#!/bin/bash
# -*- coding: utf-8 -*-
# Timestamp: "2025-11-11 06:58:09 (ywatanabe)"
# File: ./scripts/shell/compile_manuscript.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 "$0").log"
echo >"$LOG_PATH"
# 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
# Timestamp tracking
STAGE_START_TIME=0
COMPILATION_START_TIME=$(date +%s)
# New logging functions (clean format)
log_stage_start() {
local stage_name="$1"
STAGE_START_TIME=$(date +%s)
echo -e "\033[0;34m▸\033[0m \033[1m${stage_name}\033[0m"
}
log_stage_end() {
local stage_name="$1"
local end_time
end_time=$(date +%s)
local elapsed=$((end_time - STAGE_START_TIME))
echo -e "\033[0;32m✓\033[0m ${stage_name} \033[0;90m(${elapsed}s)\033[0m"
}
log_success() {
echo -e " \033[0;32m✓\033[0m $1"
}
log_warning() {
echo -e " \033[0;33m⚠\033[0m $1"
}
log_error() {
echo -e " \033[0;31m✗\033[0m $1"
}
log_info() {
if [ "${SCITEX_LOG_LEVEL:-1}" -ge 2 ]; then
echo -e " \033[0;90m→ $1\033[0m"
fi
}
# Compatibility aliases
echo_success() { log_success "$1"; }
echo_warning() { log_warning "$1"; }
echo_error() { log_error "$1"; }
echo_info() { log_info "$1"; }
echo_header() { log_stage_start "$1"; }
# Configurations
export SCITEX_WRITER_DOC_TYPE="manuscript"
source "$PROJECT_ROOT/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
# Deafult 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=false
# Colors for usage output
GRAY='\033[0;90m'
BOLD_CYAN='\033[1;36m'
GREEN='\033[0;32m'
YELLOW='\033[0;33m'
NC='\033[0m'
usage() {
echo ""
echo -e "${BOLD_CYAN}━━━ compile_manuscript.sh ━━━${NC}"
echo -e "${GRAY}Compile main manuscript document${NC}"
echo ""
echo -e "${BOLD_CYAN}━━━ Structure ━━━${NC}"
echo -e " ${GREEN}01_manuscript/${NC}"
echo -e " contents/"
echo -e " ${YELLOW}abstract.tex${NC} ${GRAY}# Abstract${NC}"
echo -e " ${YELLOW}introduction.tex${NC} ${GRAY}# Introduction${NC}"
echo -e " ${YELLOW}methods.tex${NC} ${GRAY}# Methods${NC}"
echo -e " ${YELLOW}results.tex${NC} ${GRAY}# Results${NC}"
echo -e " ${YELLOW}discussion.tex${NC} ${GRAY}# Discussion${NC}"
echo -e " figures/caption_and_media/ ${GRAY}# Figures${NC}"
echo -e " tables/caption_and_media/ ${GRAY}# Tables${NC}"
echo -e " ${GRAY}manuscript.pdf${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}01_manuscript:${NC}"
echo -e " ${GRAY}$PROJECT_ROOT/01_manuscript/contents/${NC}abstract.tex"
echo -e " ${GRAY}$PROJECT_ROOT/01_manuscript/contents/${NC}introduction.tex"
echo -e " ${GRAY}$PROJECT_ROOT/01_manuscript/contents/${NC}methods.tex"
echo -e " ${GRAY}$PROJECT_ROOT/01_manuscript/contents/${NC}results.tex"
echo -e " ${GRAY}$PROJECT_ROOT/01_manuscript/contents/${NC}discussion.tex"
echo -e " ${GRAY}$PROJECT_ROOT/01_manuscript/contents/figures/${NC}caption_and_media/"
echo -e " ${GRAY}$PROJECT_ROOT/01_manuscript/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/01_manuscript/${NC}base.tex"
echo -e " Controls section order via \\\\input{} commands:"
echo -e " ${GRAY}% \\\\input{./01_manuscript/contents/${NC}highlights${GRAY}}${NC} ${GRAY}# Commented out (optional)${NC}"
echo -e " ${GRAY}\\\\input{./01_manuscript/contents/${NC}title${GRAY}}${NC}"
echo -e " ${GRAY}\\\\input{./01_manuscript/contents/${NC}authors${GRAY}}${NC}"
echo -e " ${GRAY}\\\\input{./01_manuscript/contents/${NC}abstract${GRAY}}${NC}"
echo -e " ${GRAY}\\\\input{./01_manuscript/contents/${NC}keywords${GRAY}}${NC}"
