Created a new bindings module for fortran and python that allows a dr…

…iver program to be run directly from the Python side without using subprocess. Next step will be to fix the Simulation class so that it uses it

CMakeLists.txt

@@ -59,57 +59,24 @@ INCLUDE_DIRECTORIES($ENV{NETCDF_FORTRAN_HOME}/include;$ENV{NETCDF_HOME}/include)
 ############################################################
 
 
-
 # Define some directories
 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(TEST ${CMAKE_SOURCE_DIR}/test)
-SET(PY ${CMAKE_SOURCE_DIR}/src/python)
+SET(PY ${CMAKE_SOURCE_DIR}/python)
 
 set(CMAKE_ARCHIVE_OUTPUT_DIRECTORY ${LIB})
 set(CMAKE_LIBRARY_OUTPUT_DIRECTORY ${LIB})
 set(CMAKE_RUNTIME_OUTPUT_DIRECTORY ${BIN})
 
-
-FUNCTION(REPLACE_VERSION IN_FILE LANGUAGE)
-    # Make list of strings from file
-    FILE(STRINGS ${IN_FILE} LINES)
-
-    # Replace file with new one
-    FILE(WRITE ${IN_FILE} "")
-
-    # Look for the word "VERSION" and replace the line with the updated one
-    FOREACH(LINE IN LISTS LINES)
-        IF (LANGUAGE STREQUAL "Fortran") # This is the version found in the swiftest driver program
-            STRING(FIND "${LINE}" " VERSION =" LINE_HAS_VER)
-            IF (LINE_HAS_VER GREATER_EQUAL 0) # This is the version line
-                FILE(APPEND ${IN_FILE} "   character(*), parameter :: VERSION = \"${CMAKE_PROJECT_VERSION}\" !! Swiftest version\n")
-            ELSE ()
-                FILE(APPEND ${IN_FILE} "${LINE}\n") # No match. Put this line back like we found it
-            ENDIF ()
-        ELSEIF (LANGUAGE STREQUAL "Python") # This is the version found in the Python package
-            STRING(FIND "${LINE}" "version=" LINE_HAS_VER)
-            IF (LINE_HAS_VER GREATER_EQUAL 0) # This is the version line
-                FILE(APPEND ${IN_FILE} "      version='${CMAKE_PROJECT_VERSION}',\n")
-            ELSE () # No match. Put this line back like we found it
-                STRING(REPLACE ";" "\n" LINE "${LINE}") # Fixes an issue when parsing the list that defines the pydriver extension module
-                FILE(APPEND ${IN_FILE} "${LINE}\n") 
-            ENDIF ()
-        ENDIF ()
-    ENDFOREACH ()
-ENDFUNCTION ()
-
-REPLACE_VERSION(${SRC}/globals/globals_module.f90 "Fortran" )
-REPLACE_VERSION(${PY}/setup.py "Python")
-
-
 # Have the .mod files placed in the lib folder
 SET(CMAKE_Fortran_MODULE_DIRECTORY ${MOD})
 
 # The source for the SWIFTEST binary and have it placed in the bin folder
 ADD_SUBDIRECTORY(${SRC} ${BIN})
+ADD_SUBDIRECTORY(${PY})
 
 # # Set up test directory
 # ENABLE_TESTING()

Dockerfile

@@ -130,11 +130,9 @@ RUN wget https://repo.anaconda.com/miniconda/Miniconda3-py311_23.5.2-0-Linux-x86
   -DBUILD_SHARED_LIBS=OFF \
   ${EXTRA_CMAKE_OPTIONS} && \
   cmake --build build && \
-  cmake --install build && \
-  mv bin/CMakeFiles/swiftest.dir/__/python/swiftest/f2py/driver.f90.o python/swiftest/f2py/ && \
-  mv bin/CMakeFiles/swiftest.dir/__/python/swiftest/f2py/pydriver.f90.o python/swiftest/f2py/ 
+  cmake --install build 
 
-RUN cd swiftest/python/swiftest/f2py && \
+RUN cd swiftest/python && \
   python setup.py build_ext --inplace 
 
 
@@ -167,17 +165,17 @@ ENV LD_LIBRARY_PATH="/usr/local/lib"
 COPY --from=build_driver /usr/local/bin/swiftest_driver /opt/conda/bin/swiftest_driver
 COPY --from=build_driver /usr/local/lib/libswiftest.a  /opt/conda/lib/libswiftest.a
 COPY --from=build_driver /swiftest/include/ /opt/conda/include/swiftest/
-COPY ./python/. /opt/conda/pkgs/
+COPY ./python/. /opt/conda/pkgs/swiftest/
 COPY environment.yml .
 
