Turn to scikit-build-core

Proof-of-concept to support Python 3.12
Supports parallel build

.github/workflows/build.yml

@@ -44,3 +44,11 @@ jobs:
       run: python3 setup.py install --user --sundials-home=/usr --blas-home=/usr/lib/x86_64-linux-gnu/ --lapack-home=/usr/lib/x86_64-linux-gnu/ --superlu-home=/usr
     - name: Test
       run: python3 -m nose --verbose tests/* tests/solvers/*
+
+    - name: Build (cmake)
+      run: |
+        cmake -B build -DCMAKE_INSTALL_PREFIX=~/.local .
+        rm -r ~/.local/lib/python3.*/site-packages/assimulo
+        cmake --build build --target install --parallel 3
+    - name: Test (cmake)
+      run: python3 -m nose --verbose tests/* tests/solvers/*

CMakeLists.txt

@@ -0,0 +1,327 @@
+cmake_minimum_required (VERSION 3.17)
+
+project (assimulo LANGUAGES C)
+
+list (APPEND CMAKE_MODULE_PATH ${PROJECT_SOURCE_DIR}/cmake)
+
+option(USE_FORTRAN "build Fortran modules" ON)
+option(USE_SUNDIALS "build SUNDIALS modules" ON)
+option(USE_SUPERLU "use SUPERLU lib" ON)
+if (USE_FORTRAN)
+  enable_language(Fortran)
+endif ()
+
+find_package (Python COMPONENTS Interpreter Development.Module NumPy REQUIRED)
+include(GNUInstallDirs)
+if (NOT DEFINED PYTHON_SITE_PACKAGES)
+  if (WIN32)
+    set (PYTHON_SITE_PACKAGES Lib/site-packages CACHE PATH "site-packages dir")
+  else ()
+    set (PYTHON_SITE_PACKAGES ${CMAKE_INSTALL_LIBDIR}/python${Python_VERSION_MAJOR}.${Python_VERSION_MINOR}/site-packages CACHE PATH "site-packages dir")
+  endif ()
+endif ()
+
+find_package(LAPACK)
+
+if (USE_SUPERLU)
+  find_package (SuperLU_MT)
+endif ()
+
+if (USE_SUNDIALS)
+  find_package (SUNDIALS CONFIG)
+
+  if (SUNDIALS_FOUND)
+    message(STATUS "Found SUNDIALS: ${SUNDIALS_DIR}  (found version \"${SUNDIALS_VERSION}\")")
+  else ()
+    # fallback to our module
+    find_package (SUNDIALS MODULE)
+    set(SUNDIALS_DIR ${SUNDIALS_INCLUDE_DIRS})
+  endif ()
+
+  if (SUNDIALS_FOUND)
+    string (REGEX REPLACE "([0-9]+)\\..*" "\\1" SUNDIALS_MAJOR_VERSION "${SUNDIALS_VERSION}")
+    string (REGEX REPLACE "[0-9]+\\.([0-9]+).*" "\\1" SUNDIALS_MINOR_VERSION "${SUNDIALS_VERSION}")
+    string (REGEX REPLACE "[0-9]+\\.[0-9]+\\.([0-9]+).*" "\\1" SUNDIALS_PATCH_VERSION "${SUNDIALS_VERSION}")
+    math(EXPR SUNDIALS_VERSION_NR "100000 * ${SUNDIALS_MAJOR_VERSION} + 100 * ${SUNDIALS_MINOR_VERSION} + ${SUNDIALS_PATCH_VERSION}")
+
+    if (NOT DEFINED SUNDIALS_INCLUDE_DIR)
+      find_path (SUNDIALS_INCLUDE_DIR sundials/sundials_config.h HINTS ${SUNDIALS_DIR}/../../../../include ${SUNDIALS_DIR}/../../../include)
+    endif ()
+
+    file (STRINGS ${SUNDIALS_INCLUDE_DIR}/sundials/sundials_config.h _SUNDIALS_INT64_DEFINE REGEX "^#define SUNDIALS_INT64_T")
+    if (_SUNDIALS_INT64_DEFINE)
+      set (SUNDIALS_VECTOR_SIZE 64)
+    else ()
+      set (SUNDIALS_VECTOR_SIZE 32)
+    endif ()
+    message(STATUS "SUNDIALS has vector type size ${SUNDIALS_VECTOR_SIZE} bits")
