Merge branch 'develop' into fix_2246_rdata_tlast

CMakeLists.txt

@@ -119,6 +119,7 @@ endif()
 # find dependencies
 include(GNUInstallDirs)
 
+include(AmiciFindBLAS)
 find_package(OpenMP)
 find_package(Boost COMPONENTS chrono)
 
@@ -142,75 +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
-        "$ENV{MKL_LIB}"
-        CACHE STRING "" FORCE)
-  else()
-    set(BLAS_INCLUDE_DIRS
-        ""
-        CACHE STRING "")
-    set(BLAS_LIBRARIES
-        -lmkl
-        CACHE STRING "")
-  endif()
-elseif(
-  NOT DEFINED ENV{BLAS_LIBS}
-  AND NOT DEFINED ENV{BLAS_CFLAGS}
-  AND NOT BLAS_FOUND)
-  # if nothing is specified via environment variables, let's try FindBLAS
-  if($(CMAKE_VERSION) VERSION_GREATER_EQUAL 3.22)
-    set(BLA_SIZEOF_INTEGER 8)
-  endif()
-
-  if(APPLE AND (NOT DEFINED BLA_VENDOR OR BLA_VENDOR STREQUAL "All"))
-    set(BLA_VENDOR Apple)
-    find_package(BLAS)
-    if(BLAS_FOUND)
-      set_property(
-        TARGET BLAS::BLAS
-        APPEND
-        PROPERTY INTERFACE_COMPILE_DEFINITIONS ACCELERATE_NEW_LAPACK)
-      set_property(
-        TARGET BLAS::BLAS
-        APPEND
-        PROPERTY INTERFACE_COMPILE_DEFINITIONS ACCELERATE_LAPACK_ILP64)
-    else()
-      set(BLA_VENDOR "All")
-    endif()
-
-  endif()
-  if(NOT BLAS_FOUND)
-    find_package(BLAS)
-  endif()
-  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
@@ -285,16 +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)")
@@ -315,10 +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")
@@ -354,11 +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>
 )
 
@@ -457,16 +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)

cmake/AmiciConfig.cmake

@@ -1,12 +1,5 @@
 @PACKAGE_INIT@
 
-# TODO remove after cmake files for test models have been regenerated
-# cmake >=3.27
-if(POLICY CMP0144)
-  cmake_policy(SET CMP0144 NEW)
-endif(POLICY CMP0144)
-
-
 include(CMakeFindDependencyMacro)
 
 find_package(OpenMP)
@@ -31,11 +24,13 @@ endif()
 if(NOT DEFINED KLU_ROOT)
   set(KLU_ROOT @CMAKE_SOURCE_DIR@/ThirdParty/SuiteSparse/)
 endif()
-find_package(SuiteSparse_config REQUIRED)
-find_package(AMD REQUIRED)
-find_package(BTF REQUIRED)
-find_package(COLAMD REQUIRED)
-find_package(KLU REQUIRED)
+find_dependency(SuiteSparse_config REQUIRED)
+find_dependency(AMD REQUIRED)
+find_dependency(BTF REQUIRED)
+find_dependency(COLAMD REQUIRED)
+find_dependency(KLU REQUIRED)
+
+include("${CMAKE_CURRENT_LIST_DIR}/AmiciFindBLAS.cmake")
 
 add_library(SUNDIALS::KLU INTERFACE IMPORTED)
 target_link_libraries(
@@ -48,15 +43,15 @@ target_link_libraries(
 set_target_properties(SUNDIALS::KLU PROPERTIES INTERFACE_INCLUDE_DIRECTORIES
                                                "${KLU_INCLUDE_DIR}")
 
-find_package(SUNDIALS REQUIRED PATHS
+find_dependency(SUNDIALS REQUIRED PATHS
              "@CMAKE_SOURCE_DIR@/ThirdParty/sundials/build/@CMAKE_INSTALL_LIBDIR@/cmake/sundials/")
 
 if(@Boost_CHRONO_FOUND@)
-  find_package(Boost COMPONENTS chrono REQUIRED)
+  find_dependency(Boost COMPONENTS chrono REQUIRED)
 endif()
 
 if(@HDF5_FOUND@)
-  find_package(
+  find_dependency(
     HDF5
     COMPONENTS C HL CXX
     REQUIRED)

