Merge branch 'develop' into py312

.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-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/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:

.github/workflows/test_doc.yml

@@ -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

.github/workflows/test_install.yml

@@ -1,5 +1,5 @@
 name: Installation
-on: [push, merge_group, workflow_dispatch]
+on: [push, pull_request, merge_group, workflow_dispatch]
 
 jobs:
   archive:

.github/workflows/test_petab_test_suite.yml

@@ -85,6 +85,7 @@ jobs:
             tests/petab_test_suite/
 
       - name: Codecov
+        if: github.event_name == 'pull_request' || github.repository_owner == 'AMICI-dev'
         uses: codecov/[email protected]
         with:
           token: ${{ secrets.CODECOV_TOKEN }}

.github/workflows/test_python_cplusplus.yml

@@ -6,22 +6,16 @@ on:
   pull_request:
     branches:
       - master
+      - develop
 
 jobs:
-  build:
-    name: Tests Ubuntu
-
-    # TODO: prepare image with more deps preinstalled
+  ubuntu-cpp-python-tests:
+    name: C++/Python tests Ubuntu
     runs-on: ubuntu-22.04
 
-    env:
-      AMICI_PARALLEL_COMPILE: ""
-      ENABLE_GCOV_COVERAGE: "TRUE"
-      CI_SONARCLOUD: "TRUE"
-
     strategy:
       matrix:
-        python-version: [ 3.9 ]
+        python-version: [ "3.9" ]
 
     steps:
     - name: Set up Python ${{ matrix.python-version }}
@@ -33,48 +27,33 @@ jobs:
     - run: git fetch --prune --unshallow
 
     - run: echo "AMICI_DIR=$(pwd)" >> $GITHUB_ENV
-    - run: echo "BNGPATH=${GITHUB_WORKSPACE}/ThirdParty/BioNetGen-2.7.0" >> $GITHUB_ENV
-
-    - name: Set up Sonar tools
-      uses: ./.github/actions/setup-sonar-tools
-
-    - name: Install apt dependencies
-      uses: ./.github/actions/install-apt-dependencies
 
-    # install amici dependencies
-    - name: apt
-      run: |
-        sudo apt-get update \
-          && sudo apt-get install -y \
-            cmake \
-            python3-venv \
-            lcov
-
-    - name: Build AMICI dependencies
-      run: scripts/buildDependencies.sh
-
-    - name: Build AMICI
-      run: CI_SONARCLOUD=TRUE scripts/buildAmici.sh
+    - name: Set up AMICI C++ libraries
+      uses: ./.github/actions/setup-amici-cpp
 
     - name: C++ tests
       run: scripts/run-cpp-tests.sh
 
     - name: Install python package
       run: scripts/installAmiciSource.sh
 
-    - name: Python tests
+    - name: Check OpenMP support
+      run: source build/venv/bin/activate && python -c "import amici; import sys; sys.exit(not amici.compiledWithOpenMP())"
+
+    - name: Python tests (part 1)
       run: |
         source build/venv/bin/activate \
         && pytest \
           --ignore-glob=*petab* \
           --ignore-glob=*test_splines.py \
+          --ignore-glob=*test_splines_short.py \
+          --ignore-glob=*test_pysb.py \
           --cov=amici \
           --cov-report=xml:"${AMICI_DIR}/build/coverage_py.xml" \
           --cov-append \
           --durations=10 \
           ${AMICI_DIR}/python/tests
 
-
     - name: Python tests splines
       if: ${{ github.base_ref == 'master' || github.event.merge_group.base_ref == 'master'}}
       run: |
@@ -86,18 +65,83 @@ jobs:
           --durations=10 \
           ${AMICI_DIR}/python/tests/test_splines.py
 
