From e72484af850f60c071d81c9c3622e5a66559a714 Mon Sep 17 00:00:00 2001
From: MintoDA1 <51412913+MintoDA1@users.noreply.github.com>
Date: Tue, 15 Aug 2023 13:20:14 -0400
Subject: [PATCH] More tweaks to build scripts for robustness

---
 .gitignore                         |  2 ++
 CMakeLists.txt                     |  2 +-
 buildscripts/build_all.sh          | 29 ++++++++++++++---------------
 buildscripts/build_dependencies.sh | 29 ++++++++++++++++++++---------
 buildscripts/build_swiftest.sh     | 23 +++++++++++++++++++----
 setup.py                           |  1 +
 src/CMakeLists.txt                 |  4 ++--
 swiftest/simulation_class.py       |  1 -
 8 files changed, 59 insertions(+), 32 deletions(-)

diff --git a/.gitignore b/.gitignore
index dff4272a8..fad43d522 100644
--- a/.gitignore
+++ b/.gitignore
@@ -27,6 +27,8 @@ dump*
 !requirements.txt
 !pyproject.toml
 **/_skbuild
+*.egg*
+swiftest-*
 
 
 #Documentation
diff --git a/CMakeLists.txt b/CMakeLists.txt
index f82ba3881..29364ff6b 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -11,7 +11,7 @@
 ##################################################
 # Define the project and the depencies that it has
 ##################################################
-CMAKE_MINIMUM_REQUIRED(VERSION 3.5.0...3.27.1)
+CMAKE_MINIMUM_REQUIRED(VERSION 3.6.0...3.27.1)
 
 # Get version stored in text file
 FILE(READ "version.txt" VERSION)
diff --git a/buildscripts/build_all.sh b/buildscripts/build_all.sh
index e91d5cc0f..7647c236f 100755
--- a/buildscripts/build_all.sh
+++ b/buildscripts/build_all.sh
@@ -31,30 +31,28 @@ cd ${ROOT_DIR}
 VERSION=$( cat version.txt )
 echo "Building Swiftest version ${VERSION} for ${OS}-${ARCH}"
 
-if command -v docker &> /dev/null; then
-    echo "Docker detected"
+# if command -v docker &> /dev/null; then
+#     echo "Docker detected"
 
-    cmd="docker build --tag swiftest:latest --tag swiftest:${VERSION} --file=dockerfile.${COMPILER} --output=${ROOT_DIR}/dist/ ."
-    echo "Executing Docker build:\n${cmd}"
-    eval "$cmd"
-    exit 0
-else
-    echo "Docker not detected"
-fi
+#     cmd="docker build --tag swiftest:latest --tag swiftest:${VERSION} --file=dockerfile.${COMPILER} --output=${ROOT_DIR}/dist/ ."
+#     echo "Executing Docker build:\n${cmd}"
+#     eval "$cmd"
+#     exit 0
+# else
+#     echo "Docker not detected"
+# fi
 
 case $OS in
-        # Determine if Docker is available
-
-        ;; 
     MacOSX) 
         COMPILER="GNU-Mac"
         export MACOSX_DEPLOYMENT_TARGET=13 
         export LDFLAGS="-Wl,-no_compact_unwind"
-        echo "Building for Mac assumes using Homebrew gfortran-13, gcc-13, and g++13. Install these first if necessary."
+        ;;
+    Linux)
+        COMPILER="GNU-Linux"
         ;;
     *)
-        echo "Swiftest is currently not configured to build for platform ${OS}-${ARCH}"
-        exit 1
+        echo "This script is not tested for ${OS}-${ARCH}"
         ;;
 esac
 
@@ -63,3 +61,4 @@ ${SCRIPT_DIR}/build_dependencies.sh -c $COMPILER -p ${PREFIX} && \
 ${SCRIPT_DIR}/build_swiftest.sh -c $COMPILER -p ${PREFIX}
 
