abr protocols for liquid-classes and LLD in v8.4.0

api/src/opentrons/config/__init__.py

@@ -211,6 +211,15 @@ class ConfigElement(NamedTuple):
         " absolute path, it will be used directly. If it is a "
         "relative path it will be relative to log_dir",
     ),
+    ConfigElement(
+        "move_profile_log_file",
+        "Move Profile File",
+        Path("logs") / "profile.log",
+        ConfigElementType.FILE,
+        "The location of the file to save move profile logs to. If this is an"
+        " absolute path, it will be used directly. If it is a "
+        "relative path it will be relative to log_dir",
+    ),
     ConfigElement(
         "serial_log_file",
         "Serial Log File",

api/src/opentrons/execute.py

@@ -21,6 +21,7 @@
     Optional,
     TextIO,
     Union,
+    Any,
 )
 
 from opentrons_shared_data.labware.labware_definition import (
@@ -67,6 +68,9 @@
     create_protocol_engine,
 )
 from opentrons.protocol_engine.types import PostRunHardwareState
+from opentrons.protocol_engine.types.run_time_parameters import (
+    PrimitiveRunTimeParamValuesType,
+)
 
 from opentrons.protocol_reader import ProtocolSource
 
@@ -230,6 +234,11 @@ def get_arguments(parser: argparse.ArgumentParser) -> argparse.ArgumentParser:
         "this option and should be configured in the config file. If "
         "'none', do not show logs",
     )
+
+    parser.add_argument(
+        "--parameters", nargs="+", help="my_str=help my_bool=true my_int=1 my_float=1.0"
+    )
+
     parser.add_argument(
         "-L",
         "--custom-labware-path",
@@ -293,6 +302,7 @@ def get_arguments(parser: argparse.ArgumentParser) -> argparse.ArgumentParser:
 def execute(
     protocol_file: Union[BinaryIO, TextIO],
     protocol_name: str,
+    run_time_param_values: Optional[PrimitiveRunTimeParamValuesType] = None,
     propagate_logs: bool = False,
     log_level: str = "warning",
     emit_runlog: Optional[_EmitRunlogCallable] = None,
@@ -317,6 +327,7 @@ def execute(
     :param protocol_name: The name of the protocol file. This is required
         internally, but it may not be a thing we can get
         from the ``protocol_file`` argument.
+    :param run_time_param_values: Runtime parameter values
     :param propagate_logs: Whether this function should allow logs from the
         Opentrons stack to propagate up to the root handler.
         This can be useful if you're integrating this
@@ -430,6 +441,7 @@ def execute(
         protocol_file.seek(0)
         _run_file_pe(
             protocol=protocol,
+            run_time_param_values=run_time_param_values,
             hardware_api=_get_global_hardware_controller(_get_robot_type()),
             emit_runlog=emit_runlog,
         )
@@ -455,6 +467,42 @@ def _print_runlog(command: command_types.CommandMessage) -> None:
     return _print_runlog
 
 
+def _convert_runtime_param_value(val: str) -> Any:
+    if val.lower() == "true":
+        return True
+    elif val.lower() == "false":
+        return False
+    if "." in val:  # NOTE: arg must explicitly define a float vs int with "."
+        try:
+            return float(val)
+        except ValueError:
+            pass
+    else:
+        try:
+            return int(val)
+        except ValueError:
+            pass
+    return val
+
+
+def _parse_parameters(
+    name_value_list: List[str],
+) -> PrimitiveRunTimeParamValuesType:
+    if not name_value_list:
+        return {}
+    result: Dict[str, Any] = {}
+    for name_value in name_value_list:
+        if "=" in name_value:
+            name, value = name_value.split("=", 1)
+            if name and value:
+                result[name] = _convert_runtime_param_value(value)
+                continue
+        raise argparse.ArgumentTypeError(
+            f"Invalid argument format: '{name_value}' (expected name=value)"
+        )
+    return result
+
+
 def main() -> int:
     """Handler for command line invocation to run a protocol.
 
@@ -492,6 +540,7 @@ def main() -> int:
         execute(
             protocol_file=args.protocol,
             protocol_name=args.protocol.name,
+            run_time_param_values=_parse_parameters(args.parameters),
             custom_labware_paths=args.custom_labware_path,
             custom_data_paths=(args.custom_data_path + args.custom_data_file),
             log_level=log_level,
@@ -623,6 +672,7 @@ def _run_file_non_pe(
 
 def _run_file_pe(
     protocol: Protocol,
+    run_time_param_values: Optional[PrimitiveRunTimeParamValuesType],
     hardware_api: ThreadManagedHardware,
     emit_runlog: Optional[_EmitRunlogCallable],
 ) -> None:
@@ -668,6 +718,7 @@ async def run(protocol_source: ProtocolSource) -> None:
             result = await orchestrator.run(
                 deck_configuration=entrypoint_util.get_deck_configuration(),
                 protocol_source=protocol_source,
+                run_time_param_values=run_time_param_values,
             )
         finally:
             unsubscribe()

api/src/opentrons/hardware_control/ot3api.py

@@ -5,6 +5,7 @@
 from functools import partial, lru_cache, wraps
 from dataclasses import replace
 import logging
+import time
 from collections import OrderedDict
 from typing import (
     AsyncIterator,
@@ -27,6 +28,8 @@
 )
 
