@ -1,39 +1,138 @@
#!/usr/bin/env 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
####################################################
# This is the first bash script where I implemented the ideas outlined by
# https://betterdev.blog/minimal-safe-bash-script-template/
# I don't understand the point of traps, so I skipped "-E"
# https://vaneyckt.io/posts/safer_bash_scripts_with_set_euxo_pipefail/
set -euo pipefail
usage( ) {
cat <<EOF
Usage: $( basename " ${ BASH_SOURCE [0] } " ) [ arg1]
Compiles Rnw documents with knitr and latexmk. This is a highly customised script.
Takes zero or one arguments. The argument must be a filename with the extension "Rnw" .
If an argument is supplied, the document in question is compiled.
If no arguments are supplied, a menu is displayed offering a choice of auxiliary tasks.
This script treats certain filenames in a special manner:
+ "thesis" --> triggers a chain of special commands, see source code.
In addition, the internal execution of this script is modified by the existence of
certain files in the working directory:
+ .knitme --> use knitr::knit( ) instead of pgfSweave( ) .
+ .latexmkrc --> apply RC file to latexmk command.
+ vc --> run vc script ( integrates git with LaTeX, deprecated by gitinfo2, kept for backwards support) .
EOF
exit
}
# keep track of runtime of entire script
starttime = $( date +%s)
# in future, consider integrating this color setup with ~/.local/bin/echo-colours.sh
setup_colors( ) {
if [ [ -t 2 ] ] && [ [ -z " ${ NO_COLOR - } " ] ] && [ [ " ${ TERM - } " != "dumb" ] ] ; then
NOFORMAT = '\033[0m'
# text color
Black = '\033[0;30m' Red = '\033[0;31m' Green = '\033[0;32m' Yellow = '\033[0;33m' Blue = '\033[0;34m' Purple = '\033[0;35m' Cyan = '\033[0;36m' White = '\033[0;37m'
# bold text and color
BBlack = '\033[1;30m' BRed = '\033[1;31m' BGreen = '\033[1;32m' BYellow = '\033[1;33m' BBlue = '\033[1;34m' BPurple = '\033[1;35m' BCyan = '\033[1;36m' BWhite = '\033[1;37m'
# underline and color
UBlack = '\033[4;30m' URed = '\033[4;31m' UGreen = '\033[4;32m' UYellow = '\033[4;33m' UBlue = '\033[4;34m' UPurple = '\033[4;35m' UCyan = '\033[4;36m' UWhite = '\033[4;37m'
# text on background color
On_Black = '\033[40m' On_Red = '\033[41m' On_Green = '\033[42m' On_Yellow = '\033[43m' On_Blue = '\033[44m' On_Purple = '\033[45m' On_Cyan = '\033[46m' On_White = '\033[47m'
# high intensity color
IBlack = '\033[0;90m' IRed = '\033[0;91m' IGreen = '\033[0;92m' IYellow = '\033[0;93m' IBlue = '\033[0;94m' IPurple = '\033[0;95m' ICyan = '\033[0;96m' IWhite = '\033[0;97m'
# bold high intensity color
BIBlack = '\033[1;90m' BIRed = '\033[1;91m' BIGreen = '\033[1;92m' BIYellow = '\033[1;93m' BIBlue = '\033[1;94m' BIPurple = '\033[1;95m' BICyan = '\033[1;96m' BIWhite = '\033[1;97m'
# text on high intensity background color
On_IBlack = '\033[0;100m' On_IRed = '\033[0;101m' On_IGreen = '\033[0;102m' On_IYellow = '\033[0;103m' On_IBlue = '\033[0;104m' On_IPurple = '\033[0;105m' On_ICyan = '\033[0;106m' On_IWhite = '\033[0;107m'
else
NOFORMAT = ''
Black = '' Red = '' Green = '' Yellow = '' Blue = '' Purple = '' Cyan = '' White = ''
BBlack = '' BRed = '' BGreen = '' BYellow = '' BBlue = '' BPurple = '' BCyan = '' BWhite = ''
UBlack = '' URed = '' UGreen = '' UYellow = '' UBlue = '' UPurple = '' UCyan = '' UWhite = ''
