opentrons 8.6.0a11__py3-none-any.whl → 8.6.0a12__py3-none-any.whl

opentrons/_version.py

@@ -28,7 +28,7 @@ version_tuple: VERSION_TUPLE
 commit_id: COMMIT_ID
 __commit_id__: COMMIT_ID
 
-__version__ = version = '8.6.0a11'
-__version_tuple__ = version_tuple = (8, 6, 0, 'a11')
+__version__ = version = '8.6.0a12'
+__version_tuple__ = version_tuple = (8, 6, 0, 'a12')
 
 __commit_id__ = commit_id = None

opentrons/cli/analyze.py

@@ -1,4 +1,5 @@
 """Opentrons analyze CLI."""
+
 import click
 
 from anyio import run
@@ -24,7 +25,9 @@ from typing import (
 import logging
 import sys
 import json
+import gc
 
+from opentrons.protocol_engine import ProtocolEngine
 from opentrons.protocol_engine.types import (
     RunTimeParameter,
     CSVRuntimeParamPaths,
@@ -94,6 +97,18 @@ class _Output:
     help="Return analysis results as JSON, formatted for human eyes. Specify --human-json-output=- to use stdout, but be aware that Python protocols may contain print() which will make the output JSON invalid.",
     type=click.File(mode="wb"),
 )
+@click.option(
+    "--leaks",
+    help="Fail (via exit code) if the analysis engine has not been garbage collected after analysis is complete.",
+    is_flag=True,
+    default=False,
+)
+@click.option(
+    "--leaks-debug",
+    help="Drop into a PDB shell if a leak is detected",
+    is_flag=True,
+    default=False,
+)
 @click.option(
     "--check",
     help="Fail (via exit code) if the protocol had an error. If not specified, always succeed.",
@@ -133,6 +148,8 @@ def analyze(
     log_output: str,
     log_level: str,
     check: bool,
+    leaks: bool,
+    leaks_debug: bool,
 ) -> int:
     """Analyze a protocol.
 
@@ -147,7 +164,18 @@ def analyze(
 
     try:
         with _capture_logs(log_output, log_level):
-            sys.exit(run(_analyze, files, rtp_values, rtp_files, outputs, check))
+            sys.exit(
+                run(
+                    _analyze,
+                    files,
+                    rtp_values,
+                    rtp_files,
+                    outputs,
+                    check,
+                    leaks or leaks_debug,
+                    leaks_debug,
+                )
+            )
     except click.ClickException:
         raise
     except Exception as e:
@@ -344,12 +372,14 @@ async def _do_analyze(
     return await orchestrator.run(deck_configuration=[])
 
 
-async def _analyze(
+async def _analyze(  # noqa: C901
     files_and_dirs: Sequence[Path],
     rtp_values: str,
     rtp_files: str,
     outputs: Sequence[_Output],
     check: bool,
+    fail_on_leak: bool,
+    debug_on_leak: bool,
 ) -> int:
     input_files = _get_input_files(files_and_dirs)
     parsed_rtp_values = _get_runtime_parameter_values(rtp_values)
@@ -366,6 +396,32 @@ async def _analyze(
     analysis = await _do_analyze(protocol_source, parsed_rtp_values, rtp_paths)
     return_code = _get_return_code(analysis)
 
+    # This ugly code checks to see if an engine remains past garbage collection
+    # after analysis is complete.
+    # It should be here and open coded to make it a little easier to present
+    # the debug option.
+    if fail_on_leak or debug_on_leak:
+        gc.collect()
+        leaked_engine = next(
+            (obj for obj in gc.get_objects() if isinstance(obj, ProtocolEngine)), None
+        )
+        if leaked_engine:
+            if fail_on_leak:
+                print(
+                    "A ProtocolEngine instance exists even after garbage collection; "
+                    "some thing (likely in the protocol) has caused it to be leaked, "
+                    "likely by reference to the engine or something that refers to the "
+                    "engine after the run function ends.",
+                    file=sys.stderr,
+                )
+                return_code = -2
+            if debug_on_leak:
+                print(
+                    "You are now in an interactive PDB (https://docs.python.org/3.10/library/pdb.html) "
+                    "session; the leaked engine is bound to the variable leaked_engine."
+                )
+                breakpoint()
+
     if not outputs:
         return return_code
 

opentrons/protocol_api/core/engine/transfer_components_executor.py

@@ -5,7 +5,7 @@ import logging
 from copy import deepcopy
 from enum import Enum
 from typing import TYPE_CHECKING, Optional, Union, Literal
-from dataclasses import dataclass, field
+from dataclasses import dataclass, field, replace
 
 from opentrons_shared_data.liquid_classes.liquid_class_definition import (
     PositionReference,
@@ -21,7 +21,6 @@ from opentrons.protocol_api._liquid_properties import (
     MultiDispenseProperties,
     TouchTipProperties,
 )
-from opentrons.protocol_engine.errors import TouchTipDisabledError
 from opentrons.types import Location, Point, Mount
 from opentrons.protocols.advanced_control.transfers.transfer_liquid_utils import (
     LocationCheckDescriptors,
@@ -466,7 +465,7 @@ class TransferComponentsExecutor:
         2. If blowout is enabled and “destination”
             - Do blow-out (at the retract position)
             - Leave plunger down
-        3. Touch-tip
+        3. Touch-tip in the destination well.
         4. If not ready-to-aspirate
             - Prepare-to-aspirate (at the retract position)
         5. Air-gap (at the retract position)
@@ -479,7 +478,7 @@ class TransferComponentsExecutor:
         6. If blowout is “source” or “trash”
             - Move to location (top of Well)
             - Do blow-out (top of well)
-            - Do touch-tip (?????) (only if it’s in a non-trash location)
+            - Do touch-tip AGAIN at the source well (if blowout in a non-trash location)
             - Prepare-to-aspirate (top of well)
             - Do air-gap (top of well)
         7. If drop tip, move to drop tip location, drop tip
@@ -563,9 +562,9 @@ class TransferComponentsExecutor:
             blowout_props.enabled
             and blowout_props.location != BlowoutLocation.DESTINATION
         ):
-            # TODO: no-op touch tip if touch tip is enabled and blowout is in trash/ reservoir/ any labware with touch-tip disabled
             assert blowout_props.flow_rate is not None
             self._instrument.set_flow_rate(blow_out=blowout_props.flow_rate)
+            blowout_touch_tip_props = retract_props.touch_tip
             touch_tip_and_air_gap_location: Union[Location, TrashBin, WasteChute]
             if blowout_props.location == BlowoutLocation.SOURCE:
                 if source_location is None or source_well is None:
@@ -584,6 +583,13 @@ class TransferComponentsExecutor:
                     source_well.get_top(0), labware=source_location.labware
                 )
                 touch_tip_and_air_gap_well = source_well
+                # Skip touch tip if blowing out at the SOURCE and it's untouchable:
+                if (
+                    "touchTipDisabled"
+                    in source_location.labware.quirks_from_any_parent()
+                ):
+                    blowout_touch_tip_props = replace(blowout_touch_tip_props)
+                    blowout_touch_tip_props.enabled = False
             else:
                 self._instrument.blow_out(
                     location=trash_location,
@@ -612,7 +618,7 @@ class TransferComponentsExecutor:
             )
             # Do touch tip and air gap again after blowing out into source well or trash
             self._do_touch_tip_and_air_gap_after_dispense(
-                touch_tip_properties=retract_props.touch_tip,
+                touch_tip_properties=blowout_touch_tip_props,
                 location=touch_tip_and_air_gap_location,
                 well=touch_tip_and_air_gap_well,
                 air_gap_volume=air_gap_volume,
@@ -758,6 +764,7 @@ class TransferComponentsExecutor:
         ):
             assert blowout_props.flow_rate is not None
             self._instrument.set_flow_rate(blow_out=blowout_props.flow_rate)
+            blowout_touch_tip_props = retract_props.touch_tip
             touch_tip_and_air_gap_location: Union[Location, TrashBin, WasteChute]
             if blowout_props.location == BlowoutLocation.SOURCE:
                 if source_location is None or source_well is None:
@@ -776,6 +783,13 @@ class TransferComponentsExecutor:
                     source_well.get_top(0), labware=source_location.labware
                 )
                 touch_tip_and_air_gap_well = source_well
+                # Skip touch tip if blowing out at the SOURCE and it's untouchable:
+                if (
+                    "touchTipDisabled"
+                    in source_location.labware.quirks_from_any_parent()
+                ):
+                    blowout_touch_tip_props = replace(blowout_touch_tip_props)
+                    blowout_touch_tip_props.enabled = False
             else:
                 self._instrument.blow_out(
                     location=trash_location,
@@ -807,13 +821,13 @@ class TransferComponentsExecutor:
                 air_gap_volume = 0
             # Do touch tip and air gap again after blowing out into source well or trash
             self._do_touch_tip_and_air_gap_after_dispense(
-                touch_tip_properties=retract_props.touch_tip,
+                touch_tip_properties=blowout_touch_tip_props,
                 location=touch_tip_and_air_gap_location,
                 well=touch_tip_and_air_gap_well,
                 air_gap_volume=air_gap_volume,
             )
 
-    def _do_touch_tip_and_air_gap_after_dispense(  # noqa: C901
+    def _do_touch_tip_and_air_gap_after_dispense(
         self,
         touch_tip_properties: TouchTipProperties,
         location: Union[Location, TrashBin, WasteChute],
@@ -822,6 +836,12 @@ class TransferComponentsExecutor:
     ) -> None:
         """Perform touch tip and air gap as part of post-dispense retract.
 