-    - name: Install notebook dependencies
+    - name: Codecov Python
+      if: github.event_name == 'pull_request' || github.repository_owner == 'AMICI-dev'
+      uses: codecov/[email protected]
+      with:
+        token: ${{ secrets.CODECOV_TOKEN }}
+        file: build/coverage_py.xml
+        flags: python
+        fail_ci_if_error: true
+        verbose: true
+
+    - name: Capture coverage info (lcov)
       run: |
-        source build/venv/bin/activate \
-        && pip install jax[cpu]
+        lcov --compat-libtool --no-external \
+        -d ${AMICI_DIR}/build/CMakeFiles/amici.dir/src \
+        -b ${AMICI_DIR} -c -o coverage_cpp.info \
+        && lcov --compat-libtool --no-external \
+        -d ${AMICI_DIR}/python/sdist/build/temp_amici/CMakeFiles/amici.dir/src \
+        -b ${AMICI_DIR}/python/sdist -c -o coverage_py.info \
+        && lcov -a coverage_cpp.info -a coverage_py.info -o coverage.info
 
-    - name: example notebooks
-      run: scripts/runNotebook.sh python/examples/example_*/
+    - name: Codecov CPP
+      if: github.event_name == 'pull_request' || github.repository_owner == 'AMICI-dev'
+      uses: codecov/[email protected]
+      with:
+        token: ${{ secrets.CODECOV_TOKEN }}
+        file: coverage.info
+        flags: cpp
+        fail_ci_if_error: true
 
-    - name: doc notebooks
-      run: scripts/runNotebook.sh documentation/GettingStarted.ipynb
+    - name: Run sonar-scanner
+      if: ${{ env.SONAR_TOKEN != '' }}
+      env:
+        GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        SONAR_TOKEN: ${{ secrets.SONAR_TOKEN }}
+      run: |
+        sonar-scanner \
+         -Dsonar.cfamily.build-wrapper-output=bw-output \
+         -Dsonar.projectVersion="$(git describe --abbrev=4 --dirty=-dirty --always --tags | tr -d '\n')"
+
+  ubuntu-python-tests:
+    name: Python tests Ubuntu
+    runs-on: ubuntu-22.04
+
+    strategy:
+      matrix:
+        python-version: [ "3.9" ]
+
+    steps:
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v4
+      with:
+        python-version: ${{ matrix.python-version }}
+
+    - uses: actions/checkout@v3
+    - run: git fetch --prune --unshallow
+
+    - run: echo "AMICI_DIR=$(pwd)" >> $GITHUB_ENV
+
+    - name: Set up AMICI C++ libraries
+      uses: ./.github/actions/setup-amici-cpp
+
+    - name: Install python package
+      run: scripts/installAmiciSource.sh
+
+    - name: Python tests
+      run: |
+        source build/venv/bin/activate \
+        && pytest \
+          --cov=amici \
+          --cov-report=xml:"${AMICI_DIR}/build/coverage_py.xml" \
+          --cov-append \
+          --durations=10 \
+          ${AMICI_DIR}/python/tests/test_pysb.py \
+          ${AMICI_DIR}/python/tests/test_splines_short.py
 
     - name: Codecov Python
+      if: github.event_name == 'pull_request' || github.repository_owner == 'AMICI-dev'
       uses: codecov/[email protected]
       with:
         token: ${{ secrets.CODECOV_TOKEN }}
@@ -106,7 +150,7 @@ jobs:
         fail_ci_if_error: true
         verbose: true
 
-    - name: lcov
+    - name: Capture coverage info (lcov)
       run: |
         lcov --compat-libtool --no-external \
         -d ${AMICI_DIR}/build/CMakeFiles/amici.dir/src \
@@ -117,14 +161,16 @@ jobs:
         && lcov -a coverage_cpp.info -a coverage_py.info -o coverage.info
 
     - name: Codecov CPP
+      if: github.event_name == 'pull_request' || github.repository_owner == 'AMICI-dev'
       uses: codecov/[email protected]
       with:
         token: ${{ secrets.CODECOV_TOKEN }}
         file: coverage.info
-        flags: cpp
+        flags: cpp_python
         fail_ci_if_error: true
 
