separate scikit-build-core build using 'pip install ./pyvcell_fvsolver'

CMakeLists.txt

@@ -44,7 +44,7 @@ elseif (LINUX)
 	endif()
 endif()
 
-cmake_minimum_required(VERSION 3.13...3.27)
+cmake_minimum_required(VERSION 3.17...3.27)
 project(fvsolver)
 set(CMAKE_CXX_STANDARD 17)
 set(CMAKE_CXX_STANDARD_REQUIRED ON)
@@ -202,17 +202,14 @@ endif()
 # 
 #######################################
 
-if (${OPTION_TARGET_FV_SOLVER})
-
-		set(HDF5_USE_STATIC_LIBRARIES ON)
-		if(WINDOWS OR WIN32 OR WIN64)
-			set(HDF5_USE_STATIC_LIBRARIES OFF)
-		endif ()
-		#CMakeList.txt that comes with hdf5 switches library name if compiled with debug
-		find_package(HDF5 COMPONENTS HL CXX C)
-		set(HDF_VERSION ${HDF5_VERSION})
-		######    ${HDF5_HL_LIBRARIES} ${HDF5_CXX_LIBRARIES}
-endif()
+	set(HDF5_USE_STATIC_LIBRARIES ON)
+	if(WINDOWS OR WIN32 OR WIN64)
+		set(HDF5_USE_STATIC_LIBRARIES OFF)
+	endif ()
+	#CMakeList.txt that comes with hdf5 switches library name if compiled with debug
+	find_package(HDF5 COMPONENTS HL CXX C)
+	set(HDF_VERSION ${HDF5_VERSION})
+	######    ${HDF5_HL_LIBRARIES} ${HDF5_CXX_LIBRARIES}
 
 	add_subdirectory(VCellMessaging)
 
@@ -244,9 +241,6 @@ endif()
 	add_subdirectory(PCGPack)
 	add_subdirectory(qhull)
 
-	add_subdirectory(extern/pybind11)
-	add_subdirectory(pyvcell-fvsolver)
-
 include(FetchContent)
 FetchContent_Declare(
 		googletest

LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 1999-2024 University of Connecticut Health Center
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

noxfile.py

@@ -0,0 +1,41 @@
+from __future__ import annotations
+
+import sys
+
+import nox
+
+nox.options.sessions = ["lint", "tests"]
+
+
+@nox.session
+def lint(session: nox.Session) -> None:
+    """
+    Run the linter.
+    """
+    session.install("pre-commit")
+    session.run("pre-commit", "run", "--all-files", *session.posargs)
+
+
+@nox.session
+def tests(session: nox.Session) -> None:
+    """
+    Run the unit and regular tests.
+    """
+    session.install(".[test]")
+    session.run("pytest", *session.posargs)
+
+
+@nox.session(venv_backend="none")
+def dev(session: nox.Session) -> None:
+    """
+    Prepare a .venv folder.
+    """
+
+    session.run(sys.executable, "-m", "venv", ".venv")
+    session.run(
+        ".venv/bin/pip",
+        "install",
+        "-e.",
+        "-Ccmake.define.CMAKE_EXPORT_COMPILE_COMMANDS=1",
+        "-Cbuild-dir=build",
+    )

pyvcell-fvsolver/CMakeLists.txt

@@ -1,18 +1,165 @@
-project(pyvcell_fvsolver)
+cmake_minimum_required(VERSION 3.29)
+
+project(
+        ${SKBUILD_PROJECT_NAME}
+        VERSION ${SKBUILD_PROJECT_VERSION}
+        LANGUAGES CXX C Fortran)
+
 set(CMAKE_CXX_STANDARD 17)
 set(CMAKE_CXX_STANDARD_REQUIRED ON)
 
