fix: invalid error thrown when undefined setup variables (#7649)

## 📝 Summary

The following fails in script mode:

```python
with app.setup:
    if False:
        value = ...
```

Since we naively expect `value` to be assigned. This PR makes an
exception for setup cells in script mode, enabling this.

Author: dmadisetti

marimo/_runtime/app/script_runner.py

@@ -47,9 +47,13 @@ def __init__(
         self.cells_cancelled: set[CellId_t] = set()
         self._glbls = glbls if glbls else {}
 
-        # Prune cells that define provided refs
+        # Setup cell cannot be overridden, and it's possible that some
+        # variables are not defined, so ignore it.
         pruned_execution_order = dataflow.prune_cells_for_overrides(
-            self.app.graph, self.app.execution_order, self._glbls
+            self.app.graph,
+            self.app.execution_order,
+            self._glbls,
+            excluded=CellId_t(SETUP_CELL_NAME),
         )
 
         self.cells_to_run = [

marimo/_runtime/dataflow/__init__.py

@@ -2,7 +2,7 @@
 from __future__ import annotations
 
 from collections import deque
-from typing import TYPE_CHECKING, Any, Callable
+from typing import TYPE_CHECKING, Any, Callable, Optional
 
 from marimo import _loggers
 from marimo._ast.cell import CellImpl
@@ -136,6 +136,7 @@ def prune_cells_for_overrides(
     graph: DirectedGraph,
     execution_order: Collection[CellId_t],
     overrides: dict[str, Any],
+    excluded: Optional[CellId_t] = None,
 ) -> list[CellId_t]:
     """Prune cells from execution when their definitions are overridden.
 
@@ -148,6 +149,7 @@ def prune_cells_for_overrides(
         graph: The dataflow graph containing cell dependencies
         execution_order: Ordered collection of cells to execute
         overrides: Dictionary mapping variable names to their override values
+        excluded: CellId to ignore for closure determination.
 
     Returns:
         Filtered execution order excluding cells whose definitions are overridden
@@ -178,6 +180,8 @@ def prune_cells_for_overrides(
     # Validate that all definitions from pruned cells are provided
     missing_defs: set[str] = set()
     for cell_id in cells_to_prune:
+        if cell_id == excluded:
+            continue
         cell = graph.cells[cell_id]
         # Check all definitions this cell would have provided
         for missing in cell.defs - refs:

tests/_ast/test_app.py

@@ -195,6 +195,29 @@ def normal_cell() -> tuple[int]:
         assert defs["normal_var"] == 100
         assert "setup_var" in defs  # setup still ran
 
+    @staticmethod
+    def test_run_with_undefined_refs_in_setup_cell() -> None:
+        """Test that overriding setup cell definitions raises IncompleteRefsError."""
+        app = App()
+
+        with app.setup:
+            import os
+            a = 1
+            if a > 2:
+                setup_var = "from_setup"
+
+        @app.cell
+        def use_setup(setup_var: str) -> tuple[str]:
+            result = f"Used {setup_var}"
+            return (result,)
+
+        # Test: Trying to override setup cell variables should fail
+        # Ensure this doesn't incorrectly raise a IncompleteRefsError
+        with pytest.raises(NameError) as exc_info:
+            app.run()
+        assert "setup_var" in str(exc_info.value)
+
+
     @staticmethod
     def test_setup() -> None:
         app = App()