+
+    # only SUNDIALS_SUPERLUMT_THREAD_TYPE is consistent across sundials versions
+    file (STRINGS ${SUNDIALS_INCLUDE_DIR}/sundials/sundials_config.h _SUNDIALS_SUPERLUMT_DEFINE REGEX "^#define SUNDIALS_SUPERLUMT_THREAD_TYPE \"(PTHREAD|OPENMP)\"")
+    if (_SUNDIALS_SUPERLUMT_DEFINE)
+      set (SUNDIALS_WITH_SUPERLU True)
+    else ()
+      set (SUNDIALS_WITH_SUPERLU False)
+    endif ()
+    message(STATUS "SUNDIALS has SuperLU support: ${SUNDIALS_WITH_SUPERLU}")
+
+    file (STRINGS ${SUNDIALS_INCLUDE_DIR}/sundials/sundials_config.h _SUNDIALS_CVODE_RTOL_VEC_DEFINE REGEX "^#define SUNDIALS_CVODE_RTOL_VEC")
+    if (_SUNDIALS_CVODE_RTOL_VEC_DEFINE)
+      set (SUNDIALS_CVODE_RTOL_VEC True)
+    else ()
+      set (SUNDIALS_CVODE_RTOL_VEC False)
+    endif ()
+    message(STATUS "SUNDIALS has CVode rtol vectors support: ${SUNDIALS_CVODE_RTOL_VEC}")
+
+  endif ()
+endif ()
+
+set (cython_clones)
+# copy /src tree into CMAKE_BINARY_DIR/assimulo
+file (GLOB_RECURSE cython_sources src/*.pyx src/*.pxd src/*.py)
+foreach (file ${cython_sources})
+  if (EXISTS ${file})
+    file (RELATIVE_PATH rel_file "${CMAKE_SOURCE_DIR}/src" "${file}")
+    get_filename_component (rel_path ${rel_file} PATH)
+    file (MAKE_DIRECTORY ${CMAKE_BINARY_DIR}/assimulo/${rel_path})
+    set (cython_clone ${CMAKE_BINARY_DIR}/assimulo/${rel_file})
+    execute_process(COMMAND ${CMAKE_COMMAND} -E copy ${file} ${cython_clone})
+    add_custom_command (OUTPUT ${cython_clone}
+      COMMENT "Copying ${file}"
+      COMMAND ${CMAKE_COMMAND} -E copy ${file} ${cython_clone}
+      DEPENDS ${file}
+    )
+    list (APPEND cython_clones ${cython_clone})
+  endif ()
+endforeach ()
+
+# copy /thirdparty tree into CMAKE_BINARY_DIR
+file (GLOB_RECURSE cython_sources thirdparty/*.pyx thirdparty/*.pxd thirdparty/*.py)
+foreach (file ${cython_sources})
+  if (EXISTS ${file})
+    file (RELATIVE_PATH rel_file "${CMAKE_SOURCE_DIR}/thirdparty" "${file}")
+    get_filename_component (rel_path ${rel_file} PATH)
+    file (MAKE_DIRECTORY ${CMAKE_BINARY_DIR}/thirdparty/${rel_path})
+    set (cython_clone ${CMAKE_BINARY_DIR}/thirdparty/${rel_file})
+    execute_process(COMMAND ${CMAKE_COMMAND} -E copy ${file} ${cython_clone})
+    add_custom_command (OUTPUT ${cython_clone}
+      COMMENT "Copying ${file}"
+      COMMAND ${CMAKE_COMMAND} -E copy ${file} ${cython_clone}
+      DEPENDS ${file}
+    )
+    list (APPEND cython_clones ${cython_clone})
+  endif ()
+endforeach ()
+
+macro(assimulo_add_cython_module pyx_file)
+  cmake_parse_arguments(CMOD "" "DESTINATION" "SOURCES" ${ARGN})
+  if (NOT DEFINED CMOD_DESTINATION)
+    set (CMOD_DESTINATION assimulo)
+  endif ()
+  get_filename_component(name "${pyx_file}" NAME_WE)
+  get_filename_component(subdir "${pyx_file}" DIRECTORY)
+
+  # PYTHONNOUSERSITE=0 overrides skbuild and allows to use Cython from ~/.local when not available via system packages
