fix(ddt): Lagrangian history writes use the modern data layout (BF-04)

[lmoresi]

Summary

Fixes audit finding SWARM-06 (Track 0 item BF-04, docs/reviews/2026-07/REMEDIATION-WORKLIST.md / SWARM-SUBSYSTEM-REVIEW.md).

The Lagrangian history-update blocks in systems/ddt.py (Lagrangian and Lagrangian_Swarm) wrote per-component particle history as psi_star_0[i, j].data[:] = .... Indexing a SwarmVariable goes through MathematicalMixin.__getitem__ and returns a symbolic component (an UnderworldAppliedFunction) with no .data attribute, so the first update_pre_solve of any user-configured Lagrangian history raised AttributeError and the advertised feature (solver_template.py:92-93, solvers.py:196-197) was unusable. The only prior test (test_0007) set _history_initialised manually and never advected, so the crash was uncovered.

Reproduction

Confirmed on this branch's base (development@6451896a) by swapping the baseline ddt.py into site-packages and running the new regression tests:

AttributeError: '{\left<u^{ * }\right>}' object has no attribute 'data'
  at underworld3/systems/ddt.py:3197 (Lagrangian.initialise_history)

All three new tests fail with this error against the old write path, and pass with the fix.

Fix

At the four sites (previously ddt.py:3197, 3281, 3549, 3638-3639):

• Component writes go through the canonical (N, components) storage: psi_star_0.data[:, var._data_layout(i, j)].
• Particle coordinates are read from swarm._particle_coordinates.data instead of the deprecated swarm.data.
• The deprecated swarm.access() context wrappers around these blocks are removed.

These blocks now sit directly on the modern data-access pattern, so the Wave B migration (WB-02) has nothing left to do at these lines. No solver numerics are touched.

Tests

New: tests/test_0857_lagrangian_ddt_advecting_history.py (level_1, tier_a)

• Lagrangian scalar: auto-initialise, history shift, swarm advection; asserts history values equal psi at each particle's pre-advection position (coordinate-based, ordering-robust).
• Lagrangian vector: asserts each component lands in its own _data_layout column.
• Lagrangian_Swarm: step-averaged (phi = 1/2) blending across two updates with a user-driven swarm advection in between; asserts blend and chain-copy values.

Gate results

• Serial level_1 and tier_a, pre-fix baseline (new file excluded): 295 passed, 7 skipped, 4 xfailed, 1 xpassed — green.
• Serial level_1 and tier_a, post-fix (new file included): 298 passed, 7 skipped, 4 xfailed, 1 xpassed — green.
• MPI np2: test_0857 3 passed; test_0855_oldframe_sl_traceback 5 passed; test_1054_advdiff_monotone_mode_kwarg 6 passed, 1 failed — the failure is TestMonotoneSolverIntegration::test_pick_runs_end_to_end, which hits the intentional NotImplementedError: monotone='pick' is serial-only gate; it fails identically at the baseline (pre-existing, unrelated: the test lacks an MPI skip guard).

Underworld development team with AI support from Claude Code

[Copilot]

Pull request overview

Fixes the Lagrangian DDt history update path in ddt.py so per-component history writes use the canonical SwarmVariable storage layout (.data[:, _data_layout(i,j)]) rather than indexing into symbolic components (which previously raised AttributeError on first update_pre_solve). Adds a regression test module that actually advects particles and validates both history shifting and component layout.

Changes:

• Fix Lagrangian / Lagrangian_Swarm history initialisation and post-solve updates to write via canonical (N, components) storage and to read coordinates from swarm._particle_coordinates.data.
• Remove deprecated swarm.access() wrappers around these history update blocks.
• Add regression tests covering scalar and vector Lagrangian histories under swarm advection and step-averaging.

Reviewed changes

Copilot reviewed 2 out of 2 changed files in this pull request and generated 1 comment.

File	Description
src/underworld3/systems/ddt.py	Corrects history component writes to use modern SwarmVariable canonical data layout and modern coordinate access; removes deprecated access wrappers.
tests/test_0857_lagrangian_ddt_advecting_history.py	Adds regression coverage for advecting-history behavior and verifies component-to-column layout via _data_layout.

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