S. Riette 18 Dec 2023: update doc tools

docs/.gitignore

-# Ignore the content of doxygen directory but not the directory itself
-doxygen/**
-!doxygen/.gitkeep

docs/doxygen/.gitignore

+# Ignore the html directoru
+html

docs/doxygen/mainpage.md

+Doxygen is used to document the source code, general documentation is available
+directly in the [docs directory](../..) as Makdown files and are linked here:
+
+  - [Introduction](../PHYEX.md)
+  - [Developer](../Developer.md): package organisation, how to contribute, coding norms
+  - [Coding norms](../CodingNorms.md): coding norms
+  - [Integrator](../Integrator.md): how to merge contributions
+  - [Offline](../Offline.md): how to compile the library and the test programs, how to use the library with python and how to use the test programs
+  - [Plugging](../Plugging.md) : how to plug the physics package in a model
+  - [Tools](../Tools.md): description of the check\_commit\_\*.sh scripts (to check bit reproducibility between two commits) and of the prep\_code.sh script
+
+The main entry points of the package are:
+
+  - [ini\_phyex](@ref ini\_phyex): to setup the different schemes
+  - [rain\_ice](@ref rain\_ice): to run the ICE3/ICE4 microphysics scheme
+  - [rain\_ice\_old](@ref rain\_ice\_old): to run the old version of ICE3/ICE4 microphysics scheme
+  - [ice\_adjust](@ref ice\_adjust): to run the adjustment process linked to the ICE3/ICE4 scheme
+  - [turb](@ref turb): to run the turbulence scheme
+  - [shallow\_mf](@ref shallow\_mf): to run the shallow convection scheme
+
+In addition, some offline tools are available:
+
+  - [main\_rain\_ice](@ref main\_rain\_ice): to drive the [rain\_ice](@ref rain\_ice) subroutine
+  - [main\_rain\_ice\_old](@ref main\_rain\_ice\_old): to drive the [rain\_ice\_old](@ref rain\_ice\_old) subroutine
+  - [main\_turb](@ref main\_turb): to drive the [turb](@ref turb) subroutine
+  - [main\_ice\_adjust](@ref main\_ice\_adjust): to drive the [ice\_adjust](@ref ice\_adjust) subroutine
+  - [main\_shallow](@ref main\_shallow): to drive the [shallow\_mf](@ref shallow\_mf) subroutine

tools/generate_standalone_doc.sh

@@ -56,7 +56,7 @@ for file in $mdfiles $resources; do
   cp $PHYEXTOOLSDIR/../docs/$file $dir/
 done
 
-#Move to tep dir
+#Move to temp dir
 cd $dir
 
 #Create helper files
@@ -82,12 +82,38 @@ cat > rsvg-convert <<EOF
 #--keep-image-data
 #--no-keep-image-data
 
-#We expect to receive
-#-f pdf -a -o output_file input_file
+#We only deal with
+# -f: ignored because convert detect output format with the extension
+# -d, --dpi-x, -p, --dpi-y
+# -a: ignore ratio is always kept
+# -o
+
+format=''
+preserveratio=0
+input=''
+output=''
+dpiX=''
+dpiY=''
+while [ -n "\$1" ]; do
+  case "\$1" in
+    '-f') format=\$2; shift;;
+    '-d') dpiX=\$2; shift;;
+    '--dpi-x') dpiX=\$2; shift;;
+    '-p') dpiY=\$2; shift;;
+    '--dpi-y') dpiY=\$2; shift;;
+    '-a') preserveratio=1;;
+    '-o') output="\$2"; shift;;
+    *) input="\$1";;
+  esac
+  shift
+done
 
-if [ \$1 == '-f' -a \$2 == 'pdf' -a \$3 == '-a' -a \$4 == '-o' ]; then
-  convert \$6 \$5
+dpi=""
+if [ "\$dpiX" != "" -a "\$dpiY" != "" ]; then
+  dpi="-density \$dpiXx\$dpiY"
 fi
+
+convert \$dpi \$input \$output
 EOF
 chmod +x rsvg-convert
 
@@ -132,4 +158,5 @@ done
 pandoc --toc --toc-depth=2 --number-sections \
        --include-in-header titlesec.tex \
        -o $output \
+       --self-contained \
        title.md $mdfiles