test: run history-independent identity checks before the history lookup

Manifests and receipts unchanged. Each of the 8 group-A identity tests now
extracts its manifest's recorded commit and verifies hashes there instead of
against the current checkout. Tamper assertions and runner source refusals are
kept; missing recorded history is an explicit failure, not a skip or repin.

docs/supported_settings.md

@@ -0,0 +1,87 @@
+# Supported settings: 2D Jet + fixed multilevel refinement (candidate c95a7ba)
+
+Every entry names the guard that enforces it (file:line at c95a7ba) and, where one
+exists, an existing test that exercises it. A setting not listed here is not
+claimed. Observations at the end are tied to the exact case in which they were
+measured; they are not general bounds.
+
+## Lattice, storage, collision
+
+| Setting | Supported | Guard |
+|---|---|---|
+| Dimension / lattice | 2D D2Q9 only (3D refinement is future work) | `lbm/refinement.py:65`, `lbm/kernels/blocks.cu:25`, `lbm/kernels/refinement.cu:26` |
+| Precision / streaming | FP32 storage, double buffer | same guards |
+| Collision on refinement levels | SRT or MRT; TRT and LES rejected | `lbm/refinement.py:65` (re-checked for fine boundaries at `lbm/refinement.py:457`) |
+| Shifted (ddf_shifting) storage | only when every level is blocked; dense or mixed rejected | `lbm/refinement_stepper.py:198`, `:469`; `lbm/kernels/refinement.cu:26` (dense patch kernel unshifted only) |
+| Fine relaxation | 1/tau_fine must lie inside the configured omega guards | `lbm/refinement.py:80` |
+| Uniform blocked backend `PeriodicBlockStepper` | doubly periodic, SRT only, stationary passive circles | `lbm/block_stepper.py:84`, `:91`, `:45`-`:67` |
+
+Tests: `tests/unit/test_refinement_mrt.py`, `tests/validation/multigrid/test_refinement_mrt_gpu.py`,
+`tests/unit/test_shifted_storage.py`, `tests/unit/test_shifted_block_operators.py`.
+
+## Refinement hierarchy (`FixedPatchStepper(cfg, *, context, refinements, ...)`)
+
+| Setting | Supported | Guard |
+|---|---|---|
+| Depth | at least one refinement level; one entry per level in `level_blocks`/`level_objects`/`level_jets` | `lbm/refinement_stepper.py:72`, `:75` |
+| Single L1 rectangle | two-coarse-cell margin to the domain edge | `lbm/refinement.py:73` |
+| Several L1 rectangles (union) | require `level_blocks[0]` and `level_blocks[1]`; transfers must close (dependency checks, no fixed gap rule) | `lbm/refinement_stepper.py:84`; `lbm/refinement.py:283`-`:295` |
+| Nested levels | depth >= 3 must be all blocked; a blocked level requires blocked levels below; a scalar child needs a scalar parent | `lbm/refinement_stepper.py:82`, `:87`; `lbm/hierarchy.py:54` |
+| Nested transfer support | child only over inherited ACTIVE cells, donors/receivers uncovered ACTIVE, no child over the parent restriction footprint | `lbm/refinement.py:391`-`:407` |
+| Tile shape | positive `(by, bx)`; the level allocation must be divisible by the tile (no partial tiles yet) | `lbm/refinement_stepper.py:78`, `lbm/refinement.py:246` (shape); `lbm/blocks.py:134` (divisibility) |
+| Coarse boundary | `periodic`, `slot_reservoir` or `channel` | `lbm/refinement_stepper.py:177` |
+| `slot_reservoir` | on-site velocity bottom slot, reservoir top, velocity 0, 2 <= slot width < nx, patch rows 4..ny-4 | `lbm/refinement_stepper.py:205`, `:212`; `lbm/refinement.py:546` |
+| `channel` | all levels blocked; Zou-He inlet, pressure-NEQ outlet, stationary bounce-back walls; transfers away from the closure | `lbm/channel.py:22`, `:26`, `:43`, `:54` |
+| Explosion | `constant` (default); `projected_linear` only periodic, all-blocked SRT, no bodies/Jets, no LES (experimental) | `lbm/refinement_stepper.py:188`, `:193` |
+| L2 runtime remap (`remap_child`) | periodic three-level L2 sets only, no L0/L1 bodies, identical pinned boundary | `lbm/refinement_stepper.py:557`, `:567`-`:581` |
