From 66c61874e284865b9f7c83b6a82f19be3ebab9e6 Mon Sep 17 00:00:00 2001
From: MintoDA1 <51412913+MintoDA1@users.noreply.github.com>
Date: Wed, 9 Aug 2023 14:49:47 -0400
Subject: [PATCH] Fixed some issues related to getting the NetCDF libraries
 linked and included correctly without relying on environment variables

---
 CMakeLists.txt                  |  7 +++-
 Dockerfile                      | 59 +++++++++++++++++----------------
 cmake/Modules/SetUpNetCDF.cmake |  1 -
 setup.py                        | 17 +++++-----
 src/CMakeLists.txt              | 17 ++++++----
 swiftest/CMakeLists.txt         |  3 +-
 6 files changed, 56 insertions(+), 48 deletions(-)

diff --git a/CMakeLists.txt b/CMakeLists.txt
index 184c7c36f..eb996e7e0 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -16,7 +16,12 @@ 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")
+
+# 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)
diff --git a/Dockerfile b/Dockerfile
index 4f9be765b..4b78015f1 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -77,18 +77,6 @@ RUN cd netcdf-fortran-4.6.1 && \
 
 FROM intel/oneapi-hpckit:2023.1.0-devel-ubuntu20.04 as build_driver
 SHELL ["/bin/bash", "-c"]
-ENV INSTALL_DIR="/usr/local"
-COPY --from=build_deps ${INSTALL_DIR}/. ${INSTALL_DIR}/
-ENV PATH /root/miniconda3/bin:$PATH
-
-RUN wget https://repo.anaconda.com/miniconda/Miniconda3-py311_23.5.2-0-Linux-x86_64.sh  && \
-  /bin/bash Miniconda3-py311_23.5.2-0-Linux-x86_64.sh -b && \
-  /root/miniconda3/bin/conda init bash && \
-  source /root/.bashrc && conda update --all -y && \
-  conda install conda-libmamba-solver -y && \
-  conda config --set solver libmamba && \
-  conda install -c conda-forge scikit-build -y&& \ 
-  conda install -c anaconda cython -y
 
 # The MACHINE_CODE_VALUE argument is a string that is used when compiling the swiftest_driver. It is appended to the "-x" compiler 
 # option: (-x${MACHINE_CODE_VALUE}). The default value is set to "sse2" which allows for certain SIMD instructions to be used while 
@@ -103,39 +91,56 @@ ARG BUILD_TYPE="RELEASE"
 # Additional CMAKE options:
 ARG EXTRA_CMAKE_OPTIONS=""
 
-# Swiftest
+ENV INSTALL_DIR="/usr/local"
 ENV NETCDF_HOME=${INSTALL_DIR}
 ENV NETCDF_FORTRAN_HOME=${NETCDF_HOME}
 ENV NETCDF_LIBRARY=${NETCDF_HOME}
 ENV FOR_COARRAY_NUM_IMAGES=1
 ENV OMP_NUM_THREADS=1
-
 ENV FC="${ONEAPI_ROOT}/mpi/latest/bin/mpiifort"
 ENV CC="${ONEAPI_ROOT}/mpi/latest/bin/mpicc -cc=icx"
 ENV CXX="${ONEAPI_ROOT}/mpi/latest/bin/mpicc -cc=icpx"
 ENV FFLAGS="-fPIC -standard-semantics"
 ENV LDFLAGS="-L${INSTALL_DIR}/lib"
 ENV LIBS="-lhdf5_hl -lhdf5 -lz"
+ENV PATH /root/miniconda3/bin:$PATH
 
+COPY --from=build_deps ${INSTALL_DIR}/. ${INSTALL_DIR}/
 COPY ./cmake/ /swiftest/cmake/
 COPY ./src/ /swiftest/src/
 COPY ./CMakeLists.txt /swiftest/
-COPY ./python/ /swiftest/python/
+COPY ./swiftest/ /swiftest/swiftest/
 COPY ./version.txt /swiftest/
+COPY ./setup.py /swiftest/
+COPY ./requirements.txt /swiftest/
+COPY ./pyproject.toml /swiftest/
+COPY ./environment.yml /swiftest/
 
