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Merge branch 'main' into check_grad_sbml_test_suite
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‎.clang-tidy‎

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---
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CheckOptions:
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performance-unnecessary-value-param.AllowedTypes: "gsl::not_null"
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modernize-pass-by-value.AllowedTypes: "gsl::not_null"

‎.git-blame-ignore-revs‎

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f59fed72eb4d0cedf6abf2a96fe95087ce61478a

‎.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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shell: bash

‎.github/actions/install-macos-dependencies/action.yml‎

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name: Install AMICI dependencies for MacOS
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description: Install AMICI dependencies for MacOS
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runs:
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using: "composite"
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steps:
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# use all available cores
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- run: echo "AMICI_PARALLEL_COMPILE=" >> $GITHUB_ENV
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shell: bash
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# AMICI repository root
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- run: echo "AMICI_DIR=$(pwd)" >> $GITHUB_ENV
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shell: bash
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# BioNetGen path
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- run: echo "BNGPATH=${AMICI_DIR}/ThirdParty/BioNetGen-2.7.0" >> $GITHUB_ENV
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shell: bash
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# CMake hints
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# Ensure CMake is using the python version that we will use for the python tests later on
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- run: echo "PYTHON_EXECUTABLE=${Python3_ROOT_DIR}/bin/python3" >> $GITHUB_ENV
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shell: bash
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- run: echo "OpenMP_ROOT=$(brew --prefix)/opt/libomp" >> $GITHUB_ENV
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shell: bash
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- run: echo "BOOST_ROOT=$(brew --prefix)/opt/boost" >> $GITHUB_ENV
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shell: bash
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# install amici dependencies
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- name: homebrew
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# install hdf5 without dependencies, because pkgconf installation fails,
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# because it's already installed on the runners. install the other
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# hdf5 dependencies (libaec) manually
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run: brew install libaec && brew install --ignore-dependencies hdf5 && brew install libomp boost
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shell: bash

‎.github/actions/setup-amici-cpp/action.yml‎

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name: Set up AMICI C++
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description: |
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Build the AMICI C++ interface and set things for for coverage analysis.
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(Currently ubuntu-only).
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runs:
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using: "composite"
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steps:
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# BioNetGen Path
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- run: echo "BNGPATH=${GITHUB_WORKSPACE}/ThirdParty/BioNetGen-2.7.0" >> $GITHUB_ENV
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shell: bash
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# use all available cores
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- run: echo "AMICI_PARALLEL_COMPILE=" >> $GITHUB_ENV
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shell: bash
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# enable coverage
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- run: echo "ENABLE_GCOV_COVERAGE=TRUE" >> $GITHUB_ENV
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shell: bash
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- run: echo "PYTHONFAULTHANDLER=1" >> $GITHUB_ENV
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shell: bash
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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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- name: Install additional apt dependencies
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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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python3-venv \
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lcov
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shell: bash
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- name: Build AMICI dependencies
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run: scripts/buildDependencies.sh
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shell: bash
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- name: Build AMICI
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run: scripts/buildAmici.sh
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shell: bash
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env:
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CI_SONARCLOUD: "TRUE"

‎.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 update \
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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: '4.2.0'
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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/dependabot.yml‎

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version: 2
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updates:
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- package-ecosystem: "github-actions"
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directory: "/"
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schedule:
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interval: "weekly"
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ignore:
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- dependency-name: "*"
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update-types: ["version-update:semver-patch", "version-update:semver-minor"]
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target-branch: "develop"

‎.github/workflows/deploy_branch.yml‎

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name: Deploy Branch
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on: [push, merge_group, workflow_dispatch]
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on: [push, pull_request, merge_group, workflow_dispatch]
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jobs:
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sdist:
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name: Deploy Python Source Distribution
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runs-on: ubuntu-22.04
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runs-on: ubuntu-24.04
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strategy:
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matrix:
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python-version: [3.9]
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python-version: ["3.12"]
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steps:
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- name: Set up Python ${{ matrix.python-version }}
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uses: actions/setup-python@v4
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uses: actions/setup-python@v5
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with:
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python-version: ${{ matrix.python-version }}
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- uses: actions/checkout@v3
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- uses: actions/checkout@v4
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with:
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fetch-depth: 20
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- run: echo "AMICI_DIR=$(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: |
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scripts/buildSdist.sh
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- name: "Upload artifact: sdist"
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uses: actions/upload-artifact@v3
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uses: actions/upload-artifact@v4
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with:
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name: sdist
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path: python/sdist/dist/amici-*.gz

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