More updates to the packaging

CMakeLists.txt

@@ -11,21 +11,21 @@
 ##################################################
 # Define the project and the depencies that it has
 ##################################################
-
 CMAKE_MINIMUM_REQUIRED(VERSION 3.20.1)
 
 # Get version stored in text file
 FILE(READ "version.txt" VERSION)
 PROJECT(swiftest VERSION ${VERSION} LANGUAGES C Fortran)
+MESSAGE(STATUS "CMAKE_SOURCE_DIR: ${CMAKE_SOURCE_DIR}\nPROJECT_SOURCE_DIR: ${PROJECT_SOURCE_DIR}\n")
 
 # The following section is modified from Numpy f2py documentation
 IF(PROJECT_SOURCE_DIR STREQUAL PROJECT_BINARY_DIR)
   MESSAGE(FATAL_ERROR "In-source builds not allowed. Please make a new directory (called a build directory) and run CMake from there.\n")
 ENDIF()
 
 # Ensure scikit-build modules
+FIND_PACKAGE(Python3 COMPONENTS Interpreter Development REQUIRED)
 IF (NOT SKBUILD)
-  FIND_PACKAGE(Python3 COMPONENTS Interpreter Development REQUIRED)
   EXECUTE_PROCESS(
     COMMAND "${Python3_EXECUTABLE}"
     -c "import os, skbuild; print(os.path.dirname(skbuild.__file__))"
@@ -38,16 +38,20 @@ ENDIF()
 
 SET(PYTHON_EXTENSION_MODULE_SUFFIX ".${Python3_SOABI}" CACHE STRING "Suffix for python extension modules")
 
-INCLUDE(CTest)
+# Detect when building against a conda environment set the _using_conda variable
+# for use both in this file and in the parent
+GET_FILENAME_COMPONENT(_python_bin_dir ${Python3_EXECUTABLE} DIRECTORY)
+IF(EXISTS "${_python_bin_dir}/../conda-meta")
+  MESSAGE("-- Detected conda environment, setting INSTALL_RPATH_USE_LINK_PATH")
+  SET(_using_conda On)
+ELSE()
+  SET(_using_conda Off)
+ENDIF()
 
 # Add our local modules to the module path
 LIST(APPEND CMAKE_MODULE_PATH "${CMAKE_SOURCE_DIR}/cmake/Modules/")
 
-############################################################
-# Define the actual files and folders that make up the build
-############################################################
-
-# Define some directories
+# Define some directories that are important to the build
 SET(SRC ${CMAKE_SOURCE_DIR}/src)
 SET(LIB ${CMAKE_SOURCE_DIR}/lib)
 SET(BIN ${CMAKE_SOURCE_DIR}/bin)

distclean.cmake

@@ -19,6 +19,8 @@ ELSE()
     SET(TOPDIR "${CMAKE_SOURCE_DIR}")
 ENDIF()
 
+SET(SKBUILD_DIR "_skbuild")
+
 MACRO(GET_PARENT_DIRECTORIES search_string return_list grandparents)
     FILE(GLOB_RECURSE new_list ${search_string})
     SET(dir_list "")
@@ -61,6 +63,7 @@ SET(DEL ${TOPDIRECTORIES}
         ${CMAKEFILES}
         ${CMAKETESTING}
         ${CMAKETESTFILES}
+        ${SKBUILD_DIR}
 )
 
 # If we are not in the build dir, delete that as well

pyproject.toml

@@ -3,6 +3,7 @@ requires = [
     "setuptools>=42",
     "scikit-build>=0.13",
     "cmake>=3.20.1",
+    "cython>=3.0.0",
     "ninja",
 ]
 build-backend = "setuptools.build_meta"

setup.py

@@ -11,35 +11,24 @@
 """
 
 from skbuild import setup
-from setuptools import find_packages #, Extension
-#from Cython.Build import cythonize
-import os
 
