bash-common/chertex.sh

#!/bin/bash
## Process *.Rnw files
## Written May 14, 2010
## Taha Ahmed

####################################################
# For now, MAKE SURE that the argument consists of
# a complete filename, with extension, and 
# in the directory of the Rnw file 
####################################################

clear
echo "---------------------------------------------------------------"
echo "cheRTeX -- a script for processing R-Sweave-LaTeX-TikZ projects"
echo "^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^"
echo "MMX -- taha.ahmed@mkem.uu.se -- CHEPEC doctoral degree project"
echo "---------------------------------------------------------------"

Rfiletype="R"
TeXfiletype="tex"
tikzfiles="*.tikz"
Rnwfiles="*.Rnw"

if [ $# -eq 1 ]; then
	# Check if the argument contains a filetype
	# Assumes a complete filename was passed
	jobfilename=$1
	jobfiletype=${jobfilename#*.} # File extension
	jobname=${jobfilename%.*} # Filename without extension part

	echo "<cheRTeX> Detected filename: " $jobname
	echo "<cheRTeX> Detected extension:" $jobfiletype

	# Verifying that the file extension is *.Rnw
	if [[ $jobfiletype == "Rnw" || $jobfiletype == "rnw" || $jobfiletype == "RNW" ]]; then
		# File extension is *.Rnw
		echo "<cheRTeX> Detected *.Rnw extension"
		jobfiletype="Rnw"
	else
		# File extension is not *.Rnw
		echo "<cheRTeX> File extension should be *.Rnw"
		echo "<cheRTeX> Terminating..."
		exit 1
	fi

	# Introducing a short delay to enable on-screen reading of previous echo
	simpledelay.sh 2
	echo "Delay completed"
		
	# Tangle
	echo "<cheRTeX> Tangling..."
	R CMD Stangle $jobname.$jobfiletype
	# Weave
	echo "<cheRTeX> Weaving..."
	R CMD pgfsweave --graphics-only $jobname.$jobfiletype
	
	# Introduce delay to give time to read R CMD exit status
	echo "<cheRTeX> -------------------------"
	echo "<cheRTeX> R CMD pgfsweave completed"
	echo "<cheRTeX> -------------------------"
	simpledelay.sh 5
	
	# Run vc script if vc exists in working directory
	echo "<cheRTeX> Running vc script"
	if [ -f vc ]; then
      ./vc
   fi
	
	# Run pdflatex, bibtex, and company
	echo "<cheRTeX> Calling LaTeXMK"
	latexmk $jobname -pdf -bibtex
	
	# Don't bother with this. Let latexmk take care of cleaning up
	# Move unnecessary auxiliary files generated
	#echo "<cheRTeX> _________________________"
	#echo "<cheRTeX> ========================="
	#echo "<cheRTeX> Moving auxiliary files..."
	#mv *.aux logs
	#mv *.log logs
	#mv *.out logs	
else
	# Either no arguments, or more than one argument
	if [ $# -eq 0 ]; then
		# 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 "Any other input exits the program"
		read usrchoice
		
		# Determine number of .Rnw files in current directory
		Rnwfileno=$(ls -1 $Rnwfiles | wc -l)
		echo "No of .Rnw files: $Rnwfileno"
		
		# Check if number of .Rnw files larger than one
		if [ $Rnwfileno -gt 1 ]; then
			# If larger than one, ask for user input
			# Indicates more than one Rnw file in current directory.	
			# This introduces a naming ambiguity.
			# Resolve by asking user for current jobname
			echo "Found $Rnwfileno .Rnw files in current directory"
			echo "Please specify the jobname"
			read jobname
			if [ -z "$jobname" ]; then
				# string is null
				echo "Specified jobname cannot be parsed. Terminating..."
				exit 1
			fi
		else
		   # There is exactly one *.Rnw file is current directory
			# Fetch the jobname from the .Rnw filename by stripping off the file extension
			Rnwfilename=$(ls -1 $Rnwfiles)
			jobname=${Rnwfilename%.*}
		fi
		
		echo "Jobname set to: $jobname"
		
		if [[ $usrchoice == "pdf-all" || $usrchoice == "1" ]]; then
			echo "<1> 'pdf-all' chosen"
			# This for loop ONLY USED to determine number of *.tikz files in directory
			for tikzfiles in "$tikzfiles"; do tikzfilenumber=${#tikzfiles}; done
			echo "cheRTeX detected $tikzfilenumber TikZ files for processing"
			echo "Starting TikZ file processing..."
			simpledelay.sh 2
			
			for tikzfilename in $tikzfiles; do
				# Remove the file extension
				tikzlabel=${tikzfilename%.*}
				# Call pdfLaTeX with tikz label as jobname # See TiKZ manual section 63 for more details
				echo "Executing <pdflatex --jobname=$tikzlabel $jobname.$TeXfiletype>"
				pdflatex --jobname=$tikzlabel $jobname.$TeXfiletype
			done
			echo "Completed TikZ file processing"
		fi
		echo "Terminating..."
		
		#mv $jobname-*.pdf tikz-pdfs
		#mv *.aux logs
		#mv *.log logs
		#mv *.out logs
		
		exit 1
	fi
	
	## Here is the wild land of more than one *.Rnw file in current directory
	
	echo "<cheRTeX> This script can be run with one argument is process mode,"
	echo "<cheRTeX> or with zero arguments in post-processing mode."
	echo "<cheRTeX> Terminating..."
	exit 1
fi

exit 1