+        This function can be invoked up to 2 times for each dispense:
+        1) Once for touching tip at the dispense location.
+        2) Then again in the blowout location if it is not the dispense location.
+        For case (2), the caller should disable touch-tip in touch_tip_properties
+        if the blowout location is not touchable (such as reservoirs).
+
         If the retract location is at or above the safe location of
         AIR_GAP_LOC_Z_OFFSET_FROM_WELL_TOP, then add the air gap at the retract location
         (where the pipette is already assumed to be at).
@@ -842,18 +862,14 @@ class TransferComponentsExecutor:
             #  whether the touch tip params from transfer props should be used for
             #  both dest-well touch tip and non-dest-well touch tip.
             if isinstance(location, Location) and well is not None:
-                try:
-                    self._instrument.touch_tip(
-                        location=location,
-                        well_core=well,
-                        radius=1,
-                        z_offset=touch_tip_properties.z_offset,
-                        speed=touch_tip_properties.speed,
-                        mm_from_edge=touch_tip_properties.mm_from_edge,
-                    )
-                except TouchTipDisabledError:
-                    # TODO: log a warning
-                    pass
+                self._instrument.touch_tip(
+                    location=location,
+                    well_core=well,
+                    radius=1,
+                    z_offset=touch_tip_properties.z_offset,
+                    speed=touch_tip_properties.speed,
+                    mm_from_edge=touch_tip_properties.mm_from_edge,
+                )
 
                 # Move back to the 'retract' position
                 self._instrument.move_to(

{opentrons-8.6.0a11.dist-info → opentrons-8.6.0a12.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: opentrons
-Version: 8.6.0a11
+Version: 8.6.0a12
 Summary: The Opentrons API is a simple framework designed to make writing automated biology lab protocols easy.
 Project-URL: opentrons.com, https://www.opentrons.com
 Project-URL: Source Code On Github, https://github.com/Opentrons/opentrons/tree/edge/api
@@ -24,7 +24,7 @@ Requires-Dist: click<9,>=8.0.0
 Requires-Dist: importlib-metadata>=1.0; python_version < '3.8'
 Requires-Dist: jsonschema<4.18.0,>=3.0.1
 Requires-Dist: numpy<2,>=1.20.0
-Requires-Dist: opentrons-shared-data==8.6.0a11
+Requires-Dist: opentrons-shared-data==8.6.0a12
 Requires-Dist: packaging>=21.0
 Requires-Dist: pydantic-settings<3,>=2
 Requires-Dist: pydantic<3,>=2.0.0
@@ -32,6 +32,6 @@ Requires-Dist: pyserial>=3.5
 Requires-Dist: pyusb==1.2.1
 Requires-Dist: typing-extensions<5,>=4.0.0
 Provides-Extra: flex-hardware
-Requires-Dist: opentrons-hardware[flex]==8.6.0a11; extra == 'flex-hardware'
+Requires-Dist: opentrons-hardware[flex]==8.6.0a12; extra == 'flex-hardware'
 Provides-Extra: ot2-hardware
-Requires-Dist: opentrons-hardware==8.6.0a11; extra == 'ot2-hardware'
+Requires-Dist: opentrons-hardware==8.6.0a12; extra == 'ot2-hardware'