 
+
diff --git a/buildscripts/build_dependencies.sh b/buildscripts/build_dependencies.sh
index 266429f6f..df3155a06 100755
--- a/buildscripts/build_dependencies.sh
+++ b/buildscripts/build_dependencies.sh
@@ -53,17 +53,31 @@ printf "*********************************************************\n"
 printf "Using ${COMPILER} compilers:\nFC: ${FC}\nCC: ${CC}\nCXX: ${CXX}\n"
 printf "Installing to ${PREFIX}\n"
 printf "\n"
-export CPPFLAGS="-I{PREFIX}/include"
-export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib"
+
 export HDF5_ROOT="${PREFIX}"
 export HDF5_LIBDIR="${HDF5_ROOT}/lib"
 export HDF5_INCLUDE_DIR="${HDF5_ROOT}/include"
 export HDF5_PLUGIN_PATH="${HDF5_LIBDIR}/plugin"
 export NCDIR="${PREFIX}"
 export NFDIR="${PREFIX}"
-export LD_LIBRARY_PATH="${PREFIX}/lib"
-export LDFLAGS="-L${PREFIX}/lib"
-export CPPFLAGS="-I${PREFIX}/include"
+export LD_LIBRARY_PATH="${PREFIX}/lib:${LD_LIBRARY_PATH}"
+export CPPFLAGS="${CPPFLAGS} -isystem {$PREFIX}/include"
+export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib"
+export CPATH="${PREFIX}/include:${CPATH}"
+export CFLAGS="${CFLAGS} -Wno-unused-but-set-variable"
+
+if [ $COMPILER = "GNU-Mac" ]; then
+    export MACOSX_DEPLOYMENT_TARGET=13 
+    export LDFLAGS="${LDFLAGS} -Wl,-no_compact_unwind"
+    export CFLAGS="${CFLAGS} -Wno-deprecated-non-prototype"
+fi
+
+printf "LIBS: ${LIBS}\n"
+printf "CFLAGS: ${CFLAGS}\n"
+printf "CPPFLAGS: ${CPPFLAGS}\n"
+printf "CPATH: ${CPATH}\n"
+printf "LD_LIBRARY_PATH: ${LD_LIBRARY_PATH}\n"
+printf "LDFLAGS: ${LDFLAGS}\n"
 
 printf "*********************************************************\n"
 printf "*            BUILDING ZLIB STATIC LIBRARY               *\n"
@@ -108,10 +122,7 @@ if [ !  $COMPILER = "GNU-Mac" ]; then
     COPTS="${COPTS} --disable-libxml2"
 fi
 printf "COPTS: ${COPTS}\n"
-printf "LIBS: ${LIBS}\n"
-printf "CFLAGS: ${CFLAGS}\n"
-printf "LD_LIBRARY_PATH: ${LD_LIBRARY_PATH}\n"
-printf "LDFLAGS: ${LDFLAGS}\n"
+
 
 ./configure $COPTS
 make && make check && make install
diff --git a/buildscripts/build_swiftest.sh b/buildscripts/build_swiftest.sh
index 7a79daf14..7e4ef7b71 100755
--- a/buildscripts/build_swiftest.sh
+++ b/buildscripts/build_swiftest.sh
@@ -47,10 +47,17 @@ printf "Using ${COMPILER} compilers:\nFC: ${FC}\nCC: ${CC}\nCXX: ${CXX}\n\n"
 printf "Installing to ${PREFIX}\n"
 printf "Dependency libraries in ${PREFIX}\n"
 export DEPDIR=$PREFIX
-export CPATH=$DEPDIR/include
 export NETCDF_FORTRAN_HOME=$DEPDIR
+export LD_LIBRARY_PATH="${LD_LIBRARY_PATH}:${DEPDIR}/lib"
+export CPPFLAGS="${CPPFLAGS} -I{$DEPDIR}/include"
+export LDFLAGS="${LDFLAGS} -L${DEPDIR}/lib"
+export CPATH="${CPATH}:${DEPDIR}/include"
+
+if [ $COMPILER = "GNU-Mac" ]; then
+    export MACOSX_DEPLOYMENT_TARGET=13 
+    export LDFLAGS="${LDFLAGS} -Wl,-no_compact_unwind"
+fi
 
