Merge pull request #27 from profminton/master

Addressed many JOSS  items

.gitignore

@@ -7,7 +7,8 @@
 swiftest_driver.sh
 !CMakeLists.txt
 !*.cmake
-!COPYING.txt
+!COPYING
+!LICENSE
 !CHANGELOG 
 !README.md
 !README_figs/**
@@ -26,7 +27,6 @@ dump*
 *ipynb_checkpoints
 **/.DS_Store
 !version.txt
-!LICENSE.txt
 !requirements.txt
 !pyproject.toml
 **/_skbuild
@@ -57,4 +57,6 @@ netcdf-c-*
 netcdf-fortran-*
 zlib-*
 
-actions-runner*
+actions-runner*
+
+env/**

CMakeFiles/3.27.0/CMakeCCompiler.cmake

@@ -0,0 +1,74 @@
+set(CMAKE_C_COMPILER "/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/clang")
+set(CMAKE_C_COMPILER_ARG1 "")
+set(CMAKE_C_COMPILER_ID "AppleClang")
+set(CMAKE_C_COMPILER_VERSION "15.0.0.15000040")
+set(CMAKE_C_COMPILER_VERSION_INTERNAL "")
+set(CMAKE_C_COMPILER_WRAPPER "")
+set(CMAKE_C_STANDARD_COMPUTED_DEFAULT "17")
+set(CMAKE_C_EXTENSIONS_COMPUTED_DEFAULT "ON")
+set(CMAKE_C_COMPILE_FEATURES "c_std_90;c_function_prototypes;c_std_99;c_restrict;c_variadic_macros;c_std_11;c_static_assert;c_std_17;c_std_23")
+set(CMAKE_C90_COMPILE_FEATURES "c_std_90;c_function_prototypes")
+set(CMAKE_C99_COMPILE_FEATURES "c_std_99;c_restrict;c_variadic_macros")
+set(CMAKE_C11_COMPILE_FEATURES "c_std_11;c_static_assert")
+set(CMAKE_C17_COMPILE_FEATURES "c_std_17")
+set(CMAKE_C23_COMPILE_FEATURES "c_std_23")
+
+set(CMAKE_C_PLATFORM_ID "Darwin")
+set(CMAKE_C_SIMULATE_ID "")
+set(CMAKE_C_COMPILER_FRONTEND_VARIANT "GNU")
+set(CMAKE_C_SIMULATE_VERSION "")
+
+
+
+
+set(CMAKE_AR "/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ar")
+set(CMAKE_C_COMPILER_AR "")
+set(CMAKE_RANLIB "/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ranlib")
+set(CMAKE_C_COMPILER_RANLIB "")
+set(CMAKE_LINKER "/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ld")
+set(CMAKE_MT "")
+set(CMAKE_TAPI "/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/tapi")
+set(CMAKE_COMPILER_IS_GNUCC )
+set(CMAKE_C_COMPILER_LOADED 1)
+set(CMAKE_C_COMPILER_WORKS TRUE)
+set(CMAKE_C_ABI_COMPILED TRUE)
+
+set(CMAKE_C_COMPILER_ENV_VAR "CC")
+
+set(CMAKE_C_COMPILER_ID_RUN 1)
+set(CMAKE_C_SOURCE_FILE_EXTENSIONS c;m)
+set(CMAKE_C_IGNORE_EXTENSIONS h;H;o;O;obj;OBJ;def;DEF;rc;RC)
+set(CMAKE_C_LINKER_PREFERENCE 10)
+set(CMAKE_C_LINKER_DEPFILE_SUPPORTED FALSE)
+
+# Save compiler ABI information.
+set(CMAKE_C_SIZEOF_DATA_PTR "8")
+set(CMAKE_C_COMPILER_ABI "")
+set(CMAKE_C_BYTE_ORDER "LITTLE_ENDIAN")
+set(CMAKE_C_LIBRARY_ARCHITECTURE "")
+
+if(CMAKE_C_SIZEOF_DATA_PTR)
+  set(CMAKE_SIZEOF_VOID_P "${CMAKE_C_SIZEOF_DATA_PTR}")
+endif()
+
+if(CMAKE_C_COMPILER_ABI)
+  set(CMAKE_INTERNAL_PLATFORM_ABI "${CMAKE_C_COMPILER_ABI}")
+endif()
+
+if(CMAKE_C_LIBRARY_ARCHITECTURE)
+  set(CMAKE_LIBRARY_ARCHITECTURE "")
+endif()
+
+set(CMAKE_C_CL_SHOWINCLUDES_PREFIX "")
+if(CMAKE_C_CL_SHOWINCLUDES_PREFIX)
+  set(CMAKE_CL_SHOWINCLUDES_PREFIX "${CMAKE_C_CL_SHOWINCLUDES_PREFIX}")
+endif()
+
+
+
+
+
+set(CMAKE_C_IMPLICIT_INCLUDE_DIRECTORIES "/usr/local/include;/opt/homebrew/include;/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/lib/clang/15.0.0/include;/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX14.0.sdk/usr/include;/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include")
+set(CMAKE_C_IMPLICIT_LINK_LIBRARIES "")
+set(CMAKE_C_IMPLICIT_LINK_DIRECTORIES "/usr/local/lib;/opt/homebrew/lib")
+set(CMAKE_C_IMPLICIT_LINK_FRAMEWORK_DIRECTORIES "")

