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501 lines
22 KiB
Bash
501 lines
22 KiB
Bash
#!/usr/bin/env bash
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## Written May 14, 2010
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## Taha Ahmed
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# This is the first bash script where I implemented the ideas outlined by
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# https://betterdev.blog/minimal-safe-bash-script-template/
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# I don't understand the point of traps, so I skipped "-E"
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# https://vaneyckt.io/posts/safer_bash_scripts_with_set_euxo_pipefail/
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set -euo pipefail
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usage() {
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cat <<EOF
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Usage: $(basename "${BASH_SOURCE[0]}") <flags> job.Rnw
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Compiles R Sweave documents using knitr and LaTeXMK.
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Filename extension must be .Rnw.
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Available flags:
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+ --help --> display this usage guide
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+ --no-alert --> disable gotify alert (--silent also works)
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+ --menu --> enter "menu" mode where auxiliary commands can be run (--aux)
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This script treats certain filenames in a special manner:
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+ "thesis" --> triggers a chain of special commands, see source code.
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In addition, the internal execution of this script is modified by the existence of
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certain files in the working directory:
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+ ./.knitme --> use knitr::knit() instead of pgfSweave().
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+ ./.latexmkrc --> apply RC file to latexmk command.
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+ ./vc --> run vc script (integrates git with LaTeX, deprecated by gitinfo2, kept for backwards support).
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EOF
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exit
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}
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# keep track of runtime of entire script
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starttime=$(date +%s)
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# load colours (this script depends on colours being defined!)
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# TO-DO: to make this dependency non-critical, consider making all invocations of colour
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# optional (depending on whether colours.sh was found, or a CLI flag perhaps)
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if [ -f "/home/taha/.local/bin/echo-colours.sh" ]; then
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. "/home/taha/.local/bin/echo-colours.sh"
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fi
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msg() {
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echo >&2 -e "${1-}"
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}
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# Examples:
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# die "some message"
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# die "some message and wait 6 seconds before exiting" 6
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# die "some message and exit immediately" 0
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die() {
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local msg=$1
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msg "$msg"
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# short delay to aid reading last message in case terminal closes on exit
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# if $2 was provided, set it as delay
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# if $2 is unset or null, use a 3 second delay
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simpledelay.sh ${2:-3}
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exit 0
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}
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parse_params() {
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while :; do
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case "${1-}" in
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-h | --help) usage ;;
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-v | --verbose) set -x ;;
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--aux | --menu) show_menu=true ;;
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--no-alert | --silent) disable_alert=true ;;
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-?*) die "Unknown option: $1" ;;
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*) break ;;
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esac
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shift
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done
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args=("$@")
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# If no args were given, show aux menu mode
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# note that flags don't count as args, so as long as no jobname was given
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# (irrespective of provided flags), aux menu will be entered
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[[ ${#args[@]} -eq 0 ]] && show_menu=true
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return 0
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}
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show_menu=false
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# gotify alert is enabled by default (assuming the job takes longer than X seconds)
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disable_alert=false
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parse_params "$@"
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# setup_colors
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clear
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msg "-----------------------------------------------------------------------"
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msg "cheRTeX -- a script for processing R--Sweave/knitr--LaTeX/TikZ projects"
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msg "^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^"
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msg "MMXX -- taha@chepec.se -- CHEPEC doctoral degree project"
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msg "-----------------------------------------------------------------------"
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## If the file .latexmkrc exists in the current directory, set ltxmkrc=TRUE
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ltxmkrc=false
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msg "--- Looking for .latexmkrc"
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if [ -e .latexmkrc ]; then
