Merge branch 'edge' into robot-accuracy-recording

.github/workflows/hardware-testing.yaml

@@ -9,6 +9,9 @@ on:
     paths:
       - 'Makefile'
       - 'hardware-testing/**'
+      - 'api/**'
+      - 'shared-data/**'
+      - 'hardware/**'
       - '.github/workflows/hardware-testing.yaml'
       - '.github/actions/python/**'
     branches:

abr-testing/abr_testing/data_collection/abr_robot_error.py

@@ -203,7 +203,8 @@ def get_error_info_from_robot(
         headers_lpc,
     ) = abr_google_drive.create_data_dictionary(
         run_id, error_folder_path, issue_url, "", ""
-    )
+
+
 
     start_row = google_sheet.get_index_row() + 1
     google_sheet.batch_update_cells(runs_and_robots, "A", start_row, "0")

abr-testing/abr_testing/data_collection/read_robot_logs.py

@@ -57,7 +57,6 @@ def lpc_data(
         for item in unique_offsets:
             runs_and_lpc.append(unique_offsets[item].values())
         headers_lpc = list(unique_offsets[(slot, labware_type)].keys())
-
     return runs_and_lpc, headers_lpc
 
 
@@ -296,6 +295,7 @@ def create_abr_data_sheet(
 def get_error_info(file_results: Dict[str, Any]) -> Tuple[int, str, str, str, str]:
     """Determines if errors exist in run log and documents them."""
     error_levels = []
+    error_level = ""
     # Read error levels file
     with open(ERROR_LEVELS_PATH, "r") as error_file:
         error_levels = list(csv.reader(error_file))
@@ -329,6 +329,8 @@ def get_error_info(file_results: Dict[str, Any]) -> Tuple[int, str, str, str, st
         code_error = error[1]
         if code_error == error_code:
             error_level = error[4]
+    if len(error_level) < 1:
+        error_level = str(4)
 
     return num_of_errors, error_type, error_code, error_instrument, error_level
 

api-client/src/modules/__fixtures__/index.ts

@@ -7,6 +7,7 @@ export const mockModulesResponse = [
     hasAvailableUpdate: false,
     moduleType: 'thermocyclerModuleType',
     moduleModel: 'thermocyclerModuleV1',
+    compatibleWithRobot: true,
     data: {
       status: 'holding at target',
       currentTemperature: 3.0,
@@ -31,6 +32,7 @@ export const mockModulesResponse = [
     hasAvailableUpdate: false,
     moduleType: 'heaterShakerModuleType',
     moduleModel: 'heaterShakerModuleV1',
+    compatibleWithRobot: true,
     data: {
       status: 'idle',
       labwareLatchStatus: 'idle_unknown',
@@ -55,6 +57,7 @@ export const mockModulesResponse = [
     hasAvailableUpdate: false,
     moduleType: 'temperatureModuleType',
     moduleModel: 'temperatureModuleV1',
+    compatibleWithRobot: true,
     data: {
       status: 'holding at target',
       currentTemperature: 3.0,
@@ -75,6 +78,7 @@ export const mockModulesResponse = [
     hasAvailableUpdate: false,
     moduleType: 'magneticModuleType',
     moduleModel: 'magneticModuleV1',
+    compatibleWithRobot: true,
     data: {
       status: 'engaged',
       engaged: true,
@@ -89,6 +93,29 @@ export const mockModulesResponse = [
   },
 ]
 
+export const mockUnknownModuleResponse = [
+  ...mockModulesResponse,
+  {
+    name: 'unknown',
+    displayName: 'UnknownModule',
+    moduleModel: 'unknownModule',
+    port: '/dev/unknown',
+    usbPort: {
+      port: 0,
+      hub: false,
+      portGroup: 'unknown',
+      path: '',
+    },
+    serial: 'dummySerialMD',
+    model: 'unknown_v1.1',
+    revision: 'unknown_v1.1',
+    fwVersion: 'dummyVersionMD',
+    hasAvailableUpdate: false,
+    status: 'engaged',
+    data: {},
+  },
+]
+
 export const v2MockModulesResponse = [
   {
     name: 'thermocycler',