CMakeFiles/3.27.0/CMakeFortranCompiler.cmake

@@ -0,0 +1,64 @@
+set(CMAKE_Fortran_COMPILER "/opt/homebrew/bin/gfortran-12")
+set(CMAKE_Fortran_COMPILER_ARG1 "")
+set(CMAKE_Fortran_COMPILER_ID "GNU")
+set(CMAKE_Fortran_COMPILER_VERSION "12.3.0")
+set(CMAKE_Fortran_COMPILER_WRAPPER "")
+set(CMAKE_Fortran_PLATFORM_ID "")
+set(CMAKE_Fortran_SIMULATE_ID "")
+set(CMAKE_Fortran_COMPILER_FRONTEND_VARIANT "GNU")
+set(CMAKE_Fortran_SIMULATE_VERSION "")
+
+
+set(CMAKE_Fortran_COMPILER_SYSROOT "/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr")
+set(CMAKE_COMPILER_SYSROOT "/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr")
+
+set(CMAKE_AR "/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ar")
+set(CMAKE_Fortran_COMPILER_AR "/opt/homebrew/bin/gcc-ar-12")
+set(CMAKE_RANLIB "/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ranlib")
+set(CMAKE_TAPI "/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/tapi")
+set(CMAKE_Fortran_COMPILER_RANLIB "/opt/homebrew/bin/gcc-ranlib-12")
+set(CMAKE_COMPILER_IS_GNUG77 1)
+set(CMAKE_Fortran_COMPILER_LOADED 1)
+set(CMAKE_Fortran_COMPILER_WORKS TRUE)
+set(CMAKE_Fortran_ABI_COMPILED TRUE)
+
+set(CMAKE_Fortran_COMPILER_ENV_VAR "FC")
+
+set(CMAKE_Fortran_COMPILER_SUPPORTS_F90 1)
+
+set(CMAKE_Fortran_COMPILER_ID_RUN 1)
+set(CMAKE_Fortran_SOURCE_FILE_EXTENSIONS f;F;fpp;FPP;f77;F77;f90;F90;for;For;FOR;f95;F95;f03;F03;f08;F08)
+set(CMAKE_Fortran_IGNORE_EXTENSIONS h;H;o;O;obj;OBJ;def;DEF;rc;RC)
+set(CMAKE_Fortran_LINKER_PREFERENCE 20)
+set(CMAKE_Fortran_LINKER_DEPFILE_SUPPORTED FALSE)
+if(UNIX)
+  set(CMAKE_Fortran_OUTPUT_EXTENSION .o)
+else()
+  set(CMAKE_Fortran_OUTPUT_EXTENSION .obj)
+endif()
+
+# Save compiler ABI information.
+set(CMAKE_Fortran_SIZEOF_DATA_PTR "8")
+set(CMAKE_Fortran_COMPILER_ABI "")
+set(CMAKE_Fortran_LIBRARY_ARCHITECTURE "")
+
+if(CMAKE_Fortran_SIZEOF_DATA_PTR AND NOT CMAKE_SIZEOF_VOID_P)
+  set(CMAKE_SIZEOF_VOID_P "${CMAKE_Fortran_SIZEOF_DATA_PTR}")
+endif()
+
+if(CMAKE_Fortran_COMPILER_ABI)
+  set(CMAKE_INTERNAL_PLATFORM_ABI "${CMAKE_Fortran_COMPILER_ABI}")
+endif()
+
+if(CMAKE_Fortran_LIBRARY_ARCHITECTURE)
+  set(CMAKE_LIBRARY_ARCHITECTURE "")
+endif()
+
+
+set(CMAKE_Fortran_SYSROOT_FLAG "-isysroot")
+set(CMAKE_Fortran_OSX_DEPLOYMENT_TARGET_FLAG "-mmacosx-version-min=")
+
+set(CMAKE_Fortran_IMPLICIT_INCLUDE_DIRECTORIES "/opt/homebrew/Cellar/gcc@12/12.3.0/lib/gcc/12/gcc/aarch64-apple-darwin22/12/finclude;/usr/local/include;/opt/homebrew/include;/opt/homebrew/Cellar/gcc@12/12.3.0/lib/gcc/12/gcc/aarch64-apple-darwin22/12/include;/opt/homebrew/Cellar/gcc@12/12.3.0/lib/gcc/12/gcc/aarch64-apple-darwin22/12/include-fixed;/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX14.0.sdk/usr/include")
+set(CMAKE_Fortran_IMPLICIT_LINK_LIBRARIES "gfortran;emutls_w;gcc;quadmath;emutls_w;gcc;gcc")
+set(CMAKE_Fortran_IMPLICIT_LINK_DIRECTORIES "/usr/local/lib;/opt/homebrew/lib;/opt/homebrew/Cellar/gcc@12/12.3.0/lib/gcc/12/gcc/aarch64-apple-darwin22/12;/opt/homebrew/Cellar/gcc@12/12.3.0/lib/gcc/12/gcc;/opt/homebrew/Cellar/gcc@12/12.3.0/lib/gcc/12")
+set(CMAKE_Fortran_IMPLICIT_LINK_FRAMEWORK_DIRECTORIES "")