 
+from opentrons_hardware.hardware_control import MOVE_PROFILE_LOG_NAME
+
 from opentrons_shared_data.pipette.types import (
     PipetteName,
 )
@@ -148,6 +151,7 @@
 from .backends.errors import SubsystemUpdating
 
 mod_log = logging.getLogger(__name__)
+PROFILE_LOG = logging.getLogger(MOVE_PROFILE_LOG_NAME)
 
 AXES_IN_HOMING_ORDER: Tuple[Axis, Axis, Axis, Axis, Axis, Axis, Axis, Axis, Axis] = (
     *Axis.ot3_mount_axes(),
@@ -1462,6 +1466,8 @@ async def _move(
         expect_stalls: bool = False,
     ) -> None:
         """Worker function to apply robot motion."""
+        start = time.time()
+        PROFILE_LOG.info(f"OT3API._move\tstart\t{start}")
         machine_pos = machine_from_deck(
             deck_pos=target_position,
             attitude=self._robot_calibration.deck_calibration.attitude,
@@ -1494,11 +1500,18 @@ async def _move(
             except Exception:
                 self._log.exception("Move failed")
                 self._current_position.clear()
+                end = time.time()
+                PROFILE_LOG.info(f"OT3API._move\tfailed\t{end}")
+                PROFILE_LOG.info(f"OT3API._move\tduration\t{end - start}")
                 raise
             else:
                 await self._cache_current_position()
                 await self._cache_encoder_position()
 
+        end = time.time()
+        PROFILE_LOG.info(f"OT3API._move\tend\t{end}")
+        PROFILE_LOG.info(f"OT3API._move\tduration\t{end - start}")
+
     async def _set_plunger_current_and_home(
         self,
         axis: Axis,

api/src/opentrons/simulate.py

@@ -49,6 +49,9 @@
 from opentrons.protocol_engine.state.config import Config
 from opentrons.protocol_engine.types import DeckType, EngineStatus, PostRunHardwareState
 from opentrons.protocol_reader.protocol_source import ProtocolSource
+from opentrons.protocol_engine.types.run_time_parameters import (
+    PrimitiveRunTimeParamValuesType,
+)
 from opentrons.protocol_runner.protocol_runner import create_protocol_runner, LiveRunner
 from opentrons.protocol_runner import RunOrchestrator
 from opentrons.protocols.duration import DurationEstimator
@@ -435,6 +438,7 @@ def bundle_from_sim(
 def simulate(
     protocol_file: Union[BinaryIO, TextIO],
     file_name: Optional[str] = None,
+    run_time_param_values: Optional[PrimitiveRunTimeParamValuesType] = None,
     custom_labware_paths: Optional[List[str]] = None,
     custom_data_paths: Optional[List[str]] = None,
     propagate_logs: bool = False,
@@ -483,6 +487,7 @@ def simulate(
 
     :param protocol_file: The protocol file to simulate.
     :param file_name: The name of the file
+    :param run_time_param_values: Runtime parameter values
     :param custom_labware_paths: A list of directories to search for custom labware.
         Loads valid labware from these paths and makes them available
         to the protocol context. If this is ``None`` (the default), and
@@ -581,6 +586,7 @@ def simulate(
             protocol_file.seek(0)
             return _run_file_pe(
                 protocol=protocol,
+                run_time_param_values=run_time_param_values,
                 robot_type=protocol.robot_type,
                 hardware_api=hardware_simulator,
                 stack_logger=stack_logger,
@@ -659,6 +665,10 @@ def get_arguments(parser: argparse.ArgumentParser) -> argparse.ArgumentParser:
         'Log levels below warning can be chatty. If "none", do not show logs',
     )
 
+    parser.add_argument(
+        "--parameters", nargs="+", help="my_str=help my_bool=true my_int=1 my_float=1.0"
+    )
+
     parser.add_argument(
         "-L",
         "--custom-labware-path",
@@ -911,6 +921,7 @@ def _run_file_non_pe(
 
 def _run_file_pe(
     protocol: Protocol,
+    run_time_param_values: Optional[PrimitiveRunTimeParamValuesType],
     robot_type: RobotType,
     hardware_api: ThreadManagedHardware,
     stack_logger: logging.Logger,
@@ -965,6 +976,7 @@ async def run(protocol_source: ProtocolSource) -> _SimulateResult:
                 # the Protocol Engine config specifies use_simulated_deck_config=True.
                 deck_configuration=[],
                 protocol_source=protocol_source,
+                run_time_param_values=run_time_param_values,
             )
 
         if result.state_summary.status != EngineStatus.SUCCEEDED:
@@ -1004,6 +1016,42 @@ def _clear_live_protocol_engine_contexts() -> None:
     _LIVE_PROTOCOL_ENGINE_CONTEXTS.close()
 
