Clean headers dependencies in nrn

CMakeLists.txt

@@ -859,15 +859,6 @@ install(PROGRAMS ${CMAKE_CURRENT_SOURCE_DIR}/share/lib/cleanup
 
 # Copy NEURON headers that will be included in the installation into the build directory.
 set(headers_in_build_dir)
-foreach(header_below_src ${HEADER_FILES_TO_INSTALL})
-  get_filename_component(header_name "${header_below_src}" NAME)
-  set(output_name "${PROJECT_BINARY_DIR}/include/${header_name}")
-  cpp_cc_build_time_copy(
-    INPUT "${PROJECT_SOURCE_DIR}/src/${header_below_src}"
-    OUTPUT "${output_name}"
-    NO_TARGET)
-  list(APPEND headers_in_build_dir "${output_name}")
-endforeach()
 foreach(header_below_src ${STRUCTURED_HEADER_FILES_TO_INSTALL})
   set(output_name "${PROJECT_BINARY_DIR}/include/${header_below_src}")
   cpp_cc_build_time_copy(

bin/nrnivmodl.in

@@ -191,7 +191,7 @@ MODOBJS=
 
 {
   echo '#include <stdio.h>
-#include "hocdec.h"
+#include <oc/hocdec.h>
 extern int nrnmpi_myid;
 extern int nrn_nobanner_;
 '

bin/nrnivmodl_makefile_cmake.in

@@ -19,7 +19,7 @@ UserLDFLAGS =
 # install dirs
 bindir := ${ROOT}/@CMAKE_INSTALL_BINDIR@
 libdir := ${ROOT}/@CMAKE_INSTALL_LIBDIR@
-incdir := ${ROOT}/@CMAKE_INSTALL_INCLUDEDIR@
+incdir := -I${ROOT}/@CMAKE_INSTALL_INCLUDEDIR@ -I${ROOT}/@CMAKE_INSTALL_INCLUDEDIR@/crout -I${ROOT}/@CMAKE_INSTALL_INCLUDEDIR@/neuron -I${ROOT}/@CMAKE_INSTALL_INCLUDEDIR@/newton -I${ROOT}/@CMAKE_INSTALL_INCLUDEDIR@/nrncvode -I${ROOT}/@CMAKE_INSTALL_INCLUDEDIR@/nrniv -I${ROOT}/@CMAKE_INSTALL_INCLUDEDIR@/nrnmpi -I${ROOT}/@CMAKE_INSTALL_INCLUDEDIR@/nrnoc -I${ROOT}/@CMAKE_INSTALL_INCLUDEDIR@/oc -I${ROOT}/@CMAKE_INSTALL_INCLUDEDIR@/scopmath -I${ROOT}/@CMAKE_INSTALL_INCLUDEDIR@/sparse13
 datadir:= ${ROOT}/@CMAKE_INSTALL_DATADIR@
 datadir_lib := ${ROOT}/@CMAKE_INSTALL_DATADIR@/lib
 
@@ -47,7 +47,7 @@ OS_NAME := $(shell uname)
 _cm =,
 
 # We rebuild the include dirs since a lot of stuff changes place
-INCLUDES = -I. $(INCFLAGS) $(UserINCFLAGS) -I$(incdir)
+INCLUDES = -I. $(INCFLAGS) $(UserINCFLAGS) $(incdir)
 ifeq (@NRN_INCLUDE_MPI_HEADERS@, ON)
   INCLUDES += $(if @MPI_C_INCLUDE_PATH@, -I$(subst ;, -I,@MPI_C_INCLUDE_PATH@),)
 endif
@@ -116,14 +116,14 @@ C_GREEN := \033[32m
 # RPATH is set for DESTDIR_RPATH and coreneuron lib
 special: $(mech_lib)
 	@printf " => $(C_GREEN)LINKING$(C_RESET) executable $(special) LDFLAGS are: $(LDFLAGS)\n"
-	$(CXX_LINK_EXE) -I $(incdir) -I $(incdir)/nrncvode -DAUTO_DLOPEN_NRNMECH=0 $(datadir)/nrnmain.cpp -o $(special) \
+	$(CXX_LINK_EXE) $(incdir) -DAUTO_DLOPEN_NRNMECH=0 $(datadir)/nrnmain.cpp -o $(special) \
 	  -L$(OBJS_DIR) -l$(mech_libname) $(NRNLIB_FLAGS) -l$(mech_libname) $(extra_lib_link) -Wl,-rpath,'$(DESTDIR_RPATH)' -Wl,-rpath,$(libdir) $(LDFLAGS) $(EXTRA_LDFLAGS)
 
