nrnivmodl under cmake no longer uses symbolic links. (#850)

* nrnivmodl under cmake no longer uses symbolic links.

* windows has different signature for mkdir

* missed one

* .libs/libnrnmech.sh may not be a symlink.

* Accept reviewer suggestions.

-I<mod_file_location> before $(INCLUDES)

* Uniform 2 space per level indentation.
  But note that Make rules require a tab for indentation.

* Handle spaces in paths to mod file

* extern cfiles can be a ';' separated list of c files

* extern cfiles now is extern nrnivmodl_cfiles to list ';' separated c files.

* nrnivmodl file and folder name arg checking.

* print args only on error

* add some comments

Co-authored-by: Pramod Kumbhar <pramod.kumbhar@epfl.ch>

bin/nrnivmodl.in

@@ -3,30 +3,34 @@ set -e
 
 ARCH=@host_cpu@
 MODSUBDIR=@modsubdir@
+USER_PWD="`pwd`"
+
+UsingCMake="no"
+@USING_CMAKE_TRUE@UsingCMake="yes"
 
 if test "x${NRNHOME}" = x ; then
-	prefix=@prefix@
-	exec_prefix=@exec_prefix@
-	bindir=@bindir@
-	libdir=@libdir@
+  prefix=@prefix@
+  exec_prefix=@exec_prefix@
+  bindir=@bindir@
+  libdir=@libdir@
 else
-	prefix="$NRNHOME"
-	exec_prefix="${prefix}/${ARCH}"
-	@USING_CMAKE_FALSE@bindir="${prefix}/${ARCH}/bin"
-	@USING_CMAKE_FALSE@libdir="${prefix}/${ARCH}/lib"
-	@USING_CMAKE_TRUE@bindir="${prefix}/bin"
-	@USING_CMAKE_TRUE@libdir="${prefix}/lib"
+  prefix="$NRNHOME"
+  exec_prefix="${prefix}/${ARCH}"
+  @USING_CMAKE_FALSE@bindir="${prefix}/${ARCH}/bin"
+  @USING_CMAKE_FALSE@libdir="${prefix}/${ARCH}/lib"
+  @USING_CMAKE_TRUE@bindir="${prefix}/bin"
+  @USING_CMAKE_TRUE@libdir="${prefix}/lib"
 fi
 
 if test "${NRNHOME_EXEC}" != "" ; then
-	exec_prefix="${NRNHOME_EXEC}"
-	bindir="${exec_prefix}/bin"
-	libdir="${exec_prefix}/lib"
+  exec_prefix="${NRNHOME_EXEC}"
+  bindir="${exec_prefix}/bin"
+  libdir="${exec_prefix}/lib"
 fi
 
 # Besides NRNHOME, one may set NRNBIN to override the default location of user binaries
 if test "x$NRNBIN" = "x"; then
-	NRNBIN=$bindir
+  NRNBIN=$bindir
 fi
 
 export prefix
@@ -57,84 +61,186 @@ if [ "$1" = "-loadflags" ] ; then
        shift
 fi
 
-if [ ! -d $MODSUBDIR ] ; then
-	echo "Creating $MODSUBDIR directory for .o files."
-	echo
-	mkdir $MODSUBDIR
-fi
-
 pwd
 