echo -e " ${GRAY}\\\\input{./01_manuscript/contents/${NC}introduction${GRAY}}${NC}"
echo -e " ${GRAY}\\\\input{./01_manuscript/contents/${NC}methods${GRAY}}${NC}"
echo -e " ${GRAY}\\\\input{./01_manuscript/contents/${NC}results${GRAY}}${NC}"
echo -e " ${GRAY}\\\\input{./01_manuscript/contents/${NC}discussion${GRAY}}${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} ${YELLOW}01_manuscript/contents/figures/caption_and_media/${NC}"
echo -e " ${GREEN}Supported:${NC} PNG, JPEG, PDF, SVG, TIFF, Mermaid (.mmd)"
echo ""
echo -e " ${GREEN}Naming Rule:${NC} Prefix with 2-digit number for ordering"
echo -e " ${YELLOW}01_my_figure.png${NC} ${GRAY}# Media file${NC}"
echo -e " ${YELLOW}01_my_figure.tex${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 " ${GRAY}\\\\label{fig:my_figure_01}${NC}"
echo ""
echo -e " ${GREEN}Citing in Text:${NC} Use ${YELLOW}\\\\ref{fig:my_figure_01}${NC} or ${YELLOW}Figure~\\\\ref{fig:my_figure_01}${NC}"
echo ""
echo -e "${BOLD_CYAN}━━━ Adding Tables ━━━${NC}"
echo -e " ${GREEN}Location:${NC} ${YELLOW}01_manuscript/contents/tables/caption_and_media/${NC}"
echo -e " ${GREEN}Format:${NC} CSV auto-converts to LaTeX table"
echo ""
echo -e " ${GREEN}Naming Rule:${NC} Prefix with 2-digit number for ordering"
echo -e " ${YELLOW}01_my_table.csv${NC} ${GRAY}# Data file (CSV format)${NC}"
echo -e " ${YELLOW}01_my_table.tex${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 " ${GRAY}\\\\label{tab:my_table_01}${NC}"
echo ""
echo -e " ${GREEN}Citing in Text:${NC} Use ${YELLOW}\\\\ref{tab:my_table_01}${NC} or ${YELLOW}Table~\\\\ref{tab:my_table_01}${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_manuscript.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 [[ "$#" -gt 0 ]]; do
# Normalize option: replace underscores with hyphens for matching
local normalized_opt
normalized_opt=$(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"
# Show options only in verbose mode
if [ "${SCITEX_LOG_LEVEL:-1}" -ge 2 ] && [ -n "$options_display" ]; then
log_info "Options:$options_display"
fi
# Verbosity
export SCITEX_WRITER_VERBOSE_PDFLATEX=$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=$dark_mode
# Check dependencies
log_stage_start "Dependency Check"
"$PROJECT_ROOT/scripts/shell/modules/check_dependancy_commands.sh"
log_stage_end "Dependency Check"
# Merge bibliography files if multiple exist
log_stage_start "Bibliography Merge"
"$PROJECT_ROOT/scripts/shell/modules/merge_bibliographies.sh"
log_stage_end "Bibliography Merge"
# Apply citation style from config
log_stage_start "Citation Style"
"$PROJECT_ROOT/scripts/shell/modules/apply_citation_style.sh"
log_stage_end "Citation Style"
# Run independent processing in parallel for speed
log_stage_start "Asset Processing"
# Create temp files for parallel job outputs
local temp_dir
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
(
"$PROJECT_ROOT/scripts/shell/modules/process_figures.sh" "$no_figs" "$do_p2t" "$do_verbose" "$do_crop_tif" >"$fig_log" 2>&1
echo $? >"$temp_dir/fig_exit"
) &
local fig_pid=$!
(
"$PROJECT_ROOT/scripts/shell/modules/process_tables.sh" "$no_tables" >"$tbl_log" 2>&1
echo $? >"$temp_dir/tbl_exit"
) &
local tbl_pid=$!
(
"$PROJECT_ROOT/scripts/shell/modules/count_words.sh" >"$wrd_log" 2>&1
echo $? >"$temp_dir/wrd_exit"
) &
local wrd_pid=$!
