#!/bin/bash
# -*- coding: utf-8 -*-
# Timestamp: 2026-02-10
# File: scripts/shell/export_arxiv.sh
# Purpose: Package manuscript as arXiv-ready tarball
# Usage: export_arxiv.sh [--output-dir DIR]
set -euo pipefail
SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
PROJECT_ROOT="$(cd "$SCRIPT_DIR/../.." && pwd)"
GREEN='\033[0;32m'
YELLOW='\033[1;33m'
RED='\033[0;31m'
GRAY='\033[0;90m'
NC='\033[0m'
OUTPUT_DIR="${PROJECT_ROOT}/01_manuscript/export"
# Parse arguments
while [[ $# -gt 0 ]]; do
case "$1" in
-h | --help)
echo "Usage: $(basename "$0") [--output-dir DIR]"
echo ""
echo "Package the compiled manuscript as an arXiv-ready tarball."
echo ""
echo "Prerequisites:"
echo " Run 'make manuscript-compile' first to generate the flattened"
echo " manuscript.tex and .bbl file."
echo ""
echo "Options:"
echo " --output-dir DIR Export directory (default: 01_manuscript/export/)"
echo " -h, --help Show this help"
echo ""
echo "Output:"
echo " <output-dir>/manuscript.tar.gz arXiv-ready tarball"
echo ""
echo "The tarball contains:"
echo " manuscript.tex Flattened source with rewritten paths"
echo " manuscript.bbl Pre-compiled bibliography"
echo " bibliography.bib Source bibliography (fallback)"
echo " figures/ Figure JPGs"
echo " wordcounts/ Word count files"
echo ""
echo "Environment:"
echo " SCITEX_WRITER_EXPORT_DIR Override default output directory"
exit 0
;;
--output-dir)
OUTPUT_DIR="$2"
shift 2
;;
*)
echo -e "${RED}Unknown option: $1${NC}" >&2
echo "Use --help for usage." >&2
exit 1
;;
esac
done
# Allow env var override
OUTPUT_DIR="${SCITEX_WRITER_EXPORT_DIR:-$OUTPUT_DIR}"
# ============================================================================
# Validation
# ============================================================================
echo -e "${YELLOW}=== SciTeX Writer: arXiv Export ===${NC}"
echo ""
MANUSCRIPT_TEX="${PROJECT_ROOT}/01_manuscript/manuscript.tex"
MANUSCRIPT_DIR="${PROJECT_ROOT}/01_manuscript"
FIG_DIR="${PROJECT_ROOT}/01_manuscript/contents/figures/caption_and_media/jpg_for_compilation"
WORDCOUNT_DIR="${PROJECT_ROOT}/01_manuscript/contents/wordcounts"
BIB_FILE="${PROJECT_ROOT}/00_shared/bib_files/bibliography.bib"
# Check flattened tex exists
if [ ! -f "$MANUSCRIPT_TEX" ]; then
echo -e "${RED}Error: $MANUSCRIPT_TEX not found.${NC}" >&2
echo "Run 'make manuscript-compile' first." >&2
exit 1
fi
# Find .bbl file (could be in logs/ or manuscript dir)
BBL_FILE=""
for candidate in \
"${MANUSCRIPT_DIR}/logs/manuscript.bbl" \
"${MANUSCRIPT_DIR}/manuscript.bbl" \
"${MANUSCRIPT_DIR}/logs/"*.bbl; do
if [ -f "$candidate" ]; then
BBL_FILE="$candidate"
break
fi
done
if [ -z "$BBL_FILE" ]; then
echo -e "${YELLOW}Warning: No .bbl file found. Bibliography may not render on arXiv.${NC}"
echo "Ensure 'make manuscript-compile' ran bibtex successfully."
