opentrons 8.1.0__tar.gz → 8.2.0__tar.gz

{opentrons-8.1.0 → opentrons-8.2.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: opentrons
-Version: 8.1.0
+Version: 8.2.0
 Summary: The Opentrons API is a simple framework designed to make writing automated biology lab protocols easy.
 Author: Opentrons
 Author-email: engineering@opentrons.com
@@ -21,7 +21,7 @@ Classifier: Programming Language :: Python :: 3.10
 Classifier: Topic :: Scientific/Engineering
 Requires-Python: >=3.10
 License-File: ../LICENSE
-Requires-Dist: opentrons-shared-data==8.1.0
+Requires-Dist: opentrons-shared-data==8.2.0
 Requires-Dist: aionotify==0.3.1
 Requires-Dist: anyio<4.0.0,>=3.6.1
 Requires-Dist: jsonschema<4.18.0,>=3.0.1
@@ -30,12 +30,13 @@ Requires-Dist: pydantic<2.0.0,>=1.10.9
 Requires-Dist: pyserial>=3.5
 Requires-Dist: typing-extensions<5,>=4.0.0
 Requires-Dist: click<9,>=8.0.0
+Requires-Dist: pyusb==1.2.1
 Requires-Dist: importlib-metadata>=1.0; python_version < "3.8"
 Requires-Dist: packaging>=21.0
 Provides-Extra: ot2-hardware
-Requires-Dist: opentrons-hardware==8.1.0; extra == "ot2-hardware"
+Requires-Dist: opentrons-hardware==8.2.0; extra == "ot2-hardware"
 Provides-Extra: flex-hardware
-Requires-Dist: opentrons-hardware[FLEX]==8.1.0; extra == "flex-hardware"
+Requires-Dist: opentrons-hardware[FLEX]==8.2.0; extra == "flex-hardware"
 
 .. _Full API Documentation: http://docs.opentrons.com
 

{opentrons-8.1.0 → opentrons-8.2.0}/setup.py

@@ -65,6 +65,7 @@ INSTALL_REQUIRES = [
     "pyserial>=3.5",
     "typing-extensions>=4.0.0,<5",
     "click>=8.0.0,<9",
+    "pyusb==1.2.1",
     'importlib-metadata >= 1.0 ; python_version < "3.8"',
     "packaging>=21.0",
 ]

{opentrons-8.1.0 → opentrons-8.2.0}/src/opentrons/cli/analyze.py

@@ -23,8 +23,14 @@ from typing import (
 )
 import logging
 import sys
+import json
 
-from opentrons.protocol_engine.types import RunTimeParameter, EngineStatus
+from opentrons.protocol_engine.types import (
+    RunTimeParameter,
+    CSVRuntimeParamPaths,
+    PrimitiveRunTimeParamValuesType,
+    EngineStatus,
+)
 from opentrons.protocols.api_support.types import APIVersion
 from opentrons.protocol_reader import (
     ProtocolReader,
@@ -104,8 +110,22 @@ class _Output:
     type=click.Choice(["DEBUG", "INFO", "WARNING", "ERROR"], case_sensitive=False),
     default="WARNING",
 )
+@click.option(
+    "--rtp-values",
+    help="Serialized JSON of runtime parameter variable names to values.",
+    default="{}",
+    type=str,
+)
+@click.option(
+    "--rtp-files",
+    help="Serialized JSON of runtime parameter variable names to file paths.",
+    default="{}",
+    type=str,
+)
 def analyze(
     files: Sequence[Path],
+    rtp_values: str,
+    rtp_files: str,
     json_output: Optional[IO[bytes]],
     human_json_output: Optional[IO[bytes]],
     log_output: str,
@@ -125,7 +145,7 @@ def analyze(
 
     try:
         with _capture_logs(log_output, log_level):
-            sys.exit(run(_analyze, files, outputs, check))
+            sys.exit(run(_analyze, files, rtp_values, rtp_files, outputs, check))
     except click.ClickException:
         raise
     except Exception as e:
@@ -194,6 +214,37 @@ def _get_input_files(files_and_dirs: Sequence[Path]) -> List[Path]:
     return results
 
 
+def _get_runtime_parameter_values(
+    serialized_rtp_values: str,
+) -> PrimitiveRunTimeParamValuesType:
+    rtp_values = {}
+    try:
+        for variable_name, value in json.loads(serialized_rtp_values).items():
+            if not isinstance(value, (bool, int, float, str)):
+                raise click.BadParameter(
+                    f"Runtime parameter '{value}' is not of allowed type boolean, integer, float or string",
+                    param_hint="--rtp-values",
+                )
+            rtp_values[variable_name] = value
+    except json.JSONDecodeError as error:
+        raise click.BadParameter(
+            f"JSON decode error: {error}", param_hint="--rtp-values"
+        )
+    return rtp_values
+
+
+def _get_runtime_parameter_paths(serialized_rtp_files: str) -> CSVRuntimeParamPaths:
+    try:
+        return {
+            variable_name: Path(path_string)
+            for variable_name, path_string in json.loads(serialized_rtp_files).items()
+        }
+    except json.JSONDecodeError as error:
+        raise click.BadParameter(
+            f"JSON decode error: {error}", param_hint="--rtp-files"
+        )
+
+
 R = TypeVar("R")
 