api-client/src/modules/api-types.ts

@@ -36,6 +36,7 @@ export interface ApiBaseModule {
   firmwareVersion: string
   hasAvailableUpdate: boolean
   usbPort: PhysicalPort
+  compatibleWithRobot?: boolean
   moduleOffset?: ModuleOffset
 }
 

api-client/src/runs/commands/types.ts

@@ -15,16 +15,18 @@ export interface CommandDetail {
 }
 
 export interface CommandsLinks {
-  current: {
-    // link to the currently executing command
-    href: string
-    meta: {
-      runId: string
-      commandId: string
-      key: string
-      createdAt: string
-      index: number
-    }
+  current?: CommandsLink | null
+  currentlyRecoveringFrom?: CommandsLink | null
+}
+
+interface CommandsLink {
+  href: string
+  meta: {
+    runId: string
+    commandId: string
+    key: string
+    createdAt: string
+    index: number
   }
 }
 

api/.flake8

@@ -28,6 +28,7 @@ noqa-require-code = true
 # string lints in these modules; remove entries as they are fixed
 per-file-ignores =
     setup.py:ANN,D
+    src/opentrons/__init__.py:ANN,D
     src/opentrons/execute.py:ANN,D
     src/opentrons/simulate.py:ANN,D
     src/opentrons/types.py:ANN,D
@@ -46,6 +47,7 @@ per-file-ignores =
     src/opentrons/util/linal.py:ANN,D
     src/opentrons/util/entrypoint_util.py:ANN,D
     src/opentrons/util/helpers.py:ANN,D
+    tests/opentrons/test_init.py:ANN,D
     tests/opentrons/test_types.py:ANN,D
     tests/opentrons/conftest.py:ANN,D
     tests/opentrons/calibration_storage/*:ANN,D

api/src/opentrons/__init__.py

@@ -1,33 +1,47 @@
-# noqa: D104
+import os
 
+from pathlib import Path
 import logging
-from typing import List
-
-from opentrons.config import feature_flags as ff
+import re
+from typing import Any, List, Tuple
+
+from opentrons.drivers.serial_communication import get_ports_by_name
+from opentrons.hardware_control import (
+    API as HardwareAPI,
+    ThreadManager,
+    ThreadManagedHardware,
+    types as hw_types,
+)
+
+from opentrons.config import (
+    feature_flags as ff,
+    name,
+    robot_configs,
+    IS_ROBOT,
+    ROBOT_FIRMWARE_DIR,
+)
+from opentrons.util import logging_config
+from opentrons.protocols.types import ApiDeprecationError
+from opentrons.protocols.api_support.types import APIVersion
 
 from ._version import version
 
+HERE = os.path.abspath(os.path.dirname(__file__))
 __version__ = version
 
 
 LEGACY_MODULES = ["robot", "reset", "instruments", "containers", "labware", "modules"]
 
 
-__all__ = ["version", "__version__", "config"]
+__all__ = ["version", "__version__", "HERE", "config"]
 
 
 def __getattr__(attrname: str) -> None:
-    """Prevent import of legacy modules from global.
-
-    This is to officially deprecate Python API Version 1.0.
+    """
+    Prevent import of legacy modules from global to officially
+    deprecate Python API Version 1.0.
     """
     if attrname in LEGACY_MODULES:
-        # Local imports for performance. This case is not hit frequently, and we
-        # don't want to drag these imports in any time anything is imported from
-        # anywhere in the `opentrons` package.
-        from opentrons.protocols.types import ApiDeprecationError
-        from opentrons.protocols.api_support.types import APIVersion
-
         raise ApiDeprecationError(APIVersion(1, 0))
     raise AttributeError(attrname)
 
@@ -39,18 +53,98 @@ def __dir__() -> List[str]:
 log = logging.getLogger(__name__)
 