fi
# ============================================================================
# Export
# ============================================================================
# Clean and create export directory
rm -rf "$OUTPUT_DIR"
mkdir -p "$OUTPUT_DIR/figures" "$OUTPUT_DIR/wordcounts"
echo -e "${GRAY} Export directory: $OUTPUT_DIR${NC}"
# 1. Copy and transform manuscript.tex
cp "$MANUSCRIPT_TEX" "$OUTPUT_DIR/manuscript.tex"
TEX="$OUTPUT_DIR/manuscript.tex"
# Rewrite figure paths: ./01_manuscript/contents/figures/caption_and_media/jpg_for_compilation/ -> figures/
sed -i 's|./01_manuscript/contents/figures/caption_and_media/jpg_for_compilation/|figures/|g' "$TEX"
# Rewrite wordcount paths: ./01_manuscript/contents/wordcounts/ -> wordcounts/
sed -i 's|./01_manuscript/contents/wordcounts/|wordcounts/|g' "$TEX"
# Fix bibliography path: 01_manuscript/contents/bibliography -> bibliography
sed -i 's|\\bibliography{01_manuscript/contents/bibliography}|\\bibliography{bibliography}|g' "$TEX"
# Comment out supplementary link (fails without supplementary .aux)
sed -i 's|^\\link\[supple-\]|% [arXiv export] \\link[supple-]|g' "$TEX"
# Remove bashful package (may fail on arXiv - runs shell commands)
if grep -q 'bashful' "$TEX"; then
sed -i 's|\\usepackage\(\[.*\]\)\{0,1\}{.*bashful.*}|% [arXiv export] bashful removed (shell commands not supported)|g' "$TEX"
echo -e "${YELLOW} Note: bashful package removed (not supported on arXiv)${NC}"
fi
echo -e "${GREEN} [OK] manuscript.tex (paths rewritten)${NC}"
# 2. Copy figure JPGs
fig_count=0
if [ -d "$FIG_DIR" ]; then
for jpg in "$FIG_DIR"/*.jpg; do
[ -f "$jpg" ] || continue
cp "$jpg" "$OUTPUT_DIR/figures/"
fig_count=$((fig_count + 1))
done
fi
echo -e "${GREEN} [OK] figures/ ($fig_count files)${NC}"
# 3. Copy wordcount files
wc_count=0
if [ -d "$WORDCOUNT_DIR" ]; then
for wc in "$WORDCOUNT_DIR"/*.txt; do
[ -f "$wc" ] || continue
cp "$wc" "$OUTPUT_DIR/wordcounts/"
wc_count=$((wc_count + 1))
done
fi
echo -e "${GREEN} [OK] wordcounts/ ($wc_count files)${NC}"
# 4. Copy .bbl file
if [ -n "$BBL_FILE" ]; then
cp "$BBL_FILE" "$OUTPUT_DIR/manuscript.bbl"
echo -e "${GREEN} [OK] manuscript.bbl${NC}"
fi
# 5. Copy bibliography.bib (fallback)
if [ -f "$BIB_FILE" ]; then
cp "$BIB_FILE" "$OUTPUT_DIR/bibliography.bib"
echo -e "${GREEN} [OK] bibliography.bib${NC}"
fi
# ============================================================================
# Create tarball
# ============================================================================
TARBALL="$OUTPUT_DIR/manuscript.tar.gz"
# Build file list for tarball
tar_files=("manuscript.tex")
[ -f "$OUTPUT_DIR/manuscript.bbl" ] && tar_files+=("manuscript.bbl")
[ -f "$OUTPUT_DIR/bibliography.bib" ] && tar_files+=("bibliography.bib")
[ -d "$OUTPUT_DIR/figures" ] && tar_files+=("figures/")
[ -d "$OUTPUT_DIR/wordcounts" ] && tar_files+=("wordcounts/")
# Create tarball from inside export dir so paths are relative
(cd "$OUTPUT_DIR" && tar czf manuscript.tar.gz "${tar_files[@]}")
echo ""
echo -e "${GREEN}=== Export Complete ===${NC}"
echo ""
echo -e " Tarball: ${GREEN}$TARBALL${NC}"
local_size=$(du -h "$TARBALL" | cut -f1)
echo -e " Size: $local_size"
echo ""
# List contents
echo -e "${GRAY} Contents:${NC}"
tar tzf "$TARBALL" | sort | while read -r f; do
echo -e " ${GRAY}$f${NC}"
done
echo ""
echo "Upload this tarball to https://arxiv.org/submit"
###% EOF
/