CMakeFiles/3.27.0/CMakeSystem.cmake

@@ -0,0 +1,15 @@
+set(CMAKE_HOST_SYSTEM "Darwin-22.6.0")
+set(CMAKE_HOST_SYSTEM_NAME "Darwin")
+set(CMAKE_HOST_SYSTEM_VERSION "22.6.0")
+set(CMAKE_HOST_SYSTEM_PROCESSOR "arm64")
+
+
+
+set(CMAKE_SYSTEM "Darwin-22.6.0")
+set(CMAKE_SYSTEM_NAME "Darwin")
+set(CMAKE_SYSTEM_VERSION "22.6.0")
+set(CMAKE_SYSTEM_PROCESSOR "arm64")
+
+set(CMAKE_CROSSCOMPILING "FALSE")
+
+set(CMAKE_SYSTEM_LOADED 1)

CMakeLists.txt

@@ -24,6 +24,12 @@ IF (${CMAKE_VERSION} VERSION_GREATER_EQUAL "3.27")
     CMAKE_POLICY(SET CMP0148 OLD)
 ENDIF ()
 
+# Set some options the user may choose
+OPTION(USE_COARRAY "Use Coarray Fortran for parallelization of test particles" OFF)
+OPTION(USE_OPENMP "Use OpenMP for parallelization" ON)
+OPTION(USE_SIMD "Use SIMD vectorization" ON)
+OPTION(BUILD_SHARED_LIBS "Build using shared libraries" ON)
+
 INCLUDE(GNUInstallDirs)
 IF (SKBUILD)
     SET(INSTALL_BINDIR ${SKBUILD_PLATLIB_DIR}/${SKBUILD_PROJECT_NAME}) 
@@ -43,7 +49,7 @@ ENDIF ()
 # Have the .mod files placed in the include folder
 SET(CMAKE_Fortran_MODULE_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/mod)
 