-set(HEADER_FILES
-        include/SolverMain.h
-)
+if(POLICY CMP0057)
+    cmake_policy(SET CMP0057 NEW)
+endif()
+
+#############################################
+#
+#  Build 64bit binaries on Mac and target Macos 10.7 or later
+#
+##############################################
+if (APPLE)
+    execute_process(COMMAND uname -m OUTPUT_VARIABLE PROCESSOR_ARCHITECTURE OUTPUT_STRIP_TRAILING_WHITESPACE)
+    message("Processor Architecture: ${PROCESSOR_ARCHITECTURE}")
+    if (PROCESSOR_ARCHITECTURE STREQUAL "arm64")
+        set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -D__arm64__")
+        set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -D__arm64__")
+        set(CMAKE_OSX_ARCHITECTURES "arm64")
+    else()
+        set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -D__x86_64__")
+        set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -D__x86_64__")
+        set(CMAKE_OSX_ARCHITECTURES "x86_64")
+    endif()
+    #	set(CMAKE_Fortran_OSX_DEPLOYMENT_TARGET_FLAG "-mmacosx-version-min=10.7" CACHE PATH "")
+    #	set(CMAKE_OSX_DEPLOYMENT_TARGET "10.7" CACHE PATH "")
+    #############################################
+    #
+    #  Choose 32bit or 64bit target arch on Linux
+    #
+    ##############################################
+elseif (LINUX)
+    option(LINUX_32bit_BINARIES "Build 32bit Linux BINARIES" OFF)
+    option(LINUX_64bit_BINARIES "Build 64bit Linux BINARIES" ON)
+
+    if (LINUX_32bit_BINARIES AND LINUX_64bit_BINARIES)
+        message(FATAL_ERROR "It is required to select either 32bit or 64bit Linux Binaries, not both")
+    endif()
+
+    if (LINUX_32bit_BINARIES)
+        set (ARCH_64bit FALSE)
+        set (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -m32")
+        set (CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -m32")
+        set (CMAKE_Fortran_FLAGS "${CMAKE_Fortran_FLAGS} -m32")
+    endif()
+
+    if (LINUX_64bit_BINARIES)
+        set (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -m64")
+        set (CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -m64")
+        set (CMAKE_Fortran_FLAGS "${CMAKE_Fortran_FLAGS} -m64")
+    endif()
+endif()
+
+if(POLICY CMP0057)
+    cmake_policy(SET CMP0057 NEW)
+endif()
+
+set(CMAKE_MODULE_PATH ${CMAKE_MODULE_PATH} "${CMAKE_SOURCE_DIR}/cmake/modules/")
+
+include(GetGitRevisionDescription)
+git_describe(GIT_DESCRIBE ALLOW_LOOKING_ABOVE_CMAKE_SOURCE_DIR)
+
+include (FindZLIB)
+
+option(OPTION_TARGET_MESSAGING "Messaging (requires libcurl)" off)
+option(OPTION_TARGET_DOCS "Generate Doxygen documentation" off)
+option(OPTION_TARGET_FV_SOLVER on)
+option(OPTION_TARGET_MESSAGING "Messaging (requires libcurl)" off)
+
+
+if ("${CMAKE_CXX_COMPILER_ID}" MATCHES "Clang")
+    set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -stdlib=libc++")
+    set(CMAKE_OSX_DEPLOYMENT_TARGET "10.7" CACHE STRING "Choose minimum deploy target for Macos machines")
+endif()
+
+set(LINUX FALSE)
+if (${CMAKE_SYSTEM_NAME} MATCHES Linux)
+    set(LINUX TRUE)
+endif()
+
+set(WINDOWS FALSE)
+if (${CMAKE_SYSTEM_NAME} MATCHES Windows)
+    set(WINDOWS TRUE)
+    set(WIN32 TRUE)
+    set(MINGW TRUE)
+endif()
+
+set (ARCH_64bit FALSE)
+if (CMAKE_SIZEOF_VOID_P EQUAL 8)
+    set (ARCH_64bit TRUE)
+endif()
+
+if (NOT APPLE AND NOT LINUX AND NOT MINGW)
+    message(FATAL_ERROR "Unsupported Operating System or C/C++ Compiler.")
+endif()
+
+add_definitions(-DFORTRAN_UNDERSCORE)
+
+set(OPTION_EXE_DIRECTORY "bin" CACHE PATH "installation directory")
+set(OPTION_LIB_DIRECTORY "lib" CACHE PATH "library directory")
+set(CMAKE_INSTALL_PREFIX "${CMAKE_BINARY_DIR}")
+add_definitions(-DUNIX)
+
+set(HDF5_USE_STATIC_LIBRARIES ON)
+if(WINDOWS OR WIN32 OR WIN64)
+    set(HDF5_USE_STATIC_LIBRARIES OFF)
+endif ()
+#CMakeList.txt that comes with hdf5 switches library name if compiled with debug
+find_package(HDF5 COMPONENTS HL CXX C)
+set(HDF_VERSION ${HDF5_VERSION})
+######    ${HDF5_HL_LIBRARIES} ${HDF5_CXX_LIBRARIES}
+
+add_subdirectory(../VCellMessaging bin/VCellMessaging)
+
+add_subdirectory(../VCellZipUtils bin/VCellZipUtils)
+
+add_subdirectory(../libzip-1.2.0 bin/libzip-1.2.0)
+
+add_subdirectory(../ExpressionParser bin/ExpressionParser)
+
+add_subdirectory(../sundials bin/sundials)
+
+if (NOT APPLE)
+    add_subdirectory(../blas bin/blas)
+endif()
+
+option(OPTION_VCELL "Compile Smoldyn for VCell" ON)
+option(OPTION_NSV "Compile Smoldyn with NextSubvolume functionality" OFF)
+option(OPTION_USE_OPENGL "Build with OpenGL support" OFF)
+option(OPTION_USE_ZLIB "Build with Zlib support" ON)
+option(OPTION_USE_LIBTIFF "Build with LibTiff support" OFF)
+option(OPTION_USE_ICONV "Build with Libiconv support" OFF)
+SET(HAVE_ZLIB TRUE)
+set(OPTION_TARGET_LIBSMOLDYN ON)
+set(OPTION_VCELL ON)
+add_subdirectory(../bridgeVCellSmoldyn bin/bridgeVCellSmoldyn)
+add_subdirectory(../smoldyn-2.38 bin/smoldyn-2.38)
+
+add_subdirectory(../VCell bin/VCell)
+add_subdirectory(../PCGPack bin/PCGPack)
+add_subdirectory(../qhull bin/qhull)
+
+
 
