Continued restructuring and started adding skbuild to the python side…

… to help automate the building of the extension module

.gitignore

@@ -25,6 +25,8 @@ dump*
 **/.DS_Store
 !python/swiftest/tests/test_suite.py
 !version.txt
+**/_skbuild
+
 
 
 #Documentation

Dockerfile

@@ -76,8 +76,19 @@ RUN cd netcdf-fortran-4.6.1 && \
   make install  
 
 FROM intel/oneapi-hpckit:2023.1.0-devel-ubuntu20.04 as build_driver
-SHELL ["/bin/bash", "--login", "-c"]
+SHELL ["/bin/bash", "-c"]
 COPY --from=build_deps /usr/local/. /usr/local/
+ENV PATH /root/miniconda3/bin:$PATH
+
+RUN wget https://repo.anaconda.com/miniconda/Miniconda3-py311_23.5.2-0-Linux-x86_64.sh  && \
+  /bin/bash Miniconda3-py311_23.5.2-0-Linux-x86_64.sh -b && \
+  /root/miniconda3/bin/conda init bash && \
+  source /root/.bashrc && conda update --all -y && \
+  conda install conda-libmamba-solver -y && \
+  conda config --set solver libmamba && \
+  conda install -c conda-forge scikit-build -y&& \ 
+  conda install -c anaconda cython -y
+
 ENV INSTALL_DIR="/usr/local"
 ENV CC="${ONEAPI_ROOT}/compiler/latest/linux/bin/icx"
 ENV FC="${ONEAPI_ROOT}/compiler/latest/linux/bin/ifx"
@@ -103,26 +114,21 @@ ENV NETCDF_FORTRAN_HOME=${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/usr/local/lib"
 ENV LIBS="-lhdf5_hl -lhdf5 -lz"
-ENV PATH /root/miniconda3/bin:$PATH
 
 COPY ./cmake/ /swiftest/cmake/
 COPY ./src/ /swiftest/src/
 COPY ./CMakeLists.txt /swiftest/
 COPY ./python/ /swiftest/python/
 COPY ./version.txt /swiftest/
-RUN wget https://repo.anaconda.com/miniconda/Miniconda3-py311_23.5.2-0-Linux-x86_64.sh  && \
-  /usr/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 numpy -y&& \ 
-  conda install -c anaconda cython -y && \
-  cd swiftest && \
+
+RUN cd swiftest && \
   cmake -S . -B build -DCMAKE_INSTALL_PREFIX="${INSTALL_DIR}" \
   -DMACHINE_CODE_VALUE=${MACHINE_CODE_VALUE} \
   -DCMAKE_BUILD_TYPE=${BUILD_TYPE} \

python/CMakeLists.txt

@@ -8,3 +8,7 @@ SET(SETUP_PY_IN "${PY}/setup.py.in")
 SET(SETUP_PY_OUT "${PY}/setup.py")
 
 CONFIGURE_FILE(${SETUP_PY_IN} ${SETUP_PY_OUT})
+
+# ADD_LIBRARY(pybindings MODULE hello/_hello.cxx)
+# python_extension_module(_hello)
+# install(TARGETS _hello LIBRARY DESTINATION hello)

python/setup.py

@@ -10,7 +10,9 @@
  If not, see: https://www.gnu.org/licenses. 
 """
 
-from setuptools import setup, find_packages, Extension
+#from skbuild import setup
+from setuptools import setup
+from setuptools import find_packages, Extension
 from Cython.Build import cythonize
 import os
 
@@ -19,7 +21,7 @@
 include_dirs = "/Users/daminton/git/swiftest/apple_install/usr/local/include;/Users/daminton/git/swiftest/apple_install/usr/local/include"
 include_dirs = include_dirs.split()
 include_dirs.append(root_dir)
-link_flags = " -static-libgfortran -static-libgcc -static-libstdc++"
+link_flags = " -static-libgfortran -static-libgcc -static-libstdc++ -L/Users/daminton/git/swiftest/lib -lswiftest  /Users/daminton/git/swiftest/apple_install/usr/local/lib/libnetcdff.a /Users/daminton/git/swiftest/apple_install/usr/local/lib/libnetcdf.a -L/Users/daminton/git/swiftest/apple_install/usr/local/lib -lhdf5_hl -lhdf5 -lm -lz -lbz2 -lxml2 -lcurl"
 link_flags = link_flags.split()
 
 pybindings_extension = [Extension('swiftest.bindings',
@@ -34,5 +36,7 @@
       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),
       packages=find_packages())

python/setup.py.in

@@ -10,7 +10,9 @@
  If not, see: https://www.gnu.org/licenses. 
 """
 
-from setuptools import setup, find_packages, Extension
+#from skbuild import setup
+from setuptools import setup
+from setuptools import find_packages, Extension
 from Cython.Build import cythonize
 import os
 
@@ -19,7 +21,7 @@ root_dir = 'pybindings'
 include_dirs = "${SWIFTEST_INCLUDE_DIR}"
 include_dirs = include_dirs.split()
 include_dirs.append(root_dir)
-link_flags = "${CMAKE_Fortran_LINK_FLAGS}"
+link_flags = "${SWIFTEST_LINK_FLAGS}"
 link_flags = link_flags.split()
 
 pybindings_extension = [Extension('swiftest.bindings',
@@ -34,5 +36,7 @@ setup(name='swiftest',
       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),
       packages=find_packages())

src/CMakeLists.txt

@@ -131,7 +131,7 @@ IF(USE_COARRAY)
     SET_PROPERTY(TARGET ${SWIFTEST_LIBRARY} ${SWIFTEST_DRIVER} APPEND_STRING PROPERTY LINK_FLAGS  "${Coarray_Fortran_FLAGS} ")
 ENDIF(USE_COARRAY)
 
-STRING(REPLACE ";" " " SWIFTEST_LINK_FLAGS "${CMAKE_Fortran_LINK_FLAGS} ${CMAKE_LINK_LIBRARY_FLAG}${SWIFTEST_LIBRARY} ${NETCDF_FORTRAN_LIBRARIES} ${NETCDF_LIBRARIES} $ENV{LIBS}")
+STRING(REPLACE ";" " " SWIFTEST_LINK_FLAGS "${CMAKE_Fortran_LINK_FLAGS} -L${LIB} ${CMAKE_LINK_LIBRARY_FLAG}${SWIFTEST_LIBRARY} ${NETCDF_FORTRAN_LIBRARIES} ${NETCDF_LIBRARIES} $ENV{LIBS}")
 SET(SWIFTEST_LINK_FLAGS "${SWIFTEST_LINK_FLAGS}" CACHE STRING "Link flags to pass to setup.py")
 
 GET_TARGET_PROPERTY(SWIFTEST_INCLUDE_DIR ${SWIFTEST_DRIVER} INCLUDE_DIRECTORIES)