Merge reviewed checkpoint additions for release candidate

Test-side only; no production, manifest or pin change. Group A identity
checks (test_source_pin and the jets.py pins) are unchanged and stay
failing as recorded.

B test_refined_dfg: receipt/plan fixtures load the frozen manifest JSON
  that verify_source returns for a matching tree (frozen_manifest), and
  the two manifest-selection assertions call verify_source with only its
  working-tree hash comparison neutralised (selected_manifest), so the
  malformed/collision/observation-mode/checkout receipt checks run again.
  test_source_pin remains the single identity check.
C test_channel_root: int(owner)-1 (uint64-int became float on NumPy 1);
  test_shifted_storage: FP32 NaN fill so the arrays stay FP32. Both reach
  the intended immutable/representation/FP32/density checks.
D test_block_stepper fake gets _ddf_shifting; test_fine_surface_gpu sets
  _boundary_hosts/_level_jets instead of the read-only fine_boundary view;
  test_refinement_followup fake_backend sets _layouts/_ddf_shifting/
  _level_cfgs instead of the read-only fine_layout view (as reviewed in
  32da2d73).
E test_kernel_contracts_reject_before_upload: an inconsistent pair tau is
  now first rejected by the hierarchy chain check; the test asserts that
  rejection, then bypasses _check_chain to prove the per-level omega/tau
  guard still rejects, and asserts no mem_alloc/memcpy_htod in either case.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>

tests/integration/test_checkpoint_bodies_gpu.py

@@ -0,0 +1,66 @@
+"""Checkpoint save -> load round trip for a scene with passive bodies. Requires GPU.
+
+A fresh Simulation with the same scene, restored from the checkpoint must hold the same populations,
+flags, body count and step count, and must stay bitwise identical to the original
+after both continue for the same number of steps. Checkpoints with Jets are
+refused (documented limitation) and are not covered here.
+"""
+
+import os
+import tempfile
+import unittest
+
+import numpy as np
+
+from ._cases import make_sim
+
+# Three separated cylinders (pinball-like); cut-link receivers stay in bulk fluid.
+CIRCLES = (((40, 32), 6), ((56, 22), 6), ((56, 42), 6))
+
+
+def scene():
+    sim = make_sim()
+    sim.initialize()
+    for center, radius in CIRCLES:
+        sim.add_body("circle", center=center, radius=radius)
+    sim.sync_bodies()
+    return sim
+
+
+class CheckpointBodiesGPU(unittest.TestCase):
+    def test_round_trip_is_bitwise_and_continues_identically(self):
+        sim = scene()
+        sim.run(60)
+        with tempfile.NamedTemporaryFile(suffix=".h5", delete=False) as f:
+            path = f.name
+        restored = None
+        try:
+            saved = sim.save_checkpoint(path)
+            # The loader requires the same body count and geometry: rebuild the scene.
+            restored = scene()
+            restored.load_checkpoint(saved)
+
+            self.assertEqual(restored.bodies.count, len(CIRCLES))
+            self.assertEqual(restored.stepper.step_count, sim.stepper.step_count)
+            np.testing.assert_array_equal(restored.get_flags(), sim.get_flags())
+            a, b = sim.get_ddf(), restored.get_ddf()
+            self.assertEqual(a.dtype, b.dtype)
+            self.assertEqual(a.tobytes(), b.tobytes())
+
+            sim.run(40)
+            restored.run(40)
+            self.assertEqual(restored.stepper.step_count, sim.stepper.step_count)
+            a, b = sim.get_ddf(), restored.get_ddf()
+            self.assertTrue(np.isfinite(a).all())
+            self.assertEqual(a.tobytes(), b.tobytes())
+            for i in range(len(CIRCLES)):
+                self.assertTrue(np.all(np.isfinite(restored.read_force(i))))
+        finally:
+            if restored is not None:
+                restored.close()
+            os.unlink(path)
+            sim.close()
+
+
+if __name__ == "__main__":
+    unittest.main()

tests/unit/test_channel_root.py

@@ -50,7 +50,7 @@ def test_masks_and_minimal_footprint():
 def test_actual_closure_read_conflicts():
     pair, layout, targets = transfer((6, 6, 18, 14))
     validate_channel_transfers(pair, layout, targets)
-    for target in (layout.slot(layout.owner[5, -1]-1, 2),
+    for target in (layout.slot(int(layout.owner[5, -1]) - 1, 2),  # integer under NumPy 1 and 2
                    layout.slot(layout.owner[1, 4], 4),
                    layout.slot(layout.owner[-2, 4], 3)):
         with pytest.raises(ValueError, match="immutable"):

tests/unit/test_refined_dfg.py

@@ -141,16 +141,47 @@ def test_axis_specific_sampling_phase():
     np.testing.assert_allclose(fine_y - ((k + 43) - 0.5) * 0.00125, 0, atol=1e-15)
 