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ltxmkrc=true
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msg "+++ LaTeXMK RC file invoked"
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else
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msg "--- This job did not request LaTeXMK RC file"
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fi
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# define some constants
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path_wd=${PWD}
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dir_wd=$(basename $path_wd)
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path_thesis="/media/bay/taha/chepec/thesis"
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temp_folder="/media/bay/taha/chepec/tmp"
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# define some file types
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Rfiletype="R"
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TeXfiletype="tex"
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tikzfiles="*.tikz"
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Rnwfiles="*.Rnw"
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# aux files
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aux_4ct="*.4ct" # TOC entries for HTML output
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aux_4tc="*.4tc" # TOC entries for HTML output
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aux_acn="*.acn"
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aux_acr="*.acr"
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aux_alg="*.alg" # glossaries
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aux_aux="*.aux"
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aux_bbl="*.bbl" # bibliography
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aux_blg="*.blg" # bibliography
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aux_dep="*.dep"
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aux_dpth="*.dpth"
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aux_fdb="*.fdb*"
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aux_fig="*.figlist"
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aux_fls="*.fls"
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aux_glg="*.glg"
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aux_glo="*.glo" # glossaries
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aux_gls="*.gls*" # glossaries and bib2gls
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aux_ist="*.ist" # glossaries (makeindex style file)
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aux_lg="*.lg" # tex4ht
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aux_lob="*.lob"
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aux_lof="*.lof"
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aux_log="*.log"
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aux_lol="*.lol" # list of hyperlinks (custom, used in thesis)
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aux_lor="*.lor"
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aux_los="*.los"
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aux_lot="*.lot"
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aux_maf="*.maf" # minitoc
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aux_mtc="*.mtc*" # minitoc
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aux_out="*.out" # hyperref
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aux_lox="*.lox"
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aux_make="*.makefile"
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aux_map="*.map"
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aux_run="*.run*"
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aux_slg="*.slg"
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aux_slo="*.slo"
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aux_sls="*.sls"
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aux_stc="*.stc*" # minitoc
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aux_tikz="*-tikzDictionary"
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aux_tdo="*.tdo"
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aux_tmp="*.tmp" # tex4ht
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aux_toc="*.toc"
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aux_xdy="*.xdy" # glossaries (xindy)
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aux_xref="*.xref" # pandoc or tex4ht cross-refs
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# all aux files in a single string
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auxfiles="${aux_4ct} ${aux_4tc} ${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_lg} ${aux_lob} ${aux_lof} ${aux_log} ${aux_lol} ${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_stc} ${aux_tikz} ${aux_tdo} ${aux_toc} ${aux_xdy} ${aux_xref} ${aux_tmp}"
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if [[ $show_menu == "false" ]]; then
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# Check if the argument contains a filetype
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# (assumes a complete filename was passed)
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jobfilename=${args[0]}
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jobfiletype=${jobfilename#*.} # File extension
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jobname=${jobfilename%.*} # Filename without extension part
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msg "<cheRTeX> Detected filename: $jobname"
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msg "<cheRTeX> Detected extension: $jobfiletype"
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# Verify that the file extension is "[Rr][Nn][Ww]"
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if [[ $jobfiletype == "Rnw" || $jobfiletype == "rnw" || $jobfiletype == "RNW" ]]; then
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# File extension is indeed "[Rr][Nn][Ww]"
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msg "<cheRTeX> Detected *.Rnw extension"
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jobfiletype="Rnw"
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else
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# File extension is NOT "[Rr][Nn][Ww]"
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die "This script only supports *.Rnw files"
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fi
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# Introducing a short delay to enable on-screen reading of previous echo
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simpledelay.sh 2
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#### Special treatment for thesis
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if [[ $path_wd == "$path_thesis" && $jobname == "$dir_wd" ]]; then
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# Restore thesis.bcf from latest commit if modified in workspace
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# Background: any LaTeX run that finishes uncleanly (due to errors, etc.) leaves
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# the bcf file in an incomplete state. Since we have at least one plot in the thesis
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# that reads the bcf file, this in turn causes the subsequent chertex compilation
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# to fail. This mess could be automatically avoided if we pre-emptively check
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# if thesis.bcf is listed in the output of `git status --short`, and if so `git restore` it.
