Release 0.20.0

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

@@ -0,0 +1,16 @@
+name: Install apt dependencies
+description: Install apt dependencies for the AMICI Python package
+runs:
+  using: "composite"
+  steps:
+    - run: |
+        sudo apt-get update \
+          && sudo apt-get install -y \
+              g++ \
+              libatlas-base-dev \
+              libboost-chrono-dev \
+              libboost-math-dev \
+              libboost-serialization-dev \
+              libhdf5-serial-dev \
+              swig
+      shell: bash

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

@@ -0,0 +1,44 @@
+name: Set up AMICI C++
+description: |
+  Build the AMICI C++ interface and set things for for coverage analysis.
+  (Currently ubuntu-only).
+
+runs:
+  using: "composite"
+  steps:
+    # BioNetGen Path
+    - run: echo "BNGPATH=${GITHUB_WORKSPACE}/ThirdParty/BioNetGen-2.7.0" >> $GITHUB_ENV
+      shell: bash
+
+    # use all available cores
+    - run: echo "AMICI_PARALLEL_COMPILE=" >> $GITHUB_ENV
+      shell: bash
+
+    # enable coverage
+    - run: echo "ENABLE_GCOV_COVERAGE=TRUE" >> $GITHUB_ENV
+      shell: bash
+
+    - name: Set up Sonar tools
+      uses: ./.github/actions/setup-sonar-tools
+
+    - name: Install apt dependencies
+      uses: ./.github/actions/install-apt-dependencies
+
+    - name: Install additional apt dependencies
+      run: |
+        sudo apt-get update \
+          && sudo apt-get install -y \
+            cmake \
+            python3-venv \
+            lcov
+      shell: bash
+
+    - name: Build AMICI dependencies
+      run: scripts/buildDependencies.sh
+      shell: bash
+
+    - name: Build AMICI
+      run: scripts/buildAmici.sh
+      shell: bash
+      env:
+        CI_SONARCLOUD: "TRUE"

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

@@ -0,0 +1,20 @@
+name: Set up doxygen
+description: |
+  Download, build, and install doxygen.
+
+runs:
+  using: "composite"
+  steps:
+    - name: Install apt dependencies for doxygen
+      run: |
+        sudo apt-get update \
+          && sudo apt-get install -y \
+              bison \
+              ragel \
+              graphviz \
+              texlive-latex-extra
+      shell: bash
+
+    - name: Download and build doxygen
+      run: sudo scripts/downloadAndBuildDoxygen.sh
+      shell: bash

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

@@ -0,0 +1,26 @@
+name: Set up Sonar tools
+description: Download and install sonar-scanner and build-wrapper
+runs:
+  using: "composite"
+  steps:
+    - run: echo "SONAR_SCANNER_VERSION=5.0.1.3006" >> $GITHUB_ENV
+      shell: bash
+    - run: echo "SONAR_SCANNER_HOME=${HOME}/.sonar/sonar-scanner-$SONAR_SCANNER_VERSION-linux" >> $GITHUB_ENV
+      shell: bash
+    - run: echo "SONAR_SCANNER_OPTS=-server" >> $GITHUB_ENV
+      shell: bash
+    - run: echo "${SONAR_SCANNER_HOME}/bin" >> $GITHUB_PATH
+      shell: bash
+    - run: echo "${HOME}/.sonar/build-wrapper-linux-x86" >> $GITHUB_PATH
+      shell: bash
+
+    - name: Install sonarcloud tools
+      run: |
+        sudo apt-get install nodejs curl unzip \
+        && curl --create-dirs -sSLo $HOME/.sonar/sonar-scanner.zip \
+          https://binaries.sonarsource.com/Distribution/sonar-scanner-cli/sonar-scanner-cli-$SONAR_SCANNER_VERSION-linux.zip \
+        && unzip -o $HOME/.sonar/sonar-scanner.zip -d $HOME/.sonar/ \
+        && curl --create-dirs -sSLo $HOME/.sonar/build-wrapper-linux-x86.zip \
+          https://sonarcloud.io/static/cpp/build-wrapper-linux-x86.zip \
+        && unzip -o $HOME/.sonar/build-wrapper-linux-x86.zip -d $HOME/.sonar/ \
+      shell: bash

