Merge branch 'develop' into fix_reservedsyms

.github/workflows/deploy_release.yml

@@ -36,11 +36,6 @@ 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
 

.github/workflows/test_benchmark_collection_models.yml

@@ -61,13 +61,14 @@ jobs:
       run: |
         git clone --depth 1 https://github.com/benchmarking-initiative/Benchmark-Models-PEtab.git \
           && export BENCHMARK_COLLECTION="$(pwd)/Benchmark-Models-PEtab/Benchmark-Models/" \
+          && pip3 install -e $BENCHMARK_COLLECTION/../src/python \
           && AMICI_PARALLEL_COMPILE="" tests/benchmark-models/test_benchmark_collection.sh
 
     # run gradient checks
     - name: Run Gradient Checks
       run: |
         pip install git+https://github.com/ICB-DCM/fiddy.git \
-          && cd tests/benchmark-models && pytest ./test_petab_benchmark.py
+          && cd tests/benchmark-models && pytest --durations=10 ./test_petab_benchmark.py
 
     # upload results
     - uses: actions/upload-artifact@v4

.github/workflows/test_petab_test_suite.yml

@@ -15,7 +15,7 @@ jobs:
   build:
     name: PEtab Testsuite
 
-    runs-on: ubuntu-22.04
+    runs-on: ubuntu-latest
 
     env:
       ENABLE_GCOV_COVERAGE: TRUE
@@ -68,6 +68,12 @@ jobs:
             && source ./venv/bin/activate \
             && cd petab_test_suite && pip3 install -e .
 
+      - name: Install PEtab 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/" \
+            && source venv/bin/activate && python -m pip install -e $BENCHMARK_COLLECTION/../src/python
+
       - name: Install petab
         run: |
           source ./venv/bin/activate \

.github/workflows/test_python_cplusplus.yml

@@ -125,6 +125,13 @@ jobs:
       with:
         python-version: ${{ matrix.python-version }}
 
+    - name: Cache
+      uses: actions/cache@v4
+      with:
+        path: |
+          ~/.cache/pooch
+        key: ${{ runner.os }}-py${{ matrix.python-version }}-${{ github.job }}
+
     - uses: actions/checkout@v4
     - run: git fetch --prune --unshallow
 
@@ -201,6 +208,13 @@ jobs:
       with:
         python-version: ${{ matrix.python-version }}
 
+    - name: Cache
+      uses: actions/cache@v4
+      with:
+        path: |
+          ~/.cache/pooch
+        key: ${{ runner.os }}-py${{ matrix.python-version }}-${{ github.job }}
+
     - uses: actions/checkout@v4
     - run: git fetch --prune --unshallow
 
@@ -259,6 +273,17 @@ jobs:
     - name: C++ tests
       run: scripts/run-cpp-tests.sh
 
+    - name: Get Pooch Cache Directory
+      id: get-pooch-cache
+      run: |
+        echo "pooch-cache=$(source venv/bin/activate && python -c 'import pooch; print(pooch.os_cache("pooch"))')" >> $GITHUB_ENV
+
+    - name: Cache Pooch Directory
+      uses: actions/cache@v4
+      with:
+        path: ${{ env.pooch-cache }}
+        key: ${{ runner.os }}-py${{ matrix.python-version }}-${{ github.job }}
+
     - name: Python tests
       run: |
         scripts/run-python-tests.sh \
@@ -301,6 +326,24 @@ jobs:
     - name: Get BioNetGen
       run: scripts/buildBNGL.sh
 
+
+    - name: Get Pooch Cache Directory
+      id: get-pooch-cache
+      run: |
+        echo "pooch-cache=$(source venv/bin/activate && python -c 'import pooch; print(pooch.os_cache("pooch"))')" >> $GITHUB_ENV
+
+    - name: Cache Pooch Directory
+      uses: actions/cache@v4
+      with:
+        path: ${{ env.pooch-cache }}
+        key: ${{ runner.os }}-py${{ matrix.python-version }}-${{ github.job }}
+
+    - name: Install PEtab benchmark collection
+      run: |
+        git clone --depth 1 https://github.com/benchmarking-initiative/Benchmark-Models-PEtab.git \
+          && export BENCHMARK_COLLECTION="$(pwd)/Benchmark-Models-PEtab/Benchmark-Models/" \
+          && source venv/bin/activate && python -m pip install -e $BENCHMARK_COLLECTION/../src/python
+
     - name: Python tests
       run: |
         scripts/run-python-tests.sh \

.github/workflows/test_python_ver_matrix.yml

@@ -60,6 +60,17 @@ jobs:
     - run: source venv/bin/activate && pip3 install "sympy>=1.12.1"
       if: matrix.python-version != '3.12'
 
+    - name: Get Pooch Cache Directory
+      id: get-pooch-cache
+      run: |
+        echo "pooch-cache=$(source venv/bin/activate && python -c 'import pooch; print(pooch.os_cache("pooch"))')" >> $GITHUB_ENV
+
+    - name: Cache Pooch Directory
+      uses: actions/cache@v4
+      with:
+        path: ${{ env.pooch-cache }}
+        key: ${{ runner.os }}-py${{ matrix.python-version }}-${{ github.job }}
+
     - name: Python tests
       run: |
         source venv/bin/activate \

.github/workflows/test_windows.yml

@@ -77,6 +77,18 @@ jobs:
 
     - run: python -m amici
 
+    - name: Get Pooch Cache Directory
+      id: get-pooch-cache
+      run: |
+        echo "pooch-cache=$(python -c 'import pooch; print(pooch.os_cache("pooch"))')" >> $GITHUB_ENV
+      shell: bash
+
+    - name: Cache Pooch Directory
+      uses: actions/cache@v4
+      with:
+        path: ${{ env.pooch-cache }}
+        key: ${{ runner.os }}-py${{ matrix.python-version }}-${{ github.job }}
+
     - name: Run Python tests
       shell: bash
       run: |

.gitignore

@@ -182,6 +182,7 @@ ThirdParty/sundials/build/*
 ThirdParty/SuiteSparse/lib/*
 ThirdParty/SuiteSparse/include/
 ThirdParty/SuiteSparse/share/*
+ThirdParty/SuiteSparse/install/*
 ThirdParty/SuperLU_MT_3.1/
 ThirdParty/superlu_mt_3.1.tar.gz
 ThirdParty/swig-*
@@ -203,3 +204,4 @@ cache_fiddy/*
 debug/*
 tests/benchmark-models/cache_fiddy/*
 venv/*
+.coverage

.pre-commit-config.yaml

@@ -12,7 +12,7 @@ repos:
   - id: trailing-whitespace
 - repo: https://github.com/astral-sh/ruff-pre-commit
   # Ruff version.
-  rev: v0.4.1
+  rev: v0.6.7
   hooks:
     # Run the linter.
     - id: ruff
@@ -28,7 +28,7 @@ repos:
         - python/sdist/pyproject.toml
 
 -   repo: https://github.com/asottile/pyupgrade
-    rev: v3.15.2
+    rev: v3.17.0
     hooks:
     -   id: pyupgrade
         args: ["--py310-plus"]

CHANGELOG.md

@@ -4,6 +4,70 @@ See also our [versioning policy](https://amici.readthedocs.io/en/latest/versioni
 
 ## v0.X Series
 
+
+### v0.26.3 (2024-10-03)
+
+**Fixes**
+
+* Skip building SuiteSparse shared libraries and build all subprojects together
+  for slightly faster package installation
+
+  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2514
+  and https://github.com/AMICI-dev/AMICI/pull/2519
+
+* Got rid of petab `DeprecationWarnings` when using the `amici_import_petab`
+  CLI
+
+  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2517
+
+* Now also sundials and suitesparse are built in debug mode when installing
+  with `ENABLE_AMICI_DEBUGGING=TRUE`
+
+  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2515
+
+**Full Changelog**: https://github.com/AMICI-dev/AMICI/compare/v0.26.2...v0.26.3
+
+### v0.26.2 (2024-09-25)
+
+**Fixes**
+
+* Fixed a sympy float comparison issue in spline code that would cause
+  an `AssertionError`
+
+  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2499
+
+* Fixed some warnings from recent CMake versions
+
+  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2492
+
+* Fixed a potential issue when including AMICI in a CMake project
+
+  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2493
+
+**Full Changelog**: https://github.com/AMICI-dev/AMICI/compare/v0.26.1...v0.26.2
+
+
+### v0.26.1 (2024-07-11)
+
+**Fixes**
+
+* Fixed some C++ exception handling that previously could crash Python under
+  certain conditions
+
+  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2484
+
+* Disabled turning warnings into errors when building amici on GitHub Actions
+  in downstream projects
+
+  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2481
+
+* Fixed CMP0167 warning with CMake 3.30
+
+  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2480
+
+
+**Full Changelog**: https://github.com/AMICI-dev/AMICI/compare/v0.26.0...v0.26.1
+
 ### v0.26.0 (2024-07-02)
 
 AMICI v0.26.0 requires sympy>=1.12.1 and petab>=0.4.0.

CMakeLists.txt

@@ -1,17 +1,10 @@
 #
 # Build AMICI library
 #
-cmake_minimum_required(VERSION 3.15)
-cmake_policy(VERSION 3.15...3.27)
-
-# cmake >=3.27
-if(POLICY CMP0144)
-  cmake_policy(SET CMP0144 NEW)
-endif(POLICY CMP0144)
-# cmake >= 3.30
-if(POLICY CMP0167)
-  cmake_policy(SET CMP0167 NEW)
-endif(POLICY CMP0167)
+cmake_minimum_required(VERSION 3.22)
+# When updating the policy version, please also update it in
+# src/CMakeLists.template.cmake
+cmake_policy(VERSION 3.22...3.30)
 
 project(amici)
 
@@ -36,10 +29,11 @@ message(STATUS "CMAKE_INSTALL_PREFIX: ${CMAKE_INSTALL_PREFIX}")
 
 list(APPEND CMAKE_MODULE_PATH ${CMAKE_CURRENT_SOURCE_DIR}/cmake)
 
-if("${CMAKE_CXX_COMPILER_ID}" STREQUAL "GNU")
-  # require at least gcc 4.9, otherwise regex wont work properly
-  if(CMAKE_CXX_COMPILER_VERSION VERSION_LESS 4.9)
-    message(FATAL_ERROR "GCC version must be at least 4.9!")
+if("${CMAKE_CXX_COMPILER_ID}" STREQUAL "GNU" OR "${CMAKE_CXX_COMPILER_ID}"
+                                                STREQUAL "MINGW")
+  # require at least gcc 9.1 for proper C+17 support, e.g. std::reduce
+  if(CMAKE_CXX_COMPILER_VERSION VERSION_LESS 9.1)
+    message(FATAL_ERROR "GCC version must be at least 9.1!")
   endif()
 endif()
 
@@ -136,7 +130,8 @@ elseif(AMICI_TRY_ENABLE_HDF5)
 endif()
 
 set(VENDORED_SUNDIALS_DIR ${CMAKE_CURRENT_SOURCE_DIR}/ThirdParty/sundials)
-set(SUNDIALS_PRIVATE_INCLUDE_DIRS "${VENDORED_SUNDIALS_DIR}/src")
+set(SUNDIALS_PRIVATE_INCLUDE_DIRS
+    "${VENDORED_SUNDIALS_DIR}/src;${VENDORED_SUNDIALS_DIR}/src/sundials")
 # Handle different sundials build/install dirs, depending on whether we are
 # building the Python extension only or the full C++ interface
 if(AMICI_PYTHON_BUILD_EXT_ONLY)
@@ -147,8 +142,7 @@ else()
   set(VENDORED_SUNDIALS_INSTALL_DIR ${VENDORED_SUNDIALS_BUILD_DIR})
 endif()
 set(SUNDIALS_ROOT "${VENDORED_SUNDIALS_INSTALL_DIR}/${CMAKE_INSTALL_LIBDIR}")
-find_package(
-  SUNDIALS REQUIRED CONFIG PATHS "${SUNDIALS_ROOT}/cmake/sundials/")
+find_package(SUNDIALS REQUIRED CONFIG PATHS "${SUNDIALS_ROOT}/cmake/sundials/")
 message(STATUS "Found SUNDIALS: ${SUNDIALS_DIR}")
 
 set(GSL_LITE_INCLUDE_DIR "${CMAKE_CURRENT_SOURCE_DIR}/ThirdParty/gsl")
@@ -231,7 +225,14 @@ set(AMICI_CXX_OPTIONS
     ""
     CACHE STRING "C++ options for libamici (semicolon-separated)")
 target_compile_options(${PROJECT_NAME} PRIVATE "${AMICI_CXX_OPTIONS}")
-
+set_property(
+  SOURCE src/solver_cvodes.cpp
+  APPEND
+  PROPERTY INCLUDE_DIRECTORIES "${SUNDIALS_PRIVATE_INCLUDE_DIRS}")
+set_property(
+  SOURCE src/solver_idas.cpp
+  APPEND
+  PROPERTY INCLUDE_DIRECTORIES "${SUNDIALS_PRIVATE_INCLUDE_DIRS}")
 add_dependencies(${PROJECT_NAME} version)
 
 file(GLOB PUBLIC_HEADERS include/amici/*.h)
@@ -244,8 +245,7 @@ target_include_directories(
          $<INSTALL_INTERFACE:${CMAKE_INSTALL_INCLUDEDIR}>
          $<BUILD_INTERFACE:${GSL_LITE_INCLUDE_DIR}>
          $<INSTALL_INTERFACE:${CMAKE_INSTALL_DATADIR}/amici/swig>
-         $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/swig>
-  PRIVATE ${SUNDIALS_PRIVATE_INCLUDE_DIRS})
+         $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/swig>)
 
 if("$ENV{ENABLE_AMICI_DEBUGGING}"
    OR "$ENV{ENABLE_GCOV_COVERAGE}"
@@ -265,8 +265,7 @@ target_compile_definitions(
 
 target_link_libraries(
   ${PROJECT_NAME}
-  PUBLIC SUNDIALS::generic_static
-         SUNDIALS::nvecserial_static
+  PUBLIC SUNDIALS::nvecserial_static
          SUNDIALS::sunmatrixband_static
          SUNDIALS::sunmatrixdense_static
          SUNDIALS::sunmatrixsparse_static
@@ -377,7 +376,7 @@ export(
 include(CMakePackageConfigHelpers)
 include(version)
 configure_package_config_file(
-  cmake/AmiciConfig.cmake "${CMAKE_CURRENT_BINARY_DIR}/AmiciConfig.cmake"
+  "cmake/AmiciConfig.cmake.in" "${CMAKE_CURRENT_BINARY_DIR}/AmiciConfig.cmake"
   INSTALL_DESTINATION "${CMAKE_INSTALL_LIBDIR}/cmake/Amici")
 write_basic_package_version_file(AmiciConfigVersion.cmake
                                  COMPATIBILITY ExactVersion)