Fix mesh.X.coords stale after mesh deformation

[lmoresi]

Summary

• mesh.X.coords returned pre-deformation coordinates after _deform_mesh() because self._coords held a numpy view of the old coordinate buffer
• nuke_coords_and_rebuild (called by _deform_mesh) replaces the DM's coordinate vector via createCoordinateSpace, but self._coords was never updated to view the new buffer
• Fix: rebuild the NDArray_With_Callback wrapper from the current DM coordinate vector after nuke_coords_and_rebuild, preserving the deformation callback

Reproducer (from @NengLu)

mesh = uw.meshing.StructuredQuadBox(elementRes=(50, 50), ...)
# ... solve for displacement, compute new coords ...
mesh._deform_mesh(mesh.X.coords + displacement)

# Before fix: mesh.X.coords shows original (undeformed) coordinates
# After fix: mesh.X.coords matches mesh.dm.getCoordinatesLocal()

Test plan

• NengLu's reproducer: mesh.X.coords matches mesh.dm.getCoordinatesLocal() after deformation
• @NengLu to verify in their workflow

Closes #122

Underworld development team with AI support from Claude Code

[Copilot]

Pull request overview

This PR fixes a correctness issue in Underworld3 mesh deformation where mesh.X.coords could continue to reference the pre-deformation PETSc coordinate buffer after _deform_mesh() triggers nuke_coords_and_rebuild() (which may internally replace the DM coordinate vector via createCoordinateSpace).

Changes:

• After nuke_coords_and_rebuild(), rebuild self._coords as a fresh NDArray_With_Callback view of the current dm.getCoordinatesLocal() buffer.
• Preserve the existing deformation callback(s) by re-attaching prior callbacks to the rebuilt _coords wrapper.

---

💡 Add Copilot custom instructions for smarter, more guided reviews. Learn how to get started.

[Copilot]

When rebuilding self._coords, only the callback functions are preserved. Any existing NDArray_With_Callback state (e.g. _callback_enabled from disable_callbacks() or _disable_inplace_operators) is reset to defaults, which can silently change behavior for callers that intentionally disabled callbacks. Consider copying these flags from the old self._coords onto the new instance (and copy the callback list rather than referencing it) so the wrapper rebuild is behavior-preserving beyond just the callback functions.

Suggested change

	old_callbacks = getattr(self._coords, "_callbacks", [])
	self._coords = underworld3.utilities.NDArray_With_Callback(
	numpy.ndarray.view(
	self.dm.getCoordinatesLocal().array.reshape(-1, self.cdim)
	),
	owner=self,
	)
	old_coords = self._coords
	sentinel = object()
	old_callbacks = list(getattr(old_coords, "_callbacks", []))
	old_callback_enabled = getattr(old_coords, "_callback_enabled", sentinel)
	old_disable_inplace_operators = getattr(
	old_coords, "_disable_inplace_operators", sentinel
	)
	self._coords = underworld3.utilities.NDArray_With_Callback(
	numpy.ndarray.view(
	self.dm.getCoordinatesLocal().array.reshape(-1, self.cdim)
	),
	owner=self,
	)
	if old_callback_enabled is not sentinel:
	self._coords._callback_enabled = old_callback_enabled
	if old_disable_inplace_operators is not sentinel:
	self._coords._disable_inplace_operators = (
	old_disable_inplace_operators
	)

[NengLu]

Test shows the fix works, thanks.