docs: update README and add pixi-based tests

- Add property-based tests for PixiRunner
- Add HAN055.fna test data file
- Update README with pixi installation and usage guide
- Update .gitignore for pixi and test artifacts
- Update CLI to remove Docker-related arguments

bttoxin/cli.py

@@ -1,4 +1,16 @@
 #!/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
@@ -11,8 +23,8 @@ def main() -> int:
     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("--image", type=str, default="quay.io/biocontainers/bttoxin_digger:1.0.10--hdfd78af_0")
-    ap.add_argument("--platform", type=str, default="linux/amd64")
+    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)
@@ -21,7 +33,7 @@ def main() -> int:
     ap.add_argument("--threads", type=int, default=4)
     args = ap.parse_args()
 
-    pipe = BtSingleFnaPipeline(image=args.image, platform=args.platform, base_workdir=args.base_workdir)
+    pipe = BtSingleFnaPipeline(base_workdir=args.base_workdir)
     res = pipe.run(
         fna=args.fna,
         toxicity_csv=args.toxicity_csv,
@@ -31,6 +43,7 @@ def main() -> int:
         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"):