Index: trunk/SophyaLib/Manual/dox_sophya.conf
===================================================================
--- trunk/SophyaLib/Manual/dox_sophya.conf	(revision 974)
+++ trunk/SophyaLib/Manual/dox_sophya.conf	(revision 976)
@@ -16,5 +16,5 @@
 # if some version control system is used.
 
-PROJECT_NUMBER       = 0.9.36 V_Avr2000
+PROJECT_NUMBER       = 
 
 # The OUTPUT_DIRECTORY tag is used to specify the (relative or absolute) 
@@ -191,5 +191,5 @@
 # with spaces.
 
-INPUT = ../SysTools ../TArray ../NTools ../HiStats
+INPUT = 
 
 # If the value of the INPUT tag contains directories, you can use the 
@@ -222,5 +222,5 @@
 # the \include command).
 
-EXAMPLE_PATH         = ../SysTools ../TArray ../NTools
+EXAMPLE_PATH         = 
 
 # If the value of the EXAMPLE_PATH tag contains directories, you can use the
Index: trunk/SophyaLib/Manual/mkmf
===================================================================
--- trunk/SophyaLib/Manual/mkmf	(revision 974)
+++ trunk/SophyaLib/Manual/mkmf	(revision 976)
@@ -1,11 +1,54 @@
 #!/bin/csh
-###################################################
+#####################################################
 if( $#argv >= 1 ) then
   if( "$1" == "-h" ) then
-    echo "mkmf [module1] [module2] [...]"
+    echo "mkmf [-options] [-o dir] [module1] [module2] [...]"
     echo "  generate documentation for all Sophya"
-    echo "  or only for module [module]"
-    exit 0
+    echo "  or only for module [module...]"
+    echo "  **** [-options] :"
+    echo "  -html : generate HTML doc"
+    echo "  -latex : generate LATEX doc"
+    echo "  -man : generate MAN doc"
+    echo "  -rtf : generate RTF doc"
+    echo "  default is : html + latex"
+    echo "  **** [-o dir] : directory where doc have to be put"
+    echo "  default is ."
+    exit -1
   endif
+endif
+#####################################################
+
+##################################
+######## Decode arguments ########
+##################################
+set allmodules = ( SysTools TArray NTools HiStats )
+unset modules; unset latex; unset html; unset man; unset rtf
+set outdir = "."
+if( $#argv >= 1 ) then
+  while ( $#argv > 0)
+    if( "$1" == "-o" ) then
+      shift
+      set outdir = $1
+    else if( "$1" == "-html" ) then
+      set html
+    else if( "$1" == "-latex" ) then
+      set latex
+    else if( "$1" == "-man" ) then
+      set man
+    else if( "$1" == "-rtf" ) then
+      set rtf
+    else
+      if( ! $?modules ) set modules
+      set modules = ( $modules $1 )
+    endif
+    shift
+  end
+endif
+if( ! $?html  && ! $?latex  && ! $?man  && ! $?rtf ) then
+  set html
+  set latex
+endif
+if( ! $?modules ) then
+  set modules = ( $allmodules )
 endif
 
@@ -14,11 +57,12 @@
 ##########################################
 
+#------------
 # mydoxy.conf
+#------------
 cp dox_sophya.conf mydoxy.conf
-foreach n ( 1 2 3 4 5 )
-  echo " " >> mydoxy.conf
-end
 
+#----------
 # doxygen ?
+#----------
 which doxygen >! /dev/null
 if( $status != 0 ) then
@@ -27,5 +71,7 @@
 endif
 
+#-------------
 # doxysearch ?
+#-------------
 which doxysearch >! /dev/null
 if( $status != 0 ) then
@@ -34,6 +80,5 @@
 else
     set s = `which doxysearch`
-  echo 'doxysearch is installed in :'
-  echo $s:h
+  echo 'doxysearch is installed in : ' $s:h
   echo 'mkmf will automatically update the config file.'
     echo "BIN_ABSPATH = $s:h" >>  mydoxy.conf
@@ -41,15 +86,74 @@
 endif
 
-# partial doc ?
-if( $#argv >= 1 ) then
-  echo Partial doc generation :
-    set lf =
-    foreach f ( $* )
-      echo "... adding ../$f to INPUT"
-      set lf = ( ../$f $lf )
-    end
-    echo "INPUT = $lf" >>  mydoxy.conf
-    grep 'INPUT = ' mydoxy.conf | grep -v ^\# | tail -1
+#-----------------
+# Version number ?
+#-----------------
+set f = ../SysTools/sversion.h
+if( -e $f ) then
+  set v = `grep 'SOPHYA_VERSION'  $f | awk '{print $3}'`
+  set r = `grep 'SOPHYA_REVISION' $f | awk '{print $3}'`
+  set t = `grep 'SOPHYA_TAG'      $f | awk '{print $3}'`
+  echo "PROJECT_NUMBER = V${v}_R${r}_${t}" >>  mydoxy.conf
+else
+  echo "PROJECT_NUMBER = Not_Defined" >>  mydoxy.conf
 endif
+grep 'PROJECT_NUMBER = ' mydoxy.conf | tail -1
+
+#---------------
+# What modules ?
+#---------------
+set lf =
+foreach f ( $modules )
+  echo "... Generating doc for ../$f"
+  set lf = ( ../$f $lf )
+end
+echo "INPUT = $lf" >>  mydoxy.conf
+grep 'INPUT = ' mydoxy.conf | tail -1
+
+set lf =
+foreach f ( $allmodules )
+  set lf = ( ../$f $lf )
+end
+echo "EXAMPLE_PATH = $lf" >>  mydoxy.conf
+
+#-------------------
+# What kind of doc ?
+#-------------------
+if( $?html ) then
+  echo "GENERATE_HTML = YES" >>  mydoxy.conf
+  echo "...... generating HTML"
+else
+  echo "GENERATE_HTML = NO" >>  mydoxy.conf
+endif
+if( $?latex ) then
+  echo "GENERATE_LATEX = YES" >>  mydoxy.conf
+  echo "...... generating LATEX"
+else
+  echo "GENERATE_LATEX = NO" >>  mydoxy.conf
+endif
+if( $?man ) then
+  echo "GENERATE_MAN = YES" >>  mydoxy.conf
+  echo "...... generating MAN"
+else
+  echo "GENERATE_MAN = NO" >>  mydoxy.conf
+endif
+if( $?rtf ) then
+  echo "GENERATE_RTF = YES" >>  mydoxy.conf
+  echo "...... generating RTF"
+else
+  echo "GENERATE_RTF = NO" >>  mydoxy.conf
+endif
+
+#------------------------
+# What output directory ?
+#------------------------
+echo "OUTPUT_DIRECTORY = $outdir" >>  mydoxy.conf
+grep 'OUTPUT_DIRECTORY = ' mydoxy.conf | tail -1
+
+#--------------------------
+# Configuration file update
+#--------------------------
+doxygen -u mydoxy.conf >! /dev/null
+rm -f mydoxy.conf.bak
 
 #########################################
