feat(toolkit): ship macro_lactone_toolkit package

Unify macrolactone detection, numbering, fragmentation, and
splicing under the installable macro_lactone_toolkit package.

- replace legacy src.* modules with the new package layout
- add analyze/number/fragment CLI entrypoints and pixi tasks
- migrate tests, README, and scripts to the new package API

scripts/tylosin_splicer.py

@@ -1,10 +1,34 @@
-#!/usr/bin/env python
-"""
-Tylosin Splicing System - Main Entry Point
-"""
+from __future__ import annotations
+
+import argparse
+
+from rdkit import Chem
+
+from macro_lactone_toolkit.splicing import (
+    activate_fragment,
+    prepare_macrolactone_scaffold,
+    splice_molecule,
+)
+
+
+def main() -> None:
+    parser = argparse.ArgumentParser(description="Splice a fragment onto a prepared macrolactone scaffold.")
+    parser.add_argument("--scaffold-smiles", required=True)
+    parser.add_argument("--fragment-smiles", required=True)
+    parser.add_argument("--position", required=True, type=int)
+    parser.add_argument("--ring-size", type=int, default=None)
+    parser.add_argument("--strategy", default="smart")
+    args = parser.parse_args()
+
+    scaffold, _ = prepare_macrolactone_scaffold(
+        args.scaffold_smiles,
+        positions=[args.position],
+        ring_size=args.ring_size,
+    )
+    fragment = activate_fragment(args.fragment_smiles, strategy=args.strategy)
+    product = splice_molecule(scaffold, fragment, position=args.position)
+    print(Chem.MolToSmiles(product, isomericSmiles=True))
 
-def main():
-    print("Hello from Tylosin Splicer")
 
 if __name__ == "__main__":
     main()