     - name: Run sonar-scanner
+      if: ${{ env.SONAR_TOKEN != '' }}
       env:
         GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
         SONAR_TOKEN: ${{ secrets.SONAR_TOKEN }}
@@ -133,6 +179,45 @@ jobs:
          -Dsonar.cfamily.build-wrapper-output=bw-output \
          -Dsonar.projectVersion="$(git describe --abbrev=4 --dirty=-dirty --always --tags | tr -d '\n')"
 
+
+  ubuntu-notebook-tests:
+    name: Notebook tests Ubuntu
+    runs-on: ubuntu-22.04
+
+    strategy:
+      matrix:
+        python-version: [ "3.9" ]
+
+    steps:
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v4
+      with:
+        python-version: ${{ matrix.python-version }}
+
+    - uses: actions/checkout@v3
+    - run: git fetch --prune --unshallow
+
+    - run: echo "AMICI_DIR=$(pwd)" >> $GITHUB_ENV
+
+    - name: Set up AMICI C++ libraries
+      uses: ./.github/actions/setup-amici-cpp
+
+    - name: Install python package
+      run: scripts/installAmiciSource.sh
+
+    - name: Install notebook dependencies
+      run: |
+        source build/venv/bin/activate \
+        && pip install jax[cpu]
+
+    - name: example notebooks
+      run: scripts/runNotebook.sh python/examples/example_*/
+
+    - name: doc notebooks
+      run: scripts/runNotebook.sh documentation/GettingStarted.ipynb
+
+    # TODO: Include notebooks in coverage report
+
   osx:
     name: Tests OSX
     runs-on: macos-latest
@@ -150,22 +235,22 @@ jobs:
     - run: echo "BNGPATH=${AMICI_DIR}/ThirdParty/BioNetGen-2.7.0" >> $GITHUB_ENV
     # Ensure CMake is using the python version that we will use for the python tests later on
     - run: echo "PYTHON_EXECUTABLE=${Python3_ROOT_DIR}/bin/python3" >> $GITHUB_ENV
+    - run: echo "OpenMP_ROOT=$(brew --prefix)/opt/libomp" >> $GITHUB_ENV
+    - run: echo "BOOST_ROOT=$(brew --prefix)/opt/boost" >> $GITHUB_ENV
 
     # install amici dependencies
     - name: homebrew
-      run: |
-        brew install hdf5 swig gcc cppcheck libomp boost \
-          && brew ls -v boost \
-          && brew ls -v libomp \
-          && echo LDFLAGS="-L/usr/local/lib/ -L/usr/local/Cellar/boost/1.81.0_1/lib/" >> $GITHUB_ENV \
-          && echo CPPFLAGS="-I /usr/local/Cellar/boost/1.81.0_1/include/" >> $GITHUB_ENV
+      run: brew install hdf5 swig gcc cppcheck libomp boost
 
     - name: Build AMICI
       run: scripts/buildAll.sh
 
     - name: Install python package
       run: scripts/installAmiciSource.sh
 
+    - name: Check OpenMP support
+      run: source build/venv/bin/activate && python -c "import amici; import sys; sys.exit(not amici.compiledWithOpenMP())"
+
     - name: cppcheck
       run: scripts/run-cppcheck.sh
 

.github/workflows/test_sbml_semantic_test_suite.yml

@@ -54,6 +54,7 @@ jobs:
         path: tests/amici-semantic-results
 
     - name: Codecov SBMLSuite
+      if: github.event_name == 'pull_request' || github.repository_owner == 'AMICI-dev'
       uses: codecov/[email protected]
       with:
         token: ${{ secrets.CODECOV_TOKEN }}

.github/workflows/test_windows.yml

@@ -7,6 +7,7 @@ on:
     - cron:  '48 4 * * *'
   pull_request:
     branches:
+      - develop
       - master
 
 jobs: