Release 0.25.1

.github/dependabot.yml

@@ -8,3 +8,4 @@ updates:
     ignore:
       - dependency-name: "*"
         update-types: ["version-update:semver-patch", "version-update:semver-minor"]
+    target-branch: "develop"

.github/workflows/test_matlab.yml

@@ -21,8 +21,8 @@ jobs:
     - run: echo "AMICI_DIR=$(pwd)" >> $GITHUB_ENV
 
     - name: Install MATLAB
-      uses: matlab-actions/setup-matlab@v1
+      uses: matlab-actions/setup-matlab@v2
     - name: Run script
-      uses: matlab-actions/run-command@v1
+      uses: matlab-actions/run-command@v2
       with:
         command: cd matlab; installAMICI; addpath tests; testModels

.github/workflows/test_python_cplusplus.yml

@@ -19,7 +19,7 @@ jobs:
 
     steps:
     - name: Cache
-      uses: actions/cache@v3
+      uses: actions/cache@v4
       with:
         path: |
           ~/.cache/pooch
@@ -273,7 +273,7 @@ jobs:
 
     steps:
     - name: Cache
-      uses: actions/cache@v3
+      uses: actions/cache@v4
       with:
         path: |
           ~/Library/Caches/pooch

CHANGELOG.md

@@ -2,7 +2,23 @@
 
 ## v0.X Series
 
-### v0.25.0 (2024-05-TBD)
+### v0.25.1 (2024-05-16)
+
+**Fixes**
+* Avoid clashes with sympy-entities in `plot_expressions`
+  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2440
+* PEtab: fix KeyErrors for missing parameters in `fill_in_parameters`
+  (default values are now used if only a subset of parameters is provided)
+  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2449
+* CMake: Fix Intel MKL detection when not using environment modules
+  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2443
+* CMake: Fix some issues with multi-config generators
+  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2445
+
+**Full Changelog**: https://github.com/AMICI-dev/AMICI/compare/v0.25.0...v0.25.1
+
+
+### v0.25.0 (2024-05-08)
 
 This release requires Python >= 3.10.
 

CMakeLists.txt

@@ -90,7 +90,6 @@ if("$ENV{ENABLE_AMICI_DEBUGGING}" OR "$ENV{ENABLE_GCOV_COVERAGE}")
   else()
     add_compile_options(-O0 -g)
   endif()
-  set(CMAKE_BUILD_TYPE "Debug")
 endif()
 
 # coverage options
@@ -135,7 +134,7 @@ endif()
 set(VENDORED_SUNDIALS_DIR ${CMAKE_CURRENT_SOURCE_DIR}/ThirdParty/sundials)
 set(SUNDIALS_PRIVATE_INCLUDE_DIRS "${VENDORED_SUNDIALS_DIR}/src")
 # Handle different sundials build/install dirs, depending on whether we are
-#  building the Python extension only or the full C++ interface
+# building the Python extension only or the full C++ interface
 if(AMICI_PYTHON_BUILD_EXT_ONLY)
   set(VENDORED_SUNDIALS_BUILD_DIR ${CMAKE_CURRENT_SOURCE_DIR})
   set(VENDORED_SUNDIALS_INSTALL_DIR ${VENDORED_SUNDIALS_BUILD_DIR})

cmake/AmiciFindBLAS.cmake

@@ -12,18 +12,33 @@ 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
-        "$ENV{MKL_LIB}"
-        CACHE STRING "" FORCE)
+
+    # Was MKLROOT set by /opt/intel/oneapi/setvars.sh? then cmake will find it
+    message(STATUS "Trying to find BLAS based on MKLROOT=$ENV{MKLROOT}")
+    # give the user the option to override the BLA_VENDOR
+    if(NOT DEFINED BLA_VENDOR)
+      set(BLA_VENDOR Intel10_64lp)
+    endif()
+    message(STATUS "Trying FindBLAS with BLA_VENDOR=${BLA_VENDOR}")
+    find_package(BLAS)
+    if(BLAS_FOUND)
+      message(STATUS "Found BLAS via FindBLAS and MKLROOT")
+    else()
+      # This is set by Environment Modules and might not be compatible with
+      # FindBLAS
+      message(STATUS "Using MKL_INCDIR and MKL_LIB from environment module")
+      set(BLAS_INCLUDE_DIRS
+          "$ENV{MKL_INCDIR}"
+          CACHE STRING "" FORCE)
+      set(BLAS_LIBRARIES
+          "$ENV{MKL_LIB}"
+          CACHE STRING "" FORCE)
+    endif()
   else()
+    message(STATUS "BLAS is set to MKL, but MKLROOT is not set.")
     set(BLAS_INCLUDE_DIRS
         ""
         CACHE STRING "")
@@ -42,6 +57,7 @@ elseif(
 
