#!/bin/bash
# -*- coding: utf-8 -*-
# Timestamp: 2026-02-09
# File: scripts/shell/check_project.sh
# Purpose: Validate project structure, naming conventions, and references before compilation
# Usage: check_project.sh [-h|--help]
set -euo pipefail
SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
PROJECT_ROOT="$(cd "$SCRIPT_DIR/../.." && pwd)"
# Colors
GREEN='\033[0;32m'
YELLOW='\033[1;33m'
RED='\033[0;31m'
CYAN='\033[0;36m'
DIM='\033[0;90m'
BOLD='\033[1m'
NC='\033[0m'
# Counters
PASS_COUNT=0
WARN_COUNT=0
FAIL_COUNT=0
# Help
if [[ "${1:-}" == "-h" || "${1:-}" == "--help" ]]; then
echo "Usage: $(basename "$0") [-h|--help]"
echo ""
echo "Validate project structure and naming conventions before compilation."
echo ""
echo "Checks:"
echo " 1. Required content files exist"
echo " 2. Figure naming conventions (must start with [0-9]+_)"
echo " 3. Table naming conventions (must start with [0-9]+_)"
printf " 4. Caption content (\\\\caption{} required)\n"
echo " 5. Bibliography files"
printf " 6. Cross-references (\\\\ref{fig:*}, \\\\ref{tab:*})\n"
echo " 7. Float reference order (figures/tables referenced in sequence)"
printf " 8. References & citations (\\\\ref{}, \\\\cite{}, \\\\label{})\n"
echo ""
echo "Naming Rules:"
echo " Figures: 01_name.{jpg,png,tif,svg,...} + 01_name.tex (caption)"
echo " Panels: 01a_name.jpg (NO caption file for panels)"
echo " Tables: 01_name.csv + 01_name.tex (caption)"
echo " Bibtex: 00_shared/bib_files/*.bib (bibliography.bib is reserved)"
exit 0
fi
cd "$PROJECT_ROOT"
# --------------------------------------------------------------------------
# Helpers
# --------------------------------------------------------------------------
log_pass() {
echo -e " ${GREEN}[PASS]${NC} $1"
PASS_COUNT=$((PASS_COUNT + 1))
}
log_warn() {
echo -e " ${YELLOW}[WARN]${NC} $1"
WARN_COUNT=$((WARN_COUNT + 1))
}
log_fail() {
echo -e " ${RED}[FAIL]${NC} $1"
FAIL_COUNT=$((FAIL_COUNT + 1))
}
log_detail() {
echo -e " ${DIM}$1${NC}"
}
# --------------------------------------------------------------------------
# 1. Required content files
# --------------------------------------------------------------------------
check_required_files() {
local issues=()
local shared_files=(
"00_shared/title.tex"
"00_shared/authors.tex"
"00_shared/keywords.tex"
"00_shared/journal_name.tex"
)
local manuscript_files=(
"01_manuscript/base.tex"
"01_manuscript/contents/abstract.tex"
"01_manuscript/contents/introduction.tex"
"01_manuscript/contents/methods.tex"
"01_manuscript/contents/results.tex"
"01_manuscript/contents/discussion.tex"
)
for f in "${shared_files[@]}" "${manuscript_files[@]}"; do
if [ ! -f "$f" ]; then
issues+=("missing: $f")
fi
done
if [ ${#issues[@]} -eq 0 ]; then
log_pass "Required content files"
else
log_fail "Required content files"
for i in "${issues[@]}"; do
log_detail "$i"
done
fi
}
# --------------------------------------------------------------------------
# 2. Figure naming validation
# --------------------------------------------------------------------------
check_figures() {
local doc_dir="$1"
local doc_label="$2"
local fig_dir="$doc_dir/contents/figures/caption_and_media"
if [ ! -d "$fig_dir" ]; then
log_pass "Figure naming ($doc_label) - no figures directory"
return
fi
local issues=()
local media_exts="tif tiff jpg jpeg png svg mmd pptx pdf"
# Check media files that DON'T match required pattern
for f in "$fig_dir"/*; do
[ -e "$f" ] || continue
[ -d "$f" ] && continue # skip directories
local fname
fname=$(basename "$f")
local ext="${fname##*.}"
# Skip .tex files (checked separately), hidden files, templates
[[ "$fname" == *.tex ]] && continue
[[ "$fname" == .* ]] && continue
[[ "$fname" == templates ]] && continue
# Check if extension is a media type
local is_media=false
for mext in $media_exts; do
[[ "$ext" == "$mext" ]] && is_media=true && break
done
$is_media || continue
