feat: migrate to scikit-build-core

.github/workflows/build_wheels.yml

@@ -3,7 +3,8 @@ on:
   release:
     types: [ published ]
   workflow_dispatch:
-  pull_request:
+  pull_request: # Temporarily trigger on PRs for debugging, remove later
+    types: [opened, synchronize, reopened]
     branches:
       - "main"
 
@@ -20,8 +21,6 @@ jobs:
     runs-on: windows-latest
     steps:
       - uses: actions/checkout@v4
-        with:
-          submodules: 'true'
       - uses: actions/setup-python@v5
         with:
           python-version: 3.11
@@ -56,7 +55,7 @@ jobs:
             CMAKE_GENERATOR_PLATFORM=x64
             CMAKE_BUILD_PARALLEL_LEVEL=${{ steps.get_num_cores.outputs.count }}
           CIBW_ARCHS: AMD64
-          CIBW_BEFORE_BUILD: python -m pip install setuptools wheel delvewheel # skip CasADi and CMake
+          CIBW_BEFORE_BUILD: python -m pip install scikit-build-core delvewheel # skip CasADi and CMake
           CIBW_REPAIR_WHEEL_COMMAND: delvewheel repair --add-path C:/Windows/System32 -w {dest_dir} {wheel}
           CIBW_TEST_EXTRAS: "dev"
           CIBW_TEST_COMMAND: |
@@ -73,9 +72,6 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v4
-        with:
-          submodules: 'true'
-
       - uses: actions/setup-python@v5
         with:
           python-version: 3.11
@@ -86,8 +82,8 @@ jobs:
           CIBW_ARCHS_LINUX: x86_64
           CIBW_BEFORE_ALL_LINUX: >
             yum -y install openblas-devel lapack-devel &&
-            bash install_sundials.sh
-          CIBW_BEFORE_BUILD_LINUX: python -m pip install cmake casadi setuptools wheel
+            python install_KLU_Sundials.py
+          CIBW_BEFORE_BUILD_LINUX: python -m pip install casadi scikit-build-core cmake pybind11
           CIBW_REPAIR_WHEEL_COMMAND_LINUX: auditwheel repair -w {dest_dir} {wheel}
           CIBW_TEST_EXTRAS: "dev"
           CIBW_TEST_COMMAND: |
@@ -110,8 +106,6 @@ jobs:
       fail-fast: false
     steps:
       - uses: actions/checkout@v4
-        with:
-          submodules: 'true'
       - uses: actions/setup-python@v5
         with:
           python-version: '3.11'
@@ -211,7 +205,7 @@ jobs:
           # 10.13 for Intel (macos-13), 11.0 for Apple Silicon (macos-14 and macos-latest)
           MACOSX_DEPLOYMENT_TARGET: ${{ matrix.os == 'macos-14' && '11.0' || '10.13' }}
           CIBW_ARCHS_MACOS: auto
-          CIBW_BEFORE_BUILD: python -m pip install cmake casadi setuptools wheel delocate
+          CIBW_BEFORE_BUILD: python -m pip install casadi scikit-build-core delocate cmake pybind11
           CIBW_REPAIR_WHEEL_COMMAND: |
             if [[ $(uname -m) == "x86_64" ]]; then
               delocate-listdeps {wheel} && delocate-wheel -v -w {dest_dir} {wheel}

.github/workflows/pre-commit.yml

@@ -13,7 +13,5 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v4
-        with:
-          submodules: 'true'
       - uses: actions/setup-python@v4
       - uses: pre-commit/[email protected]

.github/workflows/unit_tests.yml

@@ -20,9 +20,6 @@ jobs:
 
     steps:
       - uses: actions/checkout@v4
-        with:
-          submodules: 'true'
-
       - name: Set up Python ${{ matrix.python-version }}
         uses: actions/setup-python@v4
         with:

