PrincetonUniversity · smiet · Jul 24, 2025 · Jul 24, 2025 · Jul 24, 2025 · Jul 24, 2025
diff --git a/Utilities/python_wrapper/CMakeLists.txt b/Utilities/python_wrapper/CMakeLists.txt
@@ -109,11 +109,13 @@ add_custom_target(${f2py_module_name} ALL
   DEPENDS ${generated_module_file} spec ${f90wrap_output_files}
 )
 
+set(f2py_build_dir ${CMAKE_CURRENT_BINARY_DIR}/f2py_build)
+
 add_custom_command(
     OUTPUT ${generated_module_file}
     COMMAND ${F2PY_EXECUTABLE} 
         -m ${f2py_module_name} 
-        --build-dir ${CMAKE_CURRENT_BINARY_DIR} 
+        --build-dir ${f2py_build_dir}
         --f90exec=${CMAKE_Fortran_COMPILER}
         --f77exec=${CMAKE_Fortran_COMPILER}
         --f90flags="-fopenmp"
@@ -123,7 +125,6 @@ add_custom_command(
         ${f90wrap_output_files} 
         -I${CMAKE_BINARY_DIR}/build/modules/spec_modules
         -I${HDF5_Fortran_INCLUDE_DIRS}
-	--verbose
         ${CMAKE_BINARY_DIR}/build/lib/libspec.a  
         ${SPEC_LINK_LIB}
     #IMPLICIT_DEPENDS Fortran ${f90wrap_output_files}
@@ -133,9 +134,11 @@ add_custom_command(
     COMMAND_EXPAND_LISTS
 )
 
-python_extension_module(${generated_module_file})
-install(FILES ${python_mod_file} ${generated_module_file} #${CMAKE_CURRENT_SOURCE_DIR}/__init__.py
-        DESTINATION Utilities/python_wrapper/spec
+install(FILES ${python_mod_file} ${generated_module_file} 
+              ${CMAKE_CURRENT_SOURCE_DIR}/spec/__init__.py
+              ${CMAKE_CURRENT_SOURCE_DIR}/spec/core.py
+        DESTINATION spec
+        COMPONENT python_wrapper
 )
 
 #set(PYINIT_STR "import sys\nimport os.path\nsys.path.append(os.path.dirname(__file__))\n\nfrom .spec import *\n")

diff --git a/Utilities/python_wrapper/cmake/FindF2PY.cmake b/Utilities/python_wrapper/cmake/FindF2PY.cmake
@@ -0,0 +1,38 @@
+# FindF2PY.cmake
+# Find f2py executable and include directories
+
+# Find Python first
+find_package(Python COMPONENTS Interpreter Development NumPy REQUIRED)
+
+# Find f2py executable
+execute_process(
+    COMMAND ${Python_EXECUTABLE} -c "import numpy.f2py; print(numpy.f2py.get_include())"
+    OUTPUT_VARIABLE F2PY_INCLUDE_DIRS
+    OUTPUT_STRIP_TRAILING_WHITESPACE
+    ERROR_QUIET
+)
+
+# Find f2py executable path
+execute_process(
+    COMMAND ${Python_EXECUTABLE} -c "import sys; import numpy.f2py as f2py; print(f2py.main.__file__.replace('__main__.py', 'f2py.py') if hasattr(f2py, 'main') else sys.executable + ' -m numpy.f2py')"
+    OUTPUT_VARIABLE F2PY_EXECUTABLE_PATH
+    OUTPUT_STRIP_TRAILING_WHITESPACE
+    ERROR_QUIET
+)
+
+# Set F2PY_EXECUTABLE - use python -m numpy.f2py for reliability
+set(F2PY_EXECUTABLE "${Python_EXECUTABLE}" "-m" "numpy.f2py")
+
+# Set include directories
+if(NOT F2PY_INCLUDE_DIRS)
+    set(F2PY_INCLUDE_DIRS ${Python_NumPy_INCLUDE_DIRS})
+endif()
+
+# Mark as found if we have Python and NumPy
+if(Python_FOUND AND Python_NumPy_FOUND)
+    set(F2PY_FOUND TRUE)
+else()
+    set(F2PY_FOUND FALSE)
+endif()
+
+mark_as_advanced(F2PY_EXECUTABLE F2PY_INCLUDE_DIRS)
diff --git a/Utilities/python_wrapper/cmake/FindNumPy.cmake b/Utilities/python_wrapper/cmake/FindNumPy.cmake
@@ -0,0 +1,11 @@
+# FindNumPy.cmake
+# Find NumPy include directories
+
+# Find Python first
+find_package(Python COMPONENTS Interpreter NumPy REQUIRED)
+
+# Set NumPy variables for compatibility
+set(NumPy_INCLUDE_DIRS ${Python_NumPy_INCLUDE_DIRS})
+set(NumPy_FOUND ${Python_NumPy_FOUND})
+
+mark_as_advanced(NumPy_INCLUDE_DIRS)
diff --git a/Utilities/python_wrapper/cmake/FindPythonExtensions.cmake b/Utilities/python_wrapper/cmake/FindPythonExtensions.cmake
@@ -0,0 +1,22 @@
+# FindPythonExtensions.cmake
+# Provides functionality for building Python extension modules
+
+# Find Python
+find_package(Python COMPONENTS Interpreter Development REQUIRED)
+
+# Get the extension suffix
+execute_process(
+    COMMAND ${Python_EXECUTABLE} -c "import sysconfig; print(sysconfig.get_config_var('EXT_SUFFIX'))"
+    OUTPUT_VARIABLE PYTHON_EXTENSION_MODULE_SUFFIX
+    OUTPUT_STRIP_TRAILING_WHITESPACE
+)
+
+# Function to mark a target as a Python extension module
+function(python_extension_module target)
+    set_target_properties(${target} PROPERTIES
+        PREFIX ""
+        SUFFIX "${PYTHON_EXTENSION_MODULE_SUFFIX}"
+    )
+endfunction()
+
+mark_as_advanced(PYTHON_EXTENSION_MODULE_SUFFIX)
diff --git a/Utilities/python_wrapper/spec/__init__.py b/Utilities/python_wrapper/spec/__init__.py
@@ -1,10 +1,8 @@
 import os.path
-#print(__file__)
-#print(os.path.dirname(__file__))
-path_to_spec_f90wrapped = os.path.dirname(__file__)
-
 import sys
-if not path_to_spec_f90wrapped in sys.path:
-  sys.path.append(path_to_spec_f90wrapped)
 