+
+Tests: `tests/unit/test_refinement_three_level_multipatch.py`, `tests/validation/multigrid/test_refinement_multipatch.py`,
+`test_refinement_three_level.py`, `test_refinement_three_level_multipatch_gpu.py`, `test_refinement_blocked_base.py`,
+`test_refinement_blocked_fine.py`, `test_channel_root_gpu.py`, `tests/unit/test_channel_root.py`,
+`tests/unit/test_projected_pair_stepper.py`, `test_runtime_child_remap_gpu.py`, `test_pinned_body_remap_gpu.py`.
+
+## Bodies and Jets on refined levels
+
+| Setting | Supported | Guard |
+|---|---|---|
+| Bodies | stationary circles without sensor/force-region roles, entirely inside the patch union, fully resolved, disjoint, stencil away from the two-hop transfer footprint | `lbm/refinement.py:474`-`:542` |
+| Level | not on L0; only on the finest level of a nested hierarchy | `lbm/refinement_stepper.py:80`, `:89` |
+| Jet condition | velocity only; `pressure` is reserved and raises NotImplementedError | `body/jets.py:148`, `:150` |
+| Jet geometry | each Jet selects resolved links of exactly one stationary body; no Jet/Jet or Jet/SurfaceActuation overlap; abs(amplitude) < 1 lattice | `body/jets.py:155`, `:175`, `:177`, `:255`, `:261`, `:263` |
+| Jets with shifted storage | only in the all-blocked stepper with SRT and no LES | `body/jets.py:249` |
+| SurfaceActuation | unshifted storage only | `body/objects.py:155` |
+| Raw boundary exchange (force) | blocked body levels only; the window ledger requires `observe_raw_exchange` | `lbm/refinement_stepper.py:264`, `:269` |
+| Checkpoint with Jets | refused | `simulation.py:687` |
+
+Raw exchange is the cut-link momentum reaction (wall + aperture), not a validated
+nozzle thrust or stress load. Jet amplitude is a lattice velocity, not a flow rate.
+
+Tests: `tests/unit/test_jets.py`, `test_jets_review.py`, `test_shifted_jets.py`, `test_raw_exchange.py`,
+`tests/validation/multigrid/test_refinement_jets.py`, `test_shifted_jets_gpu.py`, `test_raw_exchange_gpu.py`,
+`test_exchange_window.py`, `test_fine_surface_gpu.py`.
+
+## Observations from specific tested cases (not general bounds)
+
+- SRT channel root vs uniform OneStep, strict-parity test
+  `tests/validation/multigrid/test_channel_root_gpu.py::ChannelRootGPU::test_uniform_matched_root`:
+  in one of its 18 sub-cases (2 storage modes x 3 profile/clamp/damp settings x 3 blocks; which
+  one is not recorded), 1 of the 4320 compared values differs, max abs 2.33e-10, max rel 1.77e-7
+  (about 2 ULP). The test remains failed; its cause and any general bound are unresolved.
+- MRT root parity test
+  `tests/validation/multigrid/test_refinement_mrt_gpu.py::RefinementMRTGPU::test_uniform_matched_mrt_root`
+  (12 sub-cases: 2 storage modes x 2 profiles x 3 blocks, default outlet settings) passed bitwise
+  in the Horsea focused GPU run at K1 7813334 (2026-10-21).
+- Periodic Taylor-Green Re 100, measured at 36ffc8b1 (V3 matched pair, N128 depth 2):
+  every per-sample screen passed; the constant explosion's aggregate worst velocity L2,
+  0.004418, exceeds its preregistered 0.002 budget, while projected_linear passed that budget.
+- Curved-wall pressure (pilot harness, exact-q analytic annulus, tau 0.8): the coarse swirl r1
+  case exceeded its terminal density-gain cap (1.105e-4 vs 1e-4), so the frozen 9-case matrix
+  is NOT_ESTABLISHED. No validated fix exists. This is a pilot harness, not production code.
+- DFG 2D-1 Re 20 (V4, SRT, t* 60, pressure-NEQ outlet and local Zou-He inlet): refined and uniform
+  runs were NOT_STEADY under the frozen steady rule, so no interval verdict was given.
+
+## Not supported in this release
+
+3D, dynamic/automatic AMR (tagging, time-varying hierarchies beyond `remap_child`),
+moving bodies on refined levels, pressure Jets, Jet checkpoints, LES or TRT on refined
+levels, partial (non-dividing) tiles.