+  add_custom_command(
+    OUTPUT ${name}.c
+    COMMENT "Making ${name}.c from ${name}.pyx"
+    COMMAND ${CMAKE_COMMAND} -E env PYTHONNOUSERSITE=0 ${Python_EXECUTABLE} -m cython -o ${name}.c
+            --3str --fast-fail ${EXTRA_CYTHON_FLAGS}
+            -I ${CMAKE_CURRENT_SOURCE_DIR}/src
+            -I ${CMAKE_CURRENT_SOURCE_DIR}/src/lib
+            ${CMAKE_CURRENT_BINARY_DIR}/${pyx_file}
+    DEPENDS ${cython_clones} VERBATIM)
+
+  python_add_library(${name} MODULE ${name}.c ${CMOD_SOURCES} WITH_SOABI)
+  target_include_directories(${name} PRIVATE ${CMAKE_CURRENT_SOURCE_DIR}/src ${CMAKE_CURRENT_SOURCE_DIR}/${subdir})
+  target_link_libraries(${name} PRIVATE Python::NumPy)
+  target_compile_definitions(${name} PRIVATE NPY_NO_DEPRECATED_API=NPY_1_7_API_VERSION)
+  if (CMAKE_C_COMPILER_ID MATCHES "GNU")
+    target_compile_options(${name} PRIVATE $<$<COMPILE_LANGUAGE:C>:-O2 -fno-strict-aliasing>)
+  endif ()
+  install(TARGETS ${name} DESTINATION ${PYTHON_SITE_PACKAGES}/${CMOD_DESTINATION})
+endmacro()
+
+assimulo_add_cython_module(assimulo/explicit_ode.pyx
+  SOURCES src/ode_event_locator.c)
+assimulo_add_cython_module(assimulo/algebraic.pyx)
+assimulo_add_cython_module(assimulo/implicit_ode.pyx)
+assimulo_add_cython_module(assimulo/ode.pyx)
+assimulo_add_cython_module(assimulo/problem.pyx)
+assimulo_add_cython_module(assimulo/special_systems.pyx)
+assimulo_add_cython_module(assimulo/support.pyx)
+assimulo_add_cython_module(assimulo/solvers/euler.pyx
+  DESTINATION assimulo/solvers)
+
+if (SUNDIALS_FOUND)
+  set(EXTRA_CYTHON_FLAGS -E SUNDIALS_VERSION_NR=${SUNDIALS_VERSION_NR} -E SUNDIALS_VECTOR_SIZE=${SUNDIALS_VECTOR_SIZE} -E SUNDIALS_WITH_SUPERLU=${SUNDIALS_WITH_SUPERLU} -E SUNDIALS_CVODE_RTOL_VEC=${SUNDIALS_CVODE_RTOL_VEC})
+
+  assimulo_add_cython_module(assimulo/solvers/sundials.pyx
+    DESTINATION assimulo/solvers)
+  target_link_libraries(sundials PRIVATE sundials_cvodes sundials_nvecserial sundials_idas)
+  if (SUNDIALS_VERSION VERSION_GREATER_EQUAL 3)
+    target_link_libraries(sundials PRIVATE sundials_sunlinsoldense sundials_sunlinsolspgmr sundials_sunmatrixdense sundials_sunmatrixsparse)
+  endif ()
+  if (SUNDIALS_VERSION VERSION_GREATER_EQUAL 7)
+    target_link_libraries(sundials PRIVATE sundials_core)
+  endif ()
+  if (SUNDIALS_WITH_SUPERLU)
+    target_link_libraries(sundials PRIVATE SuperLU_MT::SuperLU_MT)
+    if (SUNDIALS_VERSION VERSION_GREATER_EQUAL 3)
+      target_link_libraries(sundials PRIVATE sundials_sunlinsolsuperlumt)
+    endif ()
+  endif ()
+
+  assimulo_add_cython_module(assimulo/solvers/kinsol.pyx
+    DESTINATION assimulo/solvers)
+  target_link_libraries(kinsol PRIVATE sundials_kinsol sundials_nvecserial)
+  if (SUNDIALS_VERSION VERSION_GREATER_EQUAL 7)
+    target_link_libraries(kinsol PRIVATE sundials_core)
+  endif ()
+  if (SUNDIALS_WITH_SUPERLU)