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# https://stackoverflow.com/a/25149786/1198249
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if [[ `git status --porcelain | grep $jobname.bcf` ]]; then
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msg "<thesis> -------------------------------"
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msg "<thesis> Restoring thesis.bcf"
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msg "<thesis> -------------------------------"
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git -C $path_wd restore $jobname.bcf
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simpledelay.sh 2
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fi
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# Fetch external assets by reading any assets.external files in assets/ tree
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# NOTE: be careful NOT to leave empty lines in your assets.external files
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msg "<thesis> -------------------------------"
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msg "<thesis> Getting external assets"
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msg "<thesis> -------------------------------"
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# find all files named "assets.external" in the assets/ tree
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assetsexternalfiles=$(find "$path_wd/assets/" -type f -name "assets.external")
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for externalfilepath in $assetsexternalfiles; do
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# https://stackoverflow.com/questions/10929453/read-a-file-line-by-line-assigning-the-value-to-a-variable
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while IFS='' read -r asset || [[ -n "$asset" ]]; do
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# $asset contains one line from the current external.assets
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# assetpathtarget is the directory of the current external.assets file
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assetpathtarget=$(dirname "$externalfilepath")
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# if $asset contains a space, the second element should be considered a local target folder for the copy operation
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# https://www.tutorialkart.com/bash-shell-scripting/bash-split-string/
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# https://stackoverflow.com/a/30212526
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# Using space as separator was not working if the path contains spaces
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# (I tried surrounding each path with "" or escaping each space with backslash, did not help)
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# Rather than rewriting this part, I'll change to an IFS char that's unlikely to clash with any path specification. This way, spaces in paths should not need any changes.
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IFS='>' # reset IFS
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# asset is read into an array as tokens separated by IFS
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read -ra asset_array <<< "$asset"
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# sanity check for array length
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if [ ${#asset_array[@]} -gt 2 ]; then
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die "<thesis> Cannot handle more than one $IFS character per line"
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fi
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if [ ${#asset_array[@]} -gt 1 ]; then
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# msg "Placing this asset into subdirectory ${asset_array[1]}"
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# redefine assetpathtarget to include the local subdir
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assetpathtarget="$assetpathtarget/${asset_array[1]}"
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# also redefine $asset so we keep only the asset path
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asset="${asset_array[0]}"
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# create the local subdir inside assets/<current/
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mkdir -p "$assetpathtarget" # -p suppresses error if dir already exists
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fi
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msg "<thesis> Copying $asset to $assetpathtarget"
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# cp but don't overwrite existing files
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cp --preserve=timestamps --no-clobber --recursive $asset $assetpathtarget
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# except we want to overwrite the biblatex library file (inside the assets/references/ directory)
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# as well as the zotero.sqlite file, we'll do that by checking the target dirname and only run
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# the copy operation (which will overwrite stuff) if it is "references"
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assetdirnametarget=$(basename "$assetpathtarget")
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if [[ $assetdirnametarget == "references" ]]; then
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msg "<thesis> Overwriting Zotero biblatex library and database in assets/references/"
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cp --preserve=timestamps $asset $assetpathtarget
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fi
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done < "$externalfilepath"
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done
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# Create low-res photos on-the-fly from existing photos/
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msg "<thesis> -------------------------------"
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msg "<thesis> Create low-res photos tree"
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msg "<thesis> -------------------------------"
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# copy existing photos to assets/photos/.lowres/ path
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# to save time, rsync only if highres photo has more recent timestamp (otherwise, keep lowres photo without overwriting)
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# Note: rsync usually looks at file timestamp and size, and if either has changed, copies the file (simplified explanation)
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# in this case, I'd like rsync to only compare timestamps and disregard size
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# rsync can't do that. We need to use a different tool. See e.g.
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# https://superuser.com/questions/260092/rsync-switch-to-only-compare-timestamps
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# copy only the "large" photos that have file modtimes more recent than the last time this operation was run
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photoslastrun="$path_thesis/assets/photos/.lowres/lastrun"
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if [ ! -f "$photoslastrun" ]; then
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# if, for some reason, the lastrun file does not exist
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# copy over everything and then create the file
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# (except for the .lowres tree itself, and any assets.external files)
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rsync -av "$path_thesis/assets/photos/" "$path_thesis/assets/photos/.lowres/" --exclude ".lowres/" --exclude "assets.external"
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touch "$photoslastrun"
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fi
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# Detect new photos and copy them into .lowres tree
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# https://stackoverflow.com/questions/9612090/how-to-loop-through-file-names-returned-by-find
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# https://stackoverflow.com/questions/5241625/find-and-copy-files
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cd "$path_thesis/assets/photos"
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find . -type f -cnewer $photoslastrun ! -path "./.lowres/*" ! -name "*.external" -print -exec cp --parents "{}" .lowres \;
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# revert the effects of cd above. Redirect to null suppresses the output.
