From 6918164feca59ed5c8ddf99889b14e046db6a2b6 Mon Sep 17 00:00:00 2001
From: MintoDA1 <51412913+MintoDA1@users.noreply.github.com>
Date: Tue, 8 Aug 2023 15:41:37 -0400
Subject: [PATCH] More restructuring and progress getting the scikit-build
 setup working.

---
 .gitignore                  |  3 ++-
 CMakeLists.txt              | 13 +++-------
 pyproject.toml              |  8 ++++++
 requirements.txt            | 15 +++++++++++
 setup.py                    | 50 ++++++++++++++++++++++++-------------
 src/CMakeLists.txt          |  6 ++---
 src/bindings/CMakeLists.txt | 37 +++++++++++++++++++++++++++
 swiftest/__init__.py        |  2 +-
 8 files changed, 103 insertions(+), 31 deletions(-)
 create mode 100644 pyproject.toml
 create mode 100644 requirements.txt
 create mode 100644 src/bindings/CMakeLists.txt

diff --git a/.gitignore b/.gitignore
index bfbcc463e..28d107886 100644
--- a/.gitignore
+++ b/.gitignore
@@ -25,10 +25,11 @@ dump*
 **/.DS_Store
 !python/swiftest/tests/test_suite.py
 !version.txt
+!requirements.txt
+!pyproject.toml
 **/_skbuild
 
 
-
 #Documentation
 !docs/*
 !docs/*/*
diff --git a/CMakeLists.txt b/CMakeLists.txt
index ddd78cebc..d375d3d13 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -13,6 +13,7 @@
 ##################################################
 
 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)
@@ -35,14 +36,7 @@ IF (NOT SKBUILD)
   MESSAGE(STATUS "Looking in ${SKBLD_DIR}/resources/cmake for CMake modules")
 ENDIF()
 
-# scikit-build style includes
-FIND_PACKAGE(Cython REQUIRED)
-SET(PYTHON_EXTENSION_MODULE_SUFFIX "${Python3_SOABI}" CACHE STRING "Suffix for python extension modules")
-
-# Communicate version number and other CMake build variables to the source code
-SET(SETUP_PY_IN "${PROJECT_SOURCE_DIR}/setup.py.in")
-SET(SETUP_PY_OUT "${PROJECT_SOURCE_DIR}/setup.py")
-CONFIGURE_FILE(${SETUP_PY_IN} ${SETUP_PY_OUT})
+SET(PYTHON_EXTENSION_MODULE_SUFFIX ".${Python3_SOABI}" CACHE STRING "Suffix for python extension modules")
 
 INCLUDE(CTest)
 
@@ -58,6 +52,7 @@ SET(SRC ${CMAKE_SOURCE_DIR}/src)
 SET(LIB ${CMAKE_SOURCE_DIR}/lib)
 SET(BIN ${CMAKE_SOURCE_DIR}/bin)
 SET(MOD ${CMAKE_SOURCE_DIR}/include)
+SET(PY ${CMAKE_SOURCE_DIR}/swiftest)
 #SET(TEST ${CMAKE_SOURCE_DIR}/tests)
 
 set(CMAKE_ARCHIVE_OUTPUT_DIRECTORY ${LIB})
@@ -69,7 +64,7 @@ SET(CMAKE_Fortran_MODULE_DIRECTORY ${MOD})
 
 # The source for the SWIFTEST binary and have it placed in the bin folder
 ADD_SUBDIRECTORY(${SRC} ${BIN})
-
+ADD_SUBDIRECTORY(${SRC}/bindings)
 # # Set up test directory
 # ENABLE_TESTING()
 # ADD_SUBDIRECTORY(${TEST})
diff --git a/pyproject.toml b/pyproject.toml
new file mode 100644
index 000000000..aec44a1e3
--- /dev/null
+++ b/pyproject.toml
@@ -0,0 +1,8 @@
+[build-system]
+requires = [
+    "setuptools>=42",
+    "scikit-build>=0.13",
+    "cmake>=3.20.1",
+    "ninja",
+]
+build-backend = "setuptools.build_meta"
\ No newline at end of file
diff --git a/requirements.txt b/requirements.txt
new file mode 100644
index 000000000..e27137833
--- /dev/null
+++ b/requirements.txt
@@ -0,0 +1,15 @@
+  python>=3.8
+  numpy>=1.24.3
+  pandas>=1.5.3
+  scipy>=1.10.1
+  xarray>=2022.11.0
+  dask>=2022.1
+  bottleneck>=1.3.5
+  h5netcdf>=1.0.2
+  netcdf4>=1.6.2
+  matplotlib>=3.7.1
+  astropy>=5.1
+  astroquery>=0.4.6
+  tqdm>=4.65.0
+  x264>=1!157.20191217
+  ffmpeg>=4.3.2
diff --git a/setup.py b/setup.py
index 108cee6ee..a587f2421 100644
--- a/setup.py
+++ b/setup.py
@@ -11,31 +11,47 @@
 """
 