.gitignore

@@ -11,6 +11,8 @@ setup.log
 install_KLU_Sundials
 .idaklu
 build
+dist
+*.so
 
 # Extra directories for local work
 workspace

CMakeLists.txt

@@ -36,14 +36,17 @@ endif()
 # casadi seems to compile without the newer versions of std::string
 add_compile_definitions(_GLIBCXX_USE_CXX11_ABI=0)
 
-if(NOT PYBIND11_DIR)
-  set(PYBIND11_DIR pybind11)
-endif()
-add_subdirectory(${PYBIND11_DIR})
+find_package(pybind11 CONFIG REQUIRED)
+
+find_package(Python COMPONENTS Interpreter Development.Module REQUIRED)
 
 # Check Casadi build flag
 if(NOT DEFINED PYBAMM_IDAKLU_EXPR_CASADI)
-  set(PYBAMM_IDAKLU_EXPR_CASADI ON)
+  if(DEFINED ENV{PYBAMM_IDAKLU_EXPR_CASADI})
+    set(PYBAMM_IDAKLU_EXPR_CASADI "$ENV{PYBAMM_IDAKLU_EXPR_CASADI}")
+  else()
+    set(PYBAMM_IDAKLU_EXPR_CASADI ON)
+  endif()
 endif()
 message("PYBAMM_IDAKLU_EXPR_CASADI: ${PYBAMM_IDAKLU_EXPR_CASADI}")
 
@@ -59,7 +62,11 @@ endif()
 
 # Check IREE build flag
 if(NOT DEFINED PYBAMM_IDAKLU_EXPR_IREE)
-  set(PYBAMM_IDAKLU_EXPR_IREE OFF)
+  if(DEFINED ENV{PYBAMM_IDAKLU_EXPR_IREE})
+    set(PYBAMM_IDAKLU_EXPR_IREE "$ENV{PYBAMM_IDAKLU_EXPR_IREE}")
+  else()
+    set(PYBAMM_IDAKLU_EXPR_IREE OFF)
+  endif()
 endif()
 message("PYBAMM_IDAKLU_EXPR_IREE: ${PYBAMM_IDAKLU_EXPR_IREE}")
 
@@ -116,39 +123,40 @@ pybind11_add_module(idaklu
   ${IDAKLU_EXPR_IREE_SOURCE_FILES}
 )
 
-if (NOT DEFINED USE_PYTHON_CASADI)
+if(CMAKE_SYSTEM_NAME STREQUAL "Windows")
+  set(USE_PYTHON_CASADI FALSE)
+else()
   set(USE_PYTHON_CASADI TRUE)
 endif()
 
+# Check if CASADI_PATH is set in the environment
+if(NOT DEFINED ENV{CASADI_PATH})
+  execute_process(
+      COMMAND "${PYTHON_EXECUTABLE}" -c
+      "import os; import sysconfig; print(os.path.join(sysconfig.get_path('purelib'), 'casadi', 'cmake'))"
+      OUTPUT_VARIABLE CASADI_DIR
+      OUTPUT_STRIP_TRAILING_WHITESPACE)
+else()
+  set(CASADI_DIR $ENV{CASADI_PATH})
+  message("it is alr set: ${CASADI_DIR}")
+endif()
 
-execute_process(
-    COMMAND "${PYTHON_EXECUTABLE}" -c
-    "import os; import sysconfig; print(os.path.join(sysconfig.get_path('purelib'), 'casadi', 'cmake'))"
-    OUTPUT_VARIABLE CASADI_DIR
-    OUTPUT_STRIP_TRAILING_WHITESPACE)
-
-if (CASADI_DIR)
+if(CASADI_DIR)
   file(TO_CMAKE_PATH ${CASADI_DIR} CASADI_DIR)
-  message("Found Python casadi path: ${CASADI_DIR}")
+  message("Found CasADi path: ${CASADI_DIR}")
 else()
-  message(FATAL_ERROR "Did not find casadi path}")
+  message(FATAL_ERROR "Did not find CasADi path")
 endif()
 
 if(${USE_PYTHON_CASADI})
-  message("Trying to link against Python casadi package in ${CASADI_DIR}")
+  message("Trying to link against Python CasADi package in ${CASADI_DIR}")
   find_package(casadi CONFIG PATHS ${CASADI_DIR} REQUIRED NO_DEFAULT_PATH)
 else()
-  message("Trying to link against any casadi package apart from the Python one")
+  message("Trying to link against any CasADi package apart from the Python one")
   set(CMAKE_IGNORE_PATH "${CASADI_DIR}/cmake")
   find_package(casadi CONFIG REQUIRED)
 endif()
 