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cd - >/dev/null
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# Convert all non-JPG images (except for PDF, SVG, and other non-images) to JPG
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msg "<thesis> Convert all non-JPG images to JPG"
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find "$path_thesis/assets/photos/.lowres/" -type f ! -name "*.pdf" ! -name "*.svg" ! -name "*.external" ! -name "lastrun" ! -name "*.jpg" -print -exec mogrify -format jpg "{}" \;
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# Remove the now redundant non-JPG files in .lowres/
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msg "<thesis> Delete the redundant non-JPG files in .lowres/ tree"
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find "$path_thesis/assets/photos/.lowres/" -type f ! -name "*.pdf" ! -name "*.svg" ! -name "*.external" ! -name "lastrun" ! -name "*.jpg" -print -exec rm "{}" \;
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# Shrink image filesize in-place to roughly 300kb in size
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msg "<thesis> Shrink images in .lowres/ tree to <=300K"
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# https://stackoverflow.com/questions/6917219/imagemagick-scale-jpeg-image-with-a-maximum-file-size
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find "$path_thesis/assets/photos/.lowres/" -size +500k -type f -name "*.jpg" -print -exec convert "{}" -define jpeg:extent=300kb "{}" \;
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# update the modification and access time on the photosastrun file
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touch "$photoslastrun"
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fi
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## Handle knitr or pgfSweave jobs (each requires separate treatment)
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## But how should we tell the difference between them?
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## There is no obvious way to tell the difference (apart from reading the *.Rnw file)
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## IN ALL KNITR DIRECTORIES, CREATE A FILE NAMED: .knitme
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# If the file .knitme exists in the current directory,
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# run knitr commands, otherwise run pgfsweave commands
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msg "--- Looking for .knitme"
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if [ -e .knitme ]; then
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# Run knitr commands for this job
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msg "<cheRTeX> -----------------------"
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msg "<cheRTeX> This is a job for knitr"
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msg "<cheRTeX> -----------------------"
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# Knit
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msg "<cheRTeX> Knitting..."
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Rscript -e "library(knitr); library(methods); knit('$jobname.$jobfiletype')"
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# Introduce delay to give time to read Rscript exit status
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msg "<cheRTeX> -----------------------"
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msg "<cheRTeX> Rscript knitr completed"
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msg "<cheRTeX> -----------------------"
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simpledelay.sh 2
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else
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# Run pgfSweave commands
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msg "<cheRTeX> ---------------------------"
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msg "<cheRTeX> This is a job for pgfSweave"
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msg "<cheRTeX> ---------------------------"
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# Tangle
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msg "<cheRTeX> Tangling..."
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R CMD Stangle $jobname.$jobfiletype
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# Weave
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msg "<cheRTeX> Weaving..."
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R CMD pgfsweave --graphics-only $jobname.$jobfiletype
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# Introduce delay to give time to read R CMD exit status
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msg "<cheRTeX> -------------------------"
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msg "<cheRTeX> R CMD pgfsweave completed"
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msg "<cheRTeX> -------------------------"
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simpledelay.sh 2
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fi
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# Run vc script if vc exists in working directory
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msg "<cheRTeX> Running vc script..."
