chore: 初始版本提交 - 简化架构 + 轮询改造

- 移除 Motia Streams 实时通信，改用 3 秒轮询
- 简化前端代码，移除冗余组件
- 简化后端架构，准备 FastAPI 重构
- 更新 pixi.toml 环境配置
- 保留 bttoxin_digger_v5_repro 作为参考文档

Co-Authored-By: Claude <noreply@anthropic.com>

scripts/bttoxin_shoter.py

@@ -397,7 +397,7 @@ def compute_similarity_weight(identity: float, coverage: float, hmm: bool) -> fl
 
 
 def parse_all_toxins(tsv_path: Path) -> pd.DataFrame:
-    df = pd.read_csv(tsv_path, sep="\t", dtype=str, low_memory=False)
+    df = pd.read_csv(tsv_path, sep="\t", dtype=str, engine="python")
     # Coerce needed fields
     for col in ["Identity", "Aln_length", "Hit_length"]:
         df[col] = pd.to_numeric(df[col], errors="coerce")
@@ -658,7 +658,13 @@ def main():
                 d = index.orders_for_name_or_backoff(fam)
             return bool(d)
         df = df[df.apply(_has_index_orders, axis=1)]
-    strains = sorted(df["Strain"].astype(str).unique().tolist())
+
+    # Handle empty DataFrame - preserve columns and create empty outputs
+    if df.shape[0] == 0:
+        print("[Shotter] No hits passed filters, creating empty output files")
+        strains: List[str] = []
+    else:
+        strains = sorted(df["Strain"].astype(str).unique().tolist())
 
     all_hits: List[ToxinHit] = []
     all_strain_scores: List[StrainScores] = []

scripts/run_single_fna_pipeline.py

@@ -46,6 +46,8 @@ from pathlib import Path
 from typing import Dict, Any, List
 
 # Import PixiRunner and command builders from scripts
+# Add scripts directory to path for pixi_runner import
+sys.path.insert(0, str(Path(__file__).parent))
 from pixi_runner import PixiRunner, build_shotter_command, build_plot_command
 
 

scripts/start_web.sh

@@ -0,0 +1,44 @@
+#!/bin/bash
+# Start both frontend and backend servers
+# Usage: ./scripts/start_web.sh [frontend_port] [backend_port]
+
+FRONTEND_PORT=${1:-5173}
+BACKEND_PORT=${2:-8000}
+
+echo "=========================================="
+echo "BtToxin Pipeline Web Services"
+echo "=========================================="
+echo "Frontend: http://localhost:${FRONTEND_PORT}"
+echo "Backend:  http://localhost:${BACKEND_PORT}"
+echo "=========================================="
+echo ""
+echo "Starting services..."
+
+# Create jobs directory if it doesn't exist
+mkdir -p jobs
+echo "Jobs directory: $(pwd)/jobs"
+
+# Start backend in background
+echo "[Backend] Starting FastAPI server on port ${BACKEND_PORT}..."
+uvicorn web.backend.main:app --reload --host 0.0.0.0 --port ${BACKEND_PORT} &
+BACKEND_PID=$!
+
+# Wait for backend to be ready
+sleep 2
+
+# Start frontend
+echo "[Frontend] Starting Vite dev server on port ${FRONTEND_PORT}..."
+cd frontend && pnpm dev --host --port ${FRONTEND_PORT} &
+FRONTEND_PID=$!
+
+echo ""
+echo "=========================================="
+echo "Services started:"
+echo "  - Backend (PID: ${BACKEND_PID}) on port ${BACKEND_PORT}"
+echo "  - Frontend (PID: ${FRONTEND_PID}) on port ${FRONTEND_PORT}"
+echo "=========================================="
+echo "Press Ctrl+C to stop all services"
+echo ""
+
+# Wait for any process to exit
+wait