+# Mod file paths may contain spaces which make variable lists of those
+# hard to manage as space is the item separator. Furthermore, when a
+# path is used, sometimes the spaces must be escaped (eg. a Makefile
+# dependency pattern, and sometimes it is more useful for readability to
+# enclose the path in "". To work around this issue, when creating a list
+# of paths, translate the spaces for each item to +++ and after retrieval
+# of an item, retranslate back to either a space or an escaped space.
+# Only do this for cmake
+
+hide_spaces() {
+  echo "$1" | sed 's/ /+++/g'
+}
+unhide_spaces() {
+  echo "$1" | sed 's/+++/ /g'
+}
+escape_spaces() {
+  echo "$1" | sed 's/+++/\\ /g'
+}
+
+# files is the complete list of mod files to process
 files=""
-incs=""
+@USING_CMAKE_FALSE@incs=""
 if test $# -gt 0 ; then
-	for i in "$@" ; do
-		if test -d "$i" ; then
-			set +e
-			files="$files $(unset LC_ALL; ls $i/*.mod)"
-			incs="$incs $(unset LC_ALL; ls $i/*.inc)"
-			set -e
-		else
-			files="$files $i"
-		fi
-	done
+  for i in "$@" ; do
+    i_hide=`hide_spaces "$i"`
+    if test -d "$i" ; then
+      set +e
+      if test "$UsingCMake" = "yes" ; then
+        for j in $(cd "$i"; unset LC_ALL; ls *.mod) ; do
+          files="$files $i_hide/$j"
+        done
+      else
+        files="$files $(unset LC_ALL; ls $i/*.mod)"
+        incs="$incs $(unset LC_ALL; ls $i/*.inc)"
+      fi
+      set -e
+    else
+      if test "$UsingCMake" = "yes" ; then
+        if test -e "$i" -o -e "$i.mod" ; then
+          files="$files $i_hide"
+        else
+          echo "Arg Error: \"$i\" is not a folder or mod file name or prefix"
+
+          echo ""
+          echo -n "  Mod file, folder args:"
+          for j in "$@" ; do
+            echo -n " \"$j\""
+          done
+          echo ""
+
+          exit 1
+        fi
+      else
+        files="$files $i"
+      fi
+    fi
+  done
 else
-	# Unset LC_ALL for consistent mod order
-	files=$(unset LC_ALL; ls *.mod)
+  # Unset LC_ALL for consistent mod order
+  files=$(unset LC_ALL; ls *.mod)
 fi
+
 files=`echo "$files" | sed 's/^ *//'`
 
-mfiles=""
+base_names=""
 for i in $files ; do
-	mfiles="$mfiles `basename $i`"
+  base_names="$base_names `basename -s .mod $i`"
 done
-mfiles=`echo "$mfiles" | sed 's/^ *//'`
 
-echo $files
-echo $mfiles
+if test "$UsingCMake" = "yes" ; then
+  echo -n "Mod files:"
+  for i in $files ; do
+    base_name=`basename -s .mod "$i"`
+    dir_name=`dirname "$i"`
+    echo -n " \"`unhide_spaces $dir_name`/$base_name.mod\""
+  done
+  echo ""
+  echo ""
+fi
+
+if [ ! -d $MODSUBDIR ] ; then
+  echo "Creating $MODSUBDIR directory for .o files."
+  echo
+  mkdir $MODSUBDIR
+fi
 
 files=`echo "$files" | sed 's/\.mod//g'`
 
 if test "$files" = '*' ; then
-	files=""
+  files=""
 fi
 
 cd $MODSUBDIR
-mdir=`pwd`
-for i in $files; do
-	rm -f "`basename $i`".mod
-	ln -s ../$i.mod .
-done
+mdir="`pwd`"
 
-if test "$incs" != "" ; then
-	for i in $incs ; do
-		rm -f "`basename $i`"
-		ln -s ../$i .
-	done
-fi
+if test "$UsingCMake" = "yes" ; then
+  # construct file to be included by makefile to specify mod to c rule when
+  # executed in $MODSUBDIR (child folder of launch location folder)
+  MODMAKE=makemod2c_inc
+  echo "" > $MODMAKE
+  for i in $files ; do
+    case "$i" in
+      /*) f=$i;; # absolute, fine as is
+      *)  f=../$i;; # relative
+    esac
+    base_name="`basename $f`"
+    dir_name="`dirname $f`"
+    # Note: indentation for shell lines in make rules must be a tab
+    echo "\
+./$base_name.c: `escape_spaces "$f.mod"`
+	@printf \" -> \$(C_GREEN)NMODL\$(C_RESET) \$<\\\n\"
+	(cd \"`unhide_spaces $dir_name`\"; MODLUNIT=\$(NRNUNITS) \$(NOCMODL) $base_name.mod -o \"$mdir\")
 
