Move codebase to CPP

.gitignore

@@ -3,24 +3,38 @@
 nmodlconf.h.in
 nrnconf.h.in
 build
+.DS_Store
+.eggs/
+.idea/
+CMakeFiles/
+Makefile
+Makefile.in
+.deps
+x86_64
+__pycache__
+venv
+virtualenv
+*.o 
+*.lo
 
 # These files are generated at build time
 # It would be a good idea to create them in the
 # build directory in the future.
-src/modlunit/lex.c
-src/modlunit/parse1.c
-src/modlunit/parse1.h
-src/nmodl/diffeq.c
+src/modlunit/lex.cpp
+src/modlunit/parse1.cpp
+src/modlunit/parse1.hpp
+src/nmodl/diffeq.cpp
 src/nmodl/diffeq.h
-src/nmodl/lex.c
-src/nmodl/parse1.c
-src/nmodl/parse1.h
+src/nmodl/lex.cpp
+src/nmodl/parse1.cpp
+src/nmodl/parse1.hpp
 src/nrnoc/apcount.c
 src/nrnoc/exp2syn.c
 src/nrnoc/expsyn.c
 src/nrnoc/feature.c
 src/nrnoc/hh.c
 src/nrnoc/hh.mod.orig
+src/nrnoc/hocusr.h
 src/nrnoc/intfire1.c
 src/nrnoc/intfire2.c
 src/nrnoc/intfire4.c
@@ -35,5 +49,5 @@ src/nrnoc/stim.c
 src/nrnoc/svclmp.c
 src/nrnoc/syn.c
 src/nrnoc/vclmp.c
-src/oc/parse.c
-src/oc/parse.h
+src/oc/parse.cpp
+src/oc/parse.hpp

CMakeLists.txt

@@ -221,6 +221,10 @@ if(NRN_ENABLE_MPI)
   find_package(MPI REQUIRED)
   set(NRNMPI 1)
   set(PARANEURON 1)
+  # avoid linking to C++ bindings
+  add_definitions("-DMPI_NO_CPPBIND=1")
+  add_definitions("-DOMPI_SKIP_MPICXX=1")
+  add_definitions("-DMPICH_SKIP_MPICXX=1")
 else()
   set(NRNMPI 0)
   set(PARANEURON 0)
@@ -370,7 +374,7 @@ if(READLINE_FOUND)
   # this part has to be prior to adding the nrniv subdirectory.
   execute_process(COMMAND grep -q rl_event_hook ${Readline_LIBRARY} RESULT_VARIABLE result)
   if(NOT result EQUAL 0)
-    # define for src/oc/hoc.c
+    # define for src/oc/hoc.cpp
     set(DEF_RL_GETC_FUNCTION use_rl_getc_function)
   endif()
   find_package(Curses QUIET)

bin/nrniv_makefile.in

@@ -92,7 +92,7 @@ NRNIVOBJS = $(libobjdir)/nrnmain.o $(libobjdir)/ivocmain.o $(libobjdir)/nvkludge
 	$(bindir)/nocmodl $*
 	$(COMPILE) -c $*.c
 
-mod_func.o: mod_func.c
+mod_func.o: mod_func.cpp
 	$(COMPILE) -c $<
 
 special: $(MODOBJFILES) $(COBJFILES) mod_func.o

bin/nrnivmodl.in

@@ -244,31 +244,39 @@ echo '#include <stdio.h>
 #include "hocdec.h"
 extern int nrnmpi_myid;
 extern int nrn_nobanner_;
-' > mod_func.c
+#if defined(__cplusplus)
+extern "C" {
+#endif
+' > mod_func.cpp
 for i in $base_names ; do
   echo 'extern void _'$i'_reg(void);'
-done >> mod_func.c
+done >> mod_func.cpp
 echo '
 void modl_reg(){
   if (!nrn_nobanner_) if (nrnmpi_myid < 1) {
     fprintf(stderr, "Additional mechanisms from files'$newline'");
-' >> mod_func.c
+' >> mod_func.cpp
 
 for i in $files
 do
   echo '    fprintf(stderr," \"'`unhide_spaces "$i"`'.mod\"");'
-done >>mod_func.c
+done >>mod_func.cpp
 
 echo '    fprintf(stderr, "'$newline'");
-  }' >>mod_func.c
+  }' >>mod_func.cpp
 
 for i in $base_names; do
   echo '  _'$i'_reg();'
   @USING_CMAKE_TRUE@MODOBJS="$MODOBJS ./$i.o"
   @USING_CMAKE_FALSE@MODOBJS="$MODOBJS $i.o"
-done >> mod_func.c
+done >> mod_func.cpp
 
