Release 0.23.0

Merge pull request #2372 from dweindl/release_0.23.0

.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
 

.github/workflows/deploy_protected.yml

@@ -13,9 +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:
     name: Deploy Dockerhub
-    if: github.event.pull_request.head.repo.fork == false
+    needs: [check-secret]
+    if: needs.check-secret.outputs.secrets-defined == 'true'
     runs-on: ubuntu-22.04
 
     strategy:

.github/workflows/test_petab_test_suite.yml

@@ -57,27 +57,27 @@ jobs:
 
       - name: Install petab
         run: |
-          source ./build/venv/bin/activate \
+          source ./venv/bin/activate \
             && pip3 install wheel pytest shyaml pytest-cov pysb
 
       # retrieve test models
       - name: Download and install PEtab test suite
         run: |
           git clone --depth 1 --branch main \
             https://github.com/PEtab-dev/petab_test_suite \
-            && source ./build/venv/bin/activate \
+            && source ./venv/bin/activate \
             && cd petab_test_suite && pip3 install -e .
 
       - name: Run PEtab-related unit tests
         run: |
-          source ./build/venv/bin/activate \
+          source ./venv/bin/activate \
             && pytest --cov-report=xml:coverage.xml \
               --cov=./ python/tests/test_*petab*.py python/tests/petab/
 
       # run test models
       - name: Run PEtab test suite
         run: |
-          source ./build/venv/bin/activate \
+          source ./venv/bin/activate \
           && AMICI_PARALLEL_COMPILE="" pytest -v \
             --cov-report=xml:coverage.xml \
             --cov-append \

.github/workflows/test_python_cplusplus.yml

@@ -18,6 +18,13 @@ jobs:
         python-version: [ "3.9" ]
 
     steps:
+    - name: Cache
+      uses: actions/cache@v3
+      with:
+        path: |
+          ~/.cache/pooch
+        key: ${{ runner.os }}-py${{ matrix.python-version }}-${{ github.job }}
+
     - name: Set up Python ${{ matrix.python-version }}
       uses: actions/setup-python@v5
       with:
@@ -38,11 +45,11 @@ jobs:
       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())"
+      run: source 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 \
+        source venv/bin/activate \
         && pytest \
           --ignore-glob=*petab* \
           --ignore-glob=*test_splines.py \
@@ -57,7 +64,7 @@ jobs:
     - name: Python tests splines
       if: ${{ github.base_ref == 'master' || github.event.merge_group.base_ref == 'master'}}
       run: |
-        source build/venv/bin/activate \
+        source venv/bin/activate \
         && pytest \
           --cov=amici \
           --cov-report=xml:"${AMICI_DIR}/build/coverage_py.xml" \
@@ -131,7 +138,7 @@ jobs:
 
     - name: Python tests
       run: |
-        source build/venv/bin/activate \
+        source venv/bin/activate \
         && pytest \
           --cov=amici \
           --cov-report=xml:"${AMICI_DIR}/build/coverage_py.xml" \
@@ -207,7 +214,7 @@ jobs:
 
     - name: Install notebook dependencies
       run: |
-        source build/venv/bin/activate \
+        source venv/bin/activate \
         && pip install jax[cpu]
 
     - name: example notebooks
@@ -244,7 +251,7 @@ jobs:
       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())"
+      run: source venv/bin/activate && python -c "import amici; import sys; sys.exit(not amici.compiledWithOpenMP())"
 
     - name: cppcheck
       run: scripts/run-cppcheck.sh
@@ -265,6 +272,13 @@ jobs:
     runs-on: macos-latest
 
     steps:
+    - name: Cache
+      uses: actions/cache@v3
+      with:
+        path: |
+          ~/Library/Caches/pooch
+        key: ${{ runner.os }}-py${{ matrix.python-version }}-${{ github.job }}
+
     - name: Set up Python
       uses: actions/setup-python@v5
       with:
@@ -282,7 +296,7 @@ jobs:
         scripts/installAmiciSource.sh
 
