Fix test circuit

Author: Pharmbio

cellpainter/cellpainter/commands.py

@@ -93,7 +93,7 @@ def F(cmd: Command):
                 return cmd
         return self.transform(F), did_transform
 
-    def collect(self: Command) -> list[tuple[Command, Metadata]]:
+    def collect(self: Command, flatten_sections: bool=False) -> list[tuple[Command, Metadata]]:
         match self:
             case SeqCmd():
                 return [
@@ -106,6 +106,8 @@ def collect(self: Command) -> list[tuple[Command, Metadata]]:
                     (collected_cmd, collected_metadata.merge(self.metadata))
                     for collected_cmd, collected_metadata in self.command.collect()
                 ]
+            case OptimizeSection() if flatten_sections:
+                return self.command.collect()
             # case OptimizeSection():
             #     raise ValueError(f'collect({self})')
             case _:

cellpainter/cellpainter/small_protocols.py

@@ -172,7 +172,7 @@ def test_circuit(args: SmallProtocolArgs):
     cmds = Seq(
         *[
             cmd.add(metadata)
-            for cmd, metadata in cmds.collect()
+            for cmd, metadata in cmds.collect(flatten_sections=True)
             if isinstance(cmd, RobotarmCmd)
             # if metadata.step not in {'Triton', 'Stains'}
         ],