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if [ -f vc ]; then
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./vc
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fi
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# Run pdflatex, bibtex, and company
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# Leaving this if-else for historical reasons, and also to print the message
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if $ltxmkrc; then
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msg "${On_Cyan}<cheRTeX> Calling LaTeXMK, detected .latemxkrc file${Color_Off}"
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simpledelay.sh 2
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# note: latexmk does not need us to invoke "-r .latexmkrc", it finds and uses
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# the RC file automatically (as evidenced by latexmk's output)
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latexmk -pdf -bibtex $jobname
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else
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msg "${On_Cyan}<cheRTeX> Calling LaTeXMK${Color_Off}"
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simpledelay.sh 2
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latexmk -pdf -bibtex $jobname
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fi
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else
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# Zero arguments (the case of more than one argument is handled in parse_params above)
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# In this case, present a menu of choices
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msg "This is cheRTeX POST-PROCESSING" # only one choice for now
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msg "<1> 'pdf-all' -- Process all .tikz files to pdf graphics"
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msg "<2> 'clean-up' -- Remove all auxiliary files"
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msg "<3> 'wipe-dir' -- Remove all non-essential files and subdirectories"
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msg "Any other input exits the program"
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read usrchoice
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if [[ $usrchoice == "pdf-all" || $usrchoice == "1" ]]; then
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msg "<1> 'pdf-all' chosen"
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# This for loop ONLY USED to determine number of *.tikz files in directory
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for tikzfiles in "$tikzfiles"; do tikzfilenumber=${#tikzfiles}; done
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msg "cheRTeX detected $tikzfilenumber TikZ files for processing"
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msg "Starting TikZ file processing..."
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simpledelay.sh 2
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for tikzfilename in $tikzfiles; do
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# Call tikz2pdf
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msg "<Executing> tikz2pdf $tikzfilename"
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tikz2pdf --once $tikzfilename
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done
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msg "Completed TikZ file processing"
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fi
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if [[ $usrchoice == "clean-up" || $usrchoice == "2" ]]; then
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msg "<2> 'clean-up' chosen"
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# in $auxfiles, strip "*." or "*" at beginning of each word and "*" at the
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# end of any word, and replace space between items with pipe symbol
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# using the built-in bash ${$VAR//find/replace} takes us part-way
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# $ echo "${auxfiles//\*./}"
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# acn acr alg aux bbl blg dep dpth fdb* figlist fls glg glo gls* ist lob lof log lol lor los lot maf out lox makefile map mtc* run* slg slo sls stc* *-tikzDictionary tdo toc xdy
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# https://www.baeldung.com/linux/process-a-bash-variable-with-sed
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# first, replace "*." or "*-" with empty string, then replace "* " with ".* " (to suit
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# regex syntax in the subsequent find command), finally replace each inter-word
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# spaces with pipe symbol. Also, and this is important, "*-tikzDictionary" needs to
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# be cleaned up otherwise trips up the -iregex parameter! (don't leave "*-" in the string)
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# https://unix.stackexchange.com/a/15337
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# $ echo "$auxfiles" | sed -r "s/\*\.//g" | sed -r "s/\* /\.\* /g" | sed -r "s/ /|/g"
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# acn|acr|alg|aux|bbl|blg|dep|dpth|fdb.*|figlist|fls|glg|glo|gls.*|ist|lob|lof|log|lol|lor|los|lot|maf|out|lox|makefile|map|mtc.*|run.*|slg|slo|sls|stc.*|*-tikzDictionary|tdo|toc|xdy
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auxregex=$(echo "$auxfiles" | sed -r "s/\*[\.-]//g" | sed -r "s/\* /\.\* /g" | sed -r "s/ /|/g")
|
|
# "rm -v" provides nice output of which files were cleaned up
|
|
cd "$path_wd" && find . -maxdepth 1 -type f -regextype posix-extended -iregex ".*\.($auxregex)" -exec rm -v "{}" \; && cd $OLDPWD
|
|
fi
|
|
if [[ $usrchoice == "wipe-dir" || $usrchoice == "3" ]]; then
|
|
msg "<3> 'wipe-dir' chosen"
|
|
## Remove all but non-essential files
|
|
# get a timestamp
|
|
timestamp=$(date +%s)
|
|
# create a unique tmp-dir name
|
|
tmpdirname="${timestamp}-${dir_wd}"
|
|
# make a directory in chepec/tmp with the name of the current dir
|
|
mkdir $temp_folder/$tmpdirname
|
|
# Copy the contents of the current directory to the tmp/$currdirname directory
|
|
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 $temp_folder/$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 $temp_folder/$tmpdirname/*.Rproj 2>/dev/null | wc -l`
|
|
if [ $Rprojfiles != 0 ]; then
|
|
cp $temp_folder/$tmpdirname/*.Rproj .