-export LD_LIBRARY_PATH="${DEPDIR}/lib:${LD_LIBRARY_PATH}"
 NFCFG="${DEPDIR}/bin/nf-config"
 if command -v $NFCFG &> /dev/null; then
     export LIBS=$($NFCFG --flibs)
@@ -72,8 +79,16 @@ else
     export FFLAGS="${CFLAGS}"
     export SKBUILD_CONFIGURE_OPTIONS="${SKBUILD_CONFIGURE_OPTIONS} -DMACHINE_CODE_VALUE=\"generic\""
 fi
+
+read -r OS ARCH < <($SCRIPT_DIR/get_platform.sh)
+echo $OS $ARCH
+if [ $OS = "MacOSX" ] && [ $ARCH = "arm64" ]; then
+    printf "OpenMP not supported on Apple M1 Silicon quite yet\n"
+    export SKBUILD_CONFIGURE_OPTIONS="${SKBUILD_CONFIGURE_OPTIONS} -DUSE_OPENMP=OFF"
+fi
+
 cd $ROOT_DIR
-    
 python3 -m pip install build pip
-python3 -m build --wheel
+python3 -m build
+python3 -m pip install . -v 
 
diff --git a/setup.py b/setup.py
index def08d578..43828867c 100644
--- a/setup.py
+++ b/setup.py
@@ -60,6 +60,7 @@
             'astropy>=5.1',
             'astroquery>=0.4.6',
             'tqdm>=4.65.0',
+            'py>=1.11'
       ],
       packages=['swiftest'],
       test_suite="swiftest.tests",
diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
index 59a89a4b6..f4fe40861 100644
--- a/src/CMakeLists.txt
+++ b/src/CMakeLists.txt
@@ -151,8 +151,9 @@ ADD_LIBRARY(${SWIFTEST_LIBRARY} ${SWIFTEST_src})
 SET(SWIFTEST_DRIVER swiftest_driver)
 ADD_EXECUTABLE(${SWIFTEST_DRIVER} ${DRIVER_src})
 
-TARGET_INCLUDE_DIRECTORIES(${SWIFTEST_DRIVER} PUBLIC ${NETCDF_INCLUDE_DIR})
+MESSAGE(STATUS "NetCDF Include directory: ${NETCDF_INCLUDE_DIR}")
 TARGET_INCLUDE_DIRECTORIES(${SWIFTEST_LIBRARY} PUBLIC ${NETCDF_INCLUDE_DIR})
+TARGET_INCLUDE_DIRECTORIES(${SWIFTEST_DRIVER} PUBLIC ${NETCDF_INCLUDE_DIR})
 
 IF (BUILD_SHARED_LIBS)
     TARGET_LINK_LIBRARIES(${SWIFTEST_LIBRARY} PUBLIC ${NETCDF_LIBRARIES})
@@ -174,7 +175,6 @@ IF(USE_COARRAY)
     SET_PROPERTY(TARGET ${SWIFTEST_LIBRARY} ${SWIFTEST_DRIVER} APPEND_STRING PROPERTY LINK_FLAGS  "${Coarray_Fortran_FLAGS} ")
 ENDIF(USE_COARRAY)
 
-
 # Check to see if the compiler allows for local-spec in do concurrent statements. Set a preprocessor variable if it does
 IF (USE_OPENMP)
     SET(TESTFILE "${CMAKE_BINARY_DIR}${CMAKE_FILES_DIRECTORY}")
diff --git a/swiftest/simulation_class.py b/swiftest/simulation_class.py
index 678231115..ba1d411de 100644
--- a/swiftest/simulation_class.py
+++ b/swiftest/simulation_class.py
@@ -14,7 +14,6 @@
 from swiftest import init_cond
 from swiftest import tool
 from swiftest import constants
-from swiftest import driver
 from swiftest import __file__ as _pyfile
 import json
 import os