api updates, test fixes

api/src/opentrons/execute.py

@@ -600,7 +600,9 @@ def _run_file_non_pe(
 
     context.home()
     try:
-        execute_apiv2.run_protocol(protocol, context)
+        # TODO (spp, 2024-03-18): use true run-time param overrides once enabled
+        #  for cli protocol simulation/ execution
+        execute_apiv2.run_protocol(protocol, context, run_time_param_overrides=None)
     finally:
         context.cleanup()
 

api/src/opentrons/protocol_engine/types.py

@@ -910,4 +910,6 @@ class EnumParameter(RTPBase):
 
 RunTimeParameter = Union[IntParameter, FloatParameter, EnumParameter]
 
-RTPOverridesType = Dict[str, Union[float, bool, str]]     # update value types as more RTP types are added
+RTPOverridesType = Dict[
+    str, Union[float, bool, str]
+]  # update value types as more RTP types are added

api/src/opentrons/protocol_reader/protocol_reader.py

@@ -1,6 +1,6 @@
 """Read relevant protocol information from a set of files."""
 from pathlib import Path
-from typing import Optional, Sequence, Dict, Union
+from typing import Optional, Sequence
 
 from opentrons.protocols.parse import PythonParseMode
 
@@ -55,7 +55,8 @@ def __init__(
     async def save(
         self,
         files: Sequence[BufferedFile],
-        directory: Path, content_hash: str,
+        directory: Path,
+        content_hash: str,
     ) -> ProtocolSource:
         """Compute a `ProtocolSource` from buffered files and save them as files.
 

api/src/opentrons/protocol_runner/legacy_wrappers.py

@@ -169,9 +169,15 @@ class LegacyExecutor:
     """Interface to execute Protocol API v2 protocols in a child thread."""
 
     @staticmethod
-    async def execute(protocol: LegacyProtocol, context: LegacyProtocolContext, run_time_param_overrides: Optional[RTPOverridesType]) -> None:
+    async def execute(
+        protocol: LegacyProtocol,
+        context: LegacyProtocolContext,
+        run_time_param_overrides: Optional[RTPOverridesType],
+    ) -> None:
         """Execute a PAPIv2 protocol with a given ProtocolContext in a child thread."""
-        await to_thread.run_sync(run_protocol, protocol, context, run_time_param_overrides)
+        await to_thread.run_sync(
+            run_protocol, protocol, context, run_time_param_overrides
+        )
 
 
 __all__ = [

api/src/opentrons/protocol_runner/protocol_runner.py

@@ -35,8 +35,11 @@
     LegacyExecutor,
     LegacyLoadInfo,
 )
-from ..protocol_engine.types import PostRunHardwareState, DeckConfigurationType, \
-    RTPOverridesType
+from ..protocol_engine.types import (
+    PostRunHardwareState,
+    DeckConfigurationType,
+    RTPOverridesType,
+)
 
 
 class RunResult(NamedTuple):
@@ -106,8 +109,8 @@ async def stop(self) -> None:
     async def run(
         self,
         deck_configuration: DeckConfigurationType,
-        run_time_params_overrides: Optional[RTPOverridesType],
         protocol_source: Optional[ProtocolSource] = None,
+        run_time_params_overrides: Optional[RTPOverridesType] = None,
     ) -> RunResult:
         """Run a given protocol to completion."""
 
@@ -137,17 +140,18 @@ def __init__(
         self._legacy_executor = legacy_executor or LegacyExecutor()
         # TODO(mc, 2022-01-11): replace task queue with specific implementations
         # of runner interface
-        self._task_queue = (
-            task_queue or TaskQueue()
-        )
+        self._task_queue = task_queue or TaskQueue()
         self._task_queue.set_cleanup_func(
             func=protocol_engine.finish,
             drop_tips_after_run=drop_tips_after_run,
             post_run_hardware_state=post_run_hardware_state,
         )
 
     async def load(
-        self, protocol_source: ProtocolSource, python_parse_mode: PythonParseMode, run_time_params_overrides: Optional[RTPOverridesType],
+        self,
+        protocol_source: ProtocolSource,
+        python_parse_mode: PythonParseMode,
+        run_time_params_overrides: Optional[RTPOverridesType],
     ) -> None:
         """Load a Python or JSONv5(& older) ProtocolSource into managed ProtocolEngine."""
         labware_definitions = await protocol_reader.extract_labware_definitions(
@@ -197,8 +201,8 @@ async def load(
     async def run(  # noqa: D102
         self,
         deck_configuration: DeckConfigurationType,
-        run_time_params_overrides: Optional[RTPOverridesType],
         protocol_source: Optional[ProtocolSource] = None,
+        run_time_params_overrides: Optional[RTPOverridesType] = None,
         python_parse_mode: PythonParseMode = PythonParseMode.NORMAL,
     ) -> RunResult:
         # TODO(mc, 2022-01-11): move load to runner creation, remove from `run`

api/src/opentrons/protocols/execution/execute.py

@@ -17,7 +17,11 @@
 MODULE_LOG = logging.getLogger(__name__)
 