|
|
fi
|
|
# Return *.rda files (considering peak-data files, which "cost" a lot to create)
|
|
rdafiles=`ls -1 $temp_folder/$tmpdirname/*.rda 2>/dev/null | wc -l`
|
|
if [ $rdafiles != 0 ]; then
|
|
cp $temp_folder/$tmpdirname/*.rda .
|
|
fi
|
|
# Return *.Rmd files (R markdown source files)
|
|
Rmdfiles=`ls -1 $temp_folder/$tmpdirname/*.Rmd 2>/dev/null | wc -l`
|
|
if [ $Rmdfiles != 0 ]; then
|
|
cp $temp_folder/$tmpdirname/*.Rmd .
|
|
fi
|
|
# Return *.css files (css files) [for sample-matrix]
|
|
cssfiles=`ls -1 $temp_folder/$tmpdirname/*.css 2>/dev/null | wc -l`
|
|
if [ $cssfiles != 0 ]; then
|
|
cp $temp_folder/$tmpdirname/*.css .
|
|
fi
|
|
# Return .knitme file [empty file used to indicate knitr jobs]
|
|
knitmefile=`ls -1 $temp_folder/$tmpdirname/.knitme 2>/dev/null | wc -l`
|
|
if [ $knitmefile != 0 ]; then
|
|
cp $temp_folder/$tmpdirname/.knitme .
|
|
fi
|
|
fi
|
|
|
|
die "All done. Exiting..." 0
|
|
fi
|
|
|
|
|
|
# Depending on whether the clock uses summer or wintertime, the date string length
|
|
# will differ by one (CEST vs CET).
|
|
# Just to be neat, we will take this into consideration when constructing the
|
|
# "job completed" block below.
|
|
cetcest=$(date +%Z)
|
|
|
|
# keep track of runtime of entire script
|
|
endtime=$(date +%s)
|
|
runtime=$(( $endtime - $starttime ))
|
|
|
|
# send push message to Gotify server
|
|
# if runtime is longer than X minutes (suitable limit perhaps 3 min)
|
|
if (( $runtime > 180 )) && [[ $disable_alert == "false" ]]; then
|
|
# POST request to Gotify server works without needing Gotify CLI on this box
|
|
# NOTE, multi-line bash command fails if interrupted by comment lines!
|
|
# Hide CURL response (-o /dev/null) and progress bar (--silent)
|
|
# https://gotify.net/docs/pushmsg
|
|
curl -X POST "https://gotify.chepec.se/message?token=A8nO3zYJ-R1wG__" \
|
|
-F "message=chertex.sh $@. Completed in $runtime s" \
|
|
-F "title=$dir_wd" -F "priority=5" \
|
|
-o /dev/null --silent
|
|
# https://stackoverflow.com/questions/3872427/how-to-send-line-break-with-curl
|
|
# I could not make multi-line message (to Gotify) work here, however I tried. Giving up for now.
|
|
msg "Push notification sent to Gotify"
|
|
fi
|
|
|
|
msg "${On_Cyan}-------------------------------------${Color_Off}"
|
|
# the padding for runtime makes the formatting work
|
|
# three digits for seconds is enough for just above 15 minutes
|
|
printf "${On_Cyan}=== chertex.sh completed in %03d s ===${Color_Off}\n" $runtime 1>&2
|
|
if [[ $cetcest == "CET" ]]; then
|
|
msg "${On_Cyan}=== $(date) ===${Color_Off}"
|
|
else
|
|
msg "${On_Cyan}=== $(date) ===${Color_Off}"
|
|
fi
|
|
msg "${On_Cyan}-------------------------------------${Color_Off}"
|
|
simpledelay.sh 3
|
|
|
|
exit 0
|