#!/bin/bash
# -*- coding: utf-8 -*-
# Timestamp: "2025-09-27 15:20:00 (ywatanabe)"
# File: ./paper/scripts/shell/compile_supplementary.sh
# shellcheck disable=SC1091 # Don't follow sourced files
export ORIG_DIR
ORIG_DIR="$(pwd)"
THIS_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
LOG_PATH="$THIS_DIR/.$(basename "$0").log"
# Resolve project root from script location (safe for nested repos)
# Allow override via environment variable for moved projects
PROJECT_ROOT="${PROJECT_ROOT:-$(cd "$THIS_DIR/../.." && pwd)}"
export PROJECT_ROOT
# Change to project root to ensure relative paths work
cd "$PROJECT_ROOT" || exit 1
GRAY='\033[0;90m'
GREEN='\033[0;32m'
YELLOW='\033[0;33m'
RED='\033[0;31m'
BOLD_CYAN='\033[1;36m'
NC='\033[0m' # No Color
echo_info() { echo -e "${GRAY}INFO: $1${NC}"; }
echo_success() { echo -e "${GREEN}SUCC: $1${NC}"; }
echo_warning() { echo -e "${YELLOW}WARN: $1${NC}"; }
echo_error() { echo -e "${RED}ERRO: $1${NC}"; }
echo_header() { echo_info "=== $1 ==="; }
# ---------------------------------------
# Timestamp tracking functions
STAGE_START_TIME=0
COMPILATION_START_TIME=$(date +%s)
log_stage_start() {
local stage_name="$1"
STAGE_START_TIME=$(date +%s)
local timestamp=$(date '+%H:%M:%S')
echo_info "[$timestamp] Starting: $stage_name"
}
log_stage_end() {
local stage_name="$1"
local end_time=$(date +%s)
local elapsed=$((end_time - STAGE_START_TIME))
local total_elapsed=$((end_time - COMPILATION_START_TIME))
local timestamp=$(date '+%H:%M:%S')
echo_success "[$timestamp] Completed: $stage_name (${elapsed}s elapsed, ${total_elapsed}s total)"
}
# Configurations
export SCITEX_WRITER_DOC_TYPE="supplementary"
source ./config/load_config.sh "$SCITEX_WRITER_DOC_TYPE"
echo
# Log
touch $LOG_PATH >/dev/null 2>&1
mkdir -p "$LOG_DIR" && touch "$SCITEX_WRITER_GLOBAL_LOG_FILE"
# Shell options
set -e
set -o pipefail
# Default values for arguments
do_p2t=false
no_figs=false
no_tables=false
do_verbose=false
do_crop_tif=false
do_force=false
no_diff=false
draft_mode=false
dark_mode=${SCITEX_WRITER_DARK_MODE:-false}
usage() {
echo ""
echo -e "${BOLD_CYAN}━━━ compile_supplementary.sh ━━━${NC}"
echo -e "${GRAY}Compile supplementary materials${NC}"
echo ""
echo -e "${BOLD_CYAN}━━━ Structure ━━━${NC}"
echo -e " ${GREEN}02_supplementary/${NC}"
echo -e " contents/"
echo -e " ${YELLOW}methods.tex${NC} ${GRAY}# Supplementary Methods${NC}"
echo -e " ${YELLOW}results.tex${NC} ${GRAY}# Supplementary Results${NC}"
echo -e " figures/caption_and_media/ ${GRAY}# Supplementary Figures${NC}"
echo -e " tables/caption_and_media/ ${GRAY}# Supplementary Tables${NC}"
echo -e " ${GRAY}supplementary.pdf${NC} ${GRAY}# Output${NC}"
echo ""
echo -e "${BOLD_CYAN}━━━ Editable Files ━━━${NC}"
echo -e "${GREEN}00_shared:${NC}"
echo -e " ${GRAY}$PROJECT_ROOT/00_shared/${NC}title.tex"
echo -e " ${GRAY}$PROJECT_ROOT/00_shared/${NC}authors.tex"
echo -e " ${GRAY}$PROJECT_ROOT/00_shared/${NC}keywords.tex"
echo -e " ${GRAY}$PROJECT_ROOT/00_shared/${NC}journal_name.tex"
echo -e " ${GRAY}$PROJECT_ROOT/00_shared/bib_files/${NC}*.bib"
echo ""