-bfiles=`echo "$mfiles" | sed 's/\.mod//g'`
+./$base_name.o: ./$base_name.c
+	@printf \" -> \$(C_GREEN)Compiling\$(C_RESET) \$<\\\n\"
+	\$(COMPILE) -I\"`unhide_spaces $dir_name`\" \$(INCLUDES) @CMAKE_CXX_COMPILE_OPTIONS_PIC@ -c \$< -o \$@
+" >> $MODMAKE
+  done
+  if test "$nrnivmodl_cfiles" != "" ; then
+    # I find it very difficult to construct shell variables which are
+    # space separated lists of items containing spaces. So, for a cmake build,
+    # the nrnivmodl_cfiles variable is required to be a ';' separated list
+    # of c files which may contain spaces.
+    # Save the Internal Field Separator and interpret variables as ';'
+    # separated list of items (which may contain spaces). Restore after
+    # processing nrnivmodl_cfiles.
+    ifs="$IFS"
+    IFS=';'
+    for i in $nrnivmodl_cfiles ; do
+      i_hide=`hide_spaces "$i"`
+      case "$i_hide" in
+        /*) f=$i_hide;; # absolute, fine as is
+        *)  f=../$i_hide;; # relative
+      esac
+      base_name="`basename -s .c $f`"
+      dir_name="`dirname $f`"
+      echo "\
+./$base_name.o: `escape_spaces "$f"`
+	@printf \" -> \$(C_GREEN)Compiling\$(C_RESET) \$<\\\n\"
+	(cd \"`unhide_spaces $dir_name`\"; \$(COMPILE) \$(INCLUDES) @CMAKE_CXX_COMPILE_OPTIONS_PIC@ -c $base_name.c -o \"$mdir/$base_name.o\")
+" >> $MODMAKE
+    done
+    IFS="$ifs"
+  fi
+else
+  for i in $files; do
+       rm -f "`basename $i`".mod
+       ln -s ../$i.mod .
+  done
 
-for i in $cfiles; do
-	rm -f $i
-	ln -s ../$i .
-done
+  if test "$incs" != "" ; then
+       for i in $incs ; do
+               rm -f "`basename $i`"
+               ln -s ../$i .
+       done
+  fi
+
+  for i in $nrnivmodl_cfiles; do
+       rm -f "$i"
+       ln -s "../$i" .
+  done
+fi
 
 COBJS=
 MODOBJS=
 if [ `echo "\n"` ] ; then
-	newline="\n"
+  newline="\n"
 else
-	newline="\\\\n"
+  newline="\\\\n"
 fi
 
 echo '#include <stdio.h>
 #include "hocdec.h"
 extern int nrnmpi_myid;
 extern int nrn_nobanner_;
 ' > mod_func.c
-for i in $bfiles ; do
-	echo 'extern void _'$i'_reg(void);'
+for i in $base_names ; do
+  echo 'extern void _'$i'_reg(void);'
 done >> mod_func.c
 echo '
 void modl_reg(){
@@ -144,25 +250,51 @@ void modl_reg(){
 
 for i in $files
 do
-	echo '    fprintf(stderr," '$i'.mod");'
+  echo '    fprintf(stderr," \"'`unhide_spaces "$i"`'.mod\"");'
 done >>mod_func.c
 
 echo '    fprintf(stderr, "'$newline'");
   }' >>mod_func.c
 
-for i in $bfiles; do
-	echo '  _'$i'_reg();'
-	MODOBJS="$MODOBJS $i.o"
+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
 
 echo "}" >> mod_func.c
 
+if test -n "$nrnivmodl_cfiles" ; then
+  if test "$UsingCMake" = "yes" ; then
+    sp=""
+    COBJS=""
+    ifs="$IFS"
+    IFS=';'
+    for i in $nrnivmodl_cfiles ; do
+      base_name=`basename -s .c "$i"`
+      COBJS="${COBJS}${sp}./${base_name}.o"
+      sp=" "
+    done
+    IFS="$ifs"
+  else
+    COBJS=`echo "$nrnivmodl_cfiles" | sed 's/\.c/.o/g'`
+  fi
+fi
 