On_Black = '' On_Red = '' On_Green = '' On_Yellow = '' On_Blue = '' On_Purple = '' On_Cyan = '' On_White = ''
IBlack = '' IRed = '' IGreen = '' IYellow = '' IBlue = '' IPurple = '' ICyan = '' IWhite = ''
BIBlack = '' BIRed = '' BIGreen = '' BIYellow = '' BIBlue = '' BIPurple = '' BICyan = '' BIWhite = ''
On_IBlack = '' On_IRed = '' On_IGreen = '' On_IYellow = '' On_IBlue = '' On_IPurple = '' On_ICyan = '' On_IWhite = ''
fi
}
msg( ) {
echo >& 2 -e " ${ 1 - } "
}
# examples:
# die "Some message (exiting with status 1)"
# die "Some message (exiting with status -->)" 0
die( ) {
local msg = $1
local code = ${ 2 -1 } # default exit status 1
msg " $msg "
simpledelay.sh 2 # short delay to aid reading last message in case terminal closes on exit
exit " $code "
}
parse_params( ) {
while :; do
case " ${ 1 - } " in
-h | --help) usage ; ;
-v | --verbose) set -x ; ;
--no-color) NO_COLOR = 1 ; ;
-?*) die " Unknown option: $1 " ; ;
*) break ; ;
esac
shift
done
args = ( " $@ " )
# Check number of arguments
# this script can be run with one argument is process mode or with zero arguments in post-processing mode
[ [ ${# args [@] } -gt 1 ] ] && die "More than one argument not supported"
# we use maintrack variable to keep track of whether auxiliary menu should be entered
[ [ ${# args [@] } -eq 1 ] ] && maintrack = true
return 0
}
maintrack = false # I'm not really happy with this variable *name*
parse_params " $@ "
setup_colors
clear
echo "-----------------------------------------------------------------------"
echo "cheRTeX -- a script for processing R--Sweave/knitr--LaTeX/TikZ projects"
echo "^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^"
echo "MMXVI -- taha@chepec.se -- CHEPEC doctoral degree project"
echo "-----------------------------------------------------------------------"
## If the file .latexmkrc exists in the current directory,
## set the flag ltxmkrc=TRUE
msg "-----------------------------------------------------------------------"
msg "cheRTeX -- a script for processing R--Sweave/knitr--LaTeX/TikZ projects"
msg "^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^"
msg "MMXX -- taha@chepec.se -- CHEPEC doctoral degree project"
msg "-----------------------------------------------------------------------"
## If the file .latexmkrc exists in the current directory, set ltxmkrc=TRUE
ltxmkrc = false
echo "--- Looking for .latexmkrc"
msg "--- Looking for .latexmkrc"
if [ -e .latexmkrc ] ; then
ltxmkrc = true
echo "+++ LaTeXMK RC file invoked"
msg "+++ LaTeXMK RC file invoked"
else
echo "--- This job did not request LaTeXMK RC file"
msg "--- This job did not request LaTeXMK RC file"
fi
# define some constants
path_wd = ${ PWD }
dir_wd = $( basename $path_wd )
path_thesis = "/media/bay/taha/chepec/thesis"
temp_folder = "/media/bay/taha/chepec/tmp"
# define some file types
Rfiletype = "R"
@ -80,59 +179,37 @@ aux_xdy="*.xdy" # glossaries (xindy)
auxfiles = " ${ aux_acn } ${ aux_acr } ${ aux_alg } ${ aux_aux } ${ aux_bbl } ${ aux_blg } ${ aux_dep } ${ aux_dpth } ${ aux_fdb } ${ aux_fig } ${ aux_fls } ${ aux_glg } ${ aux_glo } ${ aux_gls } ${ aux_ist } ${ aux_lob } ${ aux_lof } ${ aux_log } ${ aux_lor } ${ aux_los } ${ aux_lot } ${ aux_maf } ${ aux_out } ${ aux_lox } ${ aux_make } ${ aux_map } ${ aux_mtc } ${ aux_run } ${ aux_slg } ${ aux_slo } ${ aux_sls } ${ aux_tikz } ${ aux_tdo } ${ aux_toc } ${ aux_xdy } "
