#!/usr/bin/env python3
"""Bttoxin single-FNA pipeline CLI (pixi-based).

This CLI uses pixi environments for execution:
- digger environment: BtToxin_Digger with bioconda dependencies
- pipeline environment: Python analysis with pandas/matplotlib/seaborn

Example:
    python -m bttoxin.cli --fna tests/test_data/HAN055.fna --lang zh
    
    # With custom database
    python -m bttoxin.cli --fna tests/test_data/HAN055.fna --bttoxin_db_dir /path/to/bt_toxin
"""
from __future__ import annotations

import argparse
from pathlib import Path
from .api import BtSingleFnaPipeline


def main() -> int:
    ap = argparse.ArgumentParser(description="Bttoxin single-FNA pipeline (Digger → Shotter → Plot → Bundle)")
    ap.add_argument("--fna", type=Path, required=True, help="Path to a single .fna file")
    ap.add_argument("--toxicity_csv", type=Path, default=Path("Data/toxicity-data.csv"))
    ap.add_argument("--base_workdir", type=Path, default=None, help="Base working dir (default: runs/bttoxin under repo root)")
    ap.add_argument("--bttoxin_db_dir", type=Path, default=None,
                    help="外部 bt_toxin 数据库目录路径（默认自动检测 external_dbs/bt_toxin）")
    ap.add_argument("--min_identity", type=float, default=0.0)
    ap.add_argument("--min_coverage", type=float, default=0.0)
    ap.add_argument("--disallow_unknown_families", action="store_true", default=False)
    ap.add_argument("--require_index_hit", action="store_true", default=False)
    ap.add_argument("--lang", type=str, choices=["zh", "en"], default="zh")
    ap.add_argument("--threads", type=int, default=4)
    args = ap.parse_args()

    pipe = BtSingleFnaPipeline(base_workdir=args.base_workdir)
    res = pipe.run(
        fna=args.fna,
        toxicity_csv=args.toxicity_csv,
        min_identity=args.min_identity,
        min_coverage=args.min_coverage,
        allow_unknown_families=not args.disallow_unknown_families,
        require_index_hit=args.require_index_hit,
        lang=args.lang,
        threads=args.threads,
        bttoxin_db_dir=args.bttoxin_db_dir,
    )

    if not res.get("ok"):
        print(f"[bttoxin-run] FAILED at stage={res.get('stage')}")
        return 1

    print("[bttoxin-run] ✓ Done")
    print(f" run_root:   {res['run_root']}")
    print(f" digger:     {res['digger_dir']}")
    print(f" shotter:    {res['shotter_dir']}")
    print(f" bundle:     {res['bundle']}")
    print(f" strain:     {res.get('strain','')}")
    return 0


if __name__ == "__main__":
    raise SystemExit(main())