+    target_link_libraries(kinsol PRIVATE SuperLU_MT::SuperLU_MT)
+  endif ()
+endif ()
+
+
+assimulo_add_cython_module(thirdparty/radau5/radau5ode.pyx
+  SOURCES thirdparty/radau5/radau5.c thirdparty/radau5/radau5_io.c
+  DESTINATION assimulo/lib)
+
+if (SuperLU_MT_FOUND)
+  target_sources(radau5ode PRIVATE thirdparty/radau5/superlu_double.c thirdparty/radau5/superlu_complex.c thirdparty/radau5/superlu_util.c)
+  target_link_libraries(radau5ode PRIVATE SuperLU_MT::SuperLU_MT)
+  target_compile_definitions(radau5ode PRIVATE __RADAU5_WITH_SUPERLU)
+endif()
+
+if (USE_FORTRAN)
+
+  find_program(F2PY_EXECUTABLE NAMES f2py f2py3 REQUIRED)
+
+  if (NOT DEFINED F2PY_INCLUDE_DIR)
+    execute_process(COMMAND ${Python_EXECUTABLE} -c "from numpy import f2py; print(f2py.get_include())"
+      OUTPUT_VARIABLE F2PY_INCLUDE_DIR
+      OUTPUT_STRIP_TRAILING_WHITESPACE)
+  endif()
+  message(STATUS "Using f2py include dir: ${F2PY_INCLUDE_DIR}")
+
+  # object library with common f2py symbols
+  add_library(fortranobject OBJECT ${F2PY_INCLUDE_DIR}/fortranobject.c)
+  target_link_libraries(fortranobject PUBLIC Python::NumPy)
+  target_compile_definitions(fortranobject PUBLIC NPY_NO_DEPRECATED_API=NPY_1_7_API_VERSION)
+  target_include_directories(fortranobject PUBLIC ${F2PY_INCLUDE_DIR})
+  set_target_properties(fortranobject PROPERTIES POSITION_INDEPENDENT_CODE TRUE)
+
+  macro(assimulo_add_fortran_module name pyf_file)
+    cmake_parse_arguments(FMOD "" "" "SOURCES" ${ARGN})
+    add_custom_command(
+      OUTPUT ${name}module.c
+      COMMENT "Making ${name}module.c from ${pyf_file}"
+      COMMAND ${F2PY_EXECUTABLE} ${CMAKE_CURRENT_SOURCE_DIR}/${pyf_file}
+      DEPENDS ${pyf_file} VERBATIM)
+
+    # may be created or not
+    file(TOUCH ${CMAKE_CURRENT_BINARY_DIR}/${name}-f2pywrappers.f)
+    file(TOUCH ${CMAKE_CURRENT_BINARY_DIR}/${name}-f2pywrappers2.f90)
+
+    python_add_library(${name} MODULE ${FMOD_SOURCES}
+      ${CMAKE_CURRENT_BINARY_DIR}/${name}module.c
+      ${CMAKE_CURRENT_BINARY_DIR}/${name}-f2pywrappers.f
+      ${CMAKE_CURRENT_BINARY_DIR}/${name}-f2pywrappers2.f90
+      WITH_SOABI)
+    set_source_files_properties(${CMAKE_CURRENT_BINARY_DIR}/${name}module.c ${CMAKE_CURRENT_BINARY_DIR}/${name}-f2pywrappers.f ${CMAKE_CURRENT_BINARY_DIR}/${name}-f2pywrappers2.f90 PROPERTIES GENERATED TRUE)
+
+    target_link_libraries(${name} PRIVATE fortranobject)
+    if (CMAKE_Fortran_COMPILER_ID MATCHES "GNU")
+      target_compile_options(${name} PRIVATE $<$<COMPILE_LANGUAGE:Fortran>:-O2 --std=legacy>)
+    endif ()
+    install(TARGETS ${name} DESTINATION ${PYTHON_SITE_PACKAGES}/assimulo/lib)
+  endmacro()
+
+  assimulo_add_fortran_module(dopri5 thirdparty/hairer/dopri5.pyf
+    SOURCES thirdparty/hairer/dopri5.f)
+
+  assimulo_add_fortran_module(rodas thirdparty/hairer/rodas_decsol.pyf
+    SOURCES thirdparty/hairer/rodas_decsol.f)