 
+def frozen_manifest(observation_mode):
+    """Frozen MRT manifest JSON as recorded, without hashing the working tree."""
+    name = "source_manifest_window.json" if observation_mode == "window" else "source_manifest_mrt.json"
+    return json.loads((r.HERE / "data/refined_dfg" / name).read_text())
+
+
+def selected_manifest(collision, observation_mode):
+    """verify_source's manifest selection with its working-tree hash comparison neutralised.
+
+    Source identity is owned by test_source_pin; this exercises only which frozen manifest
+    verify_source selects and returns for (collision, observation_mode).
+    """
+    from unittest.mock import patch
+
+    class Digest(str):
+        def __ne__(self, other):
+            return False
+
+    class Hash:
+        def __init__(self, data=b""):
+            pass
+
+        def hexdigest(self):
+            return Digest()
+
+    with patch.object(r.hashlib, "sha256", Hash):
+        return r.verify_source(r.DEFAULT_SOURCE, collision, observation_mode)
+
+
 def test_full_requires_completed_pilot():
     with unittest.TestCase().assertRaisesRegex(ValueError, "pilot-results"):
-        r.verify_pilot(None, r.verify_source(r.DEFAULT_SOURCE, "MRT", "window"))
+        r.verify_pilot(None, frozen_manifest("window"))
 
 
 def pilot_fixture(path, observation_mode="window", jet_scenario="none", case_selection="both", uniform_diameter=80, placement="wide"):
     """Synthetic contract fixture only; never a physical result or run receipt."""
+    # Receipt-logic fixture: the frozen manifest verify_source returns for a matching tree.
+    # Source identity itself is checked only by test_source_pin.
     manifest = (r.verify_source(r.DEFAULT_SOURCE, "MRT", "window", jet_scenario)
-                if observation_mode == "window" else
-                json.loads((r.HERE / "data/refined_dfg/source_manifest_mrt.json").read_text()))
+                if observation_mode == "window" and jet_scenario != "none" else
+                frozen_manifest(observation_mode))
     selection = dict(case_selection=case_selection, uniform_diameter=uniform_diameter, placement=placement)
     (path / "plan.json").write_text(
         json.dumps(
@@ -348,7 +379,7 @@ def test_record_actual_checkout_separately():
     actual = checkout_provenance(r.DEFAULT_SOURCE)
     assert len(actual["checkout_revision"]) == 40
     assert isinstance(actual["checkout_dirty"], bool)
-    assert r.verify_source(r.DEFAULT_SOURCE, "MRT", "window")["production_origin_commit"].startswith("d930")
+    assert selected_manifest("MRT", "window")["production_origin_commit"].startswith("d930")
 
 
 def test_window_plan_preserves_physics():
@@ -358,7 +389,7 @@ def test_window_plan_preserves_physics():
         assert baseline.pop("observation_mode") == "last_base_step"
         assert window.pop("observation_mode") == "window"
         assert baseline == window
-        assert r.verify_source(r.DEFAULT_SOURCE, collision, "window")["observation_mode"] == "window"
+        assert selected_manifest(collision, "window")["observation_mode"] == "window"
     with unittest.TestCase().assertRaises(ValueError):
         r.verify_source(r.DEFAULT_SOURCE, "MRT", "unknown")
 

tests/unit/test_shifted_storage.py

@@ -78,13 +78,15 @@ class ShiftedStorage(unittest.TestCase):
 