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/historical_tree.py

@@ -0,0 +1,46 @@
+"""Check historical source manifests against their own recorded commit, not today's checkout."""
+
+import io
+from pathlib import Path
+import subprocess
+import tarfile
+
+ROOT = Path(__file__).resolve().parents[2]
+
+
+def _require(commit):
+    """Missing recorded history is an explicit failure, never a skip or a repin."""
+    found = subprocess.run(
+        ["git", "-C", str(ROOT), "cat-file", "-e", commit + "^{commit}"],
+        capture_output=True,
+    )
+    if found.returncode:
+        raise AssertionError(
+            f"Required history missing: commit {commit} is not in this clone; "
+            "fetch it instead of repinning or substituting"
+        )
+
+
+def tracked(commit, prefix="src"):
+    """Tracked paths under prefix at the recorded commit."""
+    _require(commit)
+    return set(
+        subprocess.check_output(
+            ["git", "-C", str(ROOT), "ls-tree", "-r", "--name-only", commit, prefix],
+            text=True,
+        ).splitlines()
+    )
+
+
+def historical_tree(commit, dest):
+    """Extract the tracked tree of the recorded commit into dest."""
+    _require(commit)
+    archive = subprocess.check_output(
+        ["git", "-C", str(ROOT), "archive", "--format=tar", commit]
+    )
+    dest = Path(dest)
+    dest.mkdir(parents=True, exist_ok=True)
+    extra = {"filter": "data"} if hasattr(tarfile, "data_filter") else {}
+    with tarfile.open(fileobj=io.BytesIO(archive)) as tar:
+        tar.extractall(dest, **extra)
+    return dest

tests/unit/test_jet_circle_cv.py

@@ -8,6 +8,7 @@ import numpy as np
 ROOT = Path(__file__).resolve().parents[2]
 REPO = ROOT
 sys.path.insert(0, str(ROOT / "tests/validation"))
+sys.path.insert(0, str(ROOT / "tests/unit"))
 sys.path.insert(0, str(REPO / "src"))
 from run_jet_circle_cv import (
     CX,
@@ -19,6 +20,7 @@ from run_jet_circle_cv import (
     cv_from_macros,
     aperture_probe,
     measured_aperture_flux,
+    PIN,
     verify,
 )
 
@@ -166,7 +168,13 @@ class Host(unittest.TestCase):
         self.assertEqual(a["steps"] * 4, b["steps"])
 
     def test_source_pin(self):
-        verify(REPO)
+        from tempfile import TemporaryDirectory
+        from historical_tree import historical_tree
+
+        with self.assertRaisesRegex(RuntimeError, "Source hash mismatch"):
+            verify(REPO)
+        with TemporaryDirectory() as directory:
+            verify(historical_tree(PIN, directory))
 
 
 if __name__ == "__main__":

tests/unit/test_les_flow_runner.py

@@ -15,6 +15,10 @@ sys.path.insert(0, str(Path(__file__).resolve().parents[1] / "validation"))
 from run_uniform_les_flow import source_guard, decode_macros, HERE, HEADER
 
 ROOT = HERE.parents[1]
+sys.path.insert(0, str(ROOT / "tests/unit"))
+from historical_tree import historical_tree, tracked
+
+A135 = "a135252ae78b47b57d7e77d19001700b3bedac8b"
 
 
 class GuardTests(unittest.TestCase):
@@ -42,19 +46,23 @@ class GuardTests(unittest.TestCase):
             decode_macros(invalid, w, cx, cy)
 
     def test_current_corrected_pins(self):
-        self.assertEqual(
-            source_guard(ROOT, "corrected", "a135252")["base_commit"],
-            "a135252ae78b47b57d7e77d19001700b3bedac8b",
-        )
+        with TemporaryDirectory() as directory:
+            root = historical_tree(A135, directory)
+            with patch("run_uniform_les_flow.subprocess.check_output", return_value="historical-tree\n"):
+                identity = source_guard(root, "corrected", "a135252")
+            # base_commit comes from the pins file; the mock only feeds checkout_commit.
+            self.assertEqual(identity["base_commit"], A135)
+            self.assertEqual(identity["checkout_commit"], "historical-tree")
 