 
@@ -238,7 +289,11 @@ class UnexpectedAnalysisError(EnumeratedError):
         )
 
 
-async def _do_analyze(protocol_source: ProtocolSource) -> RunResult:
+async def _do_analyze(
+    protocol_source: ProtocolSource,
+    rtp_values: PrimitiveRunTimeParamValuesType,
+    rtp_paths: CSVRuntimeParamPaths,
+) -> RunResult:
 
     orchestrator = await create_simulating_orchestrator(
         robot_type=protocol_source.robot_type, protocol_config=protocol_source.config
@@ -247,8 +302,8 @@ async def _do_analyze(protocol_source: ProtocolSource) -> RunResult:
         await orchestrator.load(
             protocol_source=protocol_source,
             parse_mode=ParseMode.NORMAL,
-            run_time_param_values=None,
-            run_time_param_paths=None,
+            run_time_param_values=rtp_values,
+            run_time_param_paths=rtp_paths,
         )
     except Exception as error:
         err_id = "analysis-setup-error"
@@ -275,7 +330,9 @@ async def _do_analyze(protocol_source: ProtocolSource) -> RunResult:
                 modules=[],
                 labwareOffsets=[],
                 liquids=[],
+                wells=[],
                 hasEverEnteredErrorRecovery=False,
+                files=[],
             ),
             parameters=[],
         )
@@ -284,9 +341,16 @@ async def _do_analyze(protocol_source: ProtocolSource) -> RunResult:
 
 
 async def _analyze(
-    files_and_dirs: Sequence[Path], outputs: Sequence[_Output], check: bool
+    files_and_dirs: Sequence[Path],
+    rtp_values: str,
+    rtp_files: str,
+    outputs: Sequence[_Output],
+    check: bool,
 ) -> int:
     input_files = _get_input_files(files_and_dirs)
+    parsed_rtp_values = _get_runtime_parameter_values(rtp_values)
+    rtp_paths = _get_runtime_parameter_paths(rtp_files)
+
     try:
         protocol_source = await ProtocolReader().read_saved(
             files=input_files,
@@ -295,7 +359,7 @@ async def _analyze(
     except ProtocolFilesInvalidError as error:
         raise click.ClickException(str(error))
 
-    analysis = await _do_analyze(protocol_source)
+    analysis = await _do_analyze(protocol_source, parsed_rtp_values, rtp_paths)
     return_code = _get_return_code(analysis)
 
     if not outputs:

{opentrons-8.1.0 → opentrons-8.2.0}/src/opentrons/config/__init__.py

@@ -202,6 +202,15 @@ CONFIG_ELEMENTS = (
         " absolute path, it will be used directly. If it is a "
         "relative path it will be relative to log_dir",
     ),
+    ConfigElement(
+        "sensor_log_file",
+        "Sensor Log File",
+        Path("logs") / "sensor.log",
+        ConfigElementType.FILE,
+        "The location of the file to save sensor 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",

{opentrons-8.1.0 → opentrons-8.2.0}/src/opentrons/config/advanced_settings.py

@@ -222,6 +222,17 @@ settings = [
         robot_type=[RobotTypeEnum.OT2, RobotTypeEnum.FLEX],
         internal_only=True,
     ),
+    SettingDefinition(
+        _id="allowLiquidClasses",
+        title="Allow the use of liquid classes",
+        description=(
+            "Do not enable."
+            " This is an Opentrons internal setting to allow using in-development"
+            " liquid classes."
+        ),
+        robot_type=[RobotTypeEnum.OT2, RobotTypeEnum.FLEX],
+        internal_only=True,
+    ),
 ]
 
 
@@ -715,6 +726,16 @@ def _migrate34to35(previous: SettingsMap) -> SettingsMap:
     return newmap
 
 
+def _migrate35to36(previous: SettingsMap) -> SettingsMap:
+    """Migrate to version 36 of the feature flags file.
+
+    - Adds the allowLiquidClasses config element.
+    """
+    newmap = {k: v for k, v in previous.items()}
+    newmap["allowLiquidClasses"] = None
+    return newmap
+
+
 _MIGRATIONS = [
     _migrate0to1,
     _migrate1to2,
@@ -751,6 +772,7 @@ _MIGRATIONS = [
     _migrate32to33,
     _migrate33to34,
     _migrate34to35,
+    _migrate35to36,
 ]
 """
 List of all migrations to apply, indexed by (version - 1). See _migrate below

