add pixi task to manage changes in notebooks

docs/notebooks/processing.ipynb

@@ -166,7 +166,7 @@
     "    roi.z_length = 1 # In the MIP image, the z dimension is 1\n",
     "    roi_list.append(roi)\n",
     "\n",
-    "mip_roi_table.append_rois(roi_list)\n",
+    "mip_roi_table.set_rois(roi_list, overwrite=True)\n",
     "mip_roi_table.write()\n",
     "\n",
     "mip_roi_table.table"

pyproject.toml

@@ -214,3 +214,6 @@ dev3 = { features = ["dev3"], solve-group = "v3" }
 test = { features = ["test"], solve-group = "v2_test" }
 docs = { features = ["dev2", "docs"], solve-group = "v2" }
 
+[tool.pixi.tasks]
+run_nb = "jupyter-execute ./docs/notebooks/*.ipynb"
+run_docs = "mkdocs serve"

src/ngio/tables/v1/roi_tables.py

@@ -170,15 +170,15 @@ def field_indexes(self) -> list[str]:
     def set_rois(
         self,
         rois: Iterable[WorldCooROI] | WorldCooROI,
-        mode: Literal["override", "append"] = "append",
+        overwrite: bool = False,
     ) -> None:
         """Append ROIs to the current table.
 
         Args:
             rois (Iterable[WorldCooROI] | WorldCooROI): The ROIs to append.
-            mode (str): The mode to use when appending the ROIs.
-                override: Override the current table with the new ROIs.
-                append: Append the new ROIs to the current table.
+            overwrite (bool): Whether to overwrite the ROIs if they already exist.
+                If False, the ROIs will be appended. If True, the ROIs will be
+                overwritten.
         """
         if isinstance(rois, WorldCooROI):
             rois = [rois]
@@ -205,15 +205,10 @@ def set_rois(
         table_df = self.table
         new_table_df = pd.DataFrame.from_dict(rois_dict, orient="index")
 
-        if mode == "override" or table_df.empty:
+        if overwrite or table_df.empty:
             table_df = new_table_df
-        elif mode == "append":
-            table_df = pd.concat([table_df, new_table_df], axis=0)
         else:
-            raise ValueError(
-                f"Invalid mode: {mode} for setting the ROIs. "
-                "Use 'override' or 'append'."
-            )
+            table_df = pd.concat([table_df, new_table_df], axis=0)
 
         table_df.index.name = "FieldIndex"
         table_df.index = table_df.index.astype(str)