 from skbuild import setup
-from setuptools import find_packages, Extension
-from Cython.Build import cythonize
+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 = 'pybindings'
-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,'pybindings.pyx')],
-                         extra_compile_args=['-fPIC', '-O3'],
-                         extra_link_args=link_flags,
-                         include_dirs=include_dirs,
-                         )]
+# 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='2023.8.0',
+      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),
+      #ext_modules = cythonize(pybindings_extension),
+      install_requires= [
+            'numpy>=1.24.3',
+            'pandas>=1.5.3',
+            'scipy>=1.10.1',
+            'xarray>=2022.11.0',
+            'dask>=2022.1',
+            'bottleneck>=1.3.5',
+            'h5netcdf>=1.0.2',
+            'netcdf4>=1.6.2',
+            'matplotlib>=3.7.1',
+            'astropy>=5.1',
+            'astroquery>=0.4.6',
+            'tqdm>=4.65.0',
+      ],
       packages=find_packages())
diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
index d42627f7a..ec59d460d 100644
--- a/src/CMakeLists.txt
+++ b/src/CMakeLists.txt
@@ -148,7 +148,7 @@ ADD_EXECUTABLE(${SWIFTEST_DRIVER} ${DRIVER_src})
 # Add the needed libraries and special compiler flags
 #####################################################
 
-TARGET_LINK_LIBRARIES(${SWIFTEST_DRIVER} PRIVATE ${SWIFTEST_LIBRARY} ${NETCDF_FORTRAN_LIBRARIES} ${NETCDF_LIBRARIES} $ENV{LIBS})
+TARGET_LINK_LIBRARIES(${SWIFTEST_DRIVER} PUBLIC ${SWIFTEST_LIBRARY} ${NETCDF_FORTRAN_LIBRARIES} ${NETCDF_LIBRARIES} $ENV{LIBS})
 
 IF(USE_OPENMP)
     SET_PROPERTY(TARGET ${SWIFTEST_LIBRARY} ${SWIFTEST_DRIVER} APPEND_STRING PROPERTY COMPILE_FLAGS  "${OpenMP_Fortran_FLAGS} ")
@@ -156,8 +156,8 @@ IF(USE_OPENMP)
 ENDIF(USE_OPENMP)
 
 IF(USE_COARRAY)
-    TARGET_COMPILE_DEFINITIONS(${SWIFTEST_LIBRARY} PRIVATE -DCOARRAY)
-    TARGET_COMPILE_DEFINITIONS(${SWIFTEST_DRIVER} PRIVATE -DCOARRAY)
+    TARGET_COMPILE_DEFINITIONS(${SWIFTEST_LIBRARY} PUBLIC -DCOARRAY)
+    TARGET_COMPILE_DEFINITIONS(${SWIFTEST_DRIVER} PUBLIC -DCOARRAY)
     SET_PROPERTY(TARGET ${SWIFTEST_LIBRARY} ${SWIFTEST_DRIVER} APPEND_STRING PROPERTY COMPILE_FLAGS  "${Coarray_Fortran_FLAGS} ")
     SET_PROPERTY(TARGET ${SWIFTEST_LIBRARY} ${SWIFTEST_DRIVER} APPEND_STRING PROPERTY LINK_FLAGS  "${Coarray_Fortran_FLAGS} ")
 ENDIF(USE_COARRAY)
diff --git a/src/bindings/CMakeLists.txt b/src/bindings/CMakeLists.txt
new file mode 100644
index 000000000..1fec84b18
--- /dev/null
+++ b/src/bindings/CMakeLists.txt
@@ -0,0 +1,37 @@
+# Use the old method to get Python packages, as that's what scikit-build uses
+CMAKE_POLICY(SET CMP0148 OLD)
+FIND_PACKAGE(PythonInterp REQUIRED)
+FIND_PACKAGE(Cython REQUIRED)
+FIND_PACKAGE(PythonExtensions REQUIRED)
+
+# Avoid Cython/Python3.8 minor incompatibility warnings, see
+# https://github.com/cython/cython/issues/3474. Note that this option is a bit
+# expansive, but it's a temporary fix and we'll be testing on other Python
+# versions concurrently so it shouldn't hide any real issues. ).
+IF(${PYTHON_VERSION_MAJOR} EQUAL 3
+   AND ${PYTHON_VERSION_MINOR} EQUAL 8
+   AND NOT WIN32)
+      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})
\ No newline at end of file
diff --git a/swiftest/__init__.py b/swiftest/__init__.py
index 2b9720bd7..8933c9d49 100644
--- a/swiftest/__init__.py
+++ b/swiftest/__init__.py
@@ -11,4 +11,4 @@
 
 from constants import *
 from simulation_class import Simulation
-from bindings import driver
\ No newline at end of file
+from swiftest_bindings import driver
\ No newline at end of file