-echo "}" >> mod_func.c
+echo "}" >> mod_func.cpp
+
+echo '
+#if defined(__cplusplus)
+}
+#endif' >> mod_func.cpp
 
 if test -n "$nrnivmodl_cfiles" ; then
   if test "$UsingCMake" = "yes" ; then

bin/nrnivmodl_makefile_cmake.in

@@ -61,7 +61,7 @@ mod_objs   = $(MODOBJFILES)
 c_objs = $(COBJFILES)
 
 mod_func_o = $(OBJS_DIR)/mod_func.o
-mod_func_c = $(MODC_DIR)/mod_func.c
+mod_func_cpp = $(MODC_DIR)/mod_func.cpp
 
 special  = $(OUTPUT)/special
 LIB_SUFFIX_ = $(if $(MECH_NAME),_$(MECH_NAME),)
@@ -115,7 +115,7 @@ mech_lib_static: mod_func.o $(mod_objs) $(c_objs) build_always
 	@printf " => $(C_GREEN)LINKING$(C_RESET) static library $(mech_lib)\n"
 	ar cq ${mech_lib} $(mod_func_o) $(mod_objs) $(cobjs);
 
-mod_func.o: mod_func.c
+mod_func.o: mod_func.cpp
 	@printf " -> $(C_GREEN)Compiling$(C_RESET) $<\n"
 	$(COMPILE) $(INCLUDES) @CMAKE_CXX_COMPILE_OPTIONS_PIC@ -c $< -o $@
 

bin/nrnmech_makefile.in

@@ -84,8 +84,8 @@ NRNIVOBJS = "$(libobjdir)/nrnmain.o" "$(libobjdir)/ivocmain.o" "$(libobjdir)/nvk
 	"$(bindir)/nocmodl" $*
 	$(LTCOMPILE) -c -o $@ $*.c
 
-mod_func.lo: mod_func.c
-	$(LTCOMPILE) -c -o $@ $*.c
+mod_func.lo: mod_func.cpp
+	$(LTCOMPILE) -c -o $@ $*.cpp
 
 libnrnmech_la_OBJECTS = $(MODOBJFILES) mod_func.lo $(COBJFILES)
 libnrnmech_la_LIBADD = $(NRNOCLIBS) $(NRNIVLIBS)

bin/nrnoc_makefile.in

@@ -76,7 +76,7 @@ NRNOCOBJS = $(libobjdir)/ocmain.o $(libobjdir)/nrnnoiv.o $(libobjdir)/ocnoiv.o
 	$(bindir)/nocmodl $*
 	$(COMPILE) -c $*.c
 
-mod_func.o: mod_func.c
+mod_func.o: mod_func.cpp
 	$(COMPILE) -c $<
 
 special: $(MODOBJFILES) mod_func.o

bin/nrnocmodl.in

@@ -43,22 +43,30 @@ fi
 
 echo '#include <stdio.h>
 #include "hocdec.h"
+#if defined(__cplusplus)
+extern "C"
+#endif
 modl_reg(){
 	NOT_PARALLEL_SUB(fprintf(stderr, "Additional mechanisms from files'$newline'");)
-' > mod_func.c
+' > mod_func.cpp
 
 for i in $files
 do
-	echo 'NOT_PARALLEL_SUB(fprintf(stderr," '$i'.mod");)' >>mod_func.c
+	echo 'NOT_PARALLEL_SUB(fprintf(stderr," '$i'.mod");)' >>mod_func.cpp
 done
-echo 'NOT_PARALLEL_SUB(fprintf(stderr, "'$newline'");)' >>mod_func.c
+echo 'NOT_PARALLEL_SUB(fprintf(stderr, "'$newline'");)' >>mod_func.cpp
 
 for i in $files
 do
-	echo _"$i"_reg"();" >> mod_func.c
+	echo _"$i"_reg"();" >> mod_func.cpp
 	MODOBJS="$MODOBJS $i.o"
 done
-echo "}" >> mod_func.c
+echo "}" >> mod_func.cpp
+
+echo '
+#if defined(__cplusplus)
+}
+#endif' >> mod_func.cpp
 
 make -f $MAKEFILEDIR/nrnoc_makefile "MODOBJFILES=$MODOBJS" special &&
   echo "Successfully created $MODSUBDIR/special"

cmake/CompilerFlagsHelpers.cmake

@@ -63,6 +63,7 @@ foreach(COMPILER_LANGUAGE ${SUPPORTED_COMPILER_LANGUAGE_LIST})
     set(CMAKE_${COMPILER_LANGUAGE}_POSITION_INDEPENDENT "-fPIC")
     set(CMAKE_${COMPILER_LANGUAGE}_VECTORIZE "-ftree-vectorize")
     set(IGNORE_UNKNOWN_PRAGMA_FLAGS "-Wno-unknown-pragmas")
+    set(CMAKE_${COMPILER_LANGUAGE}_IGNORE_WARNINGS "-Wno-write-strings")
 
     if(CMAKE_${COMPILER_LANGUAGE}_COMPILER_VERSION VERSION_GREATER "4.7.0")
       set(CMAKE_${COMPILER_LANGUAGE}_LINK_TIME_OPT "-flto")
@@ -87,6 +88,7 @@ foreach(COMPILER_LANGUAGE ${SUPPORTED_COMPILER_LANGUAGE_LIST})
     set(CMAKE_${COMPILER_LANGUAGE}_VECTORIZE "")
     set(IGNORE_UNKNOWN_PRAGMA_FLAGS "-Wno-unknown-pragmas")
     set(CMAKE_${COMPILER_LANGUAGE}_GEN_NATIVE "-march=native")
+    set(CMAKE_${COMPILER_LANGUAGE}_IGNORE_WARNINGS "-Wno-deprecated-register -Wno-writable-strings")
     # rest of the world
   else()
     set(CMAKE_${COMPILER_LANGUAGE}_WARNING_ALL "-Wall")
@@ -100,5 +102,8 @@ foreach(COMPILER_LANGUAGE ${SUPPORTED_COMPILER_LANGUAGE_LIST})
     if(CMAKE_${COMPILER_LANGUAGE}_COMPILER_ID STREQUAL "PGI")
       set(CMAKE_${COMPILER_LANGUAGE}_WARNING_ALL "")
     endif()
+    if(CMAKE_${COMPILER_LANGUAGE}_COMPILER_ID MATCHES "Clang|AppleClang")
+      set(CMAKE_${COMPILER_LANGUAGE}_IGNORE_WARNINGS "-Wno-deprecated-register -Wno-writable-strings")
+    endif()
   endif()
 endforeach()

cmake/MacroHelper.cmake

@@ -31,15 +31,15 @@ macro(nrn_check_dir_exists HEADER VARIABLE)
   if(${HAVE_HEADER})
     # if header is found, create a code from template
     string(REPLACE "@dir_header@" ${HEADER} CONFTEST_DIR "${CONFTEST_DIR_TPL}")
-    file(WRITE ${CMAKE_CURRENT_SOURCE_DIR}/conftest.c ${CONFTEST_DIR})
+    file(WRITE ${CMAKE_CURRENT_SOURCE_DIR}/conftest.cpp ${CONFTEST_DIR})
     # try to compile
-    try_compile(RESULT_VAR ${CMAKE_CURRENT_SOURCE_DIR} ${CMAKE_CURRENT_SOURCE_DIR}/conftest.c)
+    try_compile(RESULT_VAR ${CMAKE_CURRENT_SOURCE_DIR} ${CMAKE_CURRENT_SOURCE_DIR}/conftest.cpp)
     if(${RESULT_VAR})
       set(${VARIABLE} 1)
     else()
       set(${VARIABLE} 0)
     endif()
-    file(REMOVE "conftest.c")
+    file(REMOVE "conftest.cpp")
   endif()
 endmacro()
 
@@ -59,13 +59,13 @@ macro(nrn_check_type_exists HEADER TYPE DEFAULT_TYPE VARIABLE)
     }")
   string(REPLACE "@header@" ${HEADER} CONFTEST_TYPE "${CONFTEST_TYPE_TPL}")
   string(REPLACE "@type@" ${TYPE} CONFTEST_TYPE "${CONFTEST_TYPE}")
-  file(WRITE ${CMAKE_CURRENT_SOURCE_DIR}/conftest.c ${CONFTEST_TYPE})
+  file(WRITE ${CMAKE_CURRENT_SOURCE_DIR}/conftest.cpp ${CONFTEST_TYPE})
 
-  try_compile(RESULT_VAR ${CMAKE_CURRENT_SOURCE_DIR} ${CMAKE_CURRENT_SOURCE_DIR}/conftest.c)
+  try_compile(RESULT_VAR ${CMAKE_CURRENT_SOURCE_DIR} ${CMAKE_CURRENT_SOURCE_DIR}/conftest.cpp)
   if(NOT ${RESULT_VAR})
     set(${VARIABLE} ${DEFAULT_TYPE})
   endif()
-  file(REMOVE "conftest.c")
+  file(REMOVE "conftest.cpp")
 endmacro()
 
 # =============================================================================
@@ -81,14 +81,14 @@ macro(nrn_check_signal_return_type VARIABLE)
     int main () {
       return *(signal (0, 0)) (0) == 1;
     }")
-  file(WRITE ${CMAKE_CURRENT_SOURCE_DIR}/conftest.c ${CONFTEST_RETSIGTYPE})
-  try_compile(RESULT_VAR ${CMAKE_CURRENT_SOURCE_DIR} ${CMAKE_CURRENT_SOURCE_DIR}/conftest.c)
+  file(WRITE ${CMAKE_CURRENT_SOURCE_DIR}/conftest.cpp ${CONFTEST_RETSIGTYPE})
+  try_compile(RESULT_VAR ${CMAKE_CURRENT_SOURCE_DIR} ${CMAKE_CURRENT_SOURCE_DIR}/conftest.cpp)
   if(RESULT_VAR)
     set(${VARIABLE} int)
   else()
     set(${VARIABLE} void)
   endif()
-  file(REMOVE "conftest.c")
+  file(REMOVE "conftest.cpp")
 endmacro()
 
 # =============================================================================