-if test -n "$cfiles" ; then
-	COBJS=`echo "$cfiles" | sed 's/\.c/.o/g'`
+echo "COBJS='$COBJS'"
+# call nrnivmodl-core if CoreNEURON is enabled and requested via CLI
+if [ "$LinkCoreNEURON" = true ] ; then
+  :
+  @USING_CMAKE_FALSE@ printf "ERROR : CoreNEURON is not compatible with autotools, build with CMake build system!\n"
+  @USING_CMAKE_FALSE@ exit 1
+  @USING_CMAKE_TRUE@@CORENEURON_ENABLED_FALSE@ printf "ERROR : CoreNEURON support is not enabled!\n"
+  @USING_CMAKE_TRUE@@CORENEURON_ENABLED_FALSE@ exit 1
+  @USING_CMAKE_TRUE@@CORENEURON_ENABLED_TRUE@ cd $USER_PWD
+  @USING_CMAKE_TRUE@@CORENEURON_ENABLED_TRUE@ $bindir/nrnivmodl-core $MODSUBDIR
+  @USING_CMAKE_TRUE@@CORENEURON_ENABLED_TRUE@ cd $MODSUBDIR
 fi
 
-@NRN_BINARY_SPECIAL_TRUE@@USING_CMAKE_TRUE@make -j 4 -f "${MAKEFILEDIR}/nrnmech_makefile" "ROOT=${prefix}" "MODOBJFILES=$MODOBJS" "COBJFILES=$COBJS" "UserLDFLAGS=$UserLDFLAGS" "UserINCFLAGS=$UserINCFLAGS" special &&
+@NRN_BINARY_SPECIAL_TRUE@@USING_CMAKE_TRUE@make -j 4 -f "${MAKEFILEDIR}/nrnmech_makefile" "ROOT=${prefix}" "MODOBJFILES=$MODOBJS" "COBJFILES=$COBJS" "UserLDFLAGS=$UserLDFLAGS" "UserINCFLAGS=$UserINCFLAGS" "LinkCoreNEURON=$LinkCoreNEURON" special &&
 @NRN_BINARY_SPECIAL_TRUE@@USING_CMAKE_FALSE@make -j 4 -f "${MAKEFILEDIR}/nrniv_makefile" "ROOT=${prefix}" "MODOBJFILES=$MODOBJS" "COBJFILES=$COBJS" "UserLDFLAGS=$UserLDFLAGS" "UserINCFLAGS=$UserINCFLAGS" special &&
 @NRN_BINARY_SPECIAL_TRUE@  echo "Successfully created $MODSUBDIR/special"
 
@@ -172,7 +304,7 @@ fi
 @NRN_BINARY_SPECIAL_FALSE@  mdir='${NRNHOME}'/share/nrn/demo/release/${MODSUBDIR}
 @NRN_BINARY_SPECIAL_FALSE@fi
 @NRN_BINARY_SPECIAL_FALSE@@USING_CMAKE_FALSE@make -j 4 -f "$MAKEFILEDIR/nrnmech_makefile" "ROOT=${prefix}" "MODOBJFILES=$MODLO" "COBJFILES=$CLO" "UserLDFLAGS=$UserLDFLAGS" "UserINCFLAGS=$UserINCFLAGS" libnrnmech.la
-@NRN_BINARY_SPECIAL_FALSE@@USING_CMAKE_TRUE@make -j 4 -f "$MAKEFILEDIR/nrnmech_makefile" "ROOT=${prefix}" "MODOBJFILES=$MODOBJS" "COBJFILES=$COBJS" "UserLDFLAGS=$UserLDFLAGS" "UserINCFLAGS=$UserINCFLAGS" libnrnmech.la VERBOSE=1
+@NRN_BINARY_SPECIAL_FALSE@@USING_CMAKE_TRUE@make -j 4 -f "$MAKEFILEDIR/nrnmech_makefile" "ROOT=${prefix}" "MODOBJFILES=$MODOBJS" "COBJFILES=$COBJS" "UserLDFLAGS=$UserLDFLAGS" "UserINCFLAGS=$UserINCFLAGS" "LinkCoreNEURON=$LinkCoreNEURON" mech_lib_shared VERBOSE=1
 @NRN_BINARY_SPECIAL_FALSE@  echo '#!/bin/sh
 @NRN_BINARY_SPECIAL_FALSE@if test "x${NRNHOME}" = "x" ; then
 @NRN_BINARY_SPECIAL_FALSE@    NRNHOME='"\"${prefix}\""'