-# Add our local modules to the module path
+# Add our local modules to the module ldpath
 FILE(TO_CMAKE_PATH "${CMAKE_SOURCE_DIR}/cmake/Modules" LOCAL_MODULE_PATH)
 LIST(APPEND CMAKE_MODULE_PATH ${LOCAL_MODULE_PATH})
 
@@ -55,33 +61,40 @@ ELSE ()
     MESSAGE(FATAL_ERROR "Compiler ${CMAKE_Fortran_COMPILER_ID} not recognized!") 
 ENDIF ()
 
-# Set some options the user may choose
-OPTION(USE_COARRAY "Use Coarray Fortran for parallelization of test particles" OFF)
-OPTION(USE_OPENMP "Use OpenMP for parallelization" ON)
-OPTION(USE_SIMD "Use SIMD vectorization" ON)
-OPTION(BUILD_SHARED_LIBS "Build using shared libraries" ON)
-
 # 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()
 
+FIND_PACKAGE(NETCDF_Fortran REQUIRED)
+IF (MSVC)
+    FIND_PACKAGE(HDF5 NAMES hdf5 COMPONENTS C HL REQUIRED CONFIG)
+    MESSAGE(STATUS "HDF5_FOUND: ${HDF5_FOUND}")
+    MESSAGE(STATUS "HDF5_VERSION: ${HDF5_VERSION}")
+    MESSAGE(STATUS "HDF5_LIBRARIES: ${HDF5_LIBRARIES}")
+    MESSAGE(STATUS "HDF5_INCLUDE_DIRS: ${HDF5_INCLUDE_DIRS}")
+ELSE ()
+    FIND_PACKAGE(HDF5 COMPONENTS C HL REQUIRED)
+ENDIF ()
+
 # Ensure scikit-build modules
 FIND_PACKAGE(Python COMPONENTS Interpreter Development.Module REQUIRED)
 
-# Define some directories that are important to the build
+
 SET(SRC "${CMAKE_SOURCE_DIR}/src")
 SET(PY "${CMAKE_SOURCE_DIR}/swiftest")
 
 #####################################
 # Tell how to install this executable
 #####################################
-IF(WIN32)
+IF(CMAKE_SYSTEM_NAME STREQUAL "Windows")
     SET(CMAKE_INSTALL_PREFIX "C:\\Program Files\\swiftest")
     FILE(TO_CMAKE_PATH ${CMAKE_INSTALL_PREFIX} CMAKE_INSTALL_PREFIX)
+    SET(CMAKE_INSTALL_PREFIX ${CMAKE_INSTALL_PREFIX} CACHE PATH "Path for install")
 ELSE()
-    SET(CMAKE_INSTALL_PREFIX /usr/local)
-ENDIF(WIN32)
+    SET(CMAKE_INSTALL_PREFIX /usr/local CACHE PATH "Path for install")
+ENDIF()
+
 
 # Make sure paths are correct for Unix or Windows style
 FILE(TO_CMAKE_PATH ${SRC} SRC)
@@ -90,6 +103,17 @@ FILE(TO_CMAKE_PATH ${PY} PY)
 # Set the name of the swiftest library
 SET(SWIFTEST_LIBRARY ${SKBUILD_PROJECT_NAME})
 
+# Determine compiler options
+IF(NOT CMAKE_Fortran_COMPILER_SUPPORTS_F90)
+    MESSAGE(FATAL_ERROR "Fortran compiler does not support F90")
+ENDIF(NOT CMAKE_Fortran_COMPILER_SUPPORTS_F90)
+INCLUDE(SetParallelizationLibrary)
+
+IF (COMPILER_OPTIONS STREQUAL "Intel" AND NOT CMAKE_SYSTEM_NAME STREQUAL "Windows")
+    INCLUDE(SetMKL)
+ENDIF ()
+INCLUDE(SetSwiftestFlags) 
+
 # The source for the SWIFTEST binary and have it placed in the bin folder
 ADD_SUBDIRECTORY(${SRC} ${CMAKE_INSTALL_BINDIR})
 ADD_SUBDIRECTORY(${PY})

buildscripts/.gitignore

@@ -1 +1,2 @@
-!*.sh
+!*.sh
+!windows/*.cmake

buildscripts/_build_getopts.sh

@@ -13,9 +13,14 @@ set -a
 SCRIPT_DIR=$(realpath $(dirname $0))
 ROOT_DIR=$(realpath ${SCRIPT_DIR}/..)
 