 
+def _convert_runtime_param_value(val: str) -> Any:
+    if val.lower() == "true":
+        return True
+    elif val.lower() == "false":
+        return False
+    if "." in val:  # NOTE: arg must explicitly define a float vs int with "."
+        try:
+            return float(val)
+        except ValueError:
+            pass
+    else:
+        try:
+            return int(val)
+        except ValueError:
+            pass
+    return val
+
+
+def _parse_parameters(
+    name_value_list: List[str],
+) -> PrimitiveRunTimeParamValuesType:
+    if not name_value_list:
+        return {}
+    result: Dict[str, Any] = {}
+    for name_value in name_value_list:
+        if "=" in name_value:
+            name, value = name_value.split("=", 1)
+            if name and value:
+                result[name] = _convert_runtime_param_value(value)
+                continue
+        raise argparse.ArgumentTypeError(
+            f"Invalid argument format: '{name_value}' (expected name=value)"
+        )
+    return result
+
+
 # Note - this script is also set up as a setuptools entrypoint and thus does
 # an absolute minimum of work since setuptools does something odd generating
 # the scripts
@@ -1024,6 +1072,7 @@ def main() -> int:
         runlog, maybe_bundle = simulate(
             protocol_file=args.protocol,
             file_name=args.protocol.name,
+            run_time_param_values=_parse_parameters(args.parameters),
             custom_labware_paths=args.custom_labware_path,
             custom_data_paths=(args.custom_data_path + args.custom_data_file),
             duration_estimator=duration_estimator,

api/src/opentrons/util/logging_config.py

@@ -8,9 +8,11 @@
 
 if ARCHITECTURE is SystemArchitecture.YOCTO:
     from opentrons_hardware.sensors import SENSOR_LOG_NAME
+    from opentrons_hardware.hardware_control import MOVE_PROFILE_LOG_NAME
 else:
     # we don't use the sensor log on ot2 or host
     SENSOR_LOG_NAME = "unused"
+    MOVE_PROFILE_LOG_NAME = "unused"
 
 
 # We want this big enough to smooth over any temporary stalls in journald's ability
@@ -39,6 +41,7 @@ def _config_for_host(level_value: int) -> None:
     serial_log_filename = CONFIG["serial_log_file"]
     api_log_filename = CONFIG["api_log_file"]
     sensor_log_filename = CONFIG["sensor_log_file"]
+    move_profile_log_filename = CONFIG["move_profile_log_file"]
     config = {
         "version": 1,
         "disable_existing_loggers": False,
@@ -79,6 +82,14 @@ def _config_for_host(level_value: int) -> None:
                 "level": logging.DEBUG,
                 "backupCount": 5,
             },
+            "move_profile": {
+                "class": "logging.handlers.RotatingFileHandler",
+                "formatter": "basic",
+                "filename": move_profile_log_filename,
+                "maxBytes": 1000000,
+                "level": logging.DEBUG,
+                "backupCount": 5,
+            },
         },
         "loggers": {
             "opentrons": {
@@ -109,6 +120,11 @@ def _config_for_host(level_value: int) -> None:
                 "level": logging.DEBUG,
                 "propagate": False,
             },
+            MOVE_PROFILE_LOG_NAME: {
+                "handlers": ["move_profile"],
+                "level": logging.DEBUG,
+                "propagate": False,
+            },
             "__main__": {"handlers": ["api"], "level": level_value},
         },
     }
@@ -123,6 +139,7 @@ def _config_for_robot(level_value: int) -> None:
     from systemd.journal import JournalHandler  # type: ignore
 
     sensor_log_filename = CONFIG["sensor_log_file"]
+    move_profile_log_filename = CONFIG["move_profile_log_file"]
 
     sensor_log_queue = Queue[logging.LogRecord](maxsize=_LOG_QUEUE_SIZE)
 
@@ -167,6 +184,14 @@ def _config_for_robot(level_value: int) -> None:
                 "formatter": "message_only",
                 "queue": sensor_log_queue,
             },
+            "move_profile": {
+                "class": "logging.handlers.RotatingFileHandler",
+                "formatter": "message_only",
+                "filename": move_profile_log_filename,
+                "maxBytes": 1000000,
+                "level": logging.DEBUG,
+                "backupCount": 3,
+            },
         },
         "loggers": {
             "opentrons.drivers.asyncio.communication.serial_connection": {
@@ -197,6 +222,11 @@ def _config_for_robot(level_value: int) -> None:
                 "level": logging.DEBUG,
                 "propagate": False,
             },
+            MOVE_PROFILE_LOG_NAME: {
+                "handlers": ["move_profile"],
+                "level": logging.DEBUG,
+                "propagate": False,
+            },
             "__main__": {"handlers": ["api"], "level": level_value},
         },
     }