     def test_shifted_density_and_tag_validation(self):
         old,new = topology(A),topology(B)
-        a = tuple(np.where(m[None], np.float32(-.001), np.nan).repeat(9,axis=0) for m in old.leaf_masks)
+        a = tuple(np.where(m[None], np.float32(-.001), np.float32(np.nan)).repeat(9,axis=0)
+                  for m in old.leaf_masks)  # FP32 under NumPy 1 and 2 promotion rules
         remap(old,new,a)
         with self.assertRaisesRegex(ValueError,'representation'): remap(old,new,a,False)
         with self.assertRaisesRegex(ValueError,'FP32'): remap(old,new,tuple(x.astype(np.float64) for x in a))
         a[0][:,old.leaf_masks[0]] = -1
         with self.assertRaisesRegex(ValueError,'positive density'): remap(old,new,a)
-        rest = tuple(np.where(m[None],np.float32(0),np.nan).repeat(9,axis=0) for m in old.leaf_masks)
+        rest = tuple(np.where(m[None],np.float32(0),np.float32(np.nan)).repeat(9,axis=0)
+                     for m in old.leaf_masks)
         remap(old,new,rest)
         with self.assertRaisesRegex(ValueError,'positive density'):
             remap_synchronized(old,new,rest,base_count=7,level_steps=(7,14,28),phase='postcollision_g')

tests/validation/multigrid/test_block_stepper.py

@@ -192,6 +192,7 @@ class CpuContracts(unittest.TestCase):
         backend._lock = RLock()
         backend._status = "ready"
         backend._step_count = 0
+        backend._ddf_shifting = False  # unshifted storage, as for the default config
         backend._stream = Mock()
         backend._module = Mock()
         backend._copy = backend._step = Mock()

tests/validation/multigrid/test_fine_surface_gpu.py

@@ -282,7 +282,8 @@ def test_fine_surface_four_hops(speed):
 @pytest.mark.parametrize("missing", ["surface_velocity_gpu", "link_exchange_gpu"])
 def test_missing_surface_device_buffer_rejects_before_launch(missing):
     backend = implementation.FixedPatchStepper.__new__(implementation.FixedPatchStepper)
-    backend.fine_boundary = SimpleNamespace(objects=[object_spec(.002)])
+    backend._boundary_hosts = [None, SimpleNamespace(objects=[object_spec(.002)])]
+    backend._level_jets = [(), ()]
     backend._fine_curved = SimpleNamespace(fluid_idx_gpu=object(),
                                           surface_velocity_gpu=object(), link_exchange_gpu=object())
     setattr(backend._fine_curved, missing, None)

tests/validation/multigrid/test_refinement_followup.py

@@ -108,7 +108,9 @@ class FaultGuardsCPU(unittest.TestCase):
 
     def fake_backend(self):
         backend = PeriodicPatchStepper.__new__(PeriodicPatchStepper)
-        backend.fine_layout = None  # dense fine storage
+        backend._layouts = [None, None]  # dense storage on both levels
+        backend._ddf_shifting = False  # unshifted on every level, as _check_storage expects
+        backend._level_cfgs = [LBMConfig(nx=16, ny=16, viscosity=.1)] * 2  # ddf_shifting off
         backend.ctx = Mock(activate=nullcontext)
         backend._lock = RLock()
         backend._status = "ready"
@@ -158,10 +160,21 @@ class FaultGuardsCPU(unittest.TestCase):
             with self.assertRaisesRegex(RuntimeError, "four-cell"):
                 PeriodicPatchStepper(cfg, context=context, refinements=[(4, 4, 12, 12)])
         p = implementation.FixedPatch2D.from_config(cfg, (4, 4, 12, 12))
-        with patch.object(cuda, "Stream"), patch.object(implementation.FixedPatch2D, "from_config",
-                                                       return_value=replace(p, tau_coarse=.9)):
-            with self.assertRaisesRegex(RuntimeError, "omega/tau"):
+        from CelerisLab.lbm import hierarchy
+        bad = patch.object(implementation.FixedPatch2D, "from_config",
+                           return_value=replace(p, tau_coarse=.9))
+        # A pair tau inconsistent with its level config is rejected twice over, both before
+        # any device allocation or upload: first by the hierarchy chain check, and, if that
+        # is bypassed, by the per-level omega/tau check in _build_level.
+        with patch.object(cuda, "Stream"), bad, patch.object(cuda, "mem_alloc") as alloc, \
+                patch.object(cuda, "memcpy_htod") as upload:
+            with self.assertRaisesRegex(RuntimeError, "config chain is inconsistent"):
                 PeriodicPatchStepper(cfg, context=context, refinements=[p.bounds])
+            with patch.object(hierarchy, "_check_chain"), \
+                    self.assertRaisesRegex(RuntimeError, "omega/tau"):
+                PeriodicPatchStepper(cfg, context=context, refinements=[p.bounds])
+            alloc.assert_not_called()
+            upload.assert_not_called()
         module = Mock()
         module.get_global.return_value = (Mock(), 16)
         with patch.object(cuda, "Stream"), patch.object(compiler, "generate_config"), \