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_detection_and_numbering.py

@@ -0,0 +1,73 @@
+import pytest
+from rdkit import Chem
+
+from macro_lactone_toolkit import (
+    AmbiguousMacrolactoneError,
+    MacroLactoneAnalyzer,
+    MacrolactoneDetectionError,
+    MacrolactoneFragmenter,
+)
+
+from .helpers import build_ambiguous_smiles, build_macrolactone
+
+
+@pytest.mark.parametrize("ring_size", [12, 14, 16, 20])
+def test_analyzer_detects_supported_ring_sizes(ring_size: int):
+    built = build_macrolactone(ring_size)
+    analyzer = MacroLactoneAnalyzer()
+
+    assert analyzer.get_valid_ring_sizes(built.smiles) == [ring_size]
+
+
+def test_analyzer_rejects_non_lactone_macrocycle():
+    analyzer = MacroLactoneAnalyzer()
+
+    assert analyzer.get_valid_ring_sizes("C1CCCCCCCCCCC1") == []
+
+
+def test_fragmenter_auto_numbers_ring_with_expected_positions():
+    built = build_macrolactone(16, {5: "methyl"})
+    result = MacrolactoneFragmenter().number_molecule(built.mol)
+
+    assert result.ring_size == 16
+    assert result.position_to_atom == built.position_to_atom
+    assert set(result.position_to_atom) == set(range(1, 17))
+    assert result.atom_to_position == {
+        atom_idx: position for position, atom_idx in built.position_to_atom.items()
+    }
+
+    carbonyl_atom = built.mol.GetAtomWithIdx(result.position_to_atom[1])
+    assert carbonyl_atom.GetSymbol() == "C"
+    assert any(
+        bond.GetBondType() == Chem.BondType.DOUBLE and bond.GetOtherAtom(carbonyl_atom).GetSymbol() == "O"
+        for bond in carbonyl_atom.GetBonds()
+    )
+
+    ester_oxygen = built.mol.GetAtomWithIdx(result.position_to_atom[2])
+    assert ester_oxygen.GetSymbol() == "O"
+
+
+def test_fragmenter_requires_explicit_ring_size_for_ambiguous_molecule():
+    ambiguous_smiles = build_ambiguous_smiles()
+
+    with pytest.raises(AmbiguousMacrolactoneError):
+        MacrolactoneFragmenter().number_molecule(ambiguous_smiles)
+
+
+def test_fragmenter_raises_for_missing_macrolactone():
+    with pytest.raises(MacrolactoneDetectionError):
+        MacrolactoneFragmenter().number_molecule("CCO")
+
+
+def test_explicit_ring_size_selects_requested_ring():
+    built = build_macrolactone(14)
+    result = MacrolactoneFragmenter(ring_size=14).number_molecule(built.smiles)
+
+    assert result.ring_size == 14
+
+
+def test_explicit_ring_size_rejects_wrong_ring():
+    built = build_macrolactone(12)
+
+    with pytest.raises(MacrolactoneDetectionError):
+        MacrolactoneFragmenter(ring_size=16).number_molecule(built.smiles)