Compile only paper or only SI with dynamically set

manuscript filenames and corresponding
LaTeX template files for Markdown.
To avoid having to set overly long command
I have opted to read these values from file.

chemdtex.sh

@@ -1,5 +1,6 @@
 #!/usr/bin/env bash
-# GPL3 2023 solarchemist
+# solarchemist
+# GPL3 2023
 
 set -euo pipefail
 
@@ -7,8 +8,9 @@ usage() {
   cat <<EOF
 Usage: $(basename "${BASH_SOURCE[0]}") <flags>
 
-Compiles Markdown manuscript and SI to PDF, and optionally converts to HTML,
-ODT, or DOCX.
+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
@@ -43,6 +45,8 @@ parse_params() {
       -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
@@ -53,16 +57,76 @@ parse_params() {
 
 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 indexed bash arrays
-# https://www.cyberciti.biz/faq/bash-for-loop-array/
-declare -a MANUSCRIPT_SOURCES=("paper" "si")
-declare -a MANUSCRIPT_TEMPLATES=("templates/wiley.latex" "templates/wiley-si.latex")
 # these are just strings
 BIBLIOGRAPHIES="--bibliography ./refmngr/zotero.bib --bibliography ./references.bib"
 PANDOC=pandoc
@@ -76,16 +140,16 @@ 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
+# 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 "${!MANUSCRIPT_SOURCES[@]}"; do
-  # manuscript value in current loop
-  manuscript="${MANUSCRIPT_SOURCES[M]}"
-  # template value in current loop
-  template="${MANUSCRIPT_TEMPLATES[M]}"
+for M in "${!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