# depending on number of args and their content, do different things...
if [ $# -eq 1 ] ; then
if $maintrack ; then
# Check if the argument contains a filetype
# (assumes a complete filename was passed)
jobfilename = $1
jobfilename = ${ args [0] }
jobfiletype = ${ jobfilename #*. } # File extension
jobname = ${ jobfilename %.* } # Filename without extension part
echo "<cheRTeX> Detected filename: " $jobname
echo "<cheRTeX> Detected extension:" $jobfiletype
msg " <cheRTeX> Detected filename: $jobname "
msg " <cheRTeX> Detected extension: $jobfiletype "
# Verify that the file extension is "[Rr][Nn][Ww]"
if [ [ $jobfiletype = = "Rnw" || $jobfiletype = = "rnw" || $jobfiletype = = "RNW" ] ] ; then
# File extension is indeed "[Rr][Nn][Ww]"
echo "<cheRTeX> Detected *.Rnw extension"
msg "<cheRTeX> Detected *.Rnw extension"
jobfiletype = "Rnw"
else
# File extension is NOT "[Rr][Nn][Ww]"
echo "<cheRTeX> This script only handles *.Rnw files"
echo "<cheRTeX> Terminating..."
exit 1
die "This script only supports *.Rnw files"
fi
# Introducing a short delay to enable on-screen reading of previous echo
simpledelay.sh 2
# no need to echo it
# echo "Delay completed"
#### Special treatment for sample-matrix.Rnw
# If $jobname is sample-matrix, restart Shiny and term this script
if [ [ $jobname = = "sample-matrix" ] ] ; then
echo "<sample-matrix> -------------------------------"
echo "<sample-matrix> Restarting Shiny"
echo "<sample-matrix> -------------------------------"
# kill Shiny
pkill -f "shiny::runApp"
# start Shiny
bash -c "/media/bay/taha/chepec/chetex/common/bash/shiny-matrix.sh" &
# terminate this script
echo "<cheRTeX> Terminating..."
simpledelay.sh 2
exit 0
fi
#### Special treatment for thesis
if [ [ $path_wd = = " $path_thesis " && $jobname = = " $dir_wd " ] ] ; then
# Fetch external assets by reading any assets.external files in assets/ tree
# NOTE: be careful NOT to leave empty lines in your assets.external files
echo "<thesis> -------------------------------"
echo "<thesis> Getting external assets"
echo "<thesis> -------------------------------"
msg "<thesis> -------------------------------"
msg "<thesis> Getting external assets"
msg "<thesis> -------------------------------"
# find all files named "assets.external" in the assets/ tree
assetsexternalfiles = $( find " $path_wd /assets/ " -type f -name "assets.external" )
for externalfilepath in $assetsexternalfiles ; do
@ -152,13 +229,10 @@ if [ $# -eq 1 ]; then
read -ra asset_array <<< " $asset "
# sanity check for array length
if [ ${# asset_array [@] } -gt 2 ] ; then
echo " <thesis> Cannot handle more than one $IFS character per line "
echo "<cheRTeX> Terminating..."
simpledelay.sh 2
exit 1
die " <thesis> Cannot handle more than one $IFS character per line "
fi
if [ ${# asset_array [@] } -gt 1 ] ; then
# echo "Placing this asset into subdirectory ${asset_array[1]}"
# msg "Placing this asset into subdirectory ${asset_array[1]}"
# redefine assetpathtarget to include the local subdir
assetpathtarget = " $assetpathtarget / ${ asset_array [1] } "
# also redefine $asset so we keep only the asset path
@ -166,22 +240,22 @@ if [ $# -eq 1 ]; then
# create the local subdir inside assets/<current/
mkdir -p " $assetpathtarget " # -p suppresses error if dir already exists
fi
echo " <thesis> Copying $asset to $assetpathtarget "
msg " <thesis> Copying $asset to $assetpathtarget "
# cp but don't overwrite existing files
cp --preserve= timestamps --no-clobber --recursive $asset $assetpathtarget
# except we want to overwrite the BibTeX library files (inside the assets/references/ directory), we'll do that by checking the target dirname and only running the destructive cp operation if its "references"
assetdirnametarget = $( basename " $assetpathtarget " )
if [ [ $assetdirnametarget = = "references" ] ] ; then
echo "<thesis> Overwriting BibTeX libraries in assets/references/"
msg "<thesis> Overwriting BibTeX libraries in assets/references/"
cp --preserve= timestamps $asset $assetpathtarget
fi
done < " $externalfilepath "
done
# Create low-res photos on-the-fly from existing photos/
echo "<thesis> -------------------------------"
echo "<thesis> Create low-res photos tree"
echo "<thesis> -------------------------------"
msg "<thesis> -------------------------------"
msg "<thesis> Create low-res photos tree"
msg "<thesis> -------------------------------"
# copy existing photos to assets/photos/.lowres/ path
# to save time, rsync only if highres photo has more recent timestamp (otherwise, keep lowres photo without overwriting)
# Note: rsync usually looks at file timestamp and size, and if either has changed, copies the file (simplified explanation)