# Must start with digits
if ! [[ "$fname" =~ ^[0-9] ]]; then
issues+=("$fname: does not start with digits (will be ignored by compilation)")
fi
done
# Check main figures have caption files (skip panels)
for f in "$fig_dir"/[0-9]*; do
[ -e "$f" ] || continue
[ -d "$f" ] && continue
local fname
fname=$(basename "$f")
local ext="${fname##*.}"
[[ "$ext" == "tex" ]] && continue
local is_media=false
for mext in $media_exts; do
[[ "$ext" == "$mext" ]] && is_media=true && break
done
$is_media || continue
local base="${fname%.*}"
# Skip panels (they must NOT have captions)
if [[ "$base" =~ ^[0-9]+[a-zA-Z]_ ]]; then
# Check if panel incorrectly has a caption
if [ -f "$fig_dir/${base}.tex" ]; then
issues+=("$base.tex: panel caption file (will be auto-deleted during compilation)")
fi
continue
fi
# Main figure: must have caption
if [ ! -f "$fig_dir/${base}.tex" ]; then
issues+=("$fname: missing caption file ${base}.tex")
fi
done
# Check for orphaned caption files (tex with no media)
for f in "$fig_dir"/[0-9]*.tex; do
[ -e "$f" ] || continue
local fname
fname=$(basename "$f")
local base="${fname%.tex}"
# Skip panel patterns
[[ "$base" =~ ^[0-9]+[a-zA-Z]_ ]] && continue
local has_media=false
for mext in $media_exts; do
[ -f "$fig_dir/${base}.${mext}" ] && has_media=true && break
done
if ! $has_media; then
issues+=("$fname: orphaned caption (no matching media file)")
fi
done
if [ ${#issues[@]} -eq 0 ]; then
log_pass "Figure naming ($doc_label)"
else
log_warn "Figure naming ($doc_label)"
for i in "${issues[@]}"; do
log_detail "$i"
done
fi
}
# --------------------------------------------------------------------------
# 3. Table naming validation
# --------------------------------------------------------------------------
check_tables() {
local doc_dir="$1"
local doc_label="$2"
local tbl_dir="$doc_dir/contents/tables/caption_and_media"
if [ ! -d "$tbl_dir" ]; then
log_pass "Table naming ($doc_label) - no tables directory"
return
fi
local issues=()
# Check CSV/XLSX files that DON'T match required pattern
for f in "$tbl_dir"/*.{csv,xlsx,xls}; do
[ -e "$f" ] || continue
local fname
fname=$(basename "$f")
if ! [[ "$fname" =~ ^[0-9] ]]; then
issues+=("$fname: does not start with digits (will be ignored by compilation)")
fi
done
# Check data files have caption files
for f in "$tbl_dir"/[0-9]*.{csv,xlsx,xls}; do
[ -e "$f" ] || continue
local fname
fname=$(basename "$f")
local base="${fname%.*}"
if [ ! -f "$tbl_dir/${base}.tex" ]; then
issues+=("$fname: missing caption file ${base}.tex")
fi
done
# Check for orphaned caption files
for f in "$tbl_dir"/[0-9]*.tex; do
[ -e "$f" ] || continue
local fname
fname=$(basename "$f")
local base="${fname%.tex}"
local has_data=false
for dext in csv xlsx xls; do
[ -f "$tbl_dir/${base}.${dext}" ] && has_data=true && break
done
if ! $has_data; then
issues+=("$fname: orphaned caption (no matching CSV/XLSX)")
fi
done
if [ ${#issues[@]} -eq 0 ]; then
log_pass "Table naming ($doc_label)"
else
log_warn "Table naming ($doc_label)"
for i in "${issues[@]}"; do
log_detail "$i"
done
fi
}
# --------------------------------------------------------------------------
# 4. Caption content validation
# --------------------------------------------------------------------------
check_captions() {
local doc_dir="$1"
local doc_label="$2"
local issues=()
# Figure captions
local fig_dir="$doc_dir/contents/figures/caption_and_media"
if [ -d "$fig_dir" ]; then
for f in "$fig_dir"/[0-9]*.tex; do
[ -e "$f" ] || continue
local fname
fname=$(basename "$f")
local base="${fname%.tex}"
# Skip panels
[[ "$base" =~ ^[0-9]+[a-zA-Z]_ ]] && continue
if ! grep -q '\\caption{' "$f" 2>/dev/null; then
issues+=("figures/$fname: missing \\caption{}")
fi
done
fi
# Table captions
local tbl_dir="$doc_dir/contents/tables/caption_and_media"
if [ -d "$tbl_dir" ]; then
for f in "$tbl_dir"/[0-9]*.tex; do
[ -e "$f" ] || continue
local fname
fname=$(basename "$f")
