#!/bin/bash
# -*- coding: utf-8 -*-
# Timestamp: "2025-09-27 15:10:53 (ywatanabe)"
# File: ./paper/scripts/shell/compile_revision
# 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, ${total_elapsed}s total)"
}
################################################################################
# Description: Compiles revision response document
# Processes reviewer comments and author responses with diff highlighting
################################################################################
# Configurations
export SCITEX_WRITER_DOC_TYPE="revision"
source ./config/load_config.sh "$SCITEX_WRITER_DOC_TYPE"
echo
# Log
touch $LOG_PATH >/dev/null 2>&1
mkdir -p "$LOG_DIR" && touch "$SCITEX_WRITER_GLOBAL_LOG_FILE"
# Shell options
set -e
set -o pipefail
# Default values for arguments
no_figs=false
no_tables=false
do_verbose=false
draft_mode=false
dark_mode=${SCITEX_WRITER_DARK_MODE:-false}
usage() {
echo ""
echo -e "${BOLD_CYAN}━━━ compile_revision.sh ━━━${NC}"
echo -e "${GRAY}Compile revision response letter${NC}"
echo ""
echo -e "${BOLD_CYAN}━━━ Structure ━━━${NC}"
echo -e " ${GREEN}03_revision/${NC}"
echo -e " contents/"
echo -e " ${YELLOW}introduction.tex${NC} ${GRAY}# Response letter introduction${NC}"
echo -e " ${YELLOW}conclusion.tex${NC} ${GRAY}# Response letter conclusion${NC}"
echo -e " editor/ ${GRAY}# Editor comments & responses${NC}"
echo -e " ${YELLOW}E_01_comments.tex${NC} ${GRAY}# Copy of editor's email/comment${NC}"
echo -e " ${YELLOW}E_01_response.tex${NC} ${GRAY}# Author's response${NC}"
echo -e " ${YELLOW}E_01_revision.tex${NC} ${GRAY}# Actual manuscript changes (with \\\\DIFadd{}, \\\\DIFdel{})${NC}"
echo -e " reviewer1/ ${GRAY}# Reviewer 1 comments & responses${NC}"
echo -e " ${YELLOW}R1_01_comments.tex${NC} ${GRAY}# Copy of reviewer's comment${NC}"
echo -e " ${YELLOW}R1_01_response.tex${NC} ${GRAY}# Author's response${NC}"
echo -e " ${YELLOW}R1_01_revision.tex${NC} ${GRAY}# Actual manuscript changes${NC}"
echo -e " reviewer2/ ${GRAY}# Reviewer 2 comments & responses${NC}"
echo -e " ${YELLOW}R2_01_comments.tex${NC} ${GRAY}# Copy of reviewer's comment${NC}"
echo -e " ${YELLOW}R2_01_response.tex${NC} ${GRAY}# Author's response${NC}"
echo -e " ${YELLOW}R2_01_revision.tex${NC} ${GRAY}# Actual manuscript changes${NC}"
echo -e " ${GRAY}revision.pdf${NC} ${GRAY}# Output${NC}"
echo ""
echo -e "${BOLD_CYAN}━━━ File Types ━━━${NC}"
echo -e " ${GREEN}*_comments.tex${NC} Copy of reviewer/editor email or comment"
echo -e " ${GREEN}*_response.tex${NC} Author's response explaining changes"
echo -e " ${GREEN}*_revision.tex${NC} Actual manuscript changes with diff markup:"
echo -e " ${GRAY}\\\\DIFadd{added text}${NC} ${GRAY}# Shows added text${NC}"
echo -e " ${GRAY}\\\\DIFdel{deleted text}${NC} ${GRAY}# Shows deleted text${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}03_revision:${NC}"
echo -e " ${GRAY}$PROJECT_ROOT/03_revision/contents/${NC}introduction.tex"
echo -e " ${GRAY}$PROJECT_ROOT/03_revision/contents/${NC}conclusion.tex"
echo -e " ${GRAY}$PROJECT_ROOT/03_revision/contents/editor/${NC}E_*_comments.tex"
echo -e " ${GRAY}$PROJECT_ROOT/03_revision/contents/editor/${NC}E_*_response.tex"
echo -e " ${GRAY}$PROJECT_ROOT/03_revision/contents/editor/${NC}E_*_revision.tex"
echo -e " ${GRAY}$PROJECT_ROOT/03_revision/contents/reviewer1/${NC}R1_*_comments.tex"
echo -e " ${GRAY}$PROJECT_ROOT/03_revision/contents/reviewer1/${NC}R1_*_response.tex"
echo -e " ${GRAY}$PROJECT_ROOT/03_revision/contents/reviewer1/${NC}R1_*_revision.tex"