   if(APPLE AND (NOT DEFINED BLA_VENDOR OR BLA_VENDOR STREQUAL "All"))
     set(BLA_VENDOR Apple)
+    message(STATUS "Trying FindBLAS with BLA_VENDOR=${BLA_VENDOR}")
     find_package(BLAS)
     if(BLAS_FOUND)
       message(STATUS "Found Apple Accelerate BLAS")
@@ -59,6 +75,7 @@ elseif(
 
   endif()
   if(NOT BLAS_FOUND)
+    message(STATUS "Trying FindBLAS with BLA_VENDOR=${BLA_VENDOR}")
     find_package(BLAS)
     if(BLAS_FOUND)
       message(STATUS "Found BLAS via FindBLAS")
@@ -79,17 +96,17 @@ endif()
 # Create an imported target
 if(NOT TARGET BLAS::BLAS)
   add_library(BLAS INTERFACE)
-  set_target_properties(BLAS PROPERTIES
-    INTERFACE_INCLUDE_DIRECTORIES "${BLAS_INCLUDE_DIRS}"
-    INTERFACE_LINK_LIBRARIES "${BLAS_LIBRARIES}")
+  set_target_properties(
+    BLAS PROPERTIES INTERFACE_INCLUDE_DIRECTORIES "${BLAS_INCLUDE_DIRS}"
+                    INTERFACE_LINK_LIBRARIES "${BLAS_LIBRARIES}")
   add_library(BLAS::BLAS ALIAS BLAS)
   if("${PROJECT_NAME}" STREQUAL "amici")
-      install(TARGETS BLAS EXPORT BLAS)
-      export(EXPORT BLAS NAMESPACE BLAS::)
-      install(
-        EXPORT BLAS
-        DESTINATION "${CMAKE_INSTALL_LIBDIR}/cmake/Amici"
-        NAMESPACE BLAS::)
+    install(TARGETS BLAS EXPORT BLAS)
+    export(EXPORT BLAS NAMESPACE BLAS::)
+    install(
+      EXPORT BLAS
+      DESTINATION "${CMAKE_INSTALL_LIBDIR}/cmake/Amici"
+      NAMESPACE BLAS::)
   endif()
 
   # legacy python package environment variables:

cmake/cmakelang-tools.cmake

@@ -9,7 +9,9 @@ set(ALL_CMAKE_FILES
     tests/cpp/unittests/CMakeLists.txt
     ${CMAKE_MODULE_PATH}/cmakelang-tools.cmake
     ${CMAKE_MODULE_PATH}/clang-tools.cmake
+    ${CMAKE_MODULE_PATH}/AmiciFindBLAS.cmake
     ${CMAKE_MODULE_PATH}/version.cmake)
+
 list(JOIN ALL_CMAKE_FILES " " ALL_CMAKE_FILES)
 
 # --- cmake-format ---

documentation/rtd_requirements.txt

@@ -18,7 +18,7 @@ exhale>=0.3.7
 sphinxcontrib-matlabdomain>=0.20.0
 sphinxcontrib-napoleon>=0.7
 pygments>=2.15.1
-Jinja2==3.1.2
+Jinja2==3.1.4
 git+https://github.com/readthedocs/readthedocs-sphinx-ext
 ipykernel
 -e git+https://github.com/Benchmarking-Initiative/Benchmark-Models-PEtab.git@master#subdirectory=src/python&egg=benchmark_models_petab

pytest.ini

@@ -19,5 +19,7 @@ filterwarnings =
     ignore:The --rsyncdir command line argument and rsyncdirs config variable are deprecated.:DeprecationWarning
     ignore:.*:ImportWarning:tellurium
     ignore:.*PyDevIPCompleter6.*:DeprecationWarning
+    # ignore numpy log(0) warnings (np.log(0) = -inf)
+    ignore:divide by zero encountered in log:RuntimeWarning
 
 norecursedirs = .git amici_models build doc documentation matlab models ThirdParty amici sdist examples

python/sdist/amici/numpy.py

@@ -13,7 +13,7 @@
 import amici
 import numpy as np
 import sympy as sp
-
+from sympy.abc import _clash
 from . import ExpData, ExpDataPtr, Model, ReturnData, ReturnDataPtr
 
