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/api.py

@@ -1,4 +1,10 @@
 #!/usr/bin/env python3
+"""Bttoxin Pipeline API (pixi-based).
+
+This module provides the API for running the BtToxin pipeline using pixi environments:
+- digger environment: BtToxin_Digger with bioconda dependencies
+- pipeline environment: Python analysis with pandas/matplotlib/seaborn
+"""
 from __future__ import annotations
 
 import logging
@@ -10,16 +16,15 @@ from types import SimpleNamespace
 from typing import Dict, Any, Optional
 import sys as _sys
 
-# Ensure repo-relative imports for backend and scripts when running from installed package
+# Ensure repo-relative imports for scripts when running from installed package
 _REPO_ROOT = Path(__file__).resolve().parents[1]
-_BACKEND_DIR = _REPO_ROOT / "backend"
 _SCRIPTS_DIR = _REPO_ROOT / "scripts"
-for _p in (str(_BACKEND_DIR), str(_SCRIPTS_DIR)):
+for _p in (str(_SCRIPTS_DIR),):
     if _p not in _sys.path:
         _sys.path.append(_p)
 
-# Import DockerContainerManager from backend
-from app.utils.docker_client import DockerContainerManager  # type: ignore
+# Import PixiRunner from scripts
+from pixi_runner import PixiRunner  # type: ignore
 
 logger = logging.getLogger(__name__)
 
@@ -45,21 +50,19 @@ def _lazy_import_plotter():
 
 
 class BtToxinRunner:
-    """Wrap BtToxin_Digger docker invocation for a single FNA."""
+    """Wrap BtToxin_Digger pixi invocation for a single FNA."""
 
     def __init__(
         self,
-        image: str = "quay.io/biocontainers/bttoxin_digger:1.0.10--hdfd78af_0",
-        platform: str = "linux/amd64",
         base_workdir: Optional[Path] = None,
+        bttoxin_db_dir: Optional[Path] = None,
     ) -> None:
-        self.image = image
-        self.platform = platform
         if base_workdir is None:
             base_workdir = _REPO_ROOT / "runs" / "bttoxin"
         self.base_workdir = base_workdir
         self.base_workdir.mkdir(parents=True, exist_ok=True)
-        self.mgr = DockerContainerManager(image=self.image, platform=self.platform)
+        self.bttoxin_db_dir = bttoxin_db_dir
+        self.runner = PixiRunner(pixi_project_dir=_REPO_ROOT, env_name="digger")
 
     def _prepare_layout(self, fna_path: Path) -> tuple[Path, Path, Path, Path, str]:
         if not fna_path.exists():
@@ -86,13 +89,14 @@ class BtToxinRunner:
         fna_path = Path(fna_path)
         input_dir, digger_out, log_dir, run_root, sample_name = self._prepare_layout(fna_path)
         logger.info("Start BtToxin_Digger: %s (sample=%s)", fna_path, sample_name)
-        result = self.mgr.run_bttoxin_digger(
+        result = self.runner.run_bttoxin_digger(
             input_dir=input_dir,
             output_dir=digger_out,
             log_dir=log_dir,
             sequence_type=sequence_type,
             scaf_suffix=fna_path.suffix or ".fna",
             threads=threads,
+            bttoxin_db_dir=self.bttoxin_db_dir,
         )
         toxins_dir = digger_out / "Results" / "Toxins"
         files = {
@@ -234,15 +238,13 @@ class PlotAPI:
 
 
 class BtSingleFnaPipeline:
-    """End-to-end single-FNA pipeline: Digger → Shotter → Plot → Bundle."""
+    """End-to-end single-FNA pipeline: Digger → Shotter → Plot → Bundle (pixi-based)."""
 
     def __init__(
         self,
-        image: str = "quay.io/biocontainers/bttoxin_digger:1.0.10--hdfd78af_0",
-        platform: str = "linux/amd64",
         base_workdir: Optional[Path] = None,
     ) -> None:
-        self.digger = BtToxinRunner(image=image, platform=platform, base_workdir=base_workdir)
+        self.base_workdir = base_workdir
         self.shotter = ShotterAPI()
         self.plotter = PlotAPI()
 
@@ -256,8 +258,11 @@ class BtSingleFnaPipeline:
         require_index_hit: bool = False,
         lang: str = "zh",
         threads: int = 4,
+        bttoxin_db_dir: Optional[Path] = None,
     ) -> Dict[str, Any]:
-        dig = self.digger.run_single_fna(fna_path=fna, sequence_type="nucl", threads=threads)
+        # Create digger runner with optional external database
+        digger = BtToxinRunner(base_workdir=self.base_workdir, bttoxin_db_dir=bttoxin_db_dir)
+        dig = digger.run_single_fna(fna_path=fna, sequence_type="nucl", threads=threads)
         if not dig.get("success"):
             return {"ok": False, "stage": "digger", "detail": dig}
         run_root: Path = dig["run_root"]