echo -e " ${GRAY}$PROJECT_ROOT/03_revision/contents/reviewer2/${NC}R2_*_comments.tex"
echo -e " ${GRAY}$PROJECT_ROOT/03_revision/contents/reviewer2/${NC}R2_*_response.tex"
echo -e " ${GRAY}$PROJECT_ROOT/03_revision/contents/reviewer2/${NC}R2_*_revision.tex"
echo ""
echo -e "${BOLD_CYAN}━━━ Options ━━━${NC}"
echo " -nf, --no_figs Skip figure processing (~4s faster)"
echo " -nt, --no_tables Skip table processing (~4s faster)"
echo " -d, --draft Single-pass compilation (~5s faster)"
echo " -dm, --dark_mode Dark mode: black background, white text"
echo " -q, --quiet Minimal output"
echo " -h, --help Show this help"
echo ""
echo -e "${GRAY}Note: Options accept both hyphens and underscores${NC}"
echo -e "${GRAY}Note: Revision documents skip diff generation (changes shown inline)${NC}"
echo ""
echo -e "${BOLD_CYAN}━━━ Document Structure (base.tex) ━━━${NC}"
echo -e " ${GRAY}$PROJECT_ROOT/03_revision/${NC}base.tex"
echo -e " Controls section order via \\\\input{} commands:"
echo -e " ${GRAY}\\\\input{./03_revision/contents/${NC}introduction${GRAY}}${NC}"
echo -e " ${GRAY}\\\\input{./03_revision/contents/editor/${NC}E_01_comments${GRAY}}${NC} ${GRAY}# Reviewer's comment${NC}"
echo -e " ${GRAY}\\\\input{./03_revision/contents/editor/${NC}E_01_response${GRAY}}${NC} ${GRAY}# Your response${NC}"
echo -e " ${GRAY}\\\\input{./03_revision/contents/editor/${NC}E_01_revision${GRAY}}${NC} ${GRAY}# Manuscript changes${NC}"
echo -e " ${GRAY}\\\\input{./03_revision/contents/reviewer1/${NC}R1_01_comments${GRAY}}${NC}"
echo -e " ${GRAY}\\\\input{./03_revision/contents/reviewer1/${NC}R1_01_response${GRAY}}${NC}"
echo -e " ${GRAY}\\\\input{./03_revision/contents/reviewer1/${NC}R1_01_revision${GRAY}}${NC}"
echo -e " ${GRAY}\\\\input{./03_revision/contents/${NC}conclusion${GRAY}}${NC}"
echo -e " To add/remove sections: edit base.tex \\\\input{} lines"
echo -e " Comment out with %% to disable a section"
echo ""
echo -e "${BOLD_CYAN}━━━ Managing Bibliography ━━━${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_revision.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 ;;
-nf | --no-figs) no_figs=true ;;
-nt | --no-tables) no_tables=true ;;
-d | --draft) draft_mode=true ;;
-dm | --dark-mode) dark_mode=true ;;
-v | --verbose) do_verbose=true ;;
-q | --quiet) do_verbose=false ;;
*)
echo "Unknown option: $1"
usage
;;
esac
shift
done
}
{
parse_arguments "$@"
# Log command options
options_display=""
$no_figs && options_display="${options_display} --no_figs"
$no_tables && options_display="${options_display} --no_tables"
$draft_mode && options_display="${options_display} --draft"
$dark_mode && options_display="${options_display} --dark_mode"
$do_verbose && options_display="${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
# 1. Check dependencies
log_stage_start "Dependency Check"
./scripts/shell/modules/check_dependancy_commands.sh
if [ $? -ne 0 ]; then
echo -e "${RED}ERRO: Dependency check failed${NC}"
exit 1
fi
log_stage_end "Dependency Check"
# 2. Merge bibliography files if multiple exist
log_stage_start "Bibliography Merge"
./scripts/shell/modules/merge_bibliographies.sh
log_stage_end "Bibliography Merge"
# 3. Apply citation style from config
log_stage_start "Citation Style"
./scripts/shell/modules/apply_citation_style.sh
log_stage_end "Citation Style"
# 3. Check revision structure
log_stage_start "Revision Structure Check"
echo_info "Checking revision response structure..."
# Expected structure with simplified naming (allowing optional descriptive suffixes):
# Editor: E_01_comments[_description].tex, E_01_response[_description].tex, ...
# Reviewer1: R1_01_comments[_description].tex, R1_01_response[_description].tex, ...
# Reviewer2: R2_01_comments[_description].tex, R2_01_response[_description].tex, ...
# Examples:
# E_01_comments_about-methodology.tex
# R1_02_response_statistical-analysis.tex
check_revision_files() {
local dir="$1"
local prefix="$2" # E, R1, or R2
local name="$3" # editor, reviewer1, reviewer2 for display
if [ ! -d "$dir" ]; then
echo -e "${YELLOW}WARN: Directory $dir not found${NC}"
return 1
fi
echo -e "${BLUE} Checking $name responses...${NC}"
# Check for comment/response pairs with simplified naming (supporting descriptive suffixes)
local found_files=0
for comment_file in "$dir"/${prefix}_*_comments*.tex; do
if [ -f "$comment_file" ]; then
# Extract the base ID (e.g., E_01, R1_02)
local base_id=$(echo "$(basename $comment_file)" | sed -E "s/(${prefix}_[0-9]+)_comments.*/\1/")
# Look for corresponding response file (may have different description)
local response_found=false
for response_file in "$dir"/${base_id}_response*.tex; do
if [ -f "$response_file" ]; then
echo -e "${GREEN} ✓ $(basename $comment_file) & $(basename $response_file)${NC}"
found_files=$((found_files + 1))
response_found=true
break
fi
done
if [ "$response_found" = false ]; then
echo -e "${YELLOW} ⚠ Missing response for: $(basename $comment_file)${NC}"
fi
fi
done
if [ $found_files -eq 0 ]; then
echo -e "${YELLOW} No comment/response pairs found in $dir${NC}"
else
echo -e "${GREEN} Found $found_files comment/response pair(s)${NC}"
fi
return 0
}
# Check each reviewer directory with simplified prefixes
check_revision_files "./03_revision/contents/editor" "E" "Editor"
check_revision_files "./03_revision/contents/reviewer1" "R1" "Reviewer 1"
check_revision_files "./03_revision/contents/reviewer2" "R2" "Reviewer 2"
log_stage_end "Revision Structure Check"
# Run independent processing in parallel for speed
parallel_start=$(date +%s)
timestamp=$(date '+%H:%M:%S')
echo_info "[$timestamp] Starting: Parallel Processing (Figures, Tables)"
# Create temp files for parallel job outputs
temp_dir=$(mktemp -d)
fig_log="$temp_dir/figures.log"
tbl_log="$temp_dir/tables.log"
# Run both in parallel
(
./scripts/shell/modules/process_figures.sh "$no_figs" false false false >"$fig_log" 2>&1
echo $? >"$temp_dir/fig_exit"
) &
fig_pid=$!
(
./scripts/shell/modules/process_tables.sh "$no_tables" >"$tbl_log" 2>&1
echo $? >"$temp_dir/tbl_exit"
) &
tbl_pid=$!
# Wait for all parallel jobs
wait $fig_pid $tbl_pid
# Display outputs in order
echo_info " Figure Processing:"
cat "$fig_log" | sed 's/^/ /'
echo_info " Table Processing:"
cat "$tbl_log" | sed 's/^/ /'
# Check exit codes
fig_exit=$(cat "$temp_dir/fig_exit")
tbl_exit=$(cat "$temp_dir/tbl_exit")
rm -rf "$temp_dir"
# Fail if any job failed
if [ "$fig_exit" -ne 0 ] || [ "$tbl_exit" -ne 0 ]; then
echo_error "Parallel processing failed (fig=$fig_exit, tbl=$tbl_exit)"
exit 1
fi
parallel_end=$(date +%s)
parallel_elapsed=$((parallel_end - parallel_start))
total_elapsed=$((parallel_end - COMPILATION_START_TIME))
timestamp=$(date '+%H:%M:%S')
echo_success "[$timestamp] Completed: Parallel Processing (${parallel_elapsed}s elapsed, ${total_elapsed}s total)"
# Compile structure
log_stage_start "TeX Compilation (Structure)"
./scripts/shell/modules/compilation_structure_tex_to_compiled_tex.sh
log_stage_end "TeX Compilation (Structure)"
# Compile to PDF
log_stage_start "PDF Generation"
./scripts/shell/modules/compilation_compiled_tex_to_compiled_pdf.sh
log_stage_end "PDF Generation"
# Skip diff generation for revision (revision document already shows changes inline)
echo_info "Skipping diff generation (revision document shows changes inline)"
# Archive
log_stage_start "Archive/Versioning"
./scripts/shell/modules/process_archive.sh
log_stage_end "Archive/Versioning"
# Cleanup
log_stage_start "Cleanup"
./scripts/shell/modules/cleanup.sh
log_stage_end "Cleanup"
# Final steps
log_stage_start "Directory Tree"
./scripts/shell/modules/custom_tree.sh
log_stage_end "Directory Tree"
# Logging
echo
final_time=$(date +%s)
total_compilation_time=$((final_time - COMPILATION_START_TIME))
echo_success "===================================================="
echo_success "TOTAL COMPILATION TIME: ${total_compilation_time}s"
echo_success "===================================================="
echo_success "PDF: $SCITEX_WRITER_COMPILED_PDF"
} 2>&1 | tee -a "$LOG_PATH" "$SCITEX_WRITER_GLOBAL_LOG_FILE"
# EOF
/