{opentrons-8.6.0a11.dist-info → opentrons-8.6.0a12.dist-info}/RECORD

@@ -1,5 +1,5 @@
 opentrons/__init__.py,sha256=TQ_Ca_zzAM3iLzAysWKkFkQHG8-imihxDPQbLCYrf-E,4533
-opentrons/_version.py,sha256=XzkMHritnW-N0LeUA3PW5LD3vls19RpD5UeJgpXrBuI,714
+opentrons/_version.py,sha256=Ej-eiQxj2liXf3S-OFMSv77mR8rEtkyJT0yFtbesf_E,714
 opentrons/execute.py,sha256=Y88qICDiHWQjU0L4Ou7DI5OXXu7zZcdkUvNUYmZqIfc,29282
 opentrons/legacy_broker.py,sha256=XnuEBBlrHCThc31RFW2UR0tGqctqWZ-CZ9vSC4L9whU,1553
 opentrons/ordered_set.py,sha256=g-SB3qA14yxHu9zjGyc2wC7d2TUCBE6fKZlHAtbPzI8,4082
@@ -28,7 +28,7 @@ opentrons/calibration_storage/ot3/models/__init__.py,sha256=47DEQpj8HBSa-_TImW-5
 opentrons/calibration_storage/ot3/models/v1.py,sha256=SZU9CilK4HjPNtE-6mLcGX4ZsT3o0PGX8-RPjogmwXY,4393
 opentrons/cli/__init__.py,sha256=zP_n-SnZnZc_yzb0JnnwvUvIBiIpupGOQrqPZrSmnRs,430
 opentrons/cli/__main__.py,sha256=Jvtl3eMKDT1eX00BGULAw6WqenKe911TMTg4b97y5dA,73
-opentrons/cli/analyze.py,sha256=70ZR9bTZCedmvaYcrklRZXozgINf_gZseYgb1oSZVJ8,14837
+opentrons/cli/analyze.py,sha256=sZHRQxVyQASunYpjl0iks_Gkc8K6iX79cBuaipHfVys,16747
 opentrons/config/__init__.py,sha256=N_ls4aKFt5jrXiPg-M8g2ecc2PgEzH2qTjbPjlr2fFk,21488
 opentrons/config/advanced_settings.py,sha256=CzR1IzIMGMkvzyzwIjaVR7_ZIZ9_zr-Odgq2Ij4K4vU,27215
 opentrons/config/defaults_ot2.py,sha256=_l63QNW0aWTh0HGZcgF592ETJg8-W4M0XrQbbzkAPjA,6031
@@ -264,7 +264,7 @@ opentrons/protocol_api/core/engine/point_calculations.py,sha256=C2eF0fvJQGMqQv3D
 opentrons/protocol_api/core/engine/protocol.py,sha256=uX-qwATcTXiEUXe9gGDmp1cJ1Xd4eQnyy-q_jpiyAYY,46023
 opentrons/protocol_api/core/engine/robot.py,sha256=bzUt23NG-clD-9-QFsV_6nm3fMgSmvYEG9DyyZI1xgw,5366
 opentrons/protocol_api/core/engine/stringify.py,sha256=GwFgEhFMk-uPfFQhQG_2mkaf4cxaItiY8RW7rZwiooQ,2794
-opentrons/protocol_api/core/engine/transfer_components_executor.py,sha256=PAH4hpg5QIp9gwsq0segY113_3ZyRgDV4OnDagNSrTE,44306
+opentrons/protocol_api/core/engine/transfer_components_executor.py,sha256=mR59C-e6IHSZthlbQEwmRnh5ye8lhr6a0Qp5CNNi9n8,45211
 opentrons/protocol_api/core/engine/well.py,sha256=IaaFK-3hoUfabfn_twIT7zcAynhzAmRxDnvABss2szo,8923
 opentrons/protocol_api/core/legacy/__init__.py,sha256=_9jCJNKG3SlS_vljVu8HHkZmtLf4F-f-JHALLF5d5go,401
 opentrons/protocol_api/core/legacy/_labware_geometry.py,sha256=ugtMdfnSkUwBCC3Sdj5nP5aDUxX-Dr7BeiuPVmdjAtg,1091
@@ -594,8 +594,8 @@ opentrons/util/linal.py,sha256=IlKAP9HkNBBgULeSf4YVwSKHdx9jnCjSr7nvDvlRALg,5753
 opentrons/util/logging_config.py,sha256=7et4YYuQdWdq_e50U-8vFS_QyNBRgdnqPGAQJm8qrIo,9954
 opentrons/util/logging_queue_handler.py,sha256=ZsSJwy-oV8DXwpYiZisQ1PbYwmK2cOslD46AcyJ1E4I,2484
 opentrons/util/performance_helpers.py,sha256=ew7H8XD20iS6-2TJAzbQeyzStZkkE6PzHt_Adx3wbZQ,5172
-opentrons-8.6.0a11.dist-info/METADATA,sha256=uZEZHKsnnX6BkeHSzCP31LsjH-ipHwePKN-Ip8JI4hM,1611
-opentrons-8.6.0a11.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
-opentrons-8.6.0a11.dist-info/entry_points.txt,sha256=fTa6eGCYkvOtv0ov-KVE8LLGetgb35LQLF9x85OWPVw,106
-opentrons-8.6.0a11.dist-info/licenses/LICENSE,sha256=z8d0m5b2O9McPEK1xHG_dWgUBT6EfBDz6wA0F7xSPTA,11358
-opentrons-8.6.0a11.dist-info/RECORD,,
+opentrons-8.6.0a12.dist-info/METADATA,sha256=l9QH2vlXU_XB9ZQoxc0ls8JKOmdyxwzStTlW-DmhdUw,1611
+opentrons-8.6.0a12.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
+opentrons-8.6.0a12.dist-info/entry_points.txt,sha256=fTa6eGCYkvOtv0ov-KVE8LLGetgb35LQLF9x85OWPVw,106
+opentrons-8.6.0a12.dist-info/licenses/LICENSE,sha256=z8d0m5b2O9McPEK1xHG_dWgUBT6EfBDz6wA0F7xSPTA,11358
+opentrons-8.6.0a12.dist-info/RECORD,,