Merge branch 'develop' into test_numpy2

.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

@@ -2,10 +2,58 @@
 
 ## v0.X Series
 
+### 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.
+
+**Fixes**
+* Fixed a bug in event handling that could lead to incorrect simulation
+  results for models with events that assign to compartments *and* have
+  additional event assignments
+  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2428
+* SBML import: handle `useValuesFromTriggerTime` attribute on events.
+  This attribute was previously ignored. It is possible that now AMICI fails
+  to import models that it previously imported successfully. For cases where
+  `useValuesFromTriggerTime=True` made a difference, AMICI might have produced
+  incorrect results before.
+  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2429
+* Faster code generation for models with events if they don't have
+  state-dependent triggers
+  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2417
+* Most warnings now come with a more informative code location
+  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2421
+* `amici.ExpData` was changed so that `isinstance(edata, amici.ExpData)` works
+  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2396
+
+**Features**
+* Event-assignments to compartments are now supported. Previously, this only
+  worked for compartments that were rate rule targets.
+  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2425
+* Releases are now deployed to Docker Hub
+  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2413
+
+**Full Changelog**: https://github.com/AMICI-dev/AMICI/compare/v0.24.0...v0.25.0
+
 ### v0.24.0 (2024-04-22)
 
 This will be the last release supporting Python 3.9.
-Future releases will require Python 3.10.
+Future releases will require Python>=3.10.
 
 **Fixes**
 
@@ -27,7 +75,7 @@ Future releases will require Python 3.10.
   the correct SUNDIALS installation
   by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2397
 
-* **Features**
+**Features**
 
 * Optionally include measurements in `plot_observable_trajectories`
   by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2381

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/conf.py

@@ -104,17 +104,19 @@ def install_mtocpp():
 
 def install_doxygen():
     """Get a more recent doxygen"""
-    version = "1.9.7"
+    version = "1.11.0"
+    release = f"Release_{version.replace('.', '_')}"
+    filename = f"doxygen-{version}.linux.bin.tar.gz"
     doxygen_exe = os.path.join(
         amici_dir, "ThirdParty", f"doxygen-{version}", "bin", "doxygen"
     )
     # to create a symlink to doxygen in a location that is already on PATH
     some_dir_on_path = os.environ["PATH"].split(os.pathsep)[0]
     cmd = (
         f"cd '{os.path.join(amici_dir, 'ThirdParty')}' "
-        f"&& wget 'https://www.doxygen.nl/files/"
-        f"doxygen-{version}.linux.bin.tar.gz' "
-        f"&& tar -xzf doxygen-{version}.linux.bin.tar.gz "
+        f"&& wget 'https://github.com/doxygen/doxygen/releases/download/"
+        f"{release}/{filename}' "
+        f"&& tar -xzf '{filename}' "
         f"&& ln -sf '{doxygen_exe}' '{some_dir_on_path}'"
     )
     subprocess.run(cmd, shell=True, check=True)

documentation/python_interface.rst

@@ -26,7 +26,7 @@ AMICI can import :term:`SBML` models via the
 Status of SBML support in Python-AMICI
 ++++++++++++++++++++++++++++++++++++++
 
-Python-AMICI currently **passes 1247 out of the 1821 (~68%) test cases** from
+Python-AMICI currently **passes 1252 out of the 1821 (~68%) test cases** from
 the semantic
 `SBML Test Suite <https://github.com/sbmlteam/sbml-test-suite/>`_
 (`current status <https://github.com/AMICI-dev/AMICI/actions>`_).

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 @@ def evaluate(expr: StrOrExpr, rdata: ReturnDataView) -> np.array:
     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: