Cleanup #include cpp file (#2857)

* Create a Parallel list of files
* Remove symlink cpp files that were there for autotools

cmake/NeuronFileLists.cmake

@@ -204,14 +204,7 @@ endif()
 # =============================================================================
 set(NRNIV_FILE_LIST
     backtrace_utils.cpp
-    bbs.cpp
     bbsavestate.cpp
-    bbsdirect.cpp
-    bbslocal.cpp
-    bbslsrv.cpp
-    bbslsrv2.cpp
-    bbsrcli.cpp
-    bbssrv.cpp
     classreg.cpp
     cxprop.cpp
     datapath.cpp
@@ -243,7 +236,6 @@ set(NRNIV_FILE_LIST
     nvector_nrnserial_ld.cpp
     nvector_nrnthread.cpp
     nvector_nrnthread_ld.cpp
-    ocbbs.cpp
     ocjump.cpp
     partrans.cpp
     ppshape.cpp
@@ -424,7 +416,6 @@ set(NMODL_FILES_LIST
     simultan.cpp
     solve.cpp
     symbol.cpp
-    units.cpp
     version.cpp)
 
 set(IVOS_FILES_LIST observe.cpp resource.cpp)
@@ -433,6 +424,16 @@ set(MPI_DYNAMIC_INCLUDE nrnmpi_dynam.h nrnmpi_dynam_cinc nrnmpi_dynam_wrappers.i
 
 set(NRN_MUSIC_FILES_LIST nrnmusic.cpp)
 
+set(NRN_PARALLEL_FILES_LIST
+    bbs.cpp
+    bbsclimpi.cpp
+    bbsdirectmpi.cpp
+    bbslocal.cpp
+    bbslsrv.cpp
+    bbssrv2mpi.cpp
+    bbssrvmpi.cpp
+    ocbbs.cpp)
+
 # =============================================================================
 # Top level directories under src
 # =============================================================================
@@ -447,6 +448,7 @@ set(NRN_MODLUNIT_SRC_DIR ${PROJECT_SOURCE_DIR}/src/modlunit)
 set(NRN_NMODL_SRC_DIR ${PROJECT_SOURCE_DIR}/src/nmodl)
 set(NRN_IVOS_SRC_DIR ${PROJECT_SOURCE_DIR}/src/ivos)
 set(NRN_MUSIC_SRC_DIR ${PROJECT_SOURCE_DIR}/src/neuronmusic)
+set(NRN_PARALLEL_SRC_DIR ${PROJECT_SOURCE_DIR}/src/parallel)
 
 # =============================================================================
 # Create source file lists by gathering from various directories
@@ -460,10 +462,13 @@ nrn_create_file_list(NRN_NODEORDEROPTIM_SRC_FILES ${NRN_NODEORDEROPTIM_SRC_DIR}
 list(APPEND NRN_NODEORDEROPTIM_SRC_FILES ${PROJECT_SOURCE_DIR}/src/coreneuron/utils/lpt.cpp)
 nrn_create_file_list(NRN_NRNCVODE_SRC_FILES ${NRN_NRNCVODE_SRC_DIR} ${NRNCVODE_FILE_LIST})
 nrn_create_file_list(NRN_NRNIV_SRC_FILES ${NRN_NRNIV_SRC_DIR} ${NRNIV_FILE_LIST})
-nrn_create_file_list(NRN_PARALLEL_SRC_FILES ${PROJECT_SOURCE_DIR}/src/nrniv
-                     nvector_nrnparallel_ld.cpp)
-nrn_create_file_list(NRN_PARALLEL_SRC_FILES ${PROJECT_SOURCE_DIR}/src/sundials/shared
-                     nvector_parallel.c)
+nrn_create_file_list(NRN_PARALLEL_SRC_FILES ${NRN_PARALLEL_SRC_DIR} ${NRN_PARALLEL_FILES_LIST})
+if(NRN_ENABLE_MPI)
+  nrn_create_file_list(NRN_PARALLEL_SRC_FILES ${PROJECT_SOURCE_DIR}/src/nrniv
+                       nvector_nrnparallel_ld.cpp)
+  nrn_create_file_list(NRN_PARALLEL_SRC_FILES ${PROJECT_SOURCE_DIR}/src/sundials/shared
+                       nvector_parallel.c)
+endif()
 nrn_create_file_list(NRN_SPARSE_SRC_FILES ${PROJECT_SOURCE_DIR}/src/sparse ${SPARSE_FILES_LIST})
 nrn_create_file_list(NRN_SCOPMATH_SRC_FILES ${PROJECT_SOURCE_DIR}/src/scopmath
                      ${SCOPMATH_FILES_LIST})
@@ -480,14 +485,21 @@ nrn_create_file_list(NRNMPI_DYNAMIC_INCLUDE_FILE ${PROJECT_SOURCE_DIR}/src/nrnmp
 nrn_create_file_list(NRN_IVOS_SRC_FILES ${NRN_IVOS_SRC_DIR} ${IVOS_FILES_LIST})
 nrn_create_file_list(NRN_MUSIC_SRC_FILES ${NRN_MUSIC_SRC_DIR} ${NRN_MUSIC_FILES_LIST})
 list(APPEND NRN_OC_SRC_FILES ${PROJECT_BINARY_DIR}/src/oc/hocusr.h)
+list(APPEND NRN_NMODL_SRC_FILES ${NRN_MODLUNIT_SRC_DIR}/units.cpp)
 