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

@@ -0,0 +1,20 @@
+name: Set up SWIG
+description: |
+  Download and build SWIG and set the SWIG environment variable to the path of
+  the SWIG executable.
+
+inputs:
+  swig_version:
+    description: 'Swig version to build'
+    required: false
+    default: '4.1.1'
+
+runs:
+  using: "composite"
+  steps:
+    - name: Download and build SWIG
+      run: scripts/downloadAndBuildSwig.sh
+      shell: bash
+
+    - run: echo "SWIG=${AMICI_DIR}/ThirdParty/swig-${{ inputs.swig_version }}/install/bin/swig" >> $GITHUB_ENV
+      shell: bash

.github/workflows/deploy_branch.yml

@@ -21,12 +21,10 @@ jobs:
       with:
         fetch-depth: 20
 
-    - run: echo "AMICI_DIR=$(pwd)" >> $GITHUB_ENV
-    - run: echo "SWIG=${AMICI_DIR}/ThirdParty/swig-4.0.1/install/bin/swig" >> $GITHUB_ENV
+    - name: Set up SWIG
+      uses: ./.github/actions/setup-swig
 
-    - name: Build swig4
-      run: |
-        sudo scripts/downloadAndBuildSwig.sh
+    - run: echo "AMICI_DIR=$(pwd)" >> $GITHUB_ENV
 
     - name: Create AMICI sdist
       run: |

.github/workflows/deploy_release.yml

@@ -24,16 +24,13 @@ jobs:
       with:
         fetch-depth: 20
 
-    - run: echo "AMICI_DIR=$(pwd)" >> $GITHUB_ENV
-    - run: echo "SWIG=${AMICI_DIR}/ThirdParty/swig-4.0.1/install/bin/swig" >> $GITHUB_ENV
+    - name: Set up SWIG
+      uses: ./.github/actions/setup-swig
 
-    - name: Build swig4
-      run: |
-        sudo scripts/downloadAndBuildSwig.sh
+    - run: echo "AMICI_DIR=$(pwd)" >> $GITHUB_ENV
 
     - name: sdist
-      run: |
-        scripts/buildSdist.sh
+      run: scripts/buildSdist.sh
 
     - name: Publish a Python distribution to PyPI
       uses: pypa/gh-action-pypi-publish@release/v1

.github/workflows/test_benchmark_collection_models.yml

@@ -37,18 +37,15 @@ jobs:
       with:
         fetch-depth: 20
 
-    # install dependencies
-    - name: apt
-      run: |
-        sudo apt-get update \
-          && sudo apt-get install -y swig libatlas-base-dev
+    - name: Install apt dependencies
+      uses: ./.github/actions/install-apt-dependencies
 
     - run: echo "${HOME}/.local/bin/" >> $GITHUB_PATH
 
     # install AMICI
     - name: Create AMICI sdist
-      run: |
-        pip3 install build && cd python/sdist && python3 -m build --sdist
+      run: pip3 install build && cd python/sdist && python3 -m build --sdist
+
     - name: Install AMICI sdist
       run: |
         pip3 install --user petab[vis] && \

.github/workflows/test_doc.yml

@@ -16,7 +16,6 @@ on:
 jobs:
   doxygen:
     name: Test Doxygen
-
     runs-on: ubuntu-22.04
 
     strategy:
@@ -32,26 +31,14 @@ jobs:
     - uses: actions/checkout@v3
     - run: git fetch --prune --unshallow
 
-    - name: apt
-      run: |
-        sudo apt-get update \
-          && sudo apt-get install -y \
-          bison \
-          ragel \
-          graphviz \
-          texlive-latex-extra
-
-    - name: Build doxygen
-      run: |
-        sudo scripts/downloadAndBuildDoxygen.sh
+    - name: Set up doxygen
+      uses: ./.github/actions/setup-doxygen
 
     - name: Run doxygen
-      run: |
-        scripts/run-doxygen.sh
+      run: scripts/run-doxygen.sh
 
   sphinx:
     name: Test Sphinx
-
     runs-on: ubuntu-22.04
 
     strategy:
@@ -68,27 +55,22 @@ jobs:
       - run: git fetch --prune --unshallow
 
       - run: echo "AMICI_DIR=$(pwd)" >> $GITHUB_ENV
-      - run: echo "SWIG=${AMICI_DIR}/ThirdParty/swig-4.1.1/install/bin/swig" >> $GITHUB_ENV
 