 RUN conda update --all -y && \
   conda install conda-libmamba-solver -y && \
   conda config --set solver libmamba && \
-  conda install conda-build -y && \
   conda env create -f environment.yml && \
-  cd /opt/conda/pkgs/swiftest && conda develop . --name swiftest-env && \
   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 && \

distclean.cmake

@@ -45,6 +45,7 @@ FILE(GLOB_RECURSE MAKEFILE "${TOPDIR}/*Makefile")
 FILE(GLOB_RECURSE CMAKETESTFILES "${TOPDIR}/*CTestTestfile.cmake")
 SET(TOPDIRECTORIES "${TOPDIR}/lib" 
                    "${TOPDIR}/bin"
+                   "${TOPDIR}/include"
 )
 
 # CMake has trouble finding directories recursively, so locate these

python/CMakeLists.txt

@@ -0,0 +1,10 @@
+FIND_PACKAGE(Python COMPONENTS Interpreter REQUIRED)
+IF(NOT ${PYTHON})
+    find_program(PYTHON "python")
+ENDIF()
+
+# Communicate version number and other CMake build variables to the source code
+SET(SETUP_PY_IN "${PY}/setup.py.in")
+SET(SETUP_PY_OUT "${PY}/setup.py")
+
+CONFIGURE_FILE(${SETUP_PY_IN} ${SETUP_PY_OUT})

src/python/setup.py → python/setup.py

@@ -14,22 +14,26 @@
 from Cython.Build import cythonize
 import os
 
-# Build the pydriver extension that allows us to run the Fortran driver as a Python module. 
-root_dir = 'pydriver'
-include_dir = os.path.join(root_dir,'include')
-lib_dir = os.path.join(root_dir,'lib')
-pydriver_extension = [Extension('swiftest.pydriver',
-                         [os.path.join(root_dir,'pydriver.pyx')],
-                         extra_compile_args=['-fPIC', '-O3'],
-                         library_dirs=[lib_dir],
-                         libraries=['swiftest','netcdff','netcdf','hdf5_hl','hdf5','m','z'],
-                         include_dirs=[include_dir],
+# Build the pybindings extension that allows us to run the Fortran driver as a Python module. 
+root_dir = 'pybindings'
+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 = "-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',
+                         [os.path.join(root_dir,'pybindings.pyx')],
+                         extra_compile_args=['-fPIC', '-O3','-fopenmp'],
+                         extra_link_args=link_flags,
+                         libraries=['gfortran','omp'],
+                         include_dirs=include_dirs,
                          )]
 
 setup(name='swiftest',
       version='2023.08.00',
       author='David A. Minton',
       author_email='daminton@purdue.edu',
       url='https://github.itap.purdue.edu/MintonGroup/swiftest',
-      ext_modules = cythonize(pydriver_extension),
+      ext_modules = cythonize(pybindings_extension),
       packages=find_packages())

src/python/swiftest/__init__.py → python/swiftest/__init__.py

@@ -9,5 +9,6 @@
  If not, see: https://www.gnu.org/licenses. 
 """
 
-from swiftest.constants import *
-from swiftest.simulation_class import Simulation
+from constants import *
+from simulation_class import Simulation
+from bindings import driver

src/CMakeLists.txt

@@ -7,9 +7,10 @@
 # You should have received a copy of the GNU General Public License along with Swiftest. 
 # If not, see: https://www.gnu.org/licenses. 
 
-########################################
-# Set up how to compile the source files
-########################################
+# Communicate version number and other CMake build variables to the source code
+set(GLOBAL_MODULE_IN ${SRC}/globals/globals_module.f90.in)
+set(GLOBAL_MODULE_OUT ${SRC}/globals/globals_module.f90)
+CONFIGURE_FILE(${GLOBAL_MODULE_IN} ${GLOBAL_MODULE_OUT})
 
 # Add the source files
 SET(STRICT_MATH_FILES
@@ -48,8 +49,7 @@ SET(STRICT_MATH_FILES
             ${SRC}/whm/whm_gr.f90
             ${SRC}/whm/whm_kick.f90
             ${SRC}/whm/whm_step.f90
-            ${PY}/pydriver/src/driver.f90
-            ${PY}/pydriver/src/pydriver.f90
+            ${SRC}/bindings/bindings_module.f90
 )
 