# Wait for all parallel jobs
wait $fig_pid $tbl_pid $wrd_pid
# Display outputs only in verbose mode
if [ "${SCITEX_LOG_LEVEL:-1}" -ge 2 ]; then
log_info "Figure Processing:"
sed 's/^/ /' "$fig_log"
log_info "Table Processing:"
sed 's/^/ /' "$tbl_log"
log_info "Word Count:"
sed 's/^/ /' "$wrd_log"
fi
# Check exit codes
local fig_exit
local tbl_exit
local wrd_exit
fig_exit=$(cat "$temp_dir/fig_exit")
tbl_exit=$(cat "$temp_dir/tbl_exit")
wrd_exit=$(cat "$temp_dir/wrd_exit")
# Extract summary lines for normal mode
if [ "${SCITEX_LOG_LEVEL:-1}" -lt 2 ]; then
# Show only key results (remove file paths from grep output)
grep -hE "(figures compiled|tables compiled|Word counts updated)" "$fig_log" "$tbl_log" "$wrd_log" 2>/dev/null | sed 's/^/ /' || true
fi
rm -rf "$temp_dir"
# Fail if any job failed
if [ "$fig_exit" -ne 0 ] || [ "$tbl_exit" -ne 0 ] || [ "$wrd_exit" -ne 0 ]; then
log_error "Asset processing failed (fig=$fig_exit, tbl=$tbl_exit, wrd=$wrd_exit)"
exit 1
fi
log_stage_end "Asset Processing"
# Compile documents
log_stage_start "TeX Compilation (Structure)"
"$PROJECT_ROOT/scripts/shell/modules/compilation_structure_tex_to_compiled_tex.sh"
log_stage_end "TeX Compilation (Structure)"
# Engine Selection
log_stage_start "Engine Selection"
source "$PROJECT_ROOT/scripts/shell/modules/select_compilation_engine.sh"
# Get engine from config or default to auto
SELECTED_ENGINE="${SCITEX_WRITER_ENGINE:-auto}"
if [ "$SELECTED_ENGINE" = "auto" ]; then
# Auto-detection: try engines in order
SELECTED_ENGINE=$(auto_detect_engine)
echo_info "Auto-detected engine: $SELECTED_ENGINE"
else
# Explicit selection: verify availability
if ! verify_engine "$SELECTED_ENGINE" >/dev/null 2>&1; then
echo_warning "Requested engine '$SELECTED_ENGINE' not available"
echo_info "Falling back to auto-detection..."
SELECTED_ENGINE=$(auto_detect_engine)
echo_info "Selected engine: $SELECTED_ENGINE"
else
echo_info "Using requested engine: $SELECTED_ENGINE"
fi
fi
# Export for downstream modules
export SCITEX_WRITER_SELECTED_ENGINE="$SELECTED_ENGINE"
echo_info "$(get_engine_info "$SELECTED_ENGINE")"
log_stage_end "Engine Selection"
# TeX to PDF
log_stage_start "PDF Generation"
"$PROJECT_ROOT/scripts/shell/modules/compilation_compiled_tex_to_compiled_pdf.sh"
log_stage_end "PDF Generation"
# Diff (skip if --no_diff specified)
if [ "$no_diff" = false ]; then
log_stage_start "Diff Generation"
"$PROJECT_ROOT/scripts/shell/modules/process_diff.sh"
log_stage_end "Diff Generation"
else
echo_info "Skipping diff generation (--no_diff specified)"
fi
# Versioning
log_stage_start "Archive/Versioning"
"$PROJECT_ROOT/scripts/shell/modules/process_archive.sh"
log_stage_end "Archive/Versioning"
# Cleanup
log_stage_start "Cleanup"
"$PROJECT_ROOT/scripts/shell/modules/cleanup.sh"
log_stage_end "Cleanup"
# Final steps
log_stage_start "Directory Tree"
"$PROJECT_ROOT/scripts/shell/modules/custom_tree.sh"
log_stage_end "Directory Tree"
# Final summary
echo ""
local final_time
final_time=$(date +%s)
local total_compilation_time=$((final_time - COMPILATION_START_TIME))
echo -e "\033[1;32m━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━\033[0m"
echo -e "\033[1;32m Compilation Complete\033[0m"
echo -e "\033[0;32m Total time: ${total_compilation_time}s\033[0m"
echo -e "\033[0;32m Output: $SCITEX_WRITER_COMPILED_PDF\033[0m"
echo -e "\033[0;90m Log: $SCITEX_WRITER_GLOBAL_LOG_FILE\033[0m"
echo -e "\033[1;32m━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━\033[0m"
echo ""
}
main "$@" 2>&1 | tee -a "$LOG_PATH" "$SCITEX_WRITER_GLOBAL_LOG_FILE"
# EOF
/