 
-def run_protocol(protocol: Protocol, context: ProtocolContext, run_time_param_overrides: Optional[Dict[str, Union[float, bool, str]]]) -> None:
+def run_protocol(
+    protocol: Protocol,
+    context: ProtocolContext,
+    run_time_param_overrides: Optional[Dict[str, Union[float, bool, str]]],
+) -> None:
     """Run a protocol.
 
     :param protocol: The :py:class:`.protocols.types.Protocol` to execute

api/src/opentrons/simulate.py

@@ -866,7 +866,9 @@ def _run_file_non_pe(
     context.home()
     with scraper.scrape():
         try:
-            execute.run_protocol(protocol, context)
+            # TODO (spp, 2024-03-18): use true run-time param overrides once enabled
+            #  for cli protocol simulation/ execution
+            execute.run_protocol(protocol, context, run_time_param_overrides=None)
             if (
                 isinstance(protocol, PythonProtocol)
                 and protocol.api_level >= APIVersion(2, 0)

api/tests/opentrons/protocol_runner/smoke_tests/test_protocol_runner.py

@@ -43,7 +43,11 @@ async def test_runner_with_python(
         robot_type="OT-2 Standard",
         protocol_config=protocol_source.config,
     )
-    result = await subject.run(deck_configuration=[], protocol_source=protocol_source)
+    result = await subject.run(
+        deck_configuration=[],
+        protocol_source=protocol_source,
+        run_time_params_overrides=None,
+    )
     commands_result = result.commands
     pipettes_result = result.state_summary.pipettes
     labware_result = result.state_summary.labware
@@ -114,7 +118,10 @@ async def test_runner_with_json(json_protocol_file: Path) -> None:
     subject = await create_simulating_runner(
         robot_type="OT-2 Standard", protocol_config=protocol_source.config
     )
-    result = await subject.run(deck_configuration=[], protocol_source=protocol_source)
+    result = await subject.run(
+        deck_configuration=[],
+        protocol_source=protocol_source,
+    )
 
     commands_result = result.commands
     pipettes_result = result.state_summary.pipettes
@@ -176,7 +183,11 @@ async def test_runner_with_legacy_python(legacy_python_protocol_file: Path) -> N
         robot_type="OT-2 Standard",
         protocol_config=protocol_source.config,
     )
-    result = await subject.run(deck_configuration=[], protocol_source=protocol_source)
+    result = await subject.run(
+        deck_configuration=[],
+        protocol_source=protocol_source,
+        run_time_params_overrides=None,
+    )
 
     commands_result = result.commands
     pipettes_result = result.state_summary.pipettes
@@ -235,7 +246,11 @@ async def test_runner_with_legacy_json(legacy_json_protocol_file: Path) -> None:
     subject = await create_simulating_runner(
         robot_type="OT-2 Standard", protocol_config=protocol_source.config
     )
-    result = await subject.run(deck_configuration=[], protocol_source=protocol_source)
+    result = await subject.run(
+        deck_configuration=[],
+        protocol_source=protocol_source,
+        run_time_params_overrides=None,
+    )
 
     commands_result = result.commands
     pipettes_result = result.state_summary.pipettes

api/tests/opentrons/protocol_runner/test_protocol_runner.py

@@ -456,6 +456,7 @@ async def test_load_legacy_python(
     await legacy_python_runner_subject.load(
         legacy_protocol_source,
         python_parse_mode=PythonParseMode.ALLOW_LEGACY_METADATA_AND_REQUIREMENTS,
+        run_time_params_overrides=None,
     )
 
     decoy.verify(
@@ -526,6 +527,7 @@ async def test_load_python_with_pe_papi_core(
     await legacy_python_runner_subject.load(
         legacy_protocol_source,
         python_parse_mode=PythonParseMode.ALLOW_LEGACY_METADATA_AND_REQUIREMENTS,
+        run_time_params_overrides=None,
     )
 
     decoy.verify(protocol_engine.add_plugin(matchers.IsA(LegacyContextPlugin)), times=0)
@@ -587,6 +589,7 @@ async def test_load_legacy_json(
     await legacy_python_runner_subject.load(
         legacy_protocol_source,
         python_parse_mode=PythonParseMode.ALLOW_LEGACY_METADATA_AND_REQUIREMENTS,
+        run_time_params_overrides=None,
     )
 
     decoy.verify(