-set(SOURCE_FILES
-        src/pyvcell_fvsolver.cpp
-        src/SolverMain.cpp
-)
+# Find the module development requirements (requires FindPython from 3.17 or
+# scikit-build-core's built-in backport)
+find_package(Python REQUIRED COMPONENTS Interpreter Development.Module)
+find_package(pybind11 CONFIG REQUIRED)
 
-include_directories(${CMAKE_CURRENT_SOURCE_DIR}/include)
+# Add a library using FindPython's tooling (pybind11 also provides a helper like this)
+python_add_library(_core MODULE src/main.cpp src/SolverMain.cpp src/SolverMain.h WITH_SOABI)
+target_link_libraries(_core PRIVATE vcell pybind11::headers)
 
-pybind11_add_module(pyvcell_fvsolver ${SOURCE_FILES} ${HEADER_FILES})
+# This is passing in the version as a define just as an example
+target_compile_definitions(_core PRIVATE VERSION_INFO=${PROJECT_VERSION})
 
-target_link_libraries(pyvcell_fvsolver PRIVATE vcell)
+# The install directory is the output (wheel) directory
+install(TARGETS _core DESTINATION pyvcell_fvsolver)

pyvcell-fvsolver/README.md

@@ -0,0 +1 @@
+## pyvcell_fvsolver