-set_target_properties(
-  idaklu PROPERTIES
-  INSTALL_RPATH "${CASADI_DIR}"
-  INSTALL_RPATH_USE_LINK_PATH TRUE
-)
-
 # openmp
 if (${CMAKE_SYSTEM_NAME} MATCHES "Darwin")
   execute_process(
@@ -167,6 +175,14 @@ if(OpenMP_CXX_FOUND)
 endif()
 
 set(CMAKE_MODULE_PATH ${CMAKE_MODULE_PATH} ${PROJECT_SOURCE_DIR})
+
+if(NOT DEFINED ENV{INSTALL_DIR})
+  set(INSTALL_DIR "${CMAKE_CURRENT_SOURCE_DIR}/.idaklu")
+else()
+  set(INSTALL_DIR $ENV{INSTALL_DIR})
+endif()
+message(STATUS "Library path is set: ${INSTALL_DIR}")
+
 # Sundials
 find_package(SUNDIALS REQUIRED)
 message("SUNDIALS found in ${SUNDIALS_INCLUDE_DIR}: ${SUNDIALS_LIBRARIES}")
@@ -185,6 +201,21 @@ endif()
 include_directories(${SuiteSparse_INCLUDE_DIRS})
 target_link_libraries(idaklu PRIVATE ${SuiteSparse_LIBRARIES})
 
+if(DEFINED ENV{CIBUILDWHEEL} AND CMAKE_SYSTEM_NAME STREQUAL "Linux")
+  set(SUNDIALS_LIBRARY_DIR "${INSTALL_DIR}/lib64")
+  set(SUITESPARSE_LIBRARY_DIR "${INSTALL_DIR}/lib64")
+else()
+  set(SUNDIALS_LIBRARY_DIR "${INSTALL_DIR}/lib")
+  set(SUITESPARSE_LIBRARY_DIR "${INSTALL_DIR}/lib")
+endif()
+
+set_target_properties(idaklu PROPERTIES
+  INSTALL_RPATH "${CASADI_DIR};${SUNDIALS_LIBRARY_DIR};${SUITESPARSE_LIBRARY_DIR}"
+  INSTALL_RPATH_USE_LINK_PATH TRUE
+  BUILD_RPATH "${CASADI_DIR};${SUNDIALS_LIBRARY_DIR};${SUITESPARSE_LIBRARY_DIR}"
+)
+message("NOTE: RPATHS linking SUNDIALS, SuiteSparse and casADi are set")
+
 # IREE (MLIR compiler and runtime library) build settings
 if(${PYBAMM_IDAKLU_EXPR_IREE} STREQUAL "ON" )
   set(IREE_BUILD_COMPILER ON)
@@ -197,3 +228,9 @@ if(${PYBAMM_IDAKLU_EXPR_IREE} STREQUAL "ON" )
   target_link_libraries(idaklu PRIVATE iree_compiler_bindings_c_loader)
   target_link_libraries(idaklu PRIVATE iree_runtime_runtime)
 endif()
+
+if(DEFINED ENV{CIBUILDWHEEL})
+  install(TARGETS idaklu DESTINATION "pybammsolvers")
+else()
+  install(TARGETS idaklu DESTINATION "${CMAKE_CURRENT_SOURCE_DIR}/src/pybammsolvers")
+endif()