cmake/AmiciFindBLAS.cmake

@@ -0,0 +1,110 @@
+# Find a BLAS
+#
+# AMICI requires BLAS, currently Intel MKL, CBLAS or MATLAB BLAS can be used.
+# The latter is not supported via CMake yet.
+#
+# This module defines the BLAS::BLAS IMPORTED target.
+
+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
+        "$ENV{MKL_LIB}"
+        CACHE STRING "" FORCE)
+  else()
+    set(BLAS_INCLUDE_DIRS
+        ""
+        CACHE STRING "")
+    set(BLAS_LIBRARIES
+        -lmkl
+        CACHE STRING "")
+  endif()
+elseif(
+  NOT DEFINED ENV{BLAS_LIBS}
+  AND NOT DEFINED ENV{BLAS_CFLAGS}
+  AND NOT BLAS_FOUND)
+  # if nothing is specified via environment variables, let's try FindBLAS
+  if($(CMAKE_VERSION) VERSION_GREATER_EQUAL 3.22)
+    set(BLA_SIZEOF_INTEGER 8)
+  endif()
+
+  if(APPLE AND (NOT DEFINED BLA_VENDOR OR BLA_VENDOR STREQUAL "All"))
+    set(BLA_VENDOR Apple)
+    find_package(BLAS)
+    if(BLAS_FOUND)
+      message(STATUS "Found Apple Accelerate BLAS")
+      set_property(
+        TARGET BLAS::BLAS
+        APPEND
+        PROPERTY INTERFACE_COMPILE_DEFINITIONS ACCELERATE_NEW_LAPACK)
+      set_property(
+        TARGET BLAS::BLAS
+        APPEND
+        PROPERTY INTERFACE_COMPILE_DEFINITIONS ACCELERATE_LAPACK_ILP64)
+    else()
+      set(BLA_VENDOR "All")
+    endif()
+
+  endif()
+  if(NOT BLAS_FOUND)
+    find_package(BLAS)
+    if(BLAS_FOUND)
+      message(STATUS "Found BLAS via FindBLAS")
+    endif()
+  endif()
+  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()
+
+# 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}")
+  add_library(BLAS::BLAS ALIAS BLAS)
+  install(TARGETS BLAS EXPORT BLAS)
+  export(EXPORT BLAS NAMESPACE BLAS::)
+  install(
+    EXPORT BLAS
+    DESTINATION "${CMAKE_INSTALL_LIBDIR}/cmake/Amici"
+    NAMESPACE BLAS::)
+
+
+  # legacy python package environment variables:
+  if(DEFINED ENV{BLAS_CFLAGS})
+    target_compile_options(BLAS INTERFACE "$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(BLAS INTERFACE "$ENV{BLAS_LIBS}")
+  endif()
+
+  if(NOT "${BLAS_INCLUDE_DIRS}" STREQUAL "")
+    target_include_directories(BLAS INTERFACE ${BLAS_INCLUDE_DIRS})
+  endif()
+  target_compile_definitions(BLAS INTERFACE "AMICI_BLAS_${BLAS}")
+else()
+  target_compile_definitions(BLAS::BLAS INTERFACE "AMICI_BLAS_${BLAS}")
+endif()

python/sdist/amici/swig.py

@@ -15,6 +15,7 @@ class TypeHintFixer(ast.NodeTransformer):
         "ptrdiff_t": ast.Name("int"),
         "size_t": ast.Name("int"),
         "bool": ast.Name("bool"),
+        "boolean": ast.Name("bool"),
         "std::unique_ptr< amici::Solver >": ast.Constant("Solver"),
         "amici::InternalSensitivityMethod": ast.Constant(
             "InternalSensitivityMethod"
@@ -40,8 +41,10 @@ class TypeHintFixer(ast.NodeTransformer):
             "SteadyStateSensitivityMode"
         ),
         "amici::realtype": ast.Name("float"),
-        "DoubleVector": ast.Constant("Sequence[float]"),
+        "DoubleVector": ast.Name("Sequence[float]"),
+        "BoolVector": ast.Name("Sequence[bool]"),
         "IntVector": ast.Name("Sequence[int]"),
+        "StringVector": ast.Name("Sequence[str]"),
         "std::string": ast.Name("str"),
         "std::string const &": ast.Name("str"),
         "std::unique_ptr< amici::ExpData >": ast.Constant("ExpData"),
@@ -53,6 +56,8 @@ class TypeHintFixer(ast.NodeTransformer):
     }
 
     def visit_FunctionDef(self, node):
+        self._annotation_from_docstring(node)
+
         # Has a return type annotation?
         if node.returns:
             node.returns = self._new_annot(node.returns.value)
@@ -103,6 +108,42 @@ def _new_annot(self, old_annot: str):
 
         return ast.Constant(old_annot)
 
+    def _annotation_from_docstring(self, node: ast.FunctionDef):
+        """Add annotations based on docstring.
+
+        If any argument or return type of the function is not annotated, but
+        the corresponding docstring contains a type hint, the type hint is used
+        as the annotation.
+        """
+        docstring = ast.get_docstring(node, clean=False)
+        if not docstring or "*Overload 1:*" in docstring:
+            # skip overloaded methods
+            return
+
+        docstring = docstring.split("\n")
+        lines_to_remove = set()
+
+        for line_no, line in enumerate(docstring):
+            if match := re.match(r"\W*:rtype:\W*(.+)", line):
+                node.returns = ast.Constant(match.group(1))
+                lines_to_remove.add(line_no)
+
+            if match := re.match(r"\W*:type:\W*(\w+):\W*(.+)", line):
+                for arg in node.args.args:
+                    if arg.arg == match.group(1):
+                        arg.annotation = ast.Constant(match.group(2))
+                        lines_to_remove.add(line_no)
+
+        if lines_to_remove:
+            # Update docstring with type annotations removed
+            assert isinstance(node.body[0].value, ast.Constant)
+            new_docstring = "\n".join(
+                line
+                for line_no, line in enumerate(docstring)
+                if line_no not in lines_to_remove
+            )
+            node.body[0].value = ast.Str(new_docstring)
+
 
 def fix_typehints(infilename, outfilename):
     """Change SWIG-generated C++ typehints to Python typehints"""