echo -e "${GREEN}02_supplementary:${NC}"
echo -e " ${GRAY}$PROJECT_ROOT/02_supplementary/contents/${NC}methods.tex"
echo -e " ${GRAY}$PROJECT_ROOT/02_supplementary/contents/${NC}results.tex"
echo -e " ${GRAY}$PROJECT_ROOT/02_supplementary/contents/figures/${NC}caption_and_media/"
echo -e " ${GRAY}$PROJECT_ROOT/02_supplementary/contents/tables/${NC}caption_and_media/"
echo ""
echo -e "${BOLD_CYAN}━━━ Options ━━━${NC}"
echo " -nf, --no_figs Skip figure processing (~4s faster)"
echo " -nt, --no_tables Skip table processing (~4s faster)"
echo " -nd, --no_diff Skip diff generation (~17s faster)"
echo " -d, --draft Single-pass compilation (~5s faster)"
echo " -dm, --dark_mode Dark mode: black background, white text"
echo " -p2t, --ppt2tif Convert PowerPoint to TIF (WSL)"
echo " -c, --crop_tif Crop TIF whitespace"
echo " -q, --quiet Minimal output"
echo " --force Force full recompilation"
echo " -h, --help Show this help"
echo ""
echo -e "${GRAY}Note: Options accept both hyphens and underscores${NC}"
echo ""
echo -e "${BOLD_CYAN}━━━ Document Structure (base.tex) ━━━${NC}"
echo -e " ${GRAY}$PROJECT_ROOT/02_supplementary/${NC}base.tex"
echo -e " Controls section order via \\\\input{} commands:"
echo -e " ${GRAY}\\\\input{./02_supplementary/contents/${NC}authors${GRAY}}${NC}"
echo -e " ${GRAY}\\\\input{./02_supplementary/contents/${NC}methods${GRAY}}${NC}"
echo -e " ${GRAY}\\\\input{./02_supplementary/contents/${NC}results${GRAY}}${NC}"
echo -e " To add/remove sections: edit base.tex \\\\input{} lines"
echo -e " Comment out with %% to disable a section"
echo ""
echo -e "${BOLD_CYAN}━━━ Adding Figures ━━━${NC}"
echo -e " ${GREEN}Location:${NC} ${YELLOW}02_supplementary/contents/figures/caption_and_media/${NC}"
echo -e " ${GREEN}Supported:${NC} PNG, JPEG, PDF, SVG, TIFF, Mermaid (.mmd)"
echo ""
echo -e " ${GREEN}Naming Rule:${NC} Prefix with S + 2-digit number for ordering"
echo -e " ${YELLOW}S01_my_figure.png${NC} ${GRAY}# Media file${NC}"
echo -e " ${YELLOW}S01_my_figure.tex${NC} ${GRAY}# Caption file (same base name)${NC}"
echo ""
echo -e " ${GREEN}Caption File Format:${NC}"
echo -e " ${GRAY}%% Figure caption${NC}"
echo -e " ${GRAY}\\\\caption{Your caption here.}${NC}"
echo -e " ${GRAY}\\\\label{fig:supplementary_my_figure_01}${NC}"
echo ""
echo -e " ${GREEN}Citing in Text:${NC} Use ${YELLOW}\\\\ref{fig:supplementary_my_figure_01}${NC}"
echo ""
echo -e "${BOLD_CYAN}━━━ Adding Tables ━━━${NC}"
echo -e " ${GREEN}Location:${NC} ${YELLOW}02_supplementary/contents/tables/caption_and_media/${NC}"
echo -e " ${GREEN}Format:${NC} CSV auto-converts to LaTeX table"
echo ""
echo -e " ${GREEN}Naming Rule:${NC} Prefix with S + 2-digit number for ordering"
echo -e " ${YELLOW}S01_my_table.csv${NC} ${GRAY}# Data file (CSV format)${NC}"
echo -e " ${YELLOW}S01_my_table.tex${NC} ${GRAY}# Caption file (same base name)${NC}"
echo ""
echo -e " ${GREEN}Caption File Format:${NC}"
echo -e " ${GRAY}%% Table caption${NC}"
echo -e " ${GRAY}\\\\caption{Your caption here.}${NC}"
echo -e " ${GRAY}\\\\label{tab:supplementary_my_table_01}${NC}"
echo ""