-      - name: Build doxygen
-        run: |
-          sudo scripts/downloadAndBuildDoxygen.sh
+      - name: Set up doxygen
+        uses: ./.github/actions/setup-doxygen
 
-      # install amici dependencies
-      - name: apt
+      - name: Install apt dependencies
+        uses: ./.github/actions/install-apt-dependencies
+
+      - name: Install further dependencies
         run: |
           sudo apt-get update \
             && sudo apt-get install -y \
-              g++ \
-              libatlas-base-dev \
-              libboost-serialization-dev \
               pandoc \
-              python3-venv \
+              python3-venv
 
-      - name: Build swig
-        run: |
-          sudo scripts/downloadAndBuildSwig.sh
+      - name: Set up SWIG
+        uses: ./.github/actions/setup-swig
 
-      - name: sphinx
-        run: |
-          scripts/run-sphinx.sh
+      - name: Run sphinx
+        run: scripts/run-sphinx.sh

.github/workflows/test_install.yml

@@ -22,33 +22,26 @@ jobs:
 
     - run: echo "AMICI_DIR=$(pwd)" >> $GITHUB_ENV
 
-    # install amici dependencies
+    - name: Install apt dependencies
+      uses: ./.github/actions/install-apt-dependencies
+
     - name: apt
       run: |
         sudo apt-get update \
           && sudo apt-get install -y \
-            cmake \
-            g++ \
-            libatlas-base-dev \
-            libboost-serialization-dev \
-            libhdf5-serial-dev \
-            swig
+            cmake
 
     - name: Build suitesparse
-      run: |
-        scripts/buildSuiteSparse.sh
+      run: scripts/buildSuiteSparse.sh
 
     - name: Build sundials
-      run: |
-        scripts/buildSundials.sh
+      run: scripts/buildSundials.sh
 
     - name: Build AMICI
-      run: |
-        scripts/buildAmici.sh
+      run: scripts/buildAmici.sh
 
     - name: Install python archive
-      run: |
-        scripts/installAmiciArchive.sh
+      run: scripts/installAmiciArchive.sh
 
   sdist_ubuntu:
     name: sdist Install Ubuntu
@@ -70,28 +63,17 @@ jobs:
 
     - run: echo "AMICI_DIR=$(pwd)" >> $GITHUB_ENV
 
-    # install amici dependencies
-    - name: apt
-      run: |
-        sudo apt-get update \
-          && sudo apt-get install -y \
-            g++ \
-            libatlas-base-dev \
-            libboost-serialization-dev \
-            libhdf5-serial-dev \
-            swig
+    - name: Install apt dependencies
+      uses: ./.github/actions/install-apt-dependencies
 
     - name: Create AMICI sdist
-      run: |
-        scripts/buildSdist.sh
+      run: scripts/buildSdist.sh
 
     - name: Install python sdist
-      run: |
-        pip3 install -v --user $(ls -t python/sdist/dist/amici-*.tar.gz | head -1)
+      run: pip3 install -v --user $(ls -t python/sdist/dist/amici-*.tar.gz | head -1)
 
     - name: Test import
-      run: |
-        python -m amici
+      run: python -m amici
 
 
   sdist_macos:
@@ -124,13 +106,10 @@ jobs:
           && echo CPPFLAGS="-I /usr/local/Cellar/boost/1.81.0_1/include/" >> $GITHUB_ENV
 
     - name: Create AMICI sdist
-      run: |
-        scripts/buildSdist.sh
+      run: scripts/buildSdist.sh
 
     - name: Install python sdist
-      run: |
-        pip3 install -v --user $(ls -t python/sdist/dist/amici-*.tar.gz | head -1)
+      run: pip3 install -v --user $(ls -t python/sdist/dist/amici-*.tar.gz | head -1)
 
     - name: Test import
-      run: |
-        python -m amici
+      run: python -m amici

.github/workflows/test_performance.yml

@@ -35,11 +35,9 @@ jobs:
       with:
         fetch-depth: 20
 
-    # install dependencies
-    - name: apt
-      run: |
-        sudo apt-get update \
-          && sudo apt-get install -y swig libatlas-base-dev
+    - name: Install apt dependencies
+      uses: ./.github/actions/install-apt-dependencies
+
     - run: pip3 install petab shyaml build
 
     - run: echo "${HOME}/.local/bin/" >> $GITHUB_PATH