@ -205,21 +279,19 @@ if [ $# -eq 1 ]; then
# revert the effects of cd above. Redirect to null suppresses the output.
cd - >/dev/null
# Convert all non-JPG images (except for PDF, SVG, and other non-images) to JPG
echo "<thesis> Convert all non-JPG images to JPG"
msg "<thesis> Convert all non-JPG images to JPG"
find " $path_thesis /assets/photos/.lowres/ " -type f ! -name "*.pdf" ! -name "*.svg" ! -name "*.external" ! -name "lastrun" ! -name "*.jpg" -print -exec mogrify -format jpg "{}" \;
# Remove the now redundant non-JPG files in .lowres/
echo "<thesis> Delete the redundant non-JPG files in .lowres/ tree"
msg "<thesis> Delete the redundant non-JPG files in .lowres/ tree"
find " $path_thesis /assets/photos/.lowres/ " -type f ! -name "*.pdf" ! -name "*.svg" ! -name "*.external" ! -name "lastrun" ! -name "*.jpg" -print -exec rm "{}" \;
# Shrink image filesize in-place to roughly 300kb in size
echo "<thesis> Shrink images in .lowres/ tree to <=300K"
msg "<thesis> Shrink images in .lowres/ tree to <=300K"
# https://stackoverflow.com/questions/6917219/imagemagick-scale-jpeg-image-with-a-maximum-file-size
find " $path_thesis /assets/photos/.lowres/ " -size +500k -type f -name "*.jpg" -print -exec convert "{}" -define jpeg:extent= 300kb "{}" \;
# update the modification and access time on the photosastrun file
touch " $photoslastrun "
fi
# short delay to enable on-screen reading of previous echo
simpledelay.sh 2
## Handle knitr or pgfSweave jobs (each requires separate treatment)
@ -228,181 +300,138 @@ if [ $# -eq 1 ]; then
## IN ALL KNITR DIRECTORIES, CREATE A FILE NAMED: .knitme
# If the file .knitme exists in the current directory,
# run knitr commands, otherwise run pgfsweave commands
echo "--- Looking for .knitme"
msg "--- Looking for .knitme"
if [ -e .knitme ] ; then
# Run knitr commands for this job
echo "<cheRTeX> -----------------------"
echo "<cheRTeX> This is a job for knitr"
echo "<cheRTeX> -----------------------"
msg "<cheRTeX> -----------------------"
msg "<cheRTeX> This is a job for knitr"
msg "<cheRTeX> -----------------------"
# Knit
echo "<cheRTeX> Knitting..."
msg "<cheRTeX> Knitting..."
Rscript -e " library(knitr); library(methods); knit(' $jobname . $jobfiletype ') "
# Introduce delay to give time to read Rscript exit status
echo "<cheRTeX> -----------------------"
echo "<cheRTeX> Rscript knitr completed"
echo "<cheRTeX> -----------------------"
msg "<cheRTeX> -----------------------"
msg "<cheRTeX> Rscript knitr completed"
msg "<cheRTeX> -----------------------"
simpledelay.sh 2
else
# Run pgfSweave commands
echo "<cheRTeX> ---------------------------"
echo "<cheRTeX> This is a job for pgfSweave"
echo "<cheRTeX> ---------------------------"
msg "<cheRTeX> ---------------------------"
msg "<cheRTeX> This is a job for pgfSweave"
msg "<cheRTeX> ---------------------------"
# Tangle
echo "<cheRTeX> Tangling..."
msg "<cheRTeX> Tangling..."
