Add splicing module and related tests

- Add src/splicing/ module with scaffold_prep, fragment_prep, and engine
- Add tylosin_splicer.py entry script
- Add unit tests for splicing components

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

tests/test_env_integration.py

@@ -0,0 +1,39 @@
+import sys
+import os
+from pathlib import Path
+
+# Add SIME to path
+SIME_PATH = "/home/zly/project/SIME"
+if SIME_PATH not in sys.path:
+    sys.path.append(SIME_PATH)
+
+# Add project root to path so we can import 'src'
+PROJECT_ROOT = str(Path(__file__).parent.parent)
+if PROJECT_ROOT not in sys.path:
+    sys.path.append(PROJECT_ROOT)
+
+def test_imports():
+    """Verify that we can import from both local project and SIME."""
+    print(f"sys.path: {sys.path}")
+    
+    # 1. Test local import from src
+    try:
+        # Correct function name based on file inspection
+        from src.ring_numbering import assign_ring_numbering
+        assert callable(assign_ring_numbering)
+        print("Successfully imported src.ring_numbering.assign_ring_numbering")
+    except ImportError as e:
+        print(f"Failed to import src.ring_numbering: {e}")
+        raise
+
+    # 2. Test SIME import
+    try:
+        from utils.mole_predictor import ParallelBroadSpectrumPredictor
+        assert ParallelBroadSpectrumPredictor is not None
+        print("Successfully imported ParallelBroadSpectrumPredictor from utils.mole_predictor")
+    except ImportError as e:
+        print(f"Failed to import from SIME: {e}")
+        raise
+
+if __name__ == "__main__":
+    test_imports()