 SET(FAST_MATH_FILES
@@ -96,7 +96,7 @@ SET(COARRAY_FILES
 
 SET(DRIVER_src ${SRC}/main/main.f90)
 
-# Combine all source files (includ)
+# Combine all source files 
 set(SWIFTEST_src ${FAST_MATH_FILES} ${STRICT_MATH_FILES})
 IF(USE_COARRAY)
     set(SWIFTEST_src ${SWIFTEST_src} ${COARRAY_FILES} )
@@ -117,20 +117,25 @@ ADD_EXECUTABLE(${SWIFTEST_DRIVER} ${DRIVER_src})
 # Add the needed libraries and special compiler flags
 #####################################################
 
-TARGET_LINK_LIBRARIES(${SWIFTEST_DRIVER} PRIVATE swiftest ${NETCDF_FORTRAN_LIBRARIES} ${NETCDF_LIBRARIES} $ENV{LIBS})
+TARGET_LINK_LIBRARIES(${SWIFTEST_DRIVER} PRIVATE ${SWIFTEST_LIBRARY} ${NETCDF_FORTRAN_LIBRARIES} ${NETCDF_LIBRARIES} $ENV{LIBS})
 
 IF(USE_OPENMP)
-    SET_PROPERTY(TARGET swiftest ${SWIFTEST_DRIVER} APPEND_STRING PROPERTY COMPILE_FLAGS  "${OpenMP_Fortran_FLAGS} ")
-    SET_PROPERTY(TARGET swiftest ${SWIFTEST_DRIVER} APPEND_STRING PROPERTY LINK_FLAGS  "${OpenMP_Fortran_FLAGS} ")
+    SET_PROPERTY(TARGET ${SWIFTEST_LIBRARY} ${SWIFTEST_DRIVER} APPEND_STRING PROPERTY COMPILE_FLAGS  "${OpenMP_Fortran_FLAGS} ")
+    SET_PROPERTY(TARGET ${SWIFTEST_LIBRARY} ${SWIFTEST_DRIVER} APPEND_STRING PROPERTY LINK_FLAGS  "${OpenMP_Fortran_FLAGS} ")
 ENDIF(USE_OPENMP)
 
 IF(USE_COARRAY)
-    TARGET_COMPILE_DEFINITIONS(swiftest PRIVATE -DCOARRAY)
+    TARGET_COMPILE_DEFINITIONS(${SWIFTEST_LIBRARY} PRIVATE -DCOARRAY)
     TARGET_COMPILE_DEFINITIONS(${SWIFTEST_DRIVER} PRIVATE -DCOARRAY)
-    SET_PROPERTY(TARGET swiftest ${SWIFTEST_DRIVER} APPEND_STRING PROPERTY COMPILE_FLAGS  "${Coarray_Fortran_FLAGS} ")
-    SET_PROPERTY(TARGET swiftest ${SWIFTEST_DRIVER} APPEND_STRING PROPERTY LINK_FLAGS  "${Coarray_Fortran_FLAGS} ")
+    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)
 
+STRING(REPLACE ";" " " SWIFTEST_LINK_FLAGS "${CMAKE_LINK_LIBRARY_FLAG}${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 ${SWIFTEST_DRIVER} INCLUDE_DIRECTORIES)
+SET(SWIFTEST_INCLUDE_DIR "${SWIFTEST_INCLUDE_DIR}" CACHE STRING "Include directory needed for linking the library to an executable")
 
 #Set strict vs fast math flags
 STRING(TOUPPER "${CMAKE_BUILD_TYPE}" BT)
@@ -182,8 +187,3 @@ INSTALL(TARGETS ${SWIFTEST_DRIVER} ${SWIFTEST_LIBRARY}
     INCLUDES DESTINATION include
 )
 
-INSTALL(TARGETS ${SWIFTEST_LIBRARY}
-    LIBRARY DESTINATION "${PY}/pydriver/lib"
-    ARCHIVE DESTINATION "${PY}/pydriver/lib"
-    INCLUDES DESTINATION "${PY}pydriver/include"
-    )