echo -e " ${GREEN}Citing in Text:${NC} Use ${YELLOW}\\\\ref{tab:supplementary_my_table_01}${NC}"
echo ""
echo -e "${BOLD_CYAN}━━━ Managing Bibliography ━━━${NC}"
echo -e " Place .bib files in: ${YELLOW}$PROJECT_ROOT/00_shared/bib_files/${NC}"
echo -e " Multiple .bib files auto-merge with deduplication"
echo -e " Citation style: ${YELLOW}$PROJECT_ROOT/config/config_supplementary.yaml${NC}"
echo -e " Styles: ${GREEN}unsrtnat${NC}, ${GREEN}plainnat${NC}, ${GREEN}apalike${NC}, ${GREEN}IEEEtran${NC}, ${GREEN}naturemag${NC}"
echo ""
exit 0
}
parse_arguments() {
while [[ "$#" -gt 0 ]]; do
# Normalize option: replace underscores with hyphens for matching
local normalized_opt=$(echo "$1" | tr '_' '-')
case $normalized_opt in
-h | --help) usage ;;
-p2t | --ppt2tif) do_p2t=true ;;
-nf | --no-figs) no_figs=true ;;
-nt | --no-tables) no_tables=true ;;
-nd | --no-diff) no_diff=true ;;
-d | --draft) draft_mode=true ;;
-dm | --dark-mode) dark_mode=true ;;
-c | --crop-tif) do_crop_tif=true ;;
-v | --verbose) do_verbose=true ;;
-q | --quiet) do_verbose=false ;;
--force) do_force=true ;;
*)
echo "Unknown option: $1"
usage
;;
esac
shift
done
}
main() {
parse_arguments "$@"
# Log command options
options_display=""
$do_p2t && options_display="${options_display} --ppt2tif"
$no_figs && options_display="${options_display} --no_figs"
$no_tables && options_display="${options_display} --no_tables"
$no_diff && options_display="${options_display} --no_diff"
$draft_mode && options_display="${options_display} --draft"
$dark_mode && options_display="${options_display} --dark_mode"
$do_crop_tif && options_display="${options_display} --crop_tif"
$do_verbose && options_display="${options_display} --verbose"
echo_info "Running $0${options_display}..."
# Verbosity
export SCITEX_WRITER_VERBOSE_PDFLATEX=$do_verbose
export SCITEX_WRITER_VERBOSE_BIBTEX=$do_verbose
# Draft mode (single-pass compilation)
export SCITEX_WRITER_DRAFT_MODE=$draft_mode
# Dark mode (black background, white text)
export SCITEX_WRITER_DARK_MODE=$dark_mode
# Check dependencies
log_stage_start "Dependency Check"
./scripts/shell/modules/check_dependancy_commands.sh
log_stage_end "Dependency Check"
# Merge bibliography files if multiple exist
log_stage_start "Bibliography Merge"
./scripts/shell/modules/merge_bibliographies.sh
log_stage_end "Bibliography Merge"
# Apply citation style from config
log_stage_start "Citation Style"
./scripts/shell/modules/apply_citation_style.sh
log_stage_end "Citation Style"
# Run independent processing in parallel for speed
local parallel_start=$(date +%s)
local timestamp=$(date '+%H:%M:%S')
echo_info "[$timestamp] Starting: Parallel Processing (Figures, Tables, Word Count)"
# Create temp files for parallel job outputs
local temp_dir=$(mktemp -d)
local fig_log="$temp_dir/figures.log"
local tbl_log="$temp_dir/tables.log"
local wrd_log="$temp_dir/words.log"
# Run all three in parallel
(
./scripts/shell/modules/process_figures.sh "$no_figs" "$do_p2t" "$do_verbose" "$do_crop_tif" >"$fig_log" 2>&1
echo $? >"$temp_dir/fig_exit"
) &
local fig_pid=$!