-# Build the pybindings extension that allows us to run the Fortran driver as a Python module. 
-# root_dir = os.path.join(,'bindings')
-# include_dirs = ""
-# include_dirs = include_dirs.split()
-# include_dirs.append(root_dir)
-# link_flags = ""
-# link_flags = link_flags.split()
-
-# pybindings_extension = [Extension('swiftest.bindings',
-#                          [os.path.join(root_dir,'bindings.pyx')],
-#                          extra_compile_args=['-fPIC', '-O3'],
-#                          extra_link_args=link_flags,
-#                          include_dirs=include_dirs,
-#                          package_data={"": [os.path.join(root_dir,'bindings.h')]} 
-#                          )]
 with open('version.txt') as version_file:
     version = version_file.read().strip()
+
 setup(name='swiftest',
       version=version,
       author='David A. Minton',
       author_email='daminton@purdue.edu',
       url='https://github.itap.purdue.edu/MintonGroup/swiftest',
       python_requires=">3.8",
       license="GPLv3",
-      #ext_modules = cythonize(pybindings_extension),
+      cmake_args=[
+            '-DCMAKE_BUILD_TYPE=RELEASE',
+            '-DMACHINE_CODE_VALUE="generic"',
+            '-DUSE_COARRAY:BOOL=OFF',
+            '-DUSE_OPENMP:BOOL=ON',
+            '-DBUILD_SHARED_LIBS:BOOL=OFF'
+            ],
       install_requires= [
             'numpy>=1.24.3',
             'pandas>=1.5.3',
@@ -54,4 +43,4 @@
             'astroquery>=0.4.6',
             'tqdm>=4.65.0',
       ],
-      packages=find_packages())
+      packages=['swiftest'])

src/bindings/CMakeLists.txt

@@ -1,5 +1,9 @@
 # Use the old method to get Python packages, as that's what scikit-build uses
 CMAKE_POLICY(SET CMP0148 OLD)
+
+SET(CYTHON_FLAGS
+    "--directive binding=True,boundscheck=False,wraparound=False,embedsignature=True,always_allow_keywords=True"
+    CACHE STRING "The directives for Cython compilation.")
 FIND_PACKAGE(PythonInterp REQUIRED)
 FIND_PACKAGE(Cython REQUIRED)
 FIND_PACKAGE(PythonExtensions REQUIRED)
@@ -14,24 +18,22 @@ IF(${PYTHON_VERSION_MAJOR} EQUAL 3
       ADD_COMPILE_OPTIONS("-Wno-deprecated-declarations")
 ENDIF()
 
-
-# Detect when building against a conda environment set the _using_conda variable
-# for use both in this file and in the parent
-GET_FILENAME_COMPONENT(_python_bin_dir ${PYTHON_EXECUTABLE} DIRECTORY)
-IF(EXISTS "${_python_bin_dir}/../conda-meta")
-  MESSAGE("-- Detected conda environment, setting INSTALL_RPATH_USE_LINK_PATH")
-  SET(_using_conda On)
-  SET(_using_conda On PARENT_SCOPE)
-ELSE()
-  SET(_using_conda Off)
-  SET(_using_conda Off PARENT_SCOPE)
-ENDIF()
-
 SET(SWIFTEST_BINDINGS swiftest_bindings)
 
 INCLUDE_DIRECTORIES(${CMAKE_CURRENT_SOURCE_DIR})
 ADD_CYTHON_TARGET(${SWIFTEST_BINDINGS} bindings.pyx)
 ADD_LIBRARY(${SWIFTEST_BINDINGS} MODULE ${SWIFTEST_BINDINGS})
 TARGET_LINK_LIBRARIES(${SWIFTEST_BINDINGS} ${SWIFTEST_LIBRARY} ${SWIFTEST_LIBRARY} ${NETCDF_FORTRAN_LIBRARIES} ${NETCDF_LIBRARIES} $ENV{LIBS})
 PYTHON_EXTENSION_MODULE(${SWIFTEST_BINDINGS})
-INSTALL(TARGETS ${SWIFTEST_BINDINGS} LIBRARY DESTINATION ${PY})
+INSTALL(TARGETS ${SWIFTEST_BINDINGS} DESTINATION swiftest)
+
+IF(APPLE)
+   SET_TARGET_PROPERTIES(${SWIFTEST_BINDINGS} PROPERTIES INSTALL_RPATH "@loader_path")
+ELSE()
+   SET_TARGET_PROPERTIES(${SWIFTEST_BINDINGS} PROPERTIES INSTALL_RPATH "\$ORIGIN")
+ENDIF()
+
+IF(_using_conda OR DEFINED ENV{CIBUILDWHEEL})
+   MESSAGE(STATUS "Conda detected. Setting INSTALL_RPATH_USE_LINK_PATH to True")
+   SET_TARGET_PROPERTIES(${SWIFTEST_BINDINGS} PROPERTIES INSTALL_RPATH_USE_LINK_PATH True)
+ENDIF()

swiftest/__init__.py

@@ -9,6 +9,6 @@
  If not, see: https://www.gnu.org/licenses. 
 """
 
-from constants import *
-from simulation_class import Simulation
-from swiftest_bindings import driver
+from swiftest.constants import *
+from swiftest.simulation_class import Simulation
+from swiftest.swiftest_bindings import driver