src/bindings/bindings_module.f90

@@ -0,0 +1,44 @@
+module bindings_module
+   use iso_c_binding, only : c_char, c_null_char, c_int
+   use swiftest, only : swiftest_driver, swiftest_io_get_args, STRMAX
+   implicit none
+   contains
+
+      subroutine bindings_c2f_string(c_string, f_string)
+         implicit none
+         ! Arguments
+         character(len=1,kind=c_char),              intent(in)  :: c_string(*)
+         character(len=:),             allocatable, intent(out) :: f_string
+         ! Internals
+         integer :: i
+         character(len=STRMAX) :: tmp_string
+
+         i=1
+         tmp_string = ''
+         do while(c_string(i) /= c_null_char .and. i <= STRMAX)
+            tmp_string(i:i) = c_string(i)
+            i=i+1
+         end do
+
+         if (i > 1) then
+            f_string = trim(tmp_string)
+         else
+            f_string = ""
+         end if
+
+         return
+      end subroutine bindings_c2f_string
+
+      subroutine bindings_c_driver(c_integrator, c_param_file_name, c_display_style) bind(c)
+         implicit none
+         character(kind=c_char), dimension(*), intent(in) :: c_integrator, c_param_file_name, c_display_style
+         character(len=:), allocatable :: integrator, param_file_name, display_style
+
+         call bindings_c2f_string(c_integrator, integrator)
+         call bindings_c2f_string(c_param_file_name, param_file_name)
+         call bindings_c2f_string(c_display_style, display_style)
+
+         call swiftest_io_get_args(integrator,param_file_name,display_style,from_cli=.false.)
+         call swiftest_driver(integrator,param_file_name,display_style)
+   end subroutine bindings_c_driver
+end module bindings_module 

src/main/main.f90

@@ -20,7 +20,7 @@ program main
    character(len=:), allocatable             :: display_style     !! Style of the output display {"STANDARD", "COMPACT", "PROGRESS"}). Default is "STANDARD"
 
    ! Read in command line arguments
-   call swiftest_io_get_args(integrator, param_file_name, display_style)
+   call swiftest_io_get_args(integrator, param_file_name, display_style, from_cli=.true.)
 
    ! Execute the driver
    call swiftest_driver(integrator, param_file_name, display_style)

src/swiftest/swiftest_io.f90

@@ -446,7 +446,7 @@ module subroutine swiftest_io_dump_storage(self, param)
    end subroutine swiftest_io_dump_storage
 
 
-   module subroutine swiftest_io_get_args(integrator, param_file_name, display_style)
+   module subroutine swiftest_io_get_args(integrator, param_file_name, display_style, from_cli)
       !! author: David A. Minton
       !!
       !! Reads in the name of the parameter file from command line arguments. 
@@ -455,20 +455,41 @@ module subroutine swiftest_io_get_args(integrator, param_file_name, display_styl
       character(len=:), intent(inout), allocatable :: integrator      !! Symbolic code of the requested integrator  
       character(len=:), intent(inout), allocatable :: param_file_name !! Name of the input parameters file
       character(len=:), intent(inout), allocatable :: display_style   !! Style of the output display {"STANDARD", "COMPACT", "PROGRESS"}). Default is "STANDARD"
+      logical,          intent(in)                 :: from_cli        !! If true, get command-line arguments. Otherwise, use the values of the input variables
       ! Internals
       character(len=STRMAX), dimension(:), allocatable :: arg
+      character(len=STRMAX), dimension(3)              :: tmp_arg
       integer(I4B), dimension(:), allocatable :: ierr
       integer :: i,narg
 
-      narg = command_argument_count() 
-      if (narg > 0) then
-         allocate(arg(narg),ierr(narg))
-         do i = 1,narg
-            call get_command_argument(i, arg(i), status = ierr(i))
-         end do
-         if (any(ierr /= 0)) call base_util_exit(USAGE)
+      if (from_cli) then
+         narg = command_argument_count() 
+         if (narg > 0) then
+            allocate(arg(narg),ierr(narg))
+            do i = 1,narg
+               call get_command_argument(i, arg(i), status = ierr(i))
+            end do
+            if (any(ierr /= 0)) call base_util_exit(USAGE)
+         else
+            call base_util_exit(USAGE)
+         end if
       else
-         call base_util_exit(USAGE)
+         narg = 0
+         if (len(integrator) > 0) then
+            narg = narg + 1
+            tmp_arg(narg) = integrator
+         end if
+         if (len(param_file_name) > 0) then
+            narg = narg + 1
+            tmp_arg(narg) = param_file_name
+         end if
+         if (len(display_style) > 0) then
+            narg = narg + 1
+            tmp_arg(narg) = display_style
+         end if
+         allocate(arg(narg))
+         arg(1:narg) = tmp_arg(1:narg)
+         deallocate(integrator, param_file_name, display_style)
       end if
 
       if (narg == 1) then