bash-common/chemdtex.sh

#!/usr/bin/env bash
# solarchemist
# GPL3 2023

set -euo pipefail

usage() {
  cat <<EOF
Usage: $(basename "${BASH_SOURCE[0]}") <flags>

Compiles Markdown manuscript and SI to PDF, and optionally converts it to HTML,
ODT, and/or DOCX.
Requires .mdtemplates file to exist in the current working directory.

Available flags:
+ --help            --> display this usage guide
+ --convert-all     --> convert to HTML, ODT, or other formats
+ --convert-html    --> convert to HTML
EOF
  exit
}

msg() {
  echo >&2 -e "${1-}"
}

# Examples:
# die "some message"
# die "some message and wait 6 seconds before exiting" 6
# die "some message and exit immediately" 0
die() {
  local msg=$1
  msg "$msg"
  # short delay to aid reading last message in case terminal closes on exit
  # if $2 was provided, set it as delay
  # if $2 is unset or null, use a 3 second delay
  simpledelay.sh ${2:-3}
  exit 0
}

parse_params() {
   while :; do
      case "${1-}" in
      -h | --help) usage ;;
      -v | --verbose) set -x ;;
      --convert-all) convert_formats=true ;;
      --convert-html) convert_html=true ;;
      --paper) only_paper=true;;
      --si) only_si=true;;
      -?*) die "Unknown option: $1" ;;
      *) break ;;
      esac
      shift
   done
   return 0
}

convert_formats=false
convert_html=false
only_paper=false
only_si=false
parse_params "$@"


# https://ostechnix.com/bash-associative-array
# https://phoenixnap.com/kb/bash-associative-array
# I expect .mdtemplates to look like this:
# (note the use of "keys" named "paper" and "si", these key names should always be paper/si)
# ```
# $ cat .mdtemplates
# declare -A MANUSCRIPT=( ["paper"]="templates/pmichaillat.latex", ["si"]="templates/pmichaillat-si.latex" )
# ```
# so if your main manuscript is named something other than "paper", just adjust accordingly in your .mdtemplates
# and ditto for the relative path to your latex template file markdown should use.

msg "--- Looking for .mdtemplates"
if [ -e .mdtemplates ]; then
   msg "--- Found in .mdtemplates:"
   # https://stackoverflow.com/a/4685432/1198249
   source ./.mdtemplates
   for M in "${!MANUSCRIPT[@]}"; do
      echo "    ${M}: ${MANUSCRIPT[${M}]}"
   done
else
   die "Found no .mdtemplates file. Quitting..." 0
   # for later, add the ability define the array as arg to the --paper and --si flags
fi


if [[ $only_paper == "true" ]]; then
   # msg "Detected --paper flag"
   declare -A MANUSCRIPT_PAPER
   MANUSCRIPT_PAPER["paper"]=${MANUSCRIPT["paper"]}
   unset MANUSCRIPT
   declare -A MANUSCRIPT
   MANUSCRIPT["paper"]=${MANUSCRIPT_PAPER["paper"]}
   # declare -a MANUSCRIPT_TEMPLATES=( "templates/pmichaillat.latex" )
fi


if [[ $only_si == "true" ]]; then
   # msg "Detected --si flag"
   declare -A MANUSCRIPT_SI
   # in this assignment we lose the "si" key, gets replaced by integer
   # declare -a MANUSCRIPT_SI=${MANUSCRIPT["si"]}
   # we effectively need to build a new array from the old
   # https://unix.stackexchange.com/a/464627/411416
   MANUSCRIPT_SI["si"]=${MANUSCRIPT["si"]}
   # echo "${MANUSCRIPT_SI[@]}"
   # echo "${!MANUSCRIPT_SI[@]}"
   # echo "${#MANUSCRIPT_SI[@]}"
   # simpledelay.sh 10
   unset MANUSCRIPT
   declare -A MANUSCRIPT
   MANUSCRIPT["si"]=${MANUSCRIPT_SI["si"]}
#   declare -a MANUSCRIPT_TEMPLATES=( "templates/pmichaillat-si.latex" )
fi


# echo "${MANUSCRIPT[@]}"
# echo "${!MANUSCRIPT[@]}"
# echo "${#MANUSCRIPT[@]}"
# simpledelay.sh 15


# NOTE "templates/" is hard-coded here!
# note the colons (same function as in $PATH), they are important
export TEXINPUTS=.:${PWD}/templates/:

# these are just strings
BIBLIOGRAPHIES="--bibliography ./refmngr/zotero.bib --bibliography ./references.bib"
PANDOC=pandoc
LATEXMK=latexmk

bibtex_zotero="/media/bay/taha/chepec/literature/_refmngr/_bibrep/library.bib"
if [ -f "$bibtex_zotero" ]; then
   msg "Updating the local copy of Zotero library.bib"
   cp $bibtex_zotero ./refmngr/zotero.bib
fi

# for some reason, *.aux file is messing up the subsequent run (but not the first run):
# /paper.aux:224: Undefined control sequence. l.224 \BibFileName[0]{paper.html}
# rm -f *.aux


# note the exclamation mark in the for loop variable, makes it the loop index
# https://stackoverflow.com/a/51794732/1198249
for M in "${!MANUSCRIPT[@]}"; do
  # array key (manuscript name)
  manuscript="${M}"
  # array value (template path)
  template="${MANUSCRIPT[${M}]}"

  # The --biblatex option is not for use with the --citeproc option or with PDF output
  # https://pandoc.org/MANUAL.html#citation-rendering
  msg "pandoc $manuscript.md to TeX"
  # https://unix.stackexchange.com/questions/278502/accessing-array-index-variable-from-bash-shell-script-loop
  $PANDOC --standalone --biblatex $manuscript.md -o $manuscript.tex --template $template $BIBLIOGRAPHIES

  msg "latexmk $manuscript.tex to PDF"
  $LATEXMK -bibtex -pdf $manuscript

  if [[ $convert_formats == "true" || $convert_html == "true" ]]; then
    # TeX to HTML
    # successfully produces HTML but after lots of error-like warnings and non-zero exit
    msg "Converting $manuscript.tex to HTML"
    # this command creates a HTML file as expected, but returns a non-zero exit code
    # which causes this script to exit immediately afterwards. Circumvented by "|| true"
    # --output-dir works, but also produces all the auxiliary files in the root (very weird)
    make4ht --format html5 $manuscript.tex || true
  fi

  if [[ $convert_formats == "true" ]]; then
    # ODT is not too bad, better than html -> docx using pandoc
    # pandoc cannot find figures or images, paths must be messed up...
    msg "Converting $manuscript.html to ODT"
    pandoc -s $manuscript.html -o $manuscript.odt
    msg "Converting $manuscript.html to DOCX"
    pandoc -s $manuscript.html -o $manuscript.docx
    # to also convert to to DOC, consider abiword (works but produces broken equations and tables)
    # https://stackoverflow.com/a/8384078/1198249
    # if you want this, please run it on a workstation, not luxor
    # (abiword is installed on workstations)
    # abiword --to=doc $manuscript.odt
  fi
done


exit 0