     - name: Check OpenMP support
-      run: source build/venv/bin/activate && python -c "import amici; import sys; sys.exit(not amici.compiledWithOpenMP())"
+      run: source venv/bin/activate && python -c "import amici; import sys; sys.exit(not amici.compiledWithOpenMP())"
 
     - name: Get BioNetGen
       run: scripts/buildBNGL.sh

.github/workflows/test_python_ver_matrix.yml

@@ -50,20 +50,16 @@ jobs:
     - name: Install python package
       run: scripts/installAmiciSource.sh
 
-    # until https://github.com/dateutil/dateutil >2.8.2 is released https://github.com/dateutil/dateutil/issues/1314
-    - run: source build/venv/bin/activate && pip3 install git+https://github.com/dateutil/dateutil.git@296d419fe6bf3b22897f8f210735ac9c4e1cb796
-      if: matrix.python-version == '3.12'
-
     # install pysb before sympy to allow for sympy>=1.12 (https://github.com/pysb/pysb/commit/e83937cb8c74afc9b2fa96595b68464946745f33)
-    - run: source build/venv/bin/activate && pip3 install git+https://github.com/pysb/pysb
+    - run: source venv/bin/activate && pip3 install git+https://github.com/pysb/pysb
 
     # until sympy>1.12 is released
-    - run: source build/venv/bin/activate && pip3 install git+https://github.com/sympy/sympy.git@master
+    - run: source venv/bin/activate && pip3 install git+https://github.com/sympy/sympy.git@master
       if: matrix.python-version == '3.12'
 
     - name: Python tests
       run: |
-        source build/venv/bin/activate \
+        source venv/bin/activate \
           && python3 -m pytest \
             --durations=10 \
             --ignore-glob=*petab* \

.github/workflows/test_sbml_semantic_test_suite.yml

@@ -9,7 +9,7 @@ on:
     paths:
       - .github/workflows/test_sbml_semantic_test_suite.yml
       - python/sdist/amici/de_export.py
-      - python/sdist/amici/de_model.py
+      - python/sdist/amici/de_model_components.py
       - python/sdist/amici/sbml_import.py
       - python/sdist/amici/import_utils.py
       - scripts/run-SBMLTestsuite.sh

.gitignore

@@ -202,3 +202,4 @@ CS_Signalling_ERBB_RAS_AKT/
 cache_fiddy/*
 debug/*
 tests/benchmark-models/cache_fiddy/*
+venv/*