 $(mech_lib): $(mech_lib_type)
 
 mech_lib_shared: mod_func.o $(mod_objs) build_always
 	@printf " => $(C_GREEN)LINKING$(C_RESET) shared library $(mech_lib)\n"
-	$(CXX_LINK_SHARED) -I $(incdir) -o ${mech_lib} ${_SONAME} \
+	$(CXX_LINK_SHARED) $(incdir) -o ${mech_lib} ${_SONAME} \
 	  $(mod_func_o) $(mod_objs) $(NRNLIB_FLAGS) $(NRNLIB_RPATH_FLAGS) $(LDFLAGS)
 	rm -f $(OBJS_DIR)/.libs/libnrnmech.so ; mkdir -p $(OBJS_DIR)/.libs ; cp $(mech_lib) $(OBJS_DIR)/.libs/libnrnmech.so
 

bin/nrnocmodl.in

@@ -42,7 +42,7 @@ else
 fi
 
 echo '#include <stdio.h>
-#include "hocdec.h"
+#include <oc/hocdec.h>
 extern "C" void modl_reg() {
 	fprintf(stderr, "Additional mechanisms from files'$newline'");
 ' > mod_func.cpp

cmake/MacroHelper.cmake

@@ -83,7 +83,7 @@ endmacro()
 # Transform PROJECT_SOURCE_DIR/sdir/sfile.in to PROJECT_BINARY_DIR/bdir/bfile
 # =============================================================================
 # ~~~
-# This 4 arg macro transformsPROJECT_SOURCE_DIR/sdir/sfile.in into
+# This 4 arg macro transforms PROJECT_SOURCE_DIR/sdir/sfile.in into
 # PROJECT_BINARY_DIR/bdir/bfile .
 # THE shorter two arg form transforms PROJECT_SOURCE_DIR/dir/file.in into
 # PROJECT_BINARY_DIR/dir/file

cmake/NeuronFileLists.cmake

@@ -1,14 +1,14 @@
 # =======================================================================================
-# Lists of header files to install. Difference is whether the dir structure is preserved.
+# Lists of header files to install.
 #
-# * HEADER_FILES_TO_INSTALL: ${src}/src/dir/header.h -> {bld}/include/header.h
 # * STRUCTURED_HEADER_FILES_TO_INSTALL: {src}/src/a/b.h -> {bld}/include/a/b.h
 # =======================================================================================
 set(STRUCTURED_HEADER_FILES_TO_INSTALL
-    neuron/cache/mechanism_range.hpp neuron/container/data_handle.hpp
-    neuron/container/generic_data_handle.hpp neuron/container/non_owning_soa_identifier.hpp
-    neuron/model_data_fwd.hpp)
-set(HEADER_FILES_TO_INSTALL
+    neuron/cache/mechanism_range.hpp
+    neuron/container/data_handle.hpp
+    neuron/container/generic_data_handle.hpp
+    neuron/container/non_owning_soa_identifier.hpp
+    neuron/model_data_fwd.hpp
     nrniv/backtrace_utils.h
     nrniv/bbsavestate.h
     nrnmpi/nrnmpidec.h

mingw_files/nrnmingwenv.sh

@@ -125,8 +125,8 @@ copyinc() {
 
 # we rely on a couple of include groups, one from nocmodl and the other one hoisted from old gcc days and all (most) ModelDB include 
 copyinc '
-"mech_api.h"
-"section.h"
+<oc/mech_api.h>
+<nrnoc/section.h>
 <math.h>
 <stdio.h>
 <stdlib.h>

src/gnu/HypGeom.cpp

@@ -1,4 +1,3 @@
-
 /* 
 Copyright (C) 1988 Free Software Foundation
     written by Dirk Grunwald (grunwald@cs.uiuc.edu)

src/ivoc/apwindow.cpp

@@ -1,4 +1,4 @@
-#include <../../nrnconf.h>
+#include <nrnconf.h>
 #if HAVE_IV  // to end of file
 
 #ifdef WIN32

src/ivoc/axis.cpp

@@ -1,4 +1,4 @@
-#include <../../nrnconf.h>
+#include <nrnconf.h>
 #if HAVE_IV  // to end of file
 
