Release 0.11.13

.github/workflows/test_benchmark_collection_models.yml

@@ -28,10 +28,6 @@ jobs:
         sudo apt-get update \
           && sudo apt-get install -y swig libatlas-base-dev
 
-    - name: pip
-      run: |
-        pip3 install --upgrade --user wheel \
-          && pip3 install --upgrade --user setuptools
     - run: pip3 install pytest shyaml
 
     - run: echo "${HOME}/.local/bin/" >> $GITHUB_PATH
@@ -40,7 +36,7 @@ jobs:
     # install AMICI
     - name: Create AMICI sdist
       run: |
-        cd python/sdist && /usr/bin/python3 setup.py sdist
+        pip3 install build && cd python/sdist && python3 -m build --sdist
     - name: Install AMICI sdist
       run: |
         AMICI_PARALLEL_COMPILE=2 pip3 install -v --user \

.github/workflows/test_doc.yml

@@ -47,7 +47,7 @@ jobs:
       - run: git fetch --prune --unshallow
 
       - run: echo "AMICI_DIR=$(pwd)" >> $GITHUB_ENV
-      - run: echo "SWIG=${AMICI_DIR}/ThirdParty/swig-4.0.1/install/bin/swig" >> $GITHUB_ENV
+      - run: echo "SWIG=${AMICI_DIR}/ThirdParty/swig-4.0.2/install/bin/swig" >> $GITHUB_ENV
 
       - name: Build doxygen
         run: |
@@ -74,10 +74,6 @@ jobs:
         run: |
           sudo scripts/downloadAndBuildSwig.sh
 
-      - name: pip
-        run: |
-          pip3 install setuptools
-
       - name: sphinx
         run: |
           scripts/run-sphinx.sh

.github/workflows/test_install.yml

@@ -37,10 +37,6 @@ jobs:
       run: |
         scripts/buildCpputest.sh
 
-    - name: pip
-      run: |
-        pip3 install numpy
-
     - name: Build AMICI
       run: |
         scripts/buildAmici.sh

.github/workflows/test_performance.yml

@@ -28,10 +28,6 @@ jobs:
       run: |
         sudo apt-get update \
           && sudo apt-get install -y swig libatlas-base-dev
-    - name: pip
-      run: |
-        pip3 install --upgrade --user wheel \
-          && pip3 install --upgrade --user setuptools
     - run: pip3 install petab shyaml
 
     - run: echo "${HOME}/.local/bin/" >> $GITHUB_PATH

.github/workflows/test_petab_test_suite.yml

@@ -35,10 +35,6 @@ jobs:
             libatlas-base-dev \
             python3-venv
 
-      - name: pip
-        run: |
-          pip3 install --upgrade --user wheel \
-            && pip3 install --upgrade --user setuptools
       - run: pip3 install pytest shyaml pytest-cov pysb petab
 
       - name: Build BNGL
@@ -48,7 +44,7 @@ jobs:
       - run: |
           echo "${HOME}/.local/bin/" >> $GITHUB_PATH
           echo "${GITHUB_WORKSPACE}/tests/performance/" >> $GITHUB_PATH
-          echo "BNGPATH=${GITHUB_WORKSPACE}/ThirdParty/BioNetGen-2.3.2" >> $GITHUB_ENV
+          echo "BNGPATH=${GITHUB_WORKSPACE}/ThirdParty/BioNetGen-2.5.2" >> $GITHUB_ENV
 
       # install AMICI
       - name: Install python package
@@ -58,7 +54,7 @@ jobs:
       # retrieve test models
       - name: Download and install PEtab test suite
         run: |
-          git clone --depth 1  --branch pysb https://github.com/FFroehlich/petab_test_suite \
+          git clone --depth 1  --branch develop https://github.com/PEtab-dev/petab_test_suite \
             && source ./build/venv/bin/activate \
             && cd petab_test_suite && pip3 install -e . && cd ..
 

.github/workflows/test_python_cplusplus.yml

@@ -17,7 +17,7 @@ jobs:
     - run: git fetch --prune --unshallow
 
     - run: echo "AMICI_DIR=$(pwd)" >> $GITHUB_ENV
-    - run: echo "BNGPATH=${GITHUB_WORKSPACE}/ThirdParty/BioNetGen-2.3.2" >> $GITHUB_ENV
+    - run: echo "BNGPATH=${GITHUB_WORKSPACE}/ThirdParty/BioNetGen-2.5.2" >> $GITHUB_ENV
 
     # sonar cloud
     - run: echo "SONAR_SCANNER_VERSION=4.5.0.2216" >> $GITHUB_ENV
@@ -85,10 +85,18 @@ jobs:
           --cov-report=xml:"${AMICI_DIR}/build/coverage_py.xml" \
           --cov-append \
           ${AMICI_DIR}/python/tests
+
+    - name: example notebooks
+      run: |
+        scripts/runNotebook.sh python/examples/example_*/
+
+    - name: doc notebooks
+      run: |
+        scripts/runNotebook.sh documentation/GettingStarted.ipynb
 
     - name: Codecov Python
       uses: codecov/codecov-action@v1
-      with:
+      with: 
         token: ${{ secrets.CODECOV_TOKEN }}
         file: ./build/coverage_py.xml
         flags: python
@@ -130,7 +138,7 @@ jobs:
     - run: git fetch --prune --unshallow
 
     - run: echo "AMICI_DIR=$(pwd)" >> $GITHUB_ENV
-    - run: echo "BNGPATH=${AMICI_DIR}/ThirdParty/BioNetGen-2.3.2" >> $GITHUB_ENV
+    - run: echo "BNGPATH=${AMICI_DIR}/ThirdParty/BioNetGen-2.5.2" >> $GITHUB_ENV
 