{opentrons-8.1.0 → opentrons-8.2.0}/src/opentrons/config/defaults_ot3.py

@@ -15,7 +15,6 @@ from .types import (
     LiquidProbeSettings,
     ZSenseSettings,
     EdgeSenseSettings,
-    OutputOptions,
 )
 
 
@@ -27,9 +26,11 @@ DEFAULT_LIQUID_PROBE_SETTINGS: Final[LiquidProbeSettings] = LiquidProbeSettings(
     plunger_speed=15,
     plunger_impulse_time=0.2,
     sensor_threshold_pascals=15,
-    output_option=OutputOptions.sync_buffer_to_csv,
     aspirate_while_sensing=False,
-    data_files={InstrumentProbeType.PRIMARY: "/data/pressure_sensor_data.csv"},
+    z_overlap_between_passes_mm=0.1,
+    plunger_reset_offset=2.0,
+    samples_for_baselining=20,
+    sample_time_sec=0.004,
 )
 
 DEFAULT_CALIBRATION_SETTINGS: Final[OT3CalibrationSettings] = OT3CalibrationSettings(
@@ -39,7 +40,6 @@ DEFAULT_CALIBRATION_SETTINGS: Final[OT3CalibrationSettings] = OT3CalibrationSett
             max_overrun_distance_mm=5.0,
             speed_mm_per_s=1.0,
             sensor_threshold_pf=3.0,
-            output_option=OutputOptions.sync_only,
         ),
     ),
     edge_sense=EdgeSenseSettings(
@@ -50,7 +50,6 @@ DEFAULT_CALIBRATION_SETTINGS: Final[OT3CalibrationSettings] = OT3CalibrationSett
             max_overrun_distance_mm=0.5,
             speed_mm_per_s=1,
             sensor_threshold_pf=3.0,
-            output_option=OutputOptions.sync_only,
         ),
         search_initial_tolerance_mm=12.0,
         search_iteration_limit=8,
@@ -191,23 +190,6 @@ DEFAULT_RUN_CURRENT: Final[ByGantryLoad[Dict[OT3AxisKind, float]]] = ByGantryLoa
 )
 
 
-def _build_output_option_with_default(
-    from_conf: Any, default: OutputOptions
-) -> OutputOptions:
-    if from_conf is None:
-        return default
-    else:
-        if isinstance(from_conf, OutputOptions):
-            return from_conf
-        else:
-            try:
-                enumval = OutputOptions[from_conf]
-            except KeyError:  # not an enum entry
-                return default
-            else:
-                return enumval
-
-
 def _build_log_files_with_default(
     from_conf: Any,
     default: Optional[Dict[InstrumentProbeType, str]],
@@ -312,24 +294,12 @@ def _build_default_cap_pass(
         sensor_threshold_pf=from_conf.get(
             "sensor_threshold_pf", default.sensor_threshold_pf
         ),
-        output_option=from_conf.get("output_option", default.output_option),
     )
 
 
 def _build_default_liquid_probe(
     from_conf: Any, default: LiquidProbeSettings
 ) -> LiquidProbeSettings:
-    output_option = _build_output_option_with_default(
-        from_conf.get("output_option", None), default.output_option
-    )
-    data_files: Optional[Dict[InstrumentProbeType, str]] = None
-    if (
-        output_option is OutputOptions.sync_buffer_to_csv
-        or output_option is OutputOptions.stream_to_csv
-    ):
-        data_files = _build_log_files_with_default(
-            from_conf.get("data_files", None), default.data_files
-        )
     return LiquidProbeSettings(
         mount_speed=from_conf.get("mount_speed", default.mount_speed),
         plunger_speed=from_conf.get("plunger_speed", default.plunger_speed),
@@ -339,11 +309,19 @@ def _build_default_liquid_probe(
         sensor_threshold_pascals=from_conf.get(
             "sensor_threshold_pascals", default.sensor_threshold_pascals
         ),
-        output_option=from_conf.get("output_option", default.output_option),
         aspirate_while_sensing=from_conf.get(
             "aspirate_while_sensing", default.aspirate_while_sensing
         ),
-        data_files=data_files,
+        z_overlap_between_passes_mm=from_conf.get(
+            "z_overlap_between_passes_mm", default.z_overlap_between_passes_mm
+        ),
+        plunger_reset_offset=from_conf.get(
+            "plunger_reset_offset", default.plunger_reset_offset
+        ),
+        samples_for_baselining=from_conf.get(
+            "samples_for_baselining", default.samples_for_baselining
+        ),
+        sample_time_sec=from_conf.get("sample_time_sec", default.sample_time_sec),
     )
 
 

{opentrons-8.1.0 → opentrons-8.2.0}/src/opentrons/config/feature_flags.py

@@ -78,3 +78,7 @@ def enable_performance_metrics(robot_type: RobotTypeEnum) -> bool:
 
 def oem_mode_enabled() -> bool:
     return advs.get_setting_with_env_overload("enableOEMMode", RobotTypeEnum.FLEX)
+
+
+def allow_liquid_classes(robot_type: RobotTypeEnum) -> bool:
+    return advs.get_setting_with_env_overload("allowLiquidClasses", robot_type)

{opentrons-8.1.0 → opentrons-8.2.0}/src/opentrons/config/types.py

@@ -1,8 +1,8 @@
 from enum import Enum
 from dataclasses import dataclass, asdict, fields
-from typing import Dict, Tuple, TypeVar, Generic, List, cast, Optional
+from typing import Dict, Tuple, TypeVar, Generic, List, cast
 from typing_extensions import TypedDict, Literal
-from opentrons.hardware_control.types import OT3AxisKind, InstrumentProbeType
+from opentrons.hardware_control.types import OT3AxisKind
 
 
 class AxisDict(TypedDict):
@@ -103,25 +103,12 @@ class OT3CurrentSettings:
         )
 
 
-class OutputOptions(int, Enum):
-    """Specifies where we should report sensor data to during a sensor pass."""
-
-    stream_to_csv = 0x1  # compile sensor data stream into a csv file, in addition to can_bus_only behavior
-    sync_buffer_to_csv = 0x2  # collect sensor data on pipette mcu, then stream to robot server and compile into a csv file, in addition to can_bus_only behavior
-    can_bus_only = (
-        0x4  # stream sensor data over CAN bus, in addition to sync_only behavior
-    )
-    sync_only = 0x8  # trigger pipette sync line upon sensor's detection of something
-
-
 @dataclass(frozen=True)
 class CapacitivePassSettings:
     prep_distance_mm: float
     max_overrun_distance_mm: float
     speed_mm_per_s: float
     sensor_threshold_pf: float
-    output_option: OutputOptions
-    data_files: Optional[Dict[InstrumentProbeType, str]] = None
 
 
 @dataclass(frozen=True)
@@ -135,9 +122,11 @@ class LiquidProbeSettings:
     plunger_speed: float
     plunger_impulse_time: float
     sensor_threshold_pascals: float
-    output_option: OutputOptions
     aspirate_while_sensing: bool
-    data_files: Optional[Dict[InstrumentProbeType, str]]
+    z_overlap_between_passes_mm: float
+    plunger_reset_offset: float
+    samples_for_baselining: int
+    sample_time_sec: float
 
 
 @dataclass(frozen=True)

{opentrons-8.1.0 → opentrons-8.2.0}/src/opentrons/drivers/absorbance_reader/abstract.py

@@ -1,8 +1,10 @@
 from abc import ABC, abstractmethod
-from typing import Dict, List
+from typing import Dict, List, Optional, Tuple
 from opentrons.drivers.types import (
+    ABSMeasurementMode,
     AbsorbanceReaderLidStatus,
     AbsorbanceReaderDeviceState,
+    AbsorbanceReaderPlatePresence,
 )
 
 
@@ -31,11 +33,18 @@ class AbstractAbsorbanceReaderDriver(ABC):
         ...
 
     @abstractmethod
-    async def get_single_measurement(self, wavelength: int) -> List[float]:
+    async def initialize_measurement(
+        self,
+        wavelengths: List[int],
+        mode: ABSMeasurementMode = ABSMeasurementMode.SINGLE,
+        reference_wavelength: Optional[int] = None,
+    ) -> None:
+        """Initialize measurement for the device in single or multi mode for the given wavelengths"""
         ...
 
     @abstractmethod
-    async def initialize_measurement(self, wavelength: int) -> None:
+    async def get_measurement(self) -> List[List[float]]:
+        """Gets one or more measurements based on the current configuration."""
         ...
 
     @abstractmethod
@@ -46,3 +55,18 @@ class AbstractAbsorbanceReaderDriver(ABC):
     async def get_device_info(self) -> Dict[str, str]:
         """Get device info"""
         ...
+
+    @abstractmethod
+    async def get_uptime(self) -> int:
+        """Get device uptime"""
+        ...
+
+    @abstractmethod
+    async def get_plate_presence(self) -> AbsorbanceReaderPlatePresence:
+        """Check if there is a plate in the reader."""
+        ...
+
+    @abstractmethod
+    async def update_firmware(self, firmware_file_path: str) -> Tuple[bool, str]:
+        """Updates the firmware on the device."""
+        ...