feat: add plate_row and plate_col fields to PositionBase

Add serialized int fields to PositionBase for annotating which well a
position belongs to, enabling HCS zarr output from plain stage positions
without requiring WellPlatePlan. Also populate these fields in
WellPlatePlan.all_well_positions and selected_well_positions.

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

Author: ieivanov

src/useq/_plate.py

@@ -335,19 +335,37 @@ def _transorm_coords(self, coords: np.ndarray) -> np.ndarray:
     def all_well_positions(self) -> Sequence[Position]:
         """Return all wells (centers) as Position objects."""
         return [
-            Position(x=x * 1000, y=y * 1000, name=name)  # convert to µm
-            for (y, x), name in zip(
-                self.all_well_coordinates, self.all_well_names.reshape(-1), strict=False
+            Position(
+                x=x * 1000,
+                y=y * 1000,
+                name=name,
+                plate_row=int(row),
+                plate_col=int(col),
+            )
+            for (y, x), name, (row, col) in zip(
+                self.all_well_coordinates,
+                self.all_well_names.reshape(-1),
+                self.all_well_indices.reshape(-1, 2),
+                strict=False,
             )
         ]
 
     @cached_property
     def selected_well_positions(self) -> Sequence[Position]:
         """Return selected wells (centers) as Position objects."""
         return [
-            Position(x=x * 1000, y=y * 1000, name=name)  # convert to µm
-            for (y, x), name in zip(
-                self.selected_well_coordinates, self.selected_well_names, strict=False
+            Position(
+                x=x * 1000,
+                y=y * 1000,
+                name=name,
+                plate_row=int(row),
+                plate_col=int(col),
+            )
+            for (y, x), name, (row, col) in zip(
+                self.selected_well_coordinates,
+                self.selected_well_names,
+                self.selected_well_indices,
+                strict=False,
             )
         ]
 

src/useq/_position.py

@@ -46,6 +46,8 @@ class PositionBase(MutableModel):
     name: str | None = None
     sequence: Optional["MDASequence"] = None
     properties: list[PropertyTuple] | None = None
+    plate_row: int | None = None
+    plate_col: int | None = None
 
     # excluded from serialization
     row: int | None = Field(default=None, exclude=True)

tests/fixtures/mda.json

@@ -62,6 +62,8 @@
   "stage_positions": [
     {
       "name": null,
+      "plate_col": null,
+      "plate_row": null,
       "properties": null,
       "sequence": null,
       "x": 10.0,
@@ -70,6 +72,8 @@
     },
     {
       "name": "test_name",
+      "plate_col": null,
+      "plate_row": null,
       "properties": null,
       "sequence": {
         "autofocus_plan": null,