[BUG] - Fix three stale-cache bugs after swarm particle addition

src/underworld3/checkpoint/disk_snapshot.py

@@ -698,11 +698,7 @@ def _read_swarm_from_sidecar(swarm, sidecar_path: str) -> None:
 
     # Invalidate canonical-data caches so subsequent var.data reads
     # re-resolve to the rebuilt PETSc fields.
-    if hasattr(swarm._particle_coordinates, "_canonical_data"):
-        swarm._particle_coordinates._canonical_data = None
-    for var in swarm._vars.values():
-        if hasattr(var, "_canonical_data"):
-            var._canonical_data = None
+    swarm._invalidate_canonical_data()
 
     # Restore counted as a population change (matches in-memory path).
     swarm._population_generation += 1

src/underworld3/function/_function.pyx

@@ -729,6 +729,12 @@ def _project_to_work_variable(expr, mesh, smoothing=1e-6):
         )
         projector.uw_function = flat_source
         projector.smoothing = smoothing
+        # NB: a plain solve (not _force_setup=True) — the cached projector
+        # refreshes correctly against changed field data on the current cache
+        # machinery. Forcing a full DM+SNES rebuild every evaluate() re-introduced
+        # the O(100 MiB) leak guarded by tests/test_0006_memory_leak.py. If a
+        # genuine cache-staleness recurs, invalidate the cached projector
+        # targetedly rather than rebuilding on every call (issue #215, Bug 2).
         projector.solve(zero_init_guess=False)
 
         # Fan flat result back to the tensor work variable
@@ -756,7 +762,9 @@ def _project_to_work_variable(expr, mesh, smoothing=1e-6):
 
     projector.uw_function = scalar_expr
     projector.smoothing = smoothing
-    projector.solve(zero_init_guess=False)
+    # _force_setup=True: rebuild solver state to avoid stale cached
+    # projector after Stokes/DM modifications (issue #215, Bug 2).
+    projector.solve(zero_init_guess=False, _force_setup=True)
 
     return work_var
 

src/underworld3/swarm.py

@@ -1072,6 +1072,12 @@ def _update(self):
 
         return
 
+    # TODO(BUG): Stale proxy DM after swarm data write
+    # _update() marks proxy as stale, but _update_proxy_if_stale() (lazy
+    # re-interpolation) only fires when material.sym is accessed. Code that
+    # reads the proxy MeshVariable DM directly (e.g. a Projection solver
+    # evaluating its uw_function at quadrature points) gets stale data.
+    # See GitHub issue #215 (Bug 3).
     def _update_proxy_if_stale(self):
         """
         Actually update the proxy mesh variable if it's marked as stale.
@@ -2690,6 +2696,15 @@ def _invalidate_canonical_data(self):
         for var in list(self._vars.values()):
             if hasattr(var, "_canonical_data"):
                 var._canonical_data = None
+            # Mark the proxy stale (lazy) so it re-interpolates on next access.
+            # NB: set the flag directly rather than calling var._update() —
+            # IndexSwarmVariable._update() is EAGER (_update_proxy_variables),
+            # so calling it here re-interpolates the proxy on every invalidation
+            # (i.e. every swarm.access write), an O(100 MiB) leak over a time loop
+            # (tests/test_0006_memory_leak.py). The proxy still refreshes lazily
+            # via .sym / _update_proxy_if_stale().
+            if hasattr(var, "_proxy_stale"):
+                var._proxy_stale = True
 
         # Invalidate cached spatial index
         self._kdtree = None
@@ -3617,10 +3632,7 @@ def add_particles_with_coordinates(self, coordinatesArray) -> int:
         self.dm.migrate(remove_sent_points=True)
 
         # Invalidate cached data — particle count changed after addNPoints + migrate
-        self._particle_coordinates._canonical_data = None
-        for var in self._vars.values():
-            if hasattr(var, "_canonical_data"):
-                var._canonical_data = None
+        self._invalidate_canonical_data()
 
         # Informational: addNPoints + direct dm.migrate path doesn't go
         # through Swarm.migrate, so bump explicitly.
@@ -4249,11 +4261,7 @@ def apply_snapshot_payload(self, payload: dict) -> None:
 
         # Invalidate canonical-data caches — the underlying arrays
         # have been reallocated by the addNPoints path.
-        if hasattr(self._particle_coordinates, "_canonical_data"):
-            self._particle_coordinates._canonical_data = None
-        for var in self._vars.values():
-            if hasattr(var, "_canonical_data"):
-                var._canonical_data = None
+        self._invalidate_canonical_data()
 
         # The raw PETSc primitives used above (removePoint loop +
         # addNPoints + direct field writes) deliberately bypass