feat(step-generation, app): emit distribute_with_liquid_class for python #18603

jerader · 2025-06-11T16:33:45Z

Overview

This PR introduces distribute_with_liquid_class in distribute compound command in step-generation

Test Plan and Hands on Testing

Review code and test creating a distribute step and uploading to the app. should pass analysis

import json
from contextlib import nullcontext as pd_step
from opentrons import protocol_api, types

metadata = {
    "created": "2025-06-11T16:24:47.170Z",
    "lastModified": "2025-06-11T16:25:37.105Z",
    "protocolDesigner": "8.4.4",
    "source": "Protocol Designer",
}

requirements = {
    "robotType": "Flex",
    "apiLevel": "2.24",
}

def run(protocol: protocol_api.ProtocolContext) -> None:
    # Load Labware:
    tip_rack_1 = protocol.load_labware(
        "opentrons_flex_96_tiprack_50ul",
        location="C2",
        namespace="opentrons",
        version=1,
    )
    well_plate_1 = protocol.load_labware(
        "biorad_96_wellplate_200ul_pcr",
        location="D1",
        namespace="opentrons",
        version=3,
    )

    # Load Pipettes:
    pipette_left = protocol.load_instrument("flex_1channel_50", "left", tip_racks=[tip_rack_1])

    # Load Trash Bins:
    trash_bin_1 = protocol.load_trash_bin("A3")

    # Define Liquids:
    liquid_1 = protocol.define_liquid(
        "h20",
        display_color="#b925ff",
    )

    # Load Liquids:
    well_plate_1["A1"].load_liquid(liquid_1, 10)
    well_plate_1["B1"].load_liquid(liquid_1, 10)
    well_plate_1["C1"].load_liquid(liquid_1, 10)
    well_plate_1["D1"].load_liquid(liquid_1, 10)
    well_plate_1["E1"].load_liquid(liquid_1, 10)
    well_plate_1["F1"].load_liquid(liquid_1, 10)
    well_plate_1["G1"].load_liquid(liquid_1, 10)
    well_plate_1["H1"].load_liquid(liquid_1, 10)

    # Load Liquid Classes:
    water_v1 = protocol.get_liquid_class("water")

    # PROTOCOL STEPS

    # Step 1:
    pipette_left.distribute_with_liquid_class(
        volume=10,
        source=[well_plate_1["A1"]],
        dest=[well_plate_1["F12"], well_plate_1["G12"], well_plate_1["H12"]],
        new_tip="once",
        trash_location=trash_bin_1,
        liquid_class=protocol.define_liquid_class(
            name="distribute_step_1",
            base_liquid_class=water_v1,
            properties={
                "p50_single_flex": {"opentrons/opentrons_flex_96_tiprack_50ul/1": {
                    "aspirate": {
                        "aspirate_position": {
                            "offset": {
                                "x": 0,
                                "y": 0,
                                "z": 2,
                            },
                            "position_reference": "well-bottom",
                        },
                        "flow_rate_by_volume": [(0, 32.2)],
                        "pre_wet": False,
                        "correction_by_volume": [(0, 0)],
                        "delay": {
                            "enabled": True,
                            "duration": 0.2,
                        },
                        "mix": {"enabled": False},
                        "submerge": {
                            "delay": {"enabled": False},
                            "speed": 100,
                            "start_position": {
                                "offset": {
                                    "x": 0,
                                    "y": 0,
                                    "z": 2,
                                },
                                "position_reference": "well-top",
                            },
                        },
                        "retract": {
                            "air_gap_by_volume": [(0, 0)],
                            "delay": {"enabled": False},
                            "end_position": {
                                "offset": {
                                    "x": 0,
                                    "y": 0,
                                    "z": 2,
                                },
                                "position_reference": "well-top",
                            },
                            "speed": 50,
                            "touch_tip": {"enabled": False},
                        },
                    },
                    "dispense": {
                        "dispense_position": {
                            "offset": {
                                "x": 0,
                                "y": 0,
                                "z": 2,
                            },
                            "position_reference": "well-bottom",
                        },
                        "push_out_by_volume": [(0, 2)],
                        "flow_rate_by_volume": [(0, 50)],
                        "correction_by_volume": [(0, 0)],
                        "delay": {
                            "enabled": True,
                            "duration": 0.2,
                        },
                        "submerge": {
                            "delay": {"enabled": False},
                            "speed": 100,
                            "start_position": {
                                "offset": {
                                    "x": 0,
                                    "y": 0,
                                    "z": 2,
                                },
                                "position_reference": "well-top",
                            },
                        },
                        "mix": {"enable": False},
                        "retract": {
                            "air_gap_by_volume": [(0, 0)],
                            "delay": {"enabled": False},
                            "end_position": {
                                "offset": {
                                    "x": 0,
                                    "y": 0,
                                    "z": 2,
                                },
                                "position_reference": "well-top",
                            },
                            "speed": 50,
                            "touch_tip": {"enabled": False},
                            "blowout": {
                                "enabled": True,
                                "location": "trash",
                                "flow_rate": 50,
                            },
                            "conditioning_by_volume": [(0, 5)],
                            "disposal_by_volume": [(0, 5)],
                        },
                    },
                }},
            },
        ),
    )

DESIGNER_APPLICATION = """{"robot":{"model":"OT-3 Standard"},"designerApplication":{"name":"opentrons/protocol-designer","version":"8.5.0","data":{"pipetteTiprackAssignments":{"a6ef8103-01f5-4b11-987a-a0ee157c9db8":["opentrons/opentrons_flex_96_tiprack_50ul/1"]},"dismissedWarnings":{"form":[],"timeline":[]},"ingredients":{"0":{"displayName":"h20","displayColor":"#b925ff","liquidClass":"waterV1","description":null,"liquidGroupId":"0"}},"ingredLocations":{"8ae752f6-c1db-4961-919f-2263bb8c5ede:opentrons/biorad_96_wellplate_200ul_pcr/3":{"A1":{"0":{"volume":10}},"B1":{"0":{"volume":10}},"C1":{"0":{"volume":10}},"D1":{"0":{"volume":10}},"E1":{"0":{"volume":10}},"F1":{"0":{"volume":10}},"G1":{"0":{"volume":10}},"H1":{"0":{"volume":10}}}},"savedStepForms":{"__INITIAL_DECK_SETUP_STEP__":{"stepType":"manualIntervention","id":"__INITIAL_DECK_SETUP_STEP__","labwareLocationUpdate":{"5078453b-c146-4f7e-ae1e-ed3633312d16:opentrons/opentrons_flex_96_tiprack_50ul/1":"C2","8ae752f6-c1db-4961-919f-2263bb8c5ede:opentrons/biorad_96_wellplate_200ul_pcr/3":"D1"},"pipetteLocationUpdate":