 StrOrExpr = Union[str, sp.Expr]
@@ -497,7 +497,7 @@
     from sympy.utilities.lambdify import lambdify
 
     if isinstance(expr, str):
-        expr = sp.sympify(expr)
+        expr = sp.sympify(expr, locals=_clash)
 
     arg_names = list(sorted(expr.free_symbols, key=lambda x: x.name))
     func = lambdify(arg_names, expr, "numpy")

python/sdist/amici/petab/simulations.py

@@ -166,30 +166,33 @@ def simulate_petab(
             amici_model=amici_model,
         )
 
+    if problem_parameters is not None and not scaled_parameters:
+        problem_parameters = petab_problem.scale_parameters(problem_parameters)
+    scaled_parameters = True
+
     if problem_parameters is None:
-        # scaled PEtab nominal values
-        problem_parameters = dict(
-            zip(
-                petab_problem.x_ids,
-                petab_problem.x_nominal_scaled,
-                strict=True,
-            )
+        problem_parameters = {}
+
+    # scaled PEtab nominal values
+    default_problem_parameters = dict(
+        zip(
+            petab_problem.x_ids,
+            petab_problem.get_x_nominal(scaled=scaled_parameters),
+            strict=True,
         )
-        # depending on `fill_fixed_parameters` for parameter mapping, the
-        #  parameter mapping may contain values instead of symbols for fixed
-        #  parameters. In this case, we need to filter them here to avoid
-        #  warnings in `fill_in_parameters`.
-        free_parameters = parameter_mapping.free_symbols
-        problem_parameters = {
-            par_id: par_value
-            for par_id, par_value in problem_parameters.items()
-            if par_id in free_parameters
-        }
-
-    elif not scaled_parameters:
-        problem_parameters = petab_problem.scale_parameters(problem_parameters)
+    )
+    # depending on `fill_fixed_parameters` for parameter mapping, the
+    #  parameter mapping may contain values instead of symbols for fixed
+    #  parameters. In this case, we need to filter them here to avoid
+    #  warnings in `fill_in_parameters`.
+    free_parameters = parameter_mapping.free_symbols
+    default_problem_parameters = {
+        par_id: par_value
+        for par_id, par_value in default_problem_parameters.items()
+        if par_id in free_parameters
+    }
 
-    scaled_parameters = True
+    problem_parameters = default_problem_parameters | problem_parameters
 
     # Get edatas
     if edatas is None:

python/sdist/amici/setup.template.py

@@ -24,6 +24,11 @@ def get_extension() -> CMakeExtension:
     else:
         os.environ["CMAKE_BUILD_PARALLEL_LEVEL"] = "1"
 
+    debug_build = os.getenv("ENABLE_AMICI_DEBUGGING", "").lower() in [
+        "1",
+        "true",
+    ] or os.getenv("ENABLE_GCOV_COVERAGE", "").lower() in ["1", "true"]
+
     return CMakeExtension(
         name="model_ext",
         source_dir=os.getcwd(),
@@ -37,6 +42,7 @@ def get_extension() -> CMakeExtension:
             "-DAMICI_PYTHON_BUILD_EXT_ONLY=ON",
             f"-DPython3_EXECUTABLE={Path(sys.executable).as_posix()}",
         ],
+        cmake_build_type="Debug" if debug_build else "Release",
     )
 
 

python/sdist/pyproject.toml

@@ -11,7 +11,7 @@ requires = [
     # cf. discussion at https://github.com/numpy/numpy/issues/5888
     # (https://github.com/scipy/oldest-supported-numpy/)
     "oldest-supported-numpy",
-    "cmake-build-extension==0.5.1",
+    "cmake-build-extension==0.6.0",
 ]
 build-backend = "setuptools.build_meta"
 
@@ -21,7 +21,7 @@ dynamic = ["version"]
 description = "Advanced multi-language Interface to CVODES and IDAS"
 requires-python = ">=3.10"
 dependencies = [
-    "cmake-build-extension==0.5.1",
+    "cmake-build-extension==0.6.0",
     "sympy>=1.9",
     "numpy>=1.19.3; python_version=='3.9'",
     "numpy>=1.21.4; python_version>='3.10'",

python/sdist/setup.py

@@ -141,6 +141,10 @@ def get_extensions():
         ],
     )
     # AMICI
+    debug_build = os.getenv("ENABLE_AMICI_DEBUGGING", "").lower() in [
+        "1",
+        "true",
+    ] or os.getenv("ENABLE_GCOV_COVERAGE", "").lower() in ["1", "true"]
     amici_ext = CMakeExtension(
         name="amici",
         install_prefix="amici",
@@ -153,6 +157,7 @@ def get_extensions():
             "-DAMICI_PYTHON_BUILD_EXT_ONLY=ON",
             f"-DPython3_EXECUTABLE={Path(sys.executable).as_posix()}",
         ],
+        cmake_build_type="Debug" if debug_build else "Release",
     )
     # Order matters!
     return [suitesparse_config, amd, btf, colamd, klu, sundials, amici_ext]