+
+  assimulo_add_fortran_module(radau5 thirdparty/hairer/radau_decsol.pyf
+    SOURCES thirdparty/hairer/radau_decsol.f)
+
+  assimulo_add_fortran_module(radar5 thirdparty/hairer/radar5.pyf
+    SOURCES
+      thirdparty/hairer/contr5.f90
+      thirdparty/hairer/radar5_int.f90
+      thirdparty/hairer/radar5.f90
+      thirdparty/hairer/dontr5.f90
+      thirdparty/hairer/decsol.f90
+      thirdparty/hairer/dc_decdel.f90)
+
+  assimulo_add_fortran_module(odepack thirdparty/odepack/odepack.pyf
+    SOURCES
+      thirdparty/odepack/opkdmain.f
+      thirdparty/odepack/opkda1.f
+      thirdparty/odepack/opkda2.f
+      thirdparty/odepack/odepack_aux.f90)
+
+  assimulo_add_fortran_module(odassl thirdparty/odassl/odassl.pyf
+    SOURCES
+      thirdparty/odassl/odassl.f
+      thirdparty/odassl/odastp.f
+      thirdparty/odassl/odacor.f
+      thirdparty/odassl/odajac.f
+      thirdparty/odassl/d1mach.f
+      thirdparty/odassl/daxpy.f
+      thirdparty/odassl/ddanrm.f
+      thirdparty/odassl/ddatrp.f
+      thirdparty/odassl/ddot.f
+      thirdparty/odassl/ddwats.f
+      thirdparty/odassl/dgefa.f
+      thirdparty/odassl/dgesl.f
+      thirdparty/odassl/dscal.f
+      thirdparty/odassl/idamax.f
+      thirdparty/odassl/xerrwv.f)
+  if (CMAKE_Fortran_COMPILER_ID MATCHES "GNU")
+    target_compile_options(odassl PRIVATE $<$<COMPILE_LANGUAGE:Fortran>:-fdefault-double-8 -fdefault-real-8>)
+  endif ()
+
+  assimulo_add_fortran_module(dasp3dp thirdparty/dasp3/dasp3dp.pyf
+    SOURCES
+      thirdparty/dasp3/DASP3.f
+      thirdparty/dasp3/ANORM.f
+      thirdparty/dasp3/CTRACT.f
+      thirdparty/dasp3/DECOMP.f
+      thirdparty/dasp3/HMAX.f
+      thirdparty/dasp3/INIVAL.f
+      thirdparty/dasp3/JACEST.f
+      thirdparty/dasp3/PDERIV.f
+      thirdparty/dasp3/PREPOL.f
+      thirdparty/dasp3/SOLVE.f
+      thirdparty/dasp3/SPAPAT.f)
+
+  if (LAPACK_FOUND)
+    assimulo_add_fortran_module(glimda thirdparty/glimda/glimda_complete.pyf
+      SOURCES
+        thirdparty/glimda/glimda_complete.f)
+    target_link_libraries(glimda PRIVATE ${LAPACK_LIBRARIES})
+  endif ()
+endif ()
+
+install(FILES src/__init__.py
+  src/exception.py
+  src/problem_algebraic.py
+  DESTINATION ${PYTHON_SITE_PACKAGES}/assimulo)
+install(FILES src/lib/__init__.py
+  src/lib/radau_core.py
+  DESTINATION ${PYTHON_SITE_PACKAGES}/assimulo/lib)
+install(FILES src/solvers/__init__.py
+  src/solvers/dasp3.py
+  src/solvers/glimda.py
+  src/solvers/odassl.py
+  src/solvers/odepack.py
+  src/solvers/radar5.py
+  src/solvers/radau5.py
+  src/solvers/rosenbrock.py
+  src/solvers/runge_kutta.py
+  DESTINATION ${PYTHON_SITE_PACKAGES}/assimulo/solvers)
+install(DIRECTORY examples
+  DESTINATION ${PYTHON_SITE_PACKAGES}/assimulo)

cmake/FindSUNDIALS.cmake

@@ -0,0 +1,47 @@
+# - Find SUNDIALS
+# SUNDIALS, the SUite of Nonlinear and DIfferential/ALgebraic equation Solvers.