 # =============================================================================
 # Create mswin install lists needed for setup_exe target
 # =============================================================================
 if(MINGW)
   set(MSWIN_SRC_DIR ${PROJECT_SOURCE_DIR}/src/mswin)
   nrn_create_file_list(MSWIN_FILES ${PROJECT_SOURCE_DIR}/src/parallel test0.hoc test0.py)
+
   list(APPEND MSWIN_FILES ${MSWIN_SRC_DIR}/notes.txt)
+
+  list(APPEND NRN_MODLUNIT_SRC_FILES ${PROJECT_SOURCE_DIR}/src/mswin/extra/d2upath.cpp)
+  list(APPEND NRN_NMODL_SRC_FILES ${PROJECT_SOURCE_DIR}/src/mswin/extra/d2upath.cpp)
+  list(APPEND NRN_OC_SRC_FILES ${PROJECT_SOURCE_DIR}/src/mswin/extra/d2upath.cpp)
+
   nrn_create_file_list(MSWIN_BIN_FILES ${MSWIN_SRC_DIR} nrniv.ico nrniv10.ico nmodl2a.ico)
   nrn_create_file_list(
     MSWIN_LIB_FILES

src/modlunit/units.cpp

@@ -13,8 +13,9 @@
 #include <cstring>
 
 #ifdef MINGW
-#include "../mswin/extra/d2upath.cpp"
+#include "../mswin/extra/d2upath.h"
 #endif
+
 #if defined(WIN32)
 #include <windows.h>
 #endif
@@ -109,7 +110,7 @@ static int Getc(FILE* inp) {
 static struct unit unit_stack[UNIT_STK_SIZE], *usp{nullptr};
 
 static char* neuronhome() {
-#if defined(WIN32)
+#if defined(MINGW)
     int i;
     static char buf[256];
     GetModuleFileName(NULL, buf, 256);

src/mswin/CMakeLists.txt

@@ -31,8 +31,8 @@ if(MINGW)
     DEPENDS ${mswinsrc}/nrniv10.ico)
   set_source_files_properties(${mswinsrc}/extra/neuron.cpp ${mswinsrc}/extra/mos2nrn.cpp
                               ${mswinsrc}/extra/nrnbinstr.cpp PROPERTIES COMPILE_DEFINITIONS MINGW)
-  add_executable(neuron ${mswinsrc}/extra/neuron.cpp nrnicon.res)
-  add_executable(mos2nrn ${mswinsrc}/extra/mos2nrn.cpp)
+  add_executable(neuron ${mswinsrc}/extra/neuron.cpp ${mswinsrc}/extra/d2upath.cpp nrnicon.res)
+  add_executable(mos2nrn ${mswinsrc}/extra/mos2nrn.cpp ${mswinsrc}/extra/d2upath.cpp)
   add_executable(nrnbinstr ${mswinsrc}/extra/nrnbinstr.cpp)
   set(INCDIRS ${PROJECT_SOURCE_DIR}/src/oc)
   target_include_directories(mos2nrn PUBLIC ${INCDIRS})

src/mswin/extra/d2upath.cpp

@@ -5,18 +5,19 @@ up to 11 characters longer.
 the output string should be freed with free() when no longer needed.
 */
 
-#include <stdlib.h>
-#include <string.h>
-#include <assert.h>
+#include <cstdlib>
+#include <cstring>
+#include <cassert>
 
 char* hoc_dos2unixpath(const char* d) {
     /* translate x: and x:/ and x:\, to /cygdrive/x/ */
     /* and all backslashes to forward slashes */
     /* or, for mingw, just backslashes to forward slashes */
-    char* cp;
+    char* cp = nullptr;
     auto* const u = static_cast<char*>(malloc(strlen(d) + 12));
     assert(u);
-    int i{}, j{};
+    size_t i = 0;
+    int j = 0;
     if (d[0] && d[1] == ':') {
         strcpy(u, "/cygdrive/");
         i = strlen(u);

src/mswin/extra/d2upath.h

@@ -0,0 +1 @@
+char* hoc_dos2unixpath(const char* d);

src/mswin/extra/mos2nrn.cpp

@@ -5,7 +5,7 @@
 #include <stdio.h>
 #include <stdlib.h>
 #include <cstdio>
-#include "d2upath.cpp"
+#include "d2upath.h"
 
 char* nrnhome;
 char* nh;

src/mswin/extra/neuron.cpp

@@ -5,12 +5,12 @@
 // finally executes nrniv.exe.  Nrniv.exe can be run by itself if
 // it does not need a console or system("command")
 #include <windows.h>
-#include <stdio.h>
-#include <stdlib.h>
 
-#include "d2upath.cpp"
+#include "d2upath.h"
 
 #include <cstdio>
+#include <cstdlib>
+#include <cstring>
 
 char* nrnhome;
 char* nh;