if ! grep -q '\\caption{' "$f" 2>/dev/null; then
issues+=("tables/$fname: missing \\caption{}")
fi
done
fi
if [ ${#issues[@]} -eq 0 ]; then
log_pass "Caption content ($doc_label)"
else
log_warn "Caption content ($doc_label)"
for i in "${issues[@]}"; do
log_detail "$i"
done
fi
}
# --------------------------------------------------------------------------
# 5. Bibliography validation
# --------------------------------------------------------------------------
check_bibliography() {
local bib_dir="00_shared/bib_files"
local issues=()
if [ ! -d "$bib_dir" ]; then
log_fail "Bibliography files"
log_detail "directory not found: $bib_dir"
return
fi
# Count non-reserved bib files
local source_count=0
for f in "$bib_dir"/*.bib; do
[ -e "$f" ] || continue
local fname
fname=$(basename "$f")
[[ "$fname" == "bibliography.bib" ]] && continue
[[ "$fname" == "merged_all.bib" ]] && continue
[[ "$fname" == "enriched_all.bib" ]] && continue
[[ "$fname" == "enriched_all_v2.bib" ]] && continue
source_count=$((source_count + 1))
done
local total_bib=0
for f in "$bib_dir"/*.bib; do
[ -e "$f" ] || continue
total_bib=$((total_bib + 1))
done
if [ "$total_bib" -eq 0 ]; then
issues+=("no .bib files found in $bib_dir")
elif [ "$source_count" -eq 0 ] && [ -f "$bib_dir/bibliography.bib" ]; then
# Only bibliography.bib exists - that's fine for a template or simple project
:
fi
if [ ${#issues[@]} -eq 0 ]; then
log_pass "Bibliography files ($total_bib file(s))"
else
log_fail "Bibliography files"
for i in "${issues[@]}"; do
log_detail "$i"
done
fi
}
# --------------------------------------------------------------------------
# 6. Cross-reference check (sourced from module)
# --------------------------------------------------------------------------
# shellcheck disable=SC1091
source "$SCRIPT_DIR/modules/check_crossrefs.sh"
# --------------------------------------------------------------------------
# 7-8. Python-based checks (float order, references/citations)
# --------------------------------------------------------------------------
run_python_check() {
local script="$1"
[ -f "$script" ] && command -v python3 &>/dev/null || return 0
local output msg clean
output=$(python3 "$script" "$PROJECT_ROOT" 2>&1) || true
while IFS= read -r line; do
# Strip ANSI codes from Python output before re-wrapping
clean=$(printf '%s' "$line" | sed 's/\x1b\[[0-9;]*m//g')
case "$clean" in
*"[PASS]"*)
msg="${clean##*\[PASS\] }"
log_pass "$msg"
;;
*"[FAIL]"*)
msg="${clean##*\[FAIL\] }"
log_fail "$msg"
;;
*"[WARN]"*)
msg="${clean##*\[WARN\] }"
log_warn "$msg"
;;
*"[INFO]"*)
msg="${clean##*\[INFO\] }"
echo -e " ${DIM}[INFO] ${msg}${NC}"
;;
" "*)
msg="${clean#"${clean%%[! ]*}"}"
log_detail "$msg"
;;
esac
done <<<"$output"
}
# --------------------------------------------------------------------------
# Main
# --------------------------------------------------------------------------
echo ""
echo -e "${CYAN}${BOLD}=== SciTeX Writer: Project Check ===${NC}"
echo ""
check_required_files
# Check each document type
for doc_dir in 01_manuscript 02_supplementary; do
doc_label="${doc_dir#[0-9]*_}"
if [ -d "$doc_dir/contents" ]; then
check_figures "$doc_dir" "$doc_label"
check_tables "$doc_dir" "$doc_label"
check_captions "$doc_dir" "$doc_label"
check_crossrefs "$doc_dir" "$doc_label"
fi
done
check_bibliography
run_python_check "$SCRIPT_DIR/../python/check_float_order.py"
run_python_check "$SCRIPT_DIR/../python/check_references.py"
# Summary
echo ""
echo -e "${BOLD}Summary:${NC} ${GREEN}${PASS_COUNT} passed${NC}, ${YELLOW}${WARN_COUNT} warnings${NC}, ${RED}${FAIL_COUNT} errors${NC}"
if [ "$FAIL_COUNT" -gt 0 ]; then
echo ""
echo -e "${RED}Fix errors before compilation.${NC}"
exit 1
elif [ "$WARN_COUNT" -gt 0 ]; then
echo ""
echo -e "${YELLOW}Warnings may cause issues during compilation.${NC}"
exit 0
else
echo ""
echo -e "${GREEN}All checks passed.${NC}"
exit 0
fi
###% EOF
/