python/tests/test_misc.py

@@ -65,8 +65,9 @@ def test_cmake_compilation(sbml_example_presimulation_module):
     amici_dir = (Path(__file__).parents[2] / "build").absolute()
     cmd = (
         f"set -e; "
-        f"cmake -S {source_dir} -B '{build_dir}' -DAmici_DIR={amici_dir}; "
-        f"cmake --build '{build_dir}'"
+        f"cmake -S {source_dir} -B '{build_dir}' "
+        f"-DCMAKE_BUILD_TYPE=Debug -DAmici_DIR={amici_dir}; "
+        f"cmake --build '{build_dir}' --config Debug"
     )
 
     try:

scripts/buildAmici.sh

@@ -14,7 +14,8 @@ mkdir -p "${amici_build_dir}"
 cd "${amici_build_dir}"
 
 if [ "${GITHUB_ACTIONS:-}" = true ] ||
-  [ "${ENABLE_AMICI_DEBUGGING:-}" = TRUE ]; then
+  [ "${ENABLE_AMICI_DEBUGGING:-}" = TRUE ] ||
+  [ "${ENABLE_GCOV_COVERAGE:-}" = TRUE ]; then
   # Running on CI server
   build_type="Debug"
   # exceptions instead of terminate()

scripts/installAmiciSource.sh

@@ -33,7 +33,7 @@ fi
 export PYTHON_EXECUTABLE="${AMICI_PATH}/venv/bin/python"
 
 python -m pip install --upgrade pip wheel
-python -m pip install --upgrade pip setuptools cmake_build_extension numpy
+python -m pip install --upgrade pip setuptools cmake_build_extension==0.6.0 numpy
 python -m pip install git+https://github.com/FFroehlich/pysb@fix_pattern_matching # pin to PR for SPM with compartments
 AMICI_BUILD_TEMP="${AMICI_PATH}/python/sdist/build/temp" \
   python -m pip install --verbose -e "${AMICI_PATH}/python/sdist[petab,test,vis]" --no-build-isolation

src/CMakeLists.template.cmake

@@ -38,6 +38,10 @@ endif()
 find_package(Amici TPL_AMICI_VERSION REQUIRED HINTS
              ${CMAKE_CURRENT_LIST_DIR}/../../build)
 message(STATUS "Found AMICI ${Amici_DIR}")
+set_target_properties(Upstream::amici PROPERTIES
+    MAP_IMPORTED_CONFIG_RELWITHDEBINFO RelWithDebInfo;Release;
+    MAP_IMPORTED_CONFIG_RELEASE Release
+    MAP_IMPORTED_CONFIG_DEBUG Debug;RelWithDebInfo;)
 
 # Debug build?
 if("$ENV{ENABLE_AMICI_DEBUGGING}" OR "$ENV{ENABLE_GCOV_COVERAGE}")
@@ -47,7 +51,6 @@ if("$ENV{ENABLE_AMICI_DEBUGGING}" OR "$ENV{ENABLE_GCOV_COVERAGE}")
   else()
     add_compile_options(-O0 -g)
   endif()
-  set(CMAKE_BUILD_TYPE "Debug")
 endif()
 
 # coverage options

swig/CMakeLists.txt

@@ -20,7 +20,10 @@ find_package(
   Python3
   COMPONENTS Interpreter Development NumPy
   REQUIRED)
-message(STATUS "Found numpy ${Python3_NumPy_VERSION} include dir ${Python3_NumPy_INCLUDE_DIRS}")
+message(
+  STATUS
+    "Found numpy ${Python3_NumPy_VERSION} include dir ${Python3_NumPy_INCLUDE_DIRS}"
+)
 set(AMICI_INTERFACE_LIST
     ${CMAKE_CURRENT_SOURCE_DIR}/amici.i
     ${CMAKE_CURRENT_SOURCE_DIR}/edata.i

tests/benchmark-models/test_petab_benchmark.py

@@ -36,6 +36,7 @@
         "Isensee_JCB2018",
         "Beer_MolBioSystems2014",
         "Alkan_SciSignal2018",
+        "Lang_PLOSComputBiol2024",
         # excluded due to excessive numerical failures
         "Crauste_CellSystems2017",
         "Fujita_SciSignal2010",

version.txt

@@ -1 +1 @@
-0.25.0
+0.25.1