-RUN cd swiftest && \
-  cmake -S . -B build -DCMAKE_INSTALL_PREFIX="${INSTALL_DIR}" \
-  -DMACHINE_CODE_VALUE=${MACHINE_CODE_VALUE} \
-  -DCMAKE_BUILD_TYPE=${BUILD_TYPE} \
-  -DUSE_COARRAY=OFF \
-  -DBUILD_SHARED_LIBS=OFF \
-  ${EXTRA_CMAKE_OPTIONS} && \
-  cmake --build build && \
-  cmake --install build 
+RUN wget https://repo.anaconda.com/miniconda/Miniconda3-py311_23.5.2-0-Linux-x86_64.sh  && \
+  /bin/bash Miniconda3-py311_23.5.2-0-Linux-x86_64.sh -b && \
+  /root/miniconda3/bin/conda init bash && \
+  source /root/.bashrc && conda update --all -y && \
+  conda install conda-libmamba-solver -y && \
+  conda config --set solver libmamba && \
+  conda env create -f environment.yml && \
+  conda init bash && \
+  echo "conda activate swiftest-env" >> ~/.bashrc  && \
+  source ~/.bashrc && \
+  conda install -c conda-forge scikit-build -y&& \ 
+  conda install -c anaconda cython -y
 
-# RUN cd swiftest/python && \
-#   python setup.py build_ext --inplace 
+# RUN cd swiftest && \
+#   cmake -S . -B build -DCMAKE_INSTALL_PREFIX="${INSTALL_DIR}" \
+#   -DMACHINE_CODE_VALUE=${MACHINE_CODE_VALUE} \
+#   -DCMAKE_BUILD_TYPE=${BUILD_TYPE} \
+#   -DUSE_COARRAY=OFF \
+#   -DBUILD_SHARED_LIBS=OFF \
+#   ${EXTRA_CMAKE_OPTIONS} && \
+#   cmake --build build && \
+#   cmake --install build 
 
+# RUN cd swiftest && \
+#    pip install . -v
 
 # This build target creates a container that executes just the driver program
 FROM ubuntu:20.04 as driver
@@ -176,8 +181,6 @@ RUN conda update --all -y && \
   conda env create -f environment.yml && \
   conda init bash && \
   echo "conda activate swiftest-env" >> ~/.bashrc  && \
-  conda install -c anaconda cython -y && \
-  cd /opt/conda/pkgs/swiftest && pip install -e . && \
   conda clean --all -y && \
   mkdir -p /.astropy && \
   chmod -R 777 /.astropy && \
diff --git a/cmake/Modules/SetUpNetCDF.cmake b/cmake/Modules/SetUpNetCDF.cmake
index 318c5ce58..fad06d4f5 100644
--- a/cmake/Modules/SetUpNetCDF.cmake
+++ b/cmake/Modules/SetUpNetCDF.cmake
@@ -13,4 +13,3 @@ IF(NOT NETCDF_FOUND)
     FIND_PACKAGE(NETCDF REQUIRED)
 ENDIF(NOT NETCDF_FOUND)
 
-INCLUDE_DIRECTORIES(${NETCDF_INCLUDE_DIR})
diff --git a/setup.py b/setup.py
index 9266d5fec..8b9053d68 100644
--- a/setup.py
+++ b/setup.py
@@ -11,8 +11,13 @@
 """
 
 from skbuild import setup
-from Cython.Build import cythonize
-import os
+
+cmake_args = [
+            '-DCMAKE_BUILD_TYPE=RELEASE',
+            '-DMACHINE_CODE_VALUE="generic"',
+            '-DUSE_COARRAY:BOOL=OFF',
+            '-DUSE_OPENMP:BOOL=ON',
+            ]
 
