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_fragment_prep.py

@@ -1,95 +1,42 @@
 import pytest
 from rdkit import Chem
-from src.splicing.fragment_prep import activate_fragment
+
+from macro_lactone_toolkit.splicing.fragment_prep import activate_fragment
+
 
 def test_activate_smart_ethanol():
-    """Test 'smart' activation on Ethanol (CCO). Should attach to Oxygen."""
-    smiles = "CCO"
-    mol = activate_fragment(smiles, strategy="smart")
-    
-    # Check if we have a dummy atom
+    mol = activate_fragment("CCO", strategy="smart")
+
     assert mol is not None
-    assert mol.GetNumAtoms() == 4  # C, C, O, *
-    
-    # Check if the dummy atom is attached to Oxygen
-    # Find the dummy atom
-    dummy_atom = None
-    for atom in mol.GetAtoms():
-        if atom.GetSymbol() == '*':
-            dummy_atom = atom
-            break
-    
-    assert dummy_atom is not None
-    
-    # Check neighbors of dummy atom
-    neighbors = dummy_atom.GetNeighbors()
-    assert len(neighbors) == 1
-    assert neighbors[0].GetSymbol() == 'O'
-    
-    # Check output SMILES format
-    out_smiles = Chem.MolToSmiles(mol)
-    assert '*' in out_smiles
+    assert mol.GetNumAtoms() == 4
+    dummy_atom = next(atom for atom in mol.GetAtoms() if atom.GetAtomicNum() == 0)
+    assert dummy_atom.GetNeighbors()[0].GetSymbol() == "O"
+    assert "*" in Chem.MolToSmiles(mol)
+
 
 def test_activate_smart_amine():
-    """Test 'smart' activation on Ethylamine (CCN). Should attach to Nitrogen."""
-    smiles = "CCN"
-    mol = activate_fragment(smiles, strategy="smart")
-    
-    assert mol is not None
-    
-    # Find the dummy atom
-    dummy_atom = None
-    for atom in mol.GetAtoms():
-        if atom.GetSymbol() == '*':
-            dummy_atom = atom
-            break
-            
-    assert dummy_atom is not None
-    neighbors = dummy_atom.GetNeighbors()
-    assert neighbors[0].GetSymbol() == 'N'
+    mol = activate_fragment("CCN", strategy="smart")
+
+    dummy_atom = next(atom for atom in mol.GetAtoms() if atom.GetAtomicNum() == 0)
+    assert dummy_atom.GetNeighbors()[0].GetSymbol() == "N"
+
 
 def test_activate_random_pentane():
-    """Test 'random' activation on Pentane (CCCCC). Should attach to a Carbon."""
-    smiles = "CCCCC"
-    # Seed is not easily passed to the function unless we add it to the signature or fix it inside.
-    # For this test, any Carbon is fine.
-    mol = activate_fragment(smiles, strategy="random")
-    
-    assert mol is not None
-    assert mol.GetNumAtoms() == 6 # 5 C + 1 *
-    
-    dummy_atom = None
-    for atom in mol.GetAtoms():
-        if atom.GetSymbol() == '*':
-            dummy_atom = atom
-            break
-            
-    assert dummy_atom is not None
-    neighbors = dummy_atom.GetNeighbors()
-    assert neighbors[0].GetSymbol() == 'C'
+    mol = activate_fragment("CCCCC", strategy="random")
+
+    assert mol.GetNumAtoms() == 6
+    dummy_atom = next(atom for atom in mol.GetAtoms() if atom.GetAtomicNum() == 0)
+    assert dummy_atom.GetNeighbors()[0].GetSymbol() == "C"
+
 
 def test_activate_smart_fallback():
-    """Test 'smart' fallback when no heteroatoms are found (e.g. Propane)."""
-    smiles = "CCC"
-    # Should fall back to finding a terminal carbon or random
-    # The requirement says "fall back to a terminal Carbon" or random. 
-    # Let's assume the implementation picks a terminal carbon if possible, or just behaves like random on C.
-    mol = activate_fragment(smiles, strategy="smart")
-    
-    assert mol is not None
-    dummy_atom = None
-    for atom in mol.GetAtoms():
-        if atom.GetSymbol() == '*':
-            dummy_atom = atom
-            break
-    
-    assert dummy_atom is not None
-    neighbor = dummy_atom.GetNeighbors()[0]
-    assert neighbor.GetSymbol() == 'C'
-    # Verify it's a valid molecule
+    mol = activate_fragment("CCC", strategy="smart")
+
+    dummy_atom = next(atom for atom in mol.GetAtoms() if atom.GetAtomicNum() == 0)
+    assert dummy_atom.GetNeighbors()[0].GetSymbol() == "C"
     assert Chem.SanitizeMol(mol) == Chem.SanitizeFlags.SANITIZE_NONE
 
+
 def test_invalid_smiles():
     with pytest.raises(ValueError):
         activate_fragment("NotASmiles", strategy="smart")
-