+# Get platform and architecture
+read -r OS ARCH < <($SCRIPT_DIR/get_platform.sh)
+
 # Parse arguments
 USTMT="Usage: ${0} [-d /path/to/dependency/source] [-p /prefix/path] [-m MACOSX_DEPLOYMENT_TARGET]"
-MACOSX_DEPLOYMENT_TARGET=${MACOSX_DEPLOYMENT_TARGET:-"$(sw_vers --ProductVersion)"}
+if [ $OS = "MacOSX" ]; then
+    MACOSX_DEPLOYMENT_TARGET=${MACOSX_DEPLOYMENT_TARGET:-"$(sw_vers --ProductVersion)"}
+fi
 
 while getopts ":d:p:m:h" ARG; do
     case "${ARG}" in
@@ -44,9 +49,8 @@ while getopts ":d:p:m:h" ARG; do
     esac
 done
 
-read -r OS ARCH < <($SCRIPT_DIR/get_platform.sh)
-BUILD_DIR=${BUILD_DIR:-$(mktemp -ut swiftest_build.XXXXXXXX)}
-PREFIX=${PREFIX:-${ROOT_DIR}}
+BUILD_DIR=${BUILD_DIR:-"${HOME}/Downloads"}
+PREFIX=${PREFIX:-"/usr/local"}
 DEPENDENCY_DIR=${DEPENDENCY_DIR:-${BUILD_DIR}}
 
 mkdir -p ${DEPENDENCY_DIR}

buildscripts/build_dependencies.sh

@@ -16,21 +16,36 @@ SCRIPT_DIR=$(realpath $(dirname $0))
 set -a
 ARGS=$@
 . ${SCRIPT_DIR}/_build_getopts.sh ${ARGS}
-
+set -e
 cd $ROOT_DIR
-printf "*********************************************************\n"
-printf "*          STARTING DEPENDENCY BUILD                    *\n"
-printf "*********************************************************\n"
-printf "Using ${OS} compilers:\nFC: ${FC}\nCC: ${CC}\nCXX: ${CXX}\n"
-printf "Installing to ${PREFIX}\n"
-printf "\n"
+
+if ! command -v ninja &> /dev/null; then
+    NINJA_VER="1.11.1"
+
+    printf "*********************************************************\n"
+    printf "*             FETCHING NINJA SOURCE                      *\n"
+    printf "*********************************************************\n"
+    printf "Copying files to ${DEPENDENCY_DIR}\n"
+    mkdir -p ${DEPENDENCY_DIR}
+    if [ ! -d ${DEPENDENCY_DIR}/ninja-${NINJA_VER} ]; then
+        [ -d ${DEPENDENCY_DIR}/zlib-* ] && rm -rf ${DEPENDENCY_DIR}/zlib-*
+        curl -L https://github.com/ninja-build/ninja/archive/refs/tags/v${NINJA_VER}.tar.gz | tar xvz -C ${DEPENDENCY_DIR}
+    fi
+    cd ${DEPENDENCY_DIR}/ninja-*
+    cmake -B build -S . -DCMAKE_INSTALL_PREFIX=${PREFIX}
+    cmake --build build 
+    if [ -w ${PREFIX} ]; then
+        cmake --install build 
+    else
+        sudo cmake --install build
+    fi
+fi
 
 # Get the OpenMP Libraries
 if [ $OS = "MacOSX" ]; then
     ${SCRIPT_DIR}/get_lomp.sh ${ARGS}
 fi
 
-set -e
 ${SCRIPT_DIR}/build_zlib.sh ${ARGS}
 ${SCRIPT_DIR}/build_hdf5.sh ${ARGS}
 ${SCRIPT_DIR}/build_netcdf-c.sh ${ARGS}