 #include <cstdio>
@@ -11,7 +11,7 @@
 #include "scenevie.h"
 #include "mymath.h"
 #include "axis.h"
-#include "hocdec.h"
+#include <oc/hocdec.h>
 #include "rect.h"
 #include "graph.h"
 #include "idraw.h"

src/ivoc/bndedval.cpp

@@ -1,4 +1,4 @@
-#include <../../nrnconf.h>
+#include <nrnconf.h>
 #if HAVE_IV  // to end of file
 
 #include "bndedval.h"

src/ivoc/cbwidget.cpp

@@ -1,4 +1,4 @@
-#include <../../nrnconf.h>
+#include <nrnconf.h>
 #if HAVE_IV  // to end of file
 
 #include <InterViews/window.h>

src/ivoc/checkpnt.cpp

@@ -1,4 +1,4 @@
-#include <../../nrnconf.h>
+#include <nrnconf.h>
 #if HAVE_IV  // to end of file
 
 /*
@@ -91,17 +91,17 @@ data depending on type. eg for VAR && NOTUSER it is
 #include <OS/list.h>
 #include <OS/table.h>
 #include "oc2iv.h"
-#include "ocfunc.h"
+#include <oc/ocfunc.h>
 #if HAVE_XDR
 #include <rpc/xdr.h>
 #endif
 #include "checkpnt.h"
 
-#include "redef.h"
-#include "hoclist.h"
+#include <oc/redef.h>
+#include <oc/hoclist.h>
 #include "parse.hpp"
-#include "code.h"
-#include "equation.h"
+#include <oc/code.h>
+#include <oc/equation.h>
 int hoc_readcheckpoint(char*);
 extern int hoc_resize_toplevel(int);
 

src/ivoc/classreg.cpp

@@ -1,11 +1,11 @@
-#include <../../nrnconf.h>
+#include <nrnconf.h>
 // interface c++ class to oc
 
 #include <InterViews/resource.h>
 #include <stdio.h>
-#include "classreg.h"
+#include <oc/classreg.h>
 #ifndef OC_CLASSES
-#define OC_CLASSES "occlass.h"
+#define OC_CLASSES <ivoc/occlass.h>
 #endif
 
 #define EXTERNS 1

src/ivoc/datapath.cpp

@@ -1,18 +1,18 @@
-#include <../../nrnconf.h>
+#include <nrnconf.h>
 #include <map>
 #include <cstdio>
 #include <InterViews/resource.h>
 #include <OS/string.h>
 #include <OS/list.h>
-#include "hoclist.h"
+#include <oc/hoclist.h>
 #if HAVE_IV
 #include "graph.h"
 #endif
 #include "datapath.h"
 #include "ivocvect.h"
 
-#include "nrnoc2iv.h"
-#include "membfunc.h"
+#include <nrniv/nrnoc2iv.h>
+#include <nrnoc/membfunc.h>
 
 #include "parse.hpp"
 extern Symlist* hoc_built_in_symlist;

src/ivoc/epsprint.cpp

@@ -1,4 +1,4 @@
-#include <../../nrnconf.h>
+#include <nrnconf.h>
 #if HAVE_IV  // to end of file
 
 #include "epsprint.h"

src/ivoc/field.cpp

@@ -1,4 +1,4 @@
-#include <../../nrnconf.h>
+#include <nrnconf.h>
 #if HAVE_IV  // to end of file
 
 /*

src/ivoc/fourier.cpp

@@ -1,4 +1,4 @@
-#include <../../nrnconf.h>
+#include <nrnconf.h>
 /* (C) Copr. 1986-92 Numerical Recipes Software #.,. */
 
 /* Algorithms for Fourier Transform Spectral Methods */
@@ -18,7 +18,7 @@
 #undef myfabs
 #define myfabs fabs
 
-#include "oc_ansi.h"
+#include <oc/oc_ansi.h>
 
 // Apple LLVM version 5.1 (clang-503.0.38) generates "unsequenced modification warning".
 // #define SQUARE(a) ((x_=(a)) == 0.0 ? 0.0 : x_*x_)

src/ivoc/gifimage.cpp

@@ -1,4 +1,4 @@
-#include <../../nrnconf.h>
+#include <nrnconf.h>
 #if HAVE_IV  // to end of file
 