-# import spec_f90wrapped as spec
+# Add current directory to path if not already there
+path_to_spec_f90wrapped = os.path.dirname(__file__)
+if path_to_spec_f90wrapped not in sys.path:
+    sys.path.append(path_to_spec_f90wrapped)
+
diff --git a/cmake_config.json b/cmake_config.json
diff --git a/cmake_machines/centos7_default.json b/cmake_machines/centos7_default.json
diff --git a/cmake_machines/conda.json b/cmake_machines/conda.json
diff --git a/cmake_machines/conda_debian.json b/cmake_machines/conda_debian.json
diff --git a/cmake_machines/gfortran_arch.json b/cmake_machines/gfortran_arch.json
diff --git a/cmake_machines/gfortran_debian.json b/cmake_machines/gfortran_debian.json
diff --git a/cmake_machines/gfortran_ubuntu.json b/cmake_machines/gfortran_ubuntu.json
diff --git a/cmake_machines/intel_SUSE.json b/cmake_machines/intel_SUSE.json
diff --git a/pyproject.toml b/pyproject.toml
@@ -0,0 +1,67 @@
+[build-system]
+requires = [
+    "scikit-build-core>=0.8.0",
+    "numpy>=2.2",
+    "f90wrap",
+    "meson;python_version>='3.12'", 
+    "ninja"
+]
+build-backend = "scikit_build_core.build"
+
+[project]
+name = "spec"
+version = "0.0.3"
+description = "Stepped Pressure Equilibrium Code MHD Equilibrium Solver"
+authors = [
+    {name = "Christopher Berg Smiet", email = "christopher.smiet@epfl.ch"},
+    {name = "Stuart R. Hudson"},
+    {name = "Joaquim Loizu", email = "joaquim.loizu@epfl.ch"},
+    {name = "Bharat Medasani", email = "mbkumar@gmail.com"},
+    {name = "Caoxiang Zhu"}
+]
+readme = "README.md"
+license = {file = "LICENSE"}
+requires-python = ">=3.8"
+classifiers = [
+    "Development Status :: 4 - Beta",
+    "Intended Audience :: Science/Research",
+    "License :: OSI Approved :: GPL-3.0 License",
+    "Programming Language :: Python :: 3",
+    "Programming Language :: Python :: 3.8",
+    "Programming Language :: Python :: 3.9",
+    "Programming Language :: Python :: 3.10",
+    "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
+    "Topic :: Scientific/Engineering :: Physics",
+]
+dependencies = [
+    "numpy>=1.23.5",
+    "f90wrap",
+]
+
+
+[project.urls]
+Homepage = "https://github.com/PrincetonUniversity/SPEC"
+Documentation = "https://princetonuniversity.github.io/SPEC/"
+Repository = "https://github.com/PrincetonUniversity/SPEC.git"
+"Bug Tracker" = "https://github.com/PrincetonUniversity/SPEC/issues"
+
+[tool.scikit-build]
+# Specify the CMake source directory
+cmake.source-dir = "."
+# Set minimum CMake version
+cmake.version = ">=3.15"
+# Build directory
+build-dir = "build/{wheel_tag}"
+# Configure install components
+install.components = ["python_wrapper"]
+# Ensure wheel includes the Python wrapper package
+wheel.packages = ["spec"]
+
+[tool.scikit-build.cmake.define]
+# Ensure SKBUILD is defined for conditional Python wrapper building
+SKBUILD = "ON"
+# Set compilers and BLAS vendor from cmake_config.json
+CMAKE_C_COMPILER = {env="CMAKE_ARGS_CMAKE_C_COMPILER", default="mpicc"}
+CMAKE_Fortran_COMPILER = {env="CMAKE_ARGS_CMAKE_Fortran_COMPILER", default="mpif90"}
+BLA_VENDOR = {env="CMAKE_ARGS_BLA_VENDOR", default="OpenBLAS"}
diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
@@ -295,6 +295,16 @@ endif()
 
 add_executable(xspec ${XSPEC_OUT_FILE})
 target_link_libraries(xspec PUBLIC spec)
+
+# Ensure MPI and OpenMP are linked to xspec executable
+if(MPI_Fortran_FOUND)
+    target_link_libraries(xspec PUBLIC MPI::MPI_Fortran)
+endif()
+
+if(OpenMP_Fortran_FOUND)
+    target_link_libraries(xspec PUBLIC OpenMP::OpenMP_Fortran)
+endif()
+
 set_target_properties(xspec PROPERTIES POSITION_INDEPENDENT_CODE ON)
 
 install(TARGETS xspec spec)