git subrepo clone (merge) --branch=v0.26.1 --force git@github.com:AMI…

…CI-dev/AMICI.git deps/AMICI

subrepo:
  subdir:   "deps/AMICI"
  merged:   "b0d79fff"
upstream:
  origin:   "git@github.com:AMICI-dev/AMICI.git"
  branch:   "v0.26.1"
  commit:   "b0d79fff"
git-subrepo:
  version:  "0.4.6"
  origin:   "https://github.com/ingydotnet/git-subrepo"
  commit:   "110b9eb"

deps/AMICI/.git-blame-ignore-revs

@@ -0,0 +1 @@
+f59fed72eb4d0cedf6abf2a96fe95087ce61478a

deps/AMICI/.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

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

@@ -18,6 +18,9 @@ runs:
     - 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
 

deps/AMICI/.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/ \

deps/AMICI/.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"

deps/AMICI/.github/dependabot.yml

@@ -0,0 +1,11 @@
+version: 2
+updates:
+
+  - package-ecosystem: "github-actions"
+    directory: "/"
+    schedule:
+      interval: "weekly"
+    ignore:
+      - dependency-name: "*"
+        update-types: ["version-update:semver-patch", "version-update:semver-minor"]
+    target-branch: "develop"

deps/AMICI/.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:
@@ -9,15 +9,15 @@ jobs:
 
     strategy:
       matrix:
-        python-version: [3.9]
+        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
       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

deps/AMICI/.github/workflows/deploy_protected.yml

@@ -13,29 +13,44 @@ on:
   workflow_dispatch:
 
 jobs:
-  dockerhub:
-    # https://github.com/marketplace/actions/publish-docker
-    name: Deploy Dockerhub
+  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:
+    name: Deploy Docker Hub
+    needs: [check-secret]
+    if: needs.check-secret.outputs.secrets-defined == 'true'
     runs-on: ubuntu-22.04
 
     strategy:
       matrix:
-        python-version: [3.9]
+        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 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
+      uses: elgohr/Publish-Docker-Github-Action@v5
       with:
         name: dweindl/amici
         username: ${{ secrets.DOCKER_USERNAME }}

deps/AMICI/.github/workflows/deploy_release.yml

@@ -12,15 +12,22 @@ jobs:
 
     strategy:
       matrix:
-        python-version: [3.9]
+        python-version: ["3.11"]
+
+    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
 
@@ -29,14 +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/pyproject.toml
+
     - name: sdist
       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:
@@ -64,3 +74,29 @@ jobs:
             -H "Accept: application/vnd.github.v3+json" \
               https://api.github.com/repos/${DOWNSTREAM_REPOSITORY}/actions/workflows/${WORKFLOW_FILE}/dispatches \
             -d "{\"ref\": \"dev\", \"inputs\": {\"simulatorVersion\": \"${PACKAGE_VERSION}\", \"simulatorVersionLatest\": \"true\"}}"
+
+  dockerhub:
+    name: Release to Docker Hub
+    runs-on: ubuntu-22.04
+
+    steps:
+    - name: Set up Python
+      uses: actions/setup-python@v5
+      with:
+        python-version: "3.11"
+    - 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@v3
+    - name: Set up Docker Buildx
+      uses: docker/setup-buildx-action@v3
+    - name: Publish to Registry
+      uses: elgohr/Publish-Docker-Github-Action@v5
+      with:
+        name: dweindl/amici
+        username: ${{ secrets.DOCKER_USERNAME }}
+        password: ${{ secrets.DOCKER_PASSWORD }}
+        workdir: container/
+        dockerfile: Dockerfile
+        tag_semver: true
+        platforms: linux/amd64,linux/arm64

deps/AMICI/.github/workflows/test_benchmark_collection_models.yml

@@ -22,18 +22,18 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: [ "3.9" ]
+        python-version: [ "3.11" ]
         extract_subexpressions: ["true", "false"]
     env:
       AMICI_EXTRACT_CSE: ${{ matrix.extract_subexpressions }}
 
     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
 
@@ -49,15 +49,19 @@ jobs:
     - 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]
 
+    - run: |
+        python3 -m pip uninstall -y petab && python3 -m pip install git+https://github.com/petab-dev/libpetab-python.git@develop \
+        &&  python3 -m pip install -U sympy
+
     # 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 +70,9 @@ 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

deps/AMICI/.github/workflows/test_doc.yml

@@ -20,15 +20,15 @@ jobs:
 
     strategy:
       matrix:
-        python-version: [3.9]
+        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
 
     - name: Set up doxygen
@@ -43,15 +43,15 @@ 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
@@ -67,10 +67,10 @@ jobs:
           sudo apt-get update \
             && sudo apt-get install -y \
               pandoc \
-              python3-venv
+            && pip install tox
 
       - name: Set up SWIG
         uses: ./.github/actions/setup-swig
 
       - name: Run sphinx
-        run: scripts/run-sphinx.sh
+        run: tox -e doc