     def test_corrected_and_tamper_guard(self):
         pins = json.loads((HERE / "data/les_flow/source_pins_a135252.json").read_text())
         with TemporaryDirectory() as directory:
-            root = Path(directory)
+            origin = historical_tree(A135, Path(directory) / "origin")
+            root = Path(directory) / "fixture"
             for name in pins["sources"]:
                 dest = root / name
                 dest.parent.mkdir(parents=True, exist_ok=True)
-                shutil.copyfile(ROOT / name, dest)
+                shutil.copyfile(origin / name, dest)
             with patch(
                 "run_uniform_les_flow.subprocess.check_output",
                 return_value="isolated-fixture\n",
@@ -87,23 +95,26 @@ class GuardTests(unittest.TestCase):
 
     def test_current_manifest_pins_actual_corrected_tree(self):
         pins = json.loads((HERE / "data/les_flow/source_pins_a135252.json").read_text())
-        tracked = subprocess.check_output(["git", "-C", str(ROOT), "ls-files", "src"], text=True)
-        self.assertEqual(set(pins["sources"]), set(tracked.splitlines()))
-        for name, expected in pins["sources"].items():
-            self.assertEqual(hashlib.sha256((ROOT / name).read_bytes()).hexdigest(), expected)
-        self.assertEqual(pins["sources"][HEADER], pins["candidate_header_sha256"])
-        self.assertNotEqual(pins["sources"][HEADER], pins["baseline_header_sha256"])
-        with self.assertRaisesRegex(RuntimeError, "Source pin mismatch"):
-            source_guard(ROOT, "baseline", "a135252")
+        self.assertEqual(pins["base_commit"], A135)
+        self.assertEqual(set(pins["sources"]), tracked(A135))
+        with TemporaryDirectory() as directory:
+            root = historical_tree(A135, directory)
+            for name, expected in pins["sources"].items():
+                self.assertEqual(hashlib.sha256((root / name).read_bytes()).hexdigest(), expected)
+            self.assertEqual(pins["sources"][HEADER], pins["candidate_header_sha256"])
+            self.assertNotEqual(pins["sources"][HEADER], pins["baseline_header_sha256"])
+            with self.assertRaisesRegex(RuntimeError, "Source pin mismatch"):
+                source_guard(root, "baseline", "a135252")
 
     def test_named_baseline_accepts_only_reversed_header(self):
         pins = json.loads((HERE / "data/les_flow/source_pins_a135252.json").read_text())
         with TemporaryDirectory() as directory:
-            root = Path(directory)
+            origin = historical_tree(A135, Path(directory) / "origin")
+            root = Path(directory) / "fixture"
             for name in pins["sources"]:
                 dest = root / name
                 dest.parent.mkdir(parents=True, exist_ok=True)
-                shutil.copyfile(ROOT / name, dest)
+                shutil.copyfile(origin / name, dest)
             subprocess.run(["git", "apply", "--reverse", str(HERE / "les/data/smagorinsky_normalization.patch")], cwd=root, check=True)
             with patch("run_uniform_les_flow.subprocess.check_output", return_value="baseline-fixture\n"):
                 source_guard(root, "baseline", "a135252")

tests/unit/test_re100.py

@@ -5,6 +5,7 @@ import pytest
 
 ROOT = Path(__file__).resolve().parents[2]
 sys.path.insert(0, str(ROOT / "tests/validation"))
+sys.path.insert(0, str(ROOT / "tests/unit"))
 import re100_helpers as h
 import periodic as p
 
@@ -62,13 +63,16 @@ def test_periodic_synthetic():
     assert not p.assess(rows()[:100])["periodic"]
 
 
-def test_production_unmodified():
+def test_production_unmodified(tmp_path):
+    from historical_tree import historical_tree
+
     m = json.loads(
         (ROOT / "tests/validation/data/dfg_re100/source_manifest.json").read_text()
     )
     assert m["commit"] == h.PIN
+    origin = historical_tree(m["commit"], tmp_path)
     for name, digest in m["production_sha256"].items():
-        assert hashlib.sha256((ROOT / name).read_bytes()).hexdigest() == digest, name
+        assert hashlib.sha256((origin / name).read_bytes()).hexdigest() == digest, name
 
 
 def test_reference():

tests/unit/test_refined_dfg.py

@@ -7,7 +7,10 @@ import numpy as np
 import unittest
 
 sys.path.insert(0, str(Path(__file__).resolve().parents[1] / "validation"))
+sys.path.insert(0, str(Path(__file__).resolve().parent))
 import run_refined_dfg as r
+from historical_tree import historical_tree
+from tempfile import TemporaryDirectory
 
 h, periodic = r.helpers(r.DEFAULT_SOURCE)
 