CHANGELOG.md

@@ -2,6 +2,76 @@
 
 ## v0.X Series
 
+### v0.23.0 (2024-03-07)
+
+**Features**
+
+* SBML `InitialAssignment` are no longer absorbed into other model expressions,
+  but are available as parameters or expressions (`w`) in the amici model
+  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2304,
+  https://github.com/AMICI-dev/AMICI/pull/2305,
+  https://github.com/AMICI-dev/AMICI/pull/2345,
+  https://github.com/AMICI-dev/AMICI/pull/2359
+* Upgraded to SuiteSparse 7.6
+  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2316
+* Model expressions `w` are now split into static and dynamic expressions,
+  and only evaluated as needed
+  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2303
+* Exposed additional solver settings:
+  * `Solver.setMaxConvFails()`: maximum number of non-linear solver
+    convergence failures
+  * `Solver.setMaxNonlinIters()`: maximum number of non-linear solver
+    iterations
+  * `Solver.setMaxStepSize()`: maximum step size
+  * `Solver.setConstraints()`: for setting (non)negativity/positivity
+    constraints on state variables
+
+  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2335,
+  https://github.com/AMICI-dev/AMICI/pull/2360,
+  https://github.com/AMICI-dev/AMICI/pull/2340
+* Improved output for debugging simulation failures:
+  `ReturnData.{xdot,J}` now contain the respective
+  values from the timepoint of failure, not the last output timepoint.
+  NaN/Inf warnings now always include the timepoint at which the issue
+  occurred. Note that C++ stacktraces are now only logged for debug builds.
+  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2349,
+  https://github.com/AMICI-dev/AMICI/pull/2347,
+  https://github.com/AMICI-dev/AMICI/pull/2366
+* Updated dataframes import/export to include parameter values and scales
+  by @FFroehlich in https://github.com/AMICI-dev/AMICI/pull/2351
+
+**Fixes**
+
+* CMake: Updated BLAS detection and some minor fixes
+  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2318
+  and https://github.com/AMICI-dev/AMICI/pull/2357
+* Deterministic ordering of source files in generated `CMakeLists.txt`
+  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2322
+* Fixed size check in `Model::setStateIsNonNegative`
+  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2332
+* Fixed uncaught C++ exception in `runAmiciSimulation` that may crash Python
+  in case of invalid values for standard deviations
+  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2338
+* Fixed missing import in `amici/petab/petab_import.py`
+  by @plakrisenko in https://github.com/AMICI-dev/AMICI/pull/2342
+* Fixed `ReturnDataView` `AttributeError: messages`
+  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2341
+* Added a missing return code constant `LSETUP_FAIL`
+  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2353
+* Fixed in-place building of model wheels
+  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2352
+* Made is-zero-checks compatible with the upcoming sympy>1.12
+  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2350
+* Fixed issues with paths containing blanks for sundials
+  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2361
+* Added `amici.petab.conditions` to the API documentation
+  by @PaulJonasJost in https://github.com/AMICI-dev/AMICI/pull/2364
+* Improved type annotations in swig-wrappers
+  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2344,
+  https://github.com/AMICI-dev/AMICI/pull/2365
+
+**Full Changelog**: https://github.com/AMICI-dev/AMICI/compare/v0.22.0...v0.23.0
+
 ### v0.22.0 (2024-02-23)
 
 **Features**

CMakeLists.txt

@@ -119,6 +119,7 @@ endif()
 # find dependencies
 include(GNUInstallDirs)
 
+include(AmiciFindBLAS)
 find_package(OpenMP)
 find_package(Boost COMPONENTS chrono)
 
@@ -142,49 +143,6 @@ message(STATUS "Found SUNDIALS: ${SUNDIALS_DIR}")
 
 set(GSL_LITE_INCLUDE_DIR "${CMAKE_CURRENT_SOURCE_DIR}/ThirdParty/gsl")
 
-# AMICI requires BLAS, currently Intel MKL, CBLAS or MATLAB BLAS can be used.
-# The latter is not supported via CMake yet.
-set(BLAS
-    "CBLAS"
-    CACHE STRING "BLAS library to use")
-set_property(CACHE BLAS PROPERTY STRINGS "CBLAS" "MKL" "ACCELERATE")
-if(${BLAS} STREQUAL "MKL" OR DEFINED ENV{MKLROOT})
-  if(DEFINED ENV{MKLROOT})
-    # This is set by Environment Modules
-    message(STATUS "Using MKL_INCDIR and MKL_LIB from environment module")
-    set(BLAS
-        "MKL"
-        CACHE STRING "BLAS library to use" FORCE)
-    set(BLAS_INCLUDE_DIRS
-        "$ENV{MKL_INCDIR}"
-        CACHE STRING "" FORCE)
-    set(BLAS_LIBRARIES
-        "$ENV{MKL_LIB}"
-        CACHE STRING "" FORCE)
-  else()
-    set(BLAS_INCLUDE_DIRS
-        ""
-        CACHE STRING "")
-    set(BLAS_LIBRARIES
-        -lmkl
-        CACHE STRING "")
-  endif()
-elseif(NOT DEFINED ENV{BLAS_LIBS} AND NOT DEFINED ENV{BLAS_CFLAGS})
-  # if nothing is specified via environment variables, let's try FindBLAS
-  find_package(BLAS)
-  if(NOT BLAS_FOUND)
-    # Nothing specified by the user and FindBLAS didn't find anything; let's try
-    # if cblas is available on the system paths.
-    set(BLAS_INCLUDE_DIRS
-        ""
-        CACHE STRING "")
-    set(BLAS_LIBRARIES
-        -lcblas
-        CACHE STRING "")
-  endif()
-endif()
-add_compile_definitions(AMICI_BLAS_${BLAS})
-
 # Add target to create version file
 add_custom_target(
   version
@@ -259,16 +217,6 @@ set(AMICI_SRC_LIST
 
 add_library(${PROJECT_NAME} ${AMICI_SRC_LIST})
 