R CMD Stangle $jobname .$jobfiletype
# Weave
echo "<cheRTeX> Weaving..."
msg "<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> -------------------------"
msg "<cheRTeX> -------------------------"
msg "<cheRTeX> R CMD pgfsweave completed"
msg "<cheRTeX> -------------------------"
simpledelay.sh 2
fi
# Run vc script if vc exists in working directory
echo "<cheRTeX> Running vc script
msg "<cheRTeX> Running vc script... "
if [ -f vc ] ; then
./vc
fi
# Run pdflatex, bibtex, and company
if $ltxmkrc ; then
echo "<cheRTeX> Calling LaTeXMK with RC file
msg " ${ On_Cyan } <cheRTeX> Calling LaTeXMK with RC file ${ NOFORMAT } "
simpledelay.sh 2
latexmk -r .latexmkrc -pdf -bibtex $jobname
else
echo "<cheRTeX> Calling LaTeXMK
msg " ${ On_Cyan } <cheRTeX> Calling LaTeXMK ${ NOFORMAT } "
simpledelay.sh 2
latexmk -pdf -bibtex $jobname
fi
else
# Either no arguments, or more than one argument
if [ $# -eq 0 ] ; then
# Zero arguments. Present a menu of choices
echo "This is cheRTeX POST-PROCESSING" # only one choice for now
echo "<1> 'pdf-all' -- Process all .tikz files to pdf graphics"
echo "<2> 'clean-up' -- Remove all auxiliary files"
echo "<3> 'wipe-dir' -- Remove all non-essential files and subdirectories"
echo "Any other input exits the program"
# Zero arguments (the case of more than one argument is handled in parse_params above)
# In this case, present a menu of choices
msg "This is cheRTeX POST-PROCESSING" # only one choice for now
msg "<1> 'pdf-all' -- Process all .tikz files to pdf graphics"
msg "<2> 'clean-up' -- Remove all auxiliary files"
msg "<3> 'wipe-dir' -- Remove all non-essential files and subdirectories"
msg "Any other input exits the program"
read usrchoice
## Determine number of .Rnw files in current directory
#Rnwfileno=$(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"
msg "<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..."
msg " cheRTeX detected $tikzfilenumber TikZ files for processing "
msg "Starting TikZ file processing..."
simpledelay.sh 2
for tikzfilename in $tikzfiles ; do
# Call tikz2pdf
echo " <Executing> tikz2pdf $tikzfilename "
msg " <Executing> tikz2pdf $tikzfilename "
tikz2pdf --once $tikzfilename
done
echo "Completed TikZ file processing"
msg "Completed TikZ file processing"
fi
if [ [ $usrchoice = = "clean-up" || $usrchoice = = "2" ] ] ; then
echo "<2> 'clean-up' chosen"
msg "<2> 'clean-up' chosen"
rm $auxfiles
# Still, a rather crude way of cleaning up...
fi
if [ [ $usrchoice = = "wipe-dir" || $usrchoice = = "3" ] ] ; then
echo "<3> 'wipe-dir' chosen"
msg "<3> 'wipe-dir' chosen"
## Remove all but non-essential files
# get the name of the current directory
currdirname = ${ PWD ##*/ }
# get a timestamp
timestamp = $( date +%s)
# create a unique tmp-dir name
tmpdirname = " ${ timestamp } - ${ currdirname } "
tmpdirname = " ${ timestamp } - ${ dir_wd } "
# make a directory in chepec/tmp with the name of the current dir
mkdir /media/bay/taha/chepec/tmp /$tmpdirname
mkdir $temp_folder /$tmpdirname
# Copy the contents of the current directory to the tmp/$currdirname directory
cp * -R /media/bay/taha/chepec/tmp /$tmpdirname
cp * -R $temp_folder /$tmpdirname
# Empty the current directory of all contents
rm * -R # note: hidden files and subdir unaffected
# Return the stuff we want to keep after wipe-dir
# (we are of course assuming that the following 4 file(type)s always exist)
# (if in fact they do not exist, use conditional statements instead (see below)
cp /media/bay/taha/chepec/tmp /$tmpdirname /*.Rnw .
cp /media/bay/taha/chepec/tmp /$tmpdirname /vc .
cp /media/bay/taha/chepec/tmp /$tmpdirname /vc.tex .
cp /media/bay/taha/chepec/tmp /$tmpdirname /vc-git.awk .
cp $temp_folder /$tmpdirname /*.Rnw .
cp $temp_folder /$tmpdirname /vc .
cp $temp_folder /$tmpdirname /vc.tex .
cp $temp_folder /$tmpdirname /vc-git.awk .