 with open('version.txt') as version_file:
     version = version_file.read().strip()
@@ -43,13 +48,7 @@
         'Programming Language :: Python :: 3',
       ],
       keywords='astronomy astrophysics planetary nbody integrator symplectic wisdom-holman',
-      cmake_args=[
-            '-DCMAKE_BUILD_TYPE=RELEASE',
-            '-DMACHINE_CODE_VALUE="generic"',
-            '-DUSE_COARRAY:BOOL=OFF',
-            '-DUSE_OPENMP:BOOL=ON',
-            '-DBUILD_SHARED_LIBS:BOOL=OFF'
-            ],
+      cmake_args=cmake_args,
       install_requires= [
             'numpy>=1.24.3',
             'scipy>=1.10.1',
diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
index 9d6d9cba0..132e17971 100644
--- a/src/CMakeLists.txt
+++ b/src/CMakeLists.txt
@@ -24,12 +24,6 @@ ELSE ()
     MESSAGE(FATAL_ERROR "Compiler 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)
-
 INCLUDE(SetParallelizationLibrary)
 INCLUDE(SetUpNetCDF)
 IF (COMPILER_OPTIONS STREQUAL "Intel")
@@ -159,7 +153,16 @@ ADD_LIBRARY(${SWIFTEST_LIBRARY} ${SWIFTEST_src})
 SET(SWIFTEST_DRIVER swiftest_driver)
 ADD_EXECUTABLE(${SWIFTEST_DRIVER} ${DRIVER_src})
 
-TARGET_LINK_LIBRARIES(${SWIFTEST_DRIVER} PUBLIC ${SWIFTEST_LIBRARY} ${NETCDF_FORTRAN_LIBRARIES} ${NETCDF_LIBRARIES} $ENV{LIBS})
+TARGET_INCLUDE_DIRECTORIES(${SWIFTEST_DRIVER} PUBLIC ${NETCDF_INCLUDE_DIR})
+TARGET_INCLUDE_DIRECTORIES(${SWIFTEST_LIBRARY} PUBLIC ${NETCDF_INCLUDE_DIR})
+
+IF (BUILD_SHARED_LIBS)
+    TARGET_LINK_LIBRARIES(${SWIFTEST_LIBRARY} PUBLIC ${NETCDF_LIBRARIES})
+    TARGET_LINK_LIBRARIES(${SWIFTEST_DRIVER} PUBLIC ${SWIFTEST_LIBRARY})
+ELSE ()
+    TARGET_LINK_LIBRARIES(${SWIFTEST_LIBRARY} PUBLIC ${NETCDF_LIBRARIES} $ENV{LIBS})
+    TARGET_LINK_LIBRARIES(${SWIFTEST_DRIVER} PUBLIC ${SWIFTEST_LIBRARY} ${NETCDF_LIBRARIES} $ENV{LIBS})
+ENDIF (BUILD_SHARED_LIBS)
 
 IF(USE_OPENMP)
     SET_PROPERTY(TARGET ${SWIFTEST_LIBRARY} ${SWIFTEST_DRIVER} APPEND_STRING PROPERTY COMPILE_FLAGS  "${OpenMP_Fortran_FLAGS} ")
diff --git a/swiftest/CMakeLists.txt b/swiftest/CMakeLists.txt
index 6a1843b7a..47ef721b3 100644
--- a/swiftest/CMakeLists.txt
+++ b/swiftest/CMakeLists.txt
@@ -20,10 +20,9 @@ ENDIF()
 
 SET(SWIFTEST_BINDINGS _bindings)
 
-INCLUDE_DIRECTORIES(${CMAKE_CURRENT_SOURCE_DIR} ${MOD})
 ADD_CYTHON_TARGET(${SWIFTEST_BINDINGS})
 ADD_LIBRARY(${SWIFTEST_BINDINGS} MODULE ${SWIFTEST_BINDINGS})
-#MESSAGE(STATUS "Module linked libraries\nswiftest: ${SWIFTEST_LIBRARY}\nnetcdf: ${NETCDF_LIBRARIES}\nLIBS: $ENV{LIBS}")
 TARGET_LINK_LIBRARIES(${SWIFTEST_BINDINGS} swiftest ${NETCDF_LIBRARIES} $ENV{LIBS})
 PYTHON_EXTENSION_MODULE(${SWIFTEST_BINDINGS})
+TARGET_INCLUDE_DIRECTORIES(${SWIFTEST_BINDINGS} PUBLIC ${CMAKE_CURRENT_SOURCE_DIR} ${MOD} ${NETCDF_INCLUDE_DIR})
 INSTALL(TARGETS ${SWIFTEST_BINDINGS} LIBRARY DESTINATION swiftest)
\ No newline at end of file