Merge branch 'develop' into check_grad_sbml_test_suite

Author: dweindl

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

@@ -0,0 +1,31 @@
+name: Install AMICI dependencies for MacOS
+description: Install AMICI dependencies for MacOS
+
+runs:
+  using: "composite"
+  steps:
+    # use all available cores
+    - run: echo "AMICI_PARALLEL_COMPILE=" >> $GITHUB_ENV
+      shell: bash
+
+    # AMICI repository root
+    - run: echo "AMICI_DIR=$(pwd)" >> $GITHUB_ENV
+      shell: bash
+
+    # BioNetGen path
+    - run: echo "BNGPATH=${AMICI_DIR}/ThirdParty/BioNetGen-2.7.0" >> $GITHUB_ENV
+      shell: bash
+
+    # CMake hints
+    # Ensure CMake is using the python version that we will use for the python tests later on
+    - run: echo "PYTHON_EXECUTABLE=${Python3_ROOT_DIR}/bin/python3" >> $GITHUB_ENV
+      shell: bash
+    - run: echo "OpenMP_ROOT=$(brew --prefix)/opt/libomp" >> $GITHUB_ENV
+      shell: bash
+    - run: echo "BOOST_ROOT=$(brew --prefix)/opt/boost" >> $GITHUB_ENV
+      shell: bash
+
+    # install amici dependencies
+    - name: homebrew
+      run: brew install hdf5 swig gcc libomp boost
+      shell: bash

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

@@ -0,0 +1,47 @@
+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
+
+    - run: echo "PYTHONFAULTHANDLER=1" >> $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-sonar-tools/action.yml

@@ -16,7 +16,8 @@ runs:
 
     - name: Install sonarcloud tools
       run: |
-        sudo apt-get install nodejs curl unzip \
+        sudo apt-get update \
+        && 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/ \

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

@@ -7,7 +7,7 @@ inputs:
   swig_version:
     description: 'Swig version to build'
     required: false
-    default: '4.1.1'
+    default: '4.2.0'
 
 runs:
   using: "composite"

.github/workflows/deploy_branch.yml

@@ -1,5 +1,5 @@
 name: Deploy Branch
-on: [push, merge_group, workflow_dispatch]
+on: [push, pull_request, merge_group, workflow_dispatch]
 
 jobs:
   sdist:
@@ -13,11 +13,11 @@ jobs:
 
     steps:
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
 
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
       with:
         fetch-depth: 20
 
@@ -31,7 +31,7 @@ jobs:
         scripts/buildSdist.sh
 
     - name: "Upload artifact: sdist"
-      uses: actions/upload-artifact@v3
+      uses: actions/upload-artifact@v4
       with:
         name: sdist
         path: python/sdist/dist/amici-*.gz

.github/workflows/deploy_protected.yml

@@ -13,10 +13,25 @@ on:
   workflow_dispatch:
 
 jobs:
+  check-secret:
+    runs-on: ubuntu-latest
+    outputs:
+      secrets-defined: ${{ steps.secret-check.outputs.defined }}
+    steps:
+      - name: Check for Secret availability
+        id: secret-check
+        shell: bash
+        run: |
+          if [ "${{ secrets.DOCKER_USERNAME }}" != '' ]; then
+            echo "defined=true" >> $GITHUB_OUTPUT;
+          else
+            echo "defined=false" >> $GITHUB_OUTPUT;
+          fi
+
   dockerhub:
-    # https://github.com/marketplace/actions/publish-docker
     name: Deploy Dockerhub
-
+    needs: [check-secret]
+    if: needs.check-secret.outputs.secrets-defined == 'true'
     runs-on: ubuntu-22.04
 
     strategy:
@@ -25,15 +40,15 @@ jobs:
 
     steps:
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
     - run: git archive -o container/amici.tar.gz --format=tar.gz HEAD
     - name: Set up QEMU
-      uses: docker/setup-qemu-action@v2
+      uses: docker/setup-qemu-action@v3
     - name: Set up Docker Buildx
-      uses: docker/setup-buildx-action@v2
+      uses: docker/setup-buildx-action@v3
     - name: Publish to Registry
       uses: elgohr/Publish-Docker-Github-Action@v4
       with:

.github/workflows/deploy_release.yml

@@ -14,13 +14,20 @@ jobs:
       matrix:
         python-version: [3.9]
 
+    environment:
+      name: pypi
+      url: https://pypi.org/p/amici
+
+    permissions:
+      id-token: write
+
     steps:
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
 
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
       with:
         fetch-depth: 20
 
@@ -29,15 +36,17 @@ jobs:
 
     - run: echo "AMICI_DIR=$(pwd)" >> $GITHUB_ENV
 
+    - name: Remove direct dependencies from setup.cfg
+      # Remove any "git+https"-based dependencies that are not supported
+      #  by PyPI and are only required for testing.
+      run: sed -i '/git+https/d' python/sdist/setup.cfg
+
     - 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
       with:
-        user: __token__
-        password: ${{ secrets.pypi_password }}
         packages-dir: python/sdist/dist
 
   bioSimulatorsUpdateCliAndDockerImage:

.github/workflows/test_benchmark_collection_models.yml

@@ -29,11 +29,11 @@ jobs:
 
     steps:
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
 
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
       with:
         fetch-depth: 20
 
@@ -44,20 +44,20 @@ jobs:
 
     # 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] && \
-        AMICI_PARALLEL_COMPILE=2 pip3 install -v --user \
+        AMICI_PARALLEL_COMPILE="" pip3 install -v --user \
             $(ls -t python/sdist/dist/amici-*.tar.gz | head -1)[petab,test,vis]
 
     # retrieve test models
     - name: Download and test benchmark collection
       run: |
         git clone --depth 1 https://github.com/benchmarking-initiative/Benchmark-Models-PEtab.git \
           && export BENCHMARK_COLLECTION="$(pwd)/Benchmark-Models-PEtab/Benchmark-Models/" \
-          && AMICI_PARALLEL_COMPILE=2 tests/benchmark-models/test_benchmark_collection.sh
+          && AMICI_PARALLEL_COMPILE="" tests/benchmark-models/test_benchmark_collection.sh
 
     # run gradient checks
     - name: Run Gradient Checks
@@ -66,9 +66,9 @@ jobs:
           && cd tests/benchmark-models && pytest ./test_petab_benchmark.py
 
     # upload results
-    - uses: actions/upload-artifact@v3
+    - uses: actions/upload-artifact@v4
       with:
-        name: computation times
+        name: computation-times-${{ matrix.python-version }}-${{ matrix.extract_subexpressions }}
         path: |
           tests/benchmark-models/computation_times.csv
           tests/benchmark-models/computation_times.png

.github/workflows/test_doc.yml

@@ -24,11 +24,11 @@ jobs:
 
     steps:
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
 
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
     - run: git fetch --prune --unshallow
 
     - name: Set up doxygen
@@ -43,34 +43,34 @@ jobs:
 
     strategy:
       matrix:
-        python-version: [ "3.10" ]
+        python-version: [ "3.11" ]
 
     steps:
       - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
 
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - run: git fetch --prune --unshallow
 
       - run: echo "AMICI_DIR=$(pwd)" >> $GITHUB_ENV
 
       - 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 \
+            && pip install tox
 
-      - uses: ./.github/actions/setup-swig
+      - name: Set up SWIG
+        uses: ./.github/actions/setup-swig
 
-      - name: sphinx
-        run: scripts/run-sphinx.sh
+      - name: Run sphinx
+        run: tox -e doc