(
./scripts/shell/modules/process_tables.sh "$no_tables" >"$tbl_log" 2>&1
echo $? >"$temp_dir/tbl_exit"
) &
local tbl_pid=$!
# Wait for figures and tables to finish before counting
wait $fig_pid $tbl_pid
# Run word count after figures/tables are ready (needs compiled files)
./scripts/shell/modules/count_words.sh >"$wrd_log" 2>&1
echo $? >"$temp_dir/wrd_exit"
# Display outputs in order
echo_info " Figure Processing:"
cat "$fig_log" | sed 's/^/ /'
echo_info " Table Processing:"
cat "$tbl_log" | sed 's/^/ /'
echo_info " Word Count:"
cat "$wrd_log" | sed 's/^/ /'
# Check exit codes
local fig_exit=$(cat "$temp_dir/fig_exit")
local tbl_exit=$(cat "$temp_dir/tbl_exit")
local wrd_exit=$(cat "$temp_dir/wrd_exit")
rm -rf "$temp_dir"
# Fail if any job failed
if [ "$fig_exit" -ne 0 ] || [ "$tbl_exit" -ne 0 ] || [ "$wrd_exit" -ne 0 ]; then
echo_error "Parallel processing failed (fig=$fig_exit, tbl=$tbl_exit, wrd=$wrd_exit)"
exit 1
fi
local parallel_end=$(date +%s)
local parallel_elapsed=$((parallel_end - parallel_start))
local total_elapsed=$((parallel_end - COMPILATION_START_TIME))
timestamp=$(date '+%H:%M:%S')
echo_success "[$timestamp] Completed: Parallel Processing (${parallel_elapsed}s elapsed, ${total_elapsed}s total)"
# Compile documents
log_stage_start "TeX Compilation (Structure)"
./scripts/shell/modules/compilation_structure_tex_to_compiled_tex.sh
log_stage_end "TeX Compilation (Structure)"
# TeX to PDF
log_stage_start "PDF Generation"
./scripts/shell/modules/compilation_compiled_tex_to_compiled_pdf.sh
log_stage_end "PDF Generation"
# Diff (skip if --no_diff specified)
if [ "$no_diff" = false ]; then
log_stage_start "Diff Generation"
./scripts/shell/modules/process_diff.sh
log_stage_end "Diff Generation"
else
echo_info "Skipping diff generation (--no_diff specified)"
fi
# Versioning
log_stage_start "Archive/Versioning"
./scripts/shell/modules/process_archive.sh
log_stage_end "Archive/Versioning"
# Cleanup
log_stage_start "Cleanup"
./scripts/shell/modules/cleanup.sh
log_stage_end "Cleanup"
# Final steps
log_stage_start "Directory Tree"
./scripts/shell/modules/custom_tree.sh
log_stage_end "Directory Tree"
# Logging
echo
local final_time=$(date +%s)
local total_compilation_time=$((final_time - COMPILATION_START_TIME))
echo_success "===================================================="
echo_success "TOTAL COMPILATION TIME: ${total_compilation_time}s"
echo_success "===================================================="
echo_success "See $SCITEX_WRITER_GLOBAL_LOG_FILE"
}
main "$@" 2>&1 | tee -a "$LOG_PATH" "$SCITEX_WRITER_GLOBAL_LOG_FILE"
# EOF
/