+# https://computing.llnl.gov/projects/sundials
+#
+# The module defines the following variables:
+#  SUNDIALS_VERSION, the version string
+#  SUNDIALS_INCLUDE_DIRS, where to find sundials_dense.h, etc.
+#  SUNDIALS_LIBRARIES, the libraries needed to use SUNDIALS
+#  SUNDIALS_FOUND, If false, do not try to use SUNDIALS
+# also defined, but not for general use are
+#
+
+find_path (SUNDIALS_INCLUDE_DIR sundials/sundials_config.h)
+
+file (STRINGS ${SUNDIALS_INCLUDE_DIR}/sundials/sundials_config.h _VERSION_DEFINE_STRING REGEX "#define (SUNDIALS_VERSION|SUNDIALS_PACKAGE_VERSION) .*")
+if (_VERSION_DEFINE_STRING)
+  string (REGEX REPLACE "#define SUNDIALS[A-Z_]+VERSION \"([0-9\.]+)\"" "\\1" SUNDIALS_VERSION ${_VERSION_DEFINE_STRING})
+endif ()
+
+set(SUNDIALS_LIBRARIES)
+set(SUNDIALS_COMPONENTS sunlinsoldense sunlinsolspgmr sunmatrixdense sunmatrixsparse core sunlinsolsuperlumt kinsol nvecserial cvode cvodes)
+foreach (COMPONENT ${SUNDIALS_COMPONENTS})
+  string(TOUPPER "${COMPONENT}" COMPONENT_UPPER)
+  find_library (SUNDIALS_${COMPONENT_UPPER}_LIBRARY NAMES sundials_${COMPONENT})
+
+  if (SUNDIALS_${COMPONENT_UPPER}_LIBRARY)
+    list (APPEND SUNDIALS_LIBRARIES ${SUNDIALS_${COMPONENT_UPPER}_LIBRARY})
+  endif ()
+endforeach ()
+
+set (SUNDIALS_INCLUDE_DIRS ${SUNDIALS_INCLUDE_DIR})
+
+include(FindPackageHandleStandardArgs)
+find_package_handle_standard_args(SUNDIALS REQUIRED_VARS SUNDIALS_INCLUDE_DIR SUNDIALS_CVODES_LIBRARY VERSION_VAR SUNDIALS_VERSION)
+
+mark_as_advanced (
+  SUNDIALS_LIBRARIES
+  SUNDIALS_INCLUDE_DIR
+  SUNDIALS_INCLUDE_DIRS)
+
+if(NOT TARGET SUNDIALS::ALL)
+  add_library(SUNDIALS::ALL UNKNOWN IMPORTED)
+  set_target_properties(SUNDIALS::ALL
+    PROPERTIES
+    INTERFACE_INCLUDE_DIRECTORIES "${SUNDIALS_INCLUDE_DIRS}")
+  target_link_libraries(SUNDIALS::ALL INTERFACE ${SUNDIALS_LIBRARIES})
+endif()