Drop orphaned child tracks instead of nulling secondary targets

A listed child_track_id can fail to match any first-step row (e.g. a
secondary absorbed below the tracking threshold at birth). The
parent->child left join in _add_secondary_attributes left these as
nulls, which silently became NaN once the parquet round-tripped
through the loader's float32 padding — poisoning every later secondary
slot in that step via the cumulative "remaining budget" in
encode_secondaries, while e_sec quietly undercounted and n_sec (from
len(child_track_ids)) overcounted relative to the actual lists.

Drop orphans from both the per-secondary lists and child_track_ids
itself so downstream counts stay consistent, and thread the per-file
orphaned count back through convert_steps_to_parquet so both the
sequential and --jobs>1 batch paths in `dwarf convert` can report an
aggregate total instead of relying on grepping printed output.

Also floors encode_secondaries' slot-0 budget to _EPS (matching the
i>0 branch), fixing a harmless but noisy 0/0 divide warning on
zero-secondary steps.

Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>

tests/test_steps_to_parquet.py

@@ -22,7 +22,8 @@ def _frame() -> pl.DataFrame:
 
 
 def test_e_sec_sums_child_first_step_energy():
-    out = steps_to_parquet._add_secondary_attributes(_frame())
+    out, n_orphaned = steps_to_parquet._add_secondary_attributes(_frame())
+    assert n_orphaned == 0
     e_sec = dict(
         zip(zip(out["track_id"], out["step_no"], out["event_id"]), out["e_sec"])
     )
@@ -31,7 +32,7 @@ def test_e_sec_sums_child_first_step_energy():
 
 
 def test_e_sec_zero_when_no_children():
-    out = steps_to_parquet._add_secondary_attributes(_frame())
+    out, _ = steps_to_parquet._add_secondary_attributes(_frame())
     childless = out.filter(
         (pl.col("event_id") == 0) & (pl.col("track_id") == 1) & (pl.col("step_no") == 1)
     )
@@ -40,6 +41,38 @@ def test_e_sec_zero_when_no_children():
 
 def test_e_sec_preserves_row_count_and_order():
     df = _frame()
-    out = steps_to_parquet._add_secondary_attributes(df)
+    out, _ = steps_to_parquet._add_secondary_attributes(df)
     assert out.height == df.height
     assert out["pre_E"].to_list() == df["pre_E"].to_list()
+
+
+def test_orphaned_child_track_is_dropped_not_nulled():
+    """A listed child_track_id with no first step of its own (e.g. absorbed
+    below the tracking threshold at birth) must not leave a null in
+    sec_E_list/sec_pdg_list/etc: that null turns into NaN once the parquet
+    round-trips through the loader, poisoning every later secondary slot in
+    the step via encode_secondaries' cumulative "remaining budget". It must
+    also be dropped from child_track_ids itself, so n_sec (len(child_track_ids)
+    downstream) matches the actual, orphan-free secondary lists."""
+    df = pl.DataFrame(
+        {
+            "event_id": [0, 0, 0],
+            "track_id": [1, 1, 2],
+            "step_no": [0, 1, 0],
+            "pre_E": [100.0, 80.0, 15.0],
+            "pdg": [11, 11, 22],
+            "pre_dx": [0.0, 0.0, 1.0],
+            "pre_dy": [0.0, 0.0, 0.0],
+            "pre_dz": [1.0, 1.0, 0.0],
+            # track 3 is listed as a child but never appears with its own step.
+            "child_track_ids": [[2, 3], [], []],
+        }
+    )
+    out, n_orphaned = steps_to_parquet._add_secondary_attributes(df)
+    row = out.filter((pl.col("event_id") == 0) & (pl.col("track_id") == 1) & (pl.col("step_no") == 0))
+
+    assert n_orphaned == 1
+    assert row["child_track_ids"].to_list() == [[2]]
+    assert row["e_sec"].item() == 15.0
+    assert row["sec_E_list"].to_list() == [[15.0]]
+    assert None not in row["sec_E_list"].item()