@@ -17,11 +20,24 @@ def test_source_pin():
     assert historical["commit"].startswith("cd3a657")
     mrt_history = json.loads((r.HERE / "data/refined_dfg/source_manifest_mrt.json").read_text())
     assert mrt_history["commit"].startswith("3ea131e")
-    assert r.verify_source(r.DEFAULT_SOURCE, "MRT", "window")["commit"].startswith("a233c90")
+    with unittest.TestCase().assertRaisesRegex(RuntimeError, "Source mismatch"):
+        r.verify_source(r.DEFAULT_SOURCE, "MRT", "window")
     with unittest.TestCase().assertRaisesRegex(RuntimeError, "Source mismatch"):
         r.verify_source(r.DEFAULT_SOURCE, "MRT")
     with unittest.TestCase().assertRaisesRegex(RuntimeError, "Source mismatch"):
         r.verify_source(r.DEFAULT_SOURCE, "SRT")
+    with TemporaryDirectory() as directory:
+        for collision, mode, prefix in (
+            ("SRT", "last_base_step", "cd3a657"),
+            ("MRT", "last_base_step", "3ea131e"),
+            ("MRT", "window", "a233c90"),
+        ):
+            name = {"SRT": "source_manifest.json", "MRT": "source_manifest_mrt.json"}[collision]
+            name = "source_manifest_window.json" if mode == "window" else name
+            commit = json.loads((r.HERE / "data/refined_dfg" / name).read_text())["commit"]
+            assert commit.startswith(prefix)
+            root = historical_tree(commit, Path(directory) / commit)
+            assert r.verify_source(root, collision, mode)["commit"] == commit
 
 
 def test_matched_units_and_planes():

tests/unit/test_validation_source_provenance.py

@@ -12,13 +12,15 @@ from source_provenance import checkout_provenance
 import re100_helpers
 import run_jet_circle_cv
 
+sys.path.insert(0, str(ROOT / "tests/unit"))
+from historical_tree import historical_tree, tracked
+
 ORIGIN = "47b05bc8abfc957fe876b0c63bdb386e3c6cbaa5"
 
 
-def test_manifests_cover_current_source_and_preserve_origin():
-    names = subprocess.check_output(
-        ["git", "-C", str(ROOT), "ls-files", "src"], text=True
-    ).splitlines()
+def test_manifests_cover_current_source_and_preserve_origin(tmp_path):
+    assert re100_helpers.PIN == run_jet_circle_cv.PIN == ORIGIN
+    manifests = {}
     for group, hashes_key, revision_key in (
         ("dfg_re100", "production_sha256", "commit"),
         ("jet_circle_cv", "files", "revision"),
@@ -29,18 +31,22 @@ def test_manifests_cover_current_source_and_preserve_origin():
             ).read_text()
         )
         assert manifest[revision_key] == ORIGIN
-        assert set(manifest[hashes_key]) == set(names)
         assert manifest["source_origin_commits"][-1] == ORIGIN
         assert (
             manifest["historical_checkpoints"]["production"]
             == "d79e3f6f0a424f5bcc3a1a6d610313e49daf97a2"
         )
         assert "not inherited from d79" in manifest["experiment"]
-        for name, expected in manifest[hashes_key].items():
+        manifests[group] = manifest[hashes_key]
+    # History-dependent checks last, so a missing commit masks nothing above.
+    names = tracked(ORIGIN)
+    origin = historical_tree(ORIGIN, tmp_path)
+    for group, hashes in manifests.items():
+        assert set(hashes) == set(names), group
+        for name, expected in hashes.items():
             assert (
-                hashlib.sha256((ROOT / name).read_bytes()).hexdigest() == expected
+                hashlib.sha256((origin / name).read_bytes()).hexdigest() == expected
             ), name
-    assert re100_helpers.PIN == run_jet_circle_cv.PIN == ORIGIN
 
 
 def test_runtime_checkout_identity_is_separate_from_source_origin(tmp_path):