 #include <stdio.h>

src/ivoc/graph.cpp

@@ -1,4 +1,4 @@
-#include <../../nrnconf.h>
+#include <nrnconf.h>
 
 #include <string.h>
 #include <stdio.h>
@@ -36,7 +36,7 @@ extern Image* gif_image(const char*);
 #include "idraw.h"
 #include "symchoos.h"
 #include "scenepic.h"
-#include "oc_ansi.h"
+#include <oc/oc_ansi.h>
 #include "oc2iv.h"
 #include "objcmd.h"
 #include "ocjump.h"
@@ -46,8 +46,8 @@ extern Image* gif_image(const char*);
 #include "ivocvect.h"
 #endif /* HAVE_IV */
 
-#include "classreg.h"
-#include "gui-redirect.h"
+#include <oc/classreg.h>
+#include <nrnoc/gui-redirect.h>
 
 #if HAVE_IV
 #define Graph_Crosshair_           "Crosshair Graph"

src/ivoc/graphvec.cpp

@@ -1,4 +1,4 @@
-#include <../../nrnconf.h>
+#include <nrnconf.h>
 #if HAVE_IV  // to end of file
 
 #define USEGNU 1

src/ivoc/grglyph.cpp

@@ -1,7 +1,7 @@
-#include <../../nrnconf.h>
+#include <nrnconf.h>
 // hoc level Glyph implementation for graphing
 #include <stdio.h>
-#include "classreg.h"
+#include <oc/classreg.h>
 #include "oc2iv.h"
 #if HAVE_IV
 #include "ivoc.h"
@@ -24,7 +24,7 @@ class GrGlyph: public Resource {
 };
 #endif  // HAVE_IV
 
-#include "gui-redirect.h"
+#include <nrnoc/gui-redirect.h>
 
 double gr_addglyph(void* v) {
     TRY_GUI_REDIRECT_ACTUAL_DOUBLE("Graph.addglyph", v);

src/ivoc/grmanip.cpp

@@ -1,4 +1,4 @@
-#include <../../nrnconf.h>
+#include <nrnconf.h>
 #if HAVE_IV  // to end of file
 
 #include <InterViews/canvas.h>

src/ivoc/hocmark.cpp

@@ -1,4 +1,4 @@
-#include <../../nrnconf.h>
+#include <nrnconf.h>
 #if HAVE_IV  // to end of file
 
 #include <stdio.h>

src/ivoc/htlist.cpp

@@ -1,5 +1,5 @@
 #ifdef HAVE_CONFIG_H
-#include <../../nrnconf.h>
+#include <nrnconf.h>
 #endif
 /*
 Based on Unidraw UList but UList changed to HTList (head tail list)
@@ -34,7 +34,7 @@ for fast insertion, deletion, iteration
 
 #include <stdio.h>
 #include <OS/enter-scope.h>
-#include <htlist.h>
+#include "htlist.h"
 
 /*****************************************************************************/
 

src/ivoc/idraw.cpp

@@ -1,4 +1,4 @@
-#include <../../nrnconf.h>
+#include <nrnconf.h>
 #if HAVE_IV  // to end of file
 
 #include <stdio.h>
@@ -13,8 +13,8 @@
 #include <InterViews/style.h>
 #include <OS/string.h>
 
-#include "hocdec.h"
-#include "oc_ansi.h"
+#include <oc/hocdec.h>
+#include <oc/oc_ansi.h>
 #include "scenevie.h"
 #include "mymath.h"
 #include "idraw.h"

src/ivoc/ivoc.cpp

@@ -1,15 +1,15 @@
-#include <../../nrnconf.h>
+#include <nrnconf.h>
 
 #include <vector>
-#include <ocnotify.h>
+#include "ocnotify.h"
 #include <stdio.h>
 #include <stdlib.h>
 #include "neuron/container/soa_container.hpp"
-#include <nrnmutdec.h>
+#include "nrnmutdec.h"
 #include "oc2iv.h"
-#include "ocfunc.h"
+#include <oc/ocfunc.h>
 #include "ocnotify.h"
-#include "oc_ansi.h"
+#include <oc/oc_ansi.h>
 #include "ocjump.h"
 
 #if HAVE_IV

src/ivoc/ivoc.h

@@ -6,7 +6,7 @@
 #include <InterViews/session.h>
 #include <OS/string.h>
 #include <stdio.h>
-#include "gui-redirect.h"
+#include <nrnoc/gui-redirect.h>
 extern int nrn_err_dialog_active_;
 
 #include <ostream>

src/ivoc/ivocmac.cpp

@@ -1,4 +1,4 @@
-#include <../../nrnconf.h>
+#include <nrnconf.h>
 
 #include <CodeFragments.h>