-# legacy python package environment variables:
-if(DEFINED ENV{BLAS_CFLAGS})
-  target_compile_options(${PROJECT_NAME} PRIVATE "$ENV{BLAS_CFLAGS}")
-endif()
-if(DEFINED ENV{BLAS_LIBS})
-  # Note that, on Windows, at least for ninja, this will only work with dashes
-  # instead of slashes in any linker options
-  target_link_libraries(${PROJECT_NAME} PUBLIC "$ENV{BLAS_LIBS}")
-endif()
-
 set(AMICI_CXX_OPTIONS
     ""
     CACHE STRING "C++ options for libamici (semicolon-separated)")
@@ -289,10 +237,6 @@ target_include_directories(
          $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/swig>
   PRIVATE ${SUNDIALS_PRIVATE_INCLUDE_DIRS})
 
-if(NOT "${BLAS_INCLUDE_DIRS}" STREQUAL "")
-  target_include_directories(${PROJECT_NAME} PUBLIC ${BLAS_INCLUDE_DIRS})
-endif()
-
 if("$ENV{ENABLE_AMICI_DEBUGGING}"
    OR "$ENV{ENABLE_GCOV_COVERAGE}"
    OR CMAKE_BUILD_TYPE MATCHES "Debug")
@@ -328,11 +272,11 @@ target_link_libraries(
          SUNDIALS::sunnonlinsolfixedpoint_static
          SUNDIALS::cvodes_static
          SUNDIALS::idas_static
-         ${BLAS_LIBRARIES}
          $<$<BOOL:${Boost_CHRONO_FOUND}>:Boost::chrono>
          $<$<BOOL:${OpenMP_FOUND}>:OpenMP::OpenMP_CXX>
          ${CMAKE_DL_LIBS}
   PRIVATE
+    BLAS::BLAS
     $<$<BOOL:${SUNDIALS_SUPERLUMT_ENABLE}>:SUNDIALS::sundials_sunlinsolsuperlumt>
 )
 
@@ -431,16 +375,21 @@ install(
   EXPORT AmiciTargets
   DESTINATION "${CMAKE_INSTALL_LIBDIR}/cmake/Amici"
   NAMESPACE Upstream::)
-install(FILES ${CMAKE_CURRENT_BINARY_DIR}/AmiciConfig.cmake
-              ${CMAKE_CURRENT_BINARY_DIR}/AmiciConfigVersion.cmake
-        DESTINATION ${CMAKE_INSTALL_LIBDIR}/cmake/Amici)
+install(
+  FILES ${CMAKE_CURRENT_BINARY_DIR}/AmiciConfig.cmake
+        ${CMAKE_CURRENT_BINARY_DIR}/AmiciConfigVersion.cmake
+        ${CMAKE_CURRENT_LIST_DIR}/cmake/AmiciFindBLAS.cmake
+  DESTINATION ${CMAKE_INSTALL_LIBDIR}/cmake/Amici)
 
 install(DIRECTORY ThirdParty/gsl/gsl TYPE INCLUDE)
 # When running from setup.py, this is a symlink we need to dereference
 get_filename_component(_swig_realpath "swig" REALPATH)
 install(DIRECTORY "${_swig_realpath}"
         DESTINATION ${CMAKE_INSTALL_DATADIR}/amici)
 
+configure_file(cmake/AmiciFindBLAS.cmake
+               ${CMAKE_CURRENT_BINARY_DIR}/AmiciFindBLAS.cmake COPYONLY)
+
 # Register package?
 if(EXPORT_PACKAGE)
   export(PACKAGE Amici)