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

tests/test_splicing_engine.py

@@ -1,77 +1,51 @@
 import pytest
 from rdkit import Chem
-from src.splicing.engine import splice_molecule
+
+from macro_lactone_toolkit import MacrolactoneFragmenter
+from macro_lactone_toolkit.splicing.engine import splice_molecule
+from macro_lactone_toolkit.splicing.scaffold_prep import prepare_macrolactone_scaffold
+
+from .helpers import build_macrolactone, canonicalize
+
 
 def test_splice_benzene_methyl():
-    """
-    Test splicing a benzene scaffold (isotope 1) with a methyl fragment.
-    Scaffold: c1ccccc1[1*] (Phenyl radical-ish dummy)
-    Fragment: C* (Methyl radical-ish dummy)
-    Result: Cc1ccccc1 (Toluene)
-    """
     scaffold = Chem.MolFromSmiles("c1ccccc1[1*]")
     fragment = Chem.MolFromSmiles("C*")
-    
-    assert scaffold is not None
-    assert fragment is not None
-    
+
     product = splice_molecule(scaffold, fragment, position=1)
-    
-    # Expected result: Toluene
-    expected_smiles = "Cc1ccccc1"
-    expected_mol = Chem.MolFromSmiles(expected_smiles)
-    expected_canonical = Chem.MolToSmiles(expected_mol, isomericSmiles=True)
-    
-    product_canonical = Chem.MolToSmiles(product, isomericSmiles=True)
-    
-    assert product_canonical == expected_canonical
+
+    assert canonicalize(product) == canonicalize("Cc1ccccc1")
+
 
 def test_splice_missing_isotope():
-    """Test that error is raised if the requested position is not found on scaffold."""
-    scaffold = Chem.MolFromSmiles("c1ccccc1[2*]") # Isotope 2
+    scaffold = Chem.MolFromSmiles("c1ccccc1[2*]")
     fragment = Chem.MolFromSmiles("C*")
-    
+
     with pytest.raises(ValueError, match="Scaffold dummy atom with isotope 1 not found"):
         splice_molecule(scaffold, fragment, position=1)
 
+
 def test_splice_no_fragment_dummy():
-    """Test that error is raised if fragment has no dummy atom."""
     scaffold = Chem.MolFromSmiles("c1ccccc1[1*]")
-    fragment = Chem.MolFromSmiles("C") # Methane, no dummy
-    
+    fragment = Chem.MolFromSmiles("C")
+
     with pytest.raises(ValueError, match="Fragment does not contain a dummy atom"):
         splice_molecule(scaffold, fragment, position=1)
 
-def test_complex_splicing():
-    """
-    Test splicing with more complex structures.
-    Scaffold: Pyridine derivative n1cccc1CC[1*]
-    Fragment: Cyclopropane C1CC1*
-    Result: n1cccc1CCC1CC1
-    """
-    scaffold = Chem.MolFromSmiles("n1cccc1CC[1*]")
-    fragment = Chem.MolFromSmiles("*C1CC1")
-    
-    product = splice_molecule(scaffold, fragment, position=1)
-    
-    expected = Chem.MolFromSmiles("n1cccc1CCC1CC1")
-    
-    assert Chem.MolToSmiles(product) == Chem.MolToSmiles(expected)
 
-def test_scaffold_with_multiple_different_dummies():
-    """
-    Test splicing when scaffold has multiple dummies with different isotopes.
-    Scaffold: [1*]c1ccccc1[2*]
-    Fragment: C*
-    Target: Splicing at 1 should leave [2*] intact.
-    """
-    scaffold = Chem.MolFromSmiles("[1*]c1ccccc1[2*]")
-    fragment = Chem.MolFromSmiles("C*")
-    
-    # Splice at 1
-    product = splice_molecule(scaffold, fragment, position=1)
-    
-    # Expected: Cc1ccccc1[2*]
-    expected = Chem.MolFromSmiles("Cc1ccccc1[2*]")
-    
-    assert Chem.MolToSmiles(product) == Chem.MolToSmiles(expected)
+def test_prepare_scaffold_and_reassemble_fragment():
+    built = build_macrolactone(16, {5: "ethyl"})
+    result = MacrolactoneFragmenter(ring_size=16).fragment_molecule(built.smiles, parent_id="reassemble")
+    fragment = next(fragment for fragment in result.fragments if fragment.cleavage_position == 5)
+
+    scaffold, dummy_map = prepare_macrolactone_scaffold(
+        built.smiles,
+        positions=[5],
+        ring_size=16,
+    )
+
+    assert 5 in dummy_map
+
+    product = splice_molecule(scaffold, Chem.MolFromSmiles(fragment.fragment_smiles_labeled), position=5)
+
+    assert canonicalize(product) == canonicalize(built.mol)