Added support for latexmk shell escape in chertex.sh. Added clean-up option.

chertex.sh

@@ -16,10 +16,23 @@ echo "^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^"
 echo "MMX -- taha.ahmed@mkem.uu.se -- CHEPEC doctoral degree project"
 echo "---------------------------------------------------------------"
 
+## If the file ltxmkshellescape.rc exists in the current directory,
+## set the flag useshellescape=TRUE
+useshellescape=false
+echo "--- Looking for ltxmkshellescape.rc"
+if [ -e ltxmkshellescape.rc ]; then
+   useshellescape=true
+   echo "+++ Shell escape activated"
+else
+   echo "--- This job does not require shell escape"
+fi
+
+
 Rfiletype="R"
 TeXfiletype="tex"
 tikzfiles="*.tikz"
 Rnwfiles="*.Rnw"
+auxfiles="*.aux *.bbl *.bcf *.blg *.fdb* *.figlist *.log *.lox *.makefile *.map *.out *.run* *.toc *.dep *.dpth"
 
 if [ $# -eq 1 ]; then
 	# Check if the argument contains a filetype
@@ -58,7 +71,7 @@ if [ $# -eq 1 ]; then
 	echo "<cheRTeX> -------------------------"
 	echo "<cheRTeX> R CMD pgfsweave completed"
 	echo "<cheRTeX> -------------------------"
-	simpledelay.sh 5
+	simpledelay.sh 4
 	
 	# Run vc script if vc exists in working directory
 	echo "<cheRTeX> Running vc script"
@@ -67,8 +80,15 @@ if [ $# -eq 1 ]; then
    fi
 	
 	# Run pdflatex, bibtex, and company
+   if $useshellescape; then
+      echo "<cheRTeX> Calling LaTeXMK with shell escape"
+      simpledelay.sh 2
+      latexmk -r ltxmkshellescape.rc -pdf -bibtex $jobname
+   else
 	   echo "<cheRTeX> Calling LaTeXMK"
-	latexmk $jobname -pdf -bibtex
+      simpledelay.sh 2
+	   latexmk -pdf -bibtex $jobname
+   fi
 	#echo "<cheRTeX> Calling texi2dvi()"
 	#R CMD texi2dvi --pdf --verbose $jobname.tex
 	### Perhaps the choice should be dictated from a command-line argument?
@@ -87,6 +107,7 @@ else
 		# Zero arguments. Present a menu of choices
 		echo "This is cheRTeX POST-PROCESSING" # only one choice for now
 		echo "<1> 'pdf-all'  -- Process all .tikz files to pdf graphics"
+		echo "<2> 'clean-up' -- Remove all auxiliary files"
 		echo "Any other input exits the program"
 		read usrchoice
 		
@@ -132,12 +153,14 @@ else
 			done
 			echo "Completed TikZ file processing"
 		fi
-		echo "Terminating..."
 
-		#mv $jobname-*.pdf tikz-pdfs
-		#mv *.aux logs
-		#mv *.log logs
-		#mv *.out logs
+      if [[ $usrchoice == "clean-up" || $usrchoice == "2" ]]; then
+         echo "<2> 'clean-up' chosen"
+         rm $auxfiles
+         # Still a rather crude way of cleaning up...
+      fi
+
+		echo "Terminating..."
 		
 		exit 1
 	fi

ltxmkshellescape.rc

@@ -0,0 +1,2 @@
+$latex = "latex --shell-escape";
+$pdflatex = "pdflatex --shell-escape";