## Return stuff that may not always exist (check first...)
## The use of conditionals is mainly to avoid annoying "file does not exist" messages...
# Return *.Rproj file (removal is unnecessary and makes RStudio less useful)
Rprojfiles = ` ls -1 /media/bay/taha/chepec/tmp /$tmpdirname /*.Rproj 2>/dev/null | wc -l`
Rprojfiles = ` ls -1 $temp_folder $tmpdirname /*.Rproj 2>/dev/null | wc -l`
if [ $Rprojfiles != 0 ] ; then
cp /media/bay/taha/chepec/tmp /$tmpdirname /*.Rproj .
cp $temp_folder /$tmpdirname /*.Rproj .
fi
# Return *.rda files (considering peak-data files, which "cost" a lot to create)
rdafiles = ` ls -1 /media/bay/taha/chepec/tmp /$tmpdirname /*.rda 2>/dev/null | wc -l`
rdafiles = ` ls -1 $temp_folder $tmpdirname /*.rda 2>/dev/null | wc -l`
if [ $rdafiles != 0 ] ; then
cp /media/bay/taha/chepec/tmp /$tmpdirname /*.rda .
cp $temp_folder /$tmpdirname /*.rda .
fi
# Return *.Rmd files (R markdown source files)
Rmdfiles = ` ls -1 /media/bay/taha/chepec/tmp /$tmpdirname /*.Rmd 2>/dev/null | wc -l`
Rmdfiles = ` ls -1 $temp_folder $tmpdirname /*.Rmd 2>/dev/null | wc -l`
if [ $Rmdfiles != 0 ] ; then
cp /media/bay/taha/chepec/tmp /$tmpdirname /*.Rmd .
cp $temp_folder /$tmpdirname /*.Rmd .
fi
# Return *.css files (css files) [for sample-matrix]
cssfiles = ` ls -1 /media/bay/taha/chepec/tmp /$tmpdirname /*.css 2>/dev/null | wc -l`
cssfiles = ` ls -1 $temp_folder $tmpdirname /*.css 2>/dev/null | wc -l`
if [ $cssfiles != 0 ] ; then
cp /media/bay/taha/chepec/tmp /$tmpdirname /*.css .
cp $temp_folder /$tmpdirname /*.css .
fi
# Return .knitme file [empty file used to indicate knitr jobs]
knitmefile = ` ls -1 /media/bay/taha/chepec/tmp /$tmpdirname /.knitme 2>/dev/null | wc -l`
knitmefile = ` ls -1 $temp_folder $tmpdirname /.knitme 2>/dev/null | wc -l`
if [ $knitmefile != 0 ] ; then
cp /media/bay/taha/chepec/tmp /$tmpdirname /.knitme .
cp $temp_folder /$tmpdirname /.knitme .
fi
fi
echo "Terminating..."
exit 0
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
die "All done. Exiting..." 0
fi
@ -422,16 +451,16 @@ if (( $runtime > 180 )); then
gotify push --quiet --title " $dir_wd " --priority 5 " chertex.sh $@ \nCompleted in $runtime s "
fi
echo "-------------------------------------
msg " ${ On_Cyan } ------------------------------------- ${ NOFORMAT } "
# the padding for runtime makes the formatting work
# three digits for seconds is enough for just above 15 minutes
printf " === chertex.sh completed in %03d s ===\n" $runtime
printf " ${ On_Cyan } ${ NOFORMAT } $runtime 1>& 2
if [ [ $cetcest = = "CET" ] ] ; then
echo " === $( date) === "
msg " ${ On_Cyan } === $( date) === ${ NOFORMAT } "
else
echo " === $( date) === "
msg " ${ On_Cyan } === $( date) === ${ NOFORMAT } "
fi
echo "-------------------------------------
msg " ${ On_Cyan } ------------------------------------- ${ NOFORMAT } "
simpledelay.sh 3
exit 0