FindSUNDIALS.cmake

@@ -41,6 +41,7 @@ find_path(SUNDIALS_INCLUDE_DIR
     include
   PATHS
     ${SUNDIALS_ROOT}
+    ${INSTALL_DIR}
   )
 
 set(SUNDIALS_WANT_COMPONENTS
@@ -74,6 +75,7 @@ foreach(LIB ${SUNDIALS_WANT_COMPONENTS})
             Lib
 	PATHS
 	    ${SUNDIALS_ROOT}
+      ${INSTALL_DIR}
     )
 
     set(SUNDIALS_${LIB}_FOUND FALSE)

FindSuiteSparse.cmake

@@ -37,6 +37,20 @@
 #   system paths.
 #
 
+if(NOT CMAKE_SYSTEM_NAME STREQUAL "Darwin")
+  enable_language(Fortran)
+  set(IDAKLU_BLAS_VENDOR
+    "OpenBLAS"
+    CACHE
+      STRING
+      "Sets the BLAS/LAPACK vendor. See https://cmake.org/cmake/help/latest/module/FindBLAS.html#blas-lapack-vendors."
+  )
+  set(BLA_VENDOR ${IDAKLU_BLAS_VENDOR})
+
+  # openBLAS: include a "lib" prefix in its names
+  set(CMAKE_FIND_LIBRARY_PREFIXES "" lib)
+endif()
+
 find_package(BLAS QUIET)
 
 # look for desired componenents
@@ -60,7 +74,9 @@ endif()
 # look for library at positions given by the user
 find_library(SUITESPARSE_CONFIG_LIB
   NAMES "suitesparseconfig"
-  PATHS ${SuiteSparse_ROOT}
+  PATHS 
+    ${SuiteSparse_ROOT}
+    ${INSTALL_DIR}
   PATH_SUFFIXES "lib" "lib32" "lib64" "Lib"
   NO_DEFAULT_PATH
 )
@@ -73,7 +89,9 @@ find_library(SUITESPARSE_CONFIG_LIB
 #look for header files at positions given by the user
 find_path(SUITESPARSE_INCLUDE_DIR
   NAMES "SuiteSparse_config.h"
-  PATHS ${SuiteSparse_ROOT}
+  PATHS 
+    ${SuiteSparse_ROOT}
+    ${INSTALL_DIR}
   PATH_SUFFIXES "SuiteSparse_config" "SuiteSparse_config/include" "suitesparse" "include" "src" "SuiteSparse_config/Include"
   NO_DEFAULT_PATH
 )
@@ -89,7 +107,9 @@ foreach(_component ${SUITESPARSE_COMPONENTS})
   #look for library at positions given by the user
   find_library(${_component}_LIBRARY
     NAMES "${_componentLower}"
-    PATHS ${SuiteSparse_ROOT}
+    PATHS 
+      ${SuiteSparse_ROOT}
+      ${INSTALL_DIR}
     PATH_SUFFIXES "lib" "lib32" "lib64" "${_component}" "${_component}/Lib"
     NO_DEFAULT_PATH
   )
@@ -102,7 +122,9 @@ foreach(_component ${SUITESPARSE_COMPONENTS})
   #look for header files at positions given by the user
   find_path(${_component}_INCLUDE_DIR
     NAMES "${_componentLower}.h"
-    PATHS ${SuiteSparse_ROOT}
+    PATHS 
+      ${SuiteSparse_ROOT}
+      ${INSTALL_DIR}
     PATH_SUFFIXES "${_componentLower}" "include/${_componentLower}" "suitesparse" "include" "src" "${_component}" "${_component}/Include"
     NO_DEFAULT_PATH
   )
@@ -117,7 +139,9 @@ endforeach()
 #look for header files at positions given by the user
 find_path(SPQR_INCLUDE_DIR
   NAMES "SuiteSparseQR.hpp"
-  PATHS ${SuiteSparse_ROOT}
+  PATHS 
+    ${SuiteSparse_ROOT}
+    ${INSTALL_DIR}
   PATH_SUFFIXES "spqr" "include/spqr" "suitesparse" "include" "src" "SPQR" "SPQR/Include"
   NO_DEFAULT_PATH
 )