     # install amici dependencies
     - name: homebrew

.github/workflows/test_python_ver_matrix.yml

@@ -15,17 +15,23 @@ jobs:
     name: Python Version Matrix
 
     runs-on: ubuntu-20.04
-
+    continue-on-error: ${{ matrix.experimental }}
     env:
       AMICI_SKIP_CMAKE_TESTS: "TRUE"
 
     strategy:
+      fail-fast: false
       matrix:
-        python-version: [3.6, 3.7, 3.8, 3.9]
+        python-version: [3.7, 3.8, 3.9]
+        experimental: [false]
+# Temporarily disabled because the respective jobs somehow runs infinitely
+#        include:
+#          - python-version:  3.10.0-alpha.5
+#            experimental: true
 
     steps:
     - run: echo "AMICI_DIR=$(pwd)" >> $GITHUB_ENV
-    - run: echo "BNGPATH=${AMICI_DIR}/ThirdParty/BioNetGen-2.3.2" >> $GITHUB_ENV
+    - run: echo "BNGPATH=${AMICI_DIR}/ThirdParty/BioNetGen-2.5.2" >> $GITHUB_ENV
 
     - name: Set up Python ${{ matrix.python-version }}
       uses: actions/setup-python@v2
@@ -45,11 +51,6 @@ jobs:
           libatlas-base-dev \
           libhdf5-serial-dev \
           libboost-math-dev
-    - name: pip
-      run: |
-        pip3 install --upgrade --user wheel \
-          && pip3 install --upgrade --user setuptools
-
 
     # install AMICI
     - name: Build BNGL
@@ -65,7 +66,3 @@ jobs:
           && pip3 install pytest \
           && pip3 install git+https://github.com/pysb/pysb \
           && python3 -m pytest --ignore-glob=*petab* ${AMICI_DIR}/python/tests
-
-    - name: notebooks
-      run: |
-        scripts/runNotebook.sh python/examples/example_*/

.github/workflows/test_sbml_semantic_test_suite.yml

@@ -29,7 +29,7 @@ jobs:
     - name: apt
       run: |
         sudo apt-get update \
-          && sudo apt-get install -y swig3.0 libatlas-base-dev
+          && sudo apt-get install -y swig4.0 libatlas-base-dev
     - run: AMICI_PARALLEL_COMPILE=2 ./scripts/installAmiciSource.sh
     - run: AMICI_PARALLEL_COMPILE=2 ./scripts/run-SBMLTestsuite.sh
 

CMakeLists.txt

@@ -127,14 +127,15 @@ set(AMICI_SRC_LIST
     ${CMAKE_SOURCE_DIR}/src/rdata.cpp
     ${CMAKE_SOURCE_DIR}/src/edata.cpp
     ${CMAKE_SOURCE_DIR}/src/exception.cpp
-
+    ${CMAKE_SOURCE_DIR}/src/simulation_parameters.cpp
     ${CMAKE_SOURCE_DIR}/src/spline.cpp
     ${CMAKE_SOURCE_DIR}/src/solver.cpp
     ${CMAKE_SOURCE_DIR}/src/solver_cvodes.cpp
     ${CMAKE_SOURCE_DIR}/src/solver_idas.cpp
     ${CMAKE_SOURCE_DIR}/src/model.cpp
     ${CMAKE_SOURCE_DIR}/src/model_ode.cpp
     ${CMAKE_SOURCE_DIR}/src/model_dae.cpp
+    ${CMAKE_SOURCE_DIR}/src/model_state.cpp
     ${CMAKE_SOURCE_DIR}/src/newton_solver.cpp
     ${CMAKE_SOURCE_DIR}/src/forwardproblem.cpp
     ${CMAKE_SOURCE_DIR}/src/steadystateproblem.cpp
@@ -230,12 +231,13 @@ install(TARGETS ${PROJECT_NAME} EXPORT AmiciTargets
 export(EXPORT AmiciTargets FILE AmiciTargets.cmake
     NAMESPACE Upstream::
     )
-configure_file(cmake/AmiciConfig.cmake
-    "${CMAKE_CURRENT_BINARY_DIR}/AmiciConfig.cmake"
-    @ONLY
-    )
 include(CMakePackageConfigHelpers)
 include(version)
+configure_package_config_file(
+    cmake/AmiciConfig.cmake
+    "${CMAKE_CURRENT_BINARY_DIR}/AmiciConfig.cmake"
+    INSTALL_DESTINATION "${LIB_INSTALL_DIR}/cmake/"
+    )
 write_basic_package_version_file(AmiciConfigVersion.cmake COMPATIBILITY ExactVersion)
 install(FILES ${CMAKE_CURRENT_BINARY_DIR}/AmiciConfig.cmake
     ${CMAKE_CURRENT_BINARY_DIR}/AmiciTargets.cmake

README.md

@@ -85,7 +85,7 @@ To install AMICI, first read the installation instructions for
 [Matlab](https://amici.readthedocs.io/en/develop/matlab_installation.html).
 
 To get you started with Python-AMICI, the best way might be checking out this
-[Jupyter notebook](https://github.com/AMICI-dev/AMICI/blob/master/python/examples/example_steadystate/ExampleSteadystate.ipynb).
+[Jupyter notebook](https://github.com/AMICI-dev/AMICI/blob/master/documentation/GettingStarted.ipynb).
 
 To get started with Matlab-AMICI, various examples are available
 in [matlab/examples/](https://github.com/AMICI-dev/AMICI/tree/master/matlab/examples).