG environment variable to the path of
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the SWIG executable.
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inputs:
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swig_version:
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description: 'Swig version to build'
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required: false
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default: '4.1.1'
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runs:
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using: "composite"
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steps:
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- name: Download and build SWIG
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run: scripts/downloadAndBuildSwig.sh
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shell: bash
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- run: echo "SWIG=${AMICI_DIR}/ThirdParty/swig-${{ inputs.swig_version }}/install/bin/swig" >> $GITHUB_ENV
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shell: bash

‎.github/workflows/deploy_branch.yml‎

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with:
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fetch-depth: 20
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- run: echo "AMICI_DIR=$(pwd)" >> $GITHUB_ENV
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- run: echo "SWIG=${AMICI_DIR}/ThirdParty/swig-4.0.1/install/bin/swig" >> $GITHUB_ENV
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- name: Set up SWIG
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uses: ./.github/actions/setup-swig
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- name: Build swig4
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run: |
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sudo scripts/downloadAndBuildSwig.sh
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- run: echo "AMICI_DIR=$(pwd)" >> $GITHUB_ENV
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- name: Create AMICI sdist
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run: |

‎.github/workflows/deploy_release.yml‎

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with:
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fetch-depth: 20
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- run: echo "AMICI_DIR=$(pwd)" >> $GITHUB_ENV
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- run: echo "SWIG=${AMICI_DIR}/ThirdParty/swig-4.0.1/install/bin/swig" >> $GITHUB_ENV
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- name: Set up SWIG
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uses: ./.github/actions/setup-swig
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- name: Build swig4
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run: |
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sudo scripts/downloadAndBuildSwig.sh
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- run: echo "AMICI_DIR=$(pwd)" >> $GITHUB_ENV
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- name: sdist
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run: |

‎.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_doc.yml‎

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jobs:
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doxygen:
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name: Test Doxygen
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runs-on: ubuntu-22.04
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strategy:
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- uses: actions/checkout@v3
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- run: git fetch --prune --unshallow
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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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bison \
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ragel \
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graphviz \
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texlive-latex-extra
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- name: Build doxygen
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run: |
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sudo scripts/downloadAndBuildDoxygen.sh
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- name: Set up doxygen
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uses: ./.github/actions/setup-doxygen
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- name: Run doxygen
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run: |
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scripts/run-doxygen.sh
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run: scripts/run-doxygen.sh
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sphinx:
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name: Test Sphinx
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runs-on: ubuntu-22.04
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strategy:
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- run: git fetch --prune --unshallow
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- run: echo "AMICI_DIR=$(pwd)" >> $GITHUB_ENV
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- run: echo "SWIG=${AMICI_DIR}/ThirdParty/swig-4.1.1/install/bin/swig" >> $GITHUB_ENV
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- name: Build doxygen
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run: |
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sudo scripts/downloadAndBuildDoxygen.sh
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- name: Set up doxygen
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uses: ./.github/actions/setup-doxygen
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# install amici dependencies
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- name: apt
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pandoc \
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python3-venv \
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- name: Build swig
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run: |
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sudo scripts/downloadAndBuildSwig.sh
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- uses: ./.github/actions/setup-swig
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- name: sphinx
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run: |
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scripts/run-sphinx.sh
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run: scripts/run-sphinx.sh

‎.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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# 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

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