 
-# todo(mm, 2024-05-15): Having functions in the package's top-level __init__.py
-# can cause problems with import performance and circular dependencies. Can this
-# be moved elsewhere?
+SMOOTHIE_HEX_RE = re.compile("smoothie-(.*).hex")
+
+
+def _find_smoothie_file() -> Tuple[Path, str]:
+    resources: List[Path] = []
+
+    # Search for smoothie files in /usr/lib/firmware first then fall back to
+    # value packed in wheel
+    if IS_ROBOT:
+        resources.extend(ROBOT_FIRMWARE_DIR.iterdir())  # type: ignore
+
+    resources_path = Path(HERE) / "resources"
+    resources.extend(resources_path.iterdir())
+
+    for path in resources:
+        matches = SMOOTHIE_HEX_RE.search(path.name)
+        if matches:
+            branch_plus_ref = matches.group(1)
+            return path, branch_plus_ref
+    raise OSError(f"Could not find smoothie firmware file in {resources_path}")
+
+
+def _get_motor_control_serial_port() -> Any:
+    port = os.environ.get("OT_SMOOTHIE_EMULATOR_URI")
+
+    if port is None:
+        smoothie_id = os.environ.get("OT_SMOOTHIE_ID", "AMA")
+        # TODO(mc, 2021-08-01): raise a more informative exception than
+        # IndexError if a valid serial port is not found
+        port = get_ports_by_name(device_name=smoothie_id)[0]
+
+    log.info(f"Connecting to motor controller at port {port}")
+    return port
+
+
 def should_use_ot3() -> bool:
     """Return true if ot3 hardware controller should be used."""
     if ff.enable_ot3_hardware_controller():
         try:
-            # Try this OT-3-specific import as an extra check in case the feature
-            # flag is mistakenly enabled on an OT-2 for some reason.
             from opentrons_hardware.drivers.can_bus import CanDriver  # noqa: F401
 
             return True
         except ModuleNotFoundError:
             log.exception("Cannot use OT3 Hardware controller.")
     return False
+
+
+async def _create_thread_manager() -> ThreadManagedHardware:
+    """Build the hardware controller wrapped in a ThreadManager.
+
+    .. deprecated:: 4.6
+        ThreadManager is on its way out.
+    """
+    if os.environ.get("ENABLE_VIRTUAL_SMOOTHIE"):
+        log.info("Initialized robot using virtual Smoothie")
+        thread_manager: ThreadManagedHardware = ThreadManager(
+            HardwareAPI.build_hardware_simulator
+        )
+    elif should_use_ot3():
+        from opentrons.hardware_control.ot3api import OT3API
+
+        thread_manager = ThreadManager(
+            ThreadManager.nonblocking_builder(OT3API.build_hardware_controller),
+            use_usb_bus=ff.rear_panel_integration(),
+            status_bar_enabled=ff.status_bar_enabled(),
+            feature_flags=hw_types.HardwareFeatureFlags.build_from_ff(),
+        )
+    else:
+        thread_manager = ThreadManager(
+            ThreadManager.nonblocking_builder(HardwareAPI.build_hardware_controller),
+            port=_get_motor_control_serial_port(),
+            firmware=_find_smoothie_file(),
+            feature_flags=hw_types.HardwareFeatureFlags.build_from_ff(),
+        )
+
+    try:
+        await thread_manager.managed_thread_ready_async()
+    except RuntimeError:
+        log.exception("Could not build hardware controller, forcing virtual")
+        thread_manager = ThreadManager(HardwareAPI.build_hardware_simulator)
+
+    return thread_manager
+
+
+async def initialize() -> ThreadManagedHardware:
+    """
+    Initialize the Opentrons hardware returning a hardware instance.
+    """
+    robot_conf = robot_configs.load()
+    logging_config.log_init(robot_conf.log_level)
+
+    log.info(f"API server version: {version}")
+    log.info(f"Robot Name: {name()}")
+
+    return await _create_thread_manager()

api/src/opentrons/config/defaults_ot3.py

@@ -25,7 +25,6 @@
 DEFAULT_LIQUID_PROBE_SETTINGS: Final[LiquidProbeSettings] = LiquidProbeSettings(
     starting_mount_height=100,
     max_z_distance=40,
-    min_z_distance=5,
     mount_speed=10,
     plunger_speed=5,
     sensor_threshold_pascals=40,
@@ -337,7 +336,6 @@ def _build_default_liquid_probe(
             "starting_mount_height", default.starting_mount_height
         ),
         max_z_distance=from_conf.get("max_z_distance", default.max_z_distance),
-        min_z_distance=from_conf.get("min_z_distance", default.min_z_distance),
         mount_speed=from_conf.get("mount_speed", default.mount_speed),
         plunger_speed=from_conf.get("plunger_speed", default.plunger_speed),
         sensor_threshold_pascals=from_conf.get(