Restructured Python and created pydriver extension module

The pydriver extension module will (eventually) allow us to run the swiftest fortran driver from a module instead of via a subprocess call to the CLI program.

CMakeLists.txt

@@ -66,7 +66,7 @@ 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}/python/swiftest)
+SET(PY ${CMAKE_SOURCE_DIR}/src/python)
 
 set(CMAKE_ARCHIVE_OUTPUT_DIRECTORY ${LIB})
 set(CMAKE_LIBRARY_OUTPUT_DIRECTORY ${LIB})
@@ -93,8 +93,9 @@ FUNCTION(REPLACE_VERSION IN_FILE LANGUAGE)
             STRING(FIND "${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 ()
-                FILE(APPEND ${IN_FILE} "${LINE}\n") # No match. Put this line back like we found it
+            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 ()

Dockerfile

@@ -76,6 +76,7 @@ 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"]
 COPY --from=build_deps /usr/local/. /usr/local/
 ENV INSTALL_DIR="/usr/local"
 ENV CC="${ONEAPI_ROOT}/compiler/latest/linux/bin/icx"
@@ -106,20 +107,36 @@ ENV FC="${ONEAPI_ROOT}/mpi/latest/bin/mpiifort"
 ENV FFLAGS="-fPIC -standard-semantics"
 ENV LDFLAGS="-L/usr/local/lib"
 ENV LIBS="-lhdf5_hl -lhdf5 -lz"
+ENV PATH /root/miniconda3/bin:$PATH
+
 COPY ./cmake/ /swiftest/cmake/
 COPY ./src/ /swiftest/src/
 COPY ./CMakeLists.txt /swiftest/
 COPY ./python/ /swiftest/python/
 COPY ./version.txt /swiftest/
-RUN cd swiftest && \
+RUN wget https://repo.anaconda.com/miniconda/Miniconda3-py311_23.5.2-0-Linux-x86_64.sh  && \
+  /usr/bin/bash Miniconda3-py311_23.5.2-0-Linux-x86_64.sh -b && \
+  /root/miniconda3/bin/conda init bash && \
+  source /root/.bashrc && conda update --all -y && \
+  conda install conda-libmamba-solver -y && \
+  conda config --set solver libmamba && \
+  conda install -c conda-forge numpy -y&& \ 
+  conda install -c anaconda cython -y && \
+  cd swiftest && \
   cmake -S . -B build -DCMAKE_INSTALL_PREFIX="${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
+  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/ 
+
+RUN cd swiftest/python/swiftest/f2py && \
+  python setup.py build_ext --inplace 
+
 
 # This build target creates a container that executes just the driver program
 FROM ubuntu:20.04 as driver

src/CMakeLists.txt

@@ -48,6 +48,8 @@ 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
 )
 
 SET(FAST_MATH_FILES
@@ -81,7 +83,6 @@ SET(FAST_MATH_FILES
             ${SRC}/symba/symba_util.f90
             ${SRC}/walltime/walltime_implementations.f90
             ${SRC}/whm/whm_util.f90
-
 )
 
 SET(COARRAY_FILES
@@ -131,7 +132,6 @@ IF(USE_COARRAY)
 ENDIF(USE_COARRAY)
 
 
-
 #Set strict vs fast math flags
 STRING(TOUPPER "${CMAKE_BUILD_TYPE}" BT)
 IF(BT STREQUAL "RELEASE" OR BT STREQUAL "PROFILE")
@@ -176,9 +176,14 @@ ELSE()
     SET(CMAKE_INSTALL_PREFIX /usr/local)
 ENDIF(WIN32)
 INSTALL(TARGETS ${SWIFTEST_DRIVER} ${SWIFTEST_LIBRARY}
-        RUNTIME DESTINATION bin
-        LIBRARY DESTINATION lib
-        ARCHIVE DESTINATION lib
+    RUNTIME DESTINATION bin
+    LIBRARY DESTINATION lib
+    ARCHIVE DESTINATION lib
+    INCLUDES DESTINATION include
 )
-INSTALL(FILES ${MOD}/swiftest.mod DESTINATION include)
 
+INSTALL(TARGETS ${SWIFTEST_LIBRARY}
+    LIBRARY DESTINATION "${PY}/pydriver/lib"
+    ARCHIVE DESTINATION "${PY}/pydriver/lib"
+    INCLUDES DESTINATION "${PY}pydriver/include"
+    )

src/python/pydriver/src/driver.f90

@@ -0,0 +1,26 @@
+module pydriver_module
+   use swiftest, only : swiftest_driver
+   implicit none
+
+   contains 
+   subroutine driver(integrator, param_file_name, display_style)
+
+      !! author: David A. Minton
+      !!
+      !! Driver program for the Swiftest integrators. Unlike the earlier Swift and Swifter drivers, in Swiftest all integrators 
+      !!    are run from this single program. 
+      !!
+      !! Adapted from Swifter by David E. Kaufmann's Swifter driver programs swifter_[bs,helio,ra15,rmvs,symba,tu4,whm].f90
+      !! Adapted from Hal Levison and Martin Duncan's Swift driver programs
+      implicit none
+
+      ! Arguments
+      character(len=:), intent(in), allocatable :: integrator      !! Symbolic code of the requested integrator  
+      character(len=:), intent(in), allocatable :: param_file_name !! Name of the input parameters file
+      character(len=:), intent(in), allocatable :: display_style   !! Style of the output display {"STANDARD", "COMPACT", "PROGRESS"}). Default is "STANDARD")
+
+      call swiftest_driver(integrator, param_file_name, display_style)
+
+      return
+   end subroutine driver
+end module pydriver_module

src/python/pydriver/src/pydriver.f90

@@ -0,0 +1,9 @@
+module pydriver_interface
+   use iso_c_binding, only : c_char
+   use pydriver_module, only : driver
+   implicit none
+   contains
+      subroutine c_driver(integrator, param_file_name, display_style) bind(c)
+      character(kind=c_char) :: integrator(:), param_file_name(:), display_style(:)
+   end subroutine c_driver
+end module pydriver_interface

src/python/setup.py

@@ -0,0 +1,35 @@
+"""
+ Copyright 2022 - David Minton, Carlisle Wishard, Jennifer Pouplin, Jake Elliott, & Dana Singh
+ This file is part of Swiftest.
+ Swiftest is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License 
+ as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ Swiftest is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY
+ without even the implied warranty 
+ of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
+ You should have received a copy of the GNU General Public License along with Swiftest. 
+ If not, see: https://www.gnu.org/licenses. 
+"""
+
+from setuptools import setup, find_packages, Extension
+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],
+                         )]
+
+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),
+      packages=find_packages())