Error on missing secondary lists instead of silently zeroing Stage-2 targets

A parquet that carries child_track_ids/e_sec but was never run through the
parent->child join lacks the per-secondary columns (sec_E_list/sec_pdg_list/
sec_dir_list). build_features would fall back to all-zero sec_cont/sec_pdg_idx,
collapsing every secondary to PDG index 0 and a constant energy fraction — a
broken Stage 2 that trained with no error (single-species validation tables).

Add an opt-in require_secondaries flag that raises when n_sec > 0 but the lists
are absent, and enable it on the training paths (StreamingStepsDataset and the
normalizer-fit pass). giant predict keeps the default False for Stage-1-only use.

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>

tests/test_transforms.py

@@ -239,3 +239,51 @@ def test_build_features_clamps_n_sec_label_to_k_max():
 
     assert n_sec.max() <= K_MAX
     np.testing.assert_array_equal(n_sec, [0, 5, K_MAX])
+
+
+def _step_data_no_sec_lists(n_sec: np.ndarray) -> dict:
+    """Minimal build_features input with n_sec but no per-secondary list columns
+    (mimics a parquet that skipped the parent->child join)."""
+    N = len(n_sec)
+    rng = np.random.default_rng(0)
+    return {
+        "pdg": np.full(N, 11, dtype=np.int32),
+        "material": np.full(N, "PbWO4", dtype=object),
+        "pre_pos": rng.standard_normal((N, 3)).astype(np.float32),
+        "pre_E": np.full(N, 10.0, dtype=np.float32),
+        "pre_dir": np.tile(np.array([0, 0, 1], dtype=np.float32), (N, 1)),
+        "layer_id": np.zeros(N, dtype=np.int32),
+        "n_sec": np.asarray(n_sec, dtype=np.int32),
+        "e_sec": np.full(N, 1.0, dtype=np.float32),
+        "step_length": np.full(N, 1.0, dtype=np.float32),
+        "post_E": np.full(N, 9.0, dtype=np.float32),
+        "edep": np.full(N, 1.0, dtype=np.float32),
+        "post_dir": np.tile(np.array([0, 0, 1], dtype=np.float32), (N, 1)),
+        "post_pos": rng.standard_normal((N, 3)).astype(np.float32),
+    }
+
+
+def test_build_features_require_secondaries_raises_when_lists_missing():
+    """A parquet with n_sec > 0 but no per-secondary list columns was never run
+    through the parent->child join; require_secondaries must catch it instead of
+    silently zeroing every Stage-2 target (regression: this collapsed the
+    secondary species to a single PDG index during training)."""
+    data = _step_data_no_sec_lists(np.array([0, 2, 1]))
+    pdg_map, mat_map = {11: 0}, {"PbWO4": 0}
+
+    with pytest.raises(ValueError, match="per-secondary columns"):
+        build_features(data, pdg_map, mat_map, require_secondaries=True)
+
+
+def test_build_features_require_secondaries_ok_when_no_secondaries():
+    """require_secondaries only fires when secondaries actually exist; a file
+    with n_sec == 0 everywhere (e.g. Stage-1-only) must still load."""
+    data = _step_data_no_sec_lists(np.zeros(3, dtype=np.int32))
+    pdg_map, mat_map = {11: 0}, {"PbWO4": 0}
+
+    _, _, _, _, sec_cont, sec_pdg_idx, _, _ = build_features(
+        data, pdg_map, mat_map, require_secondaries=True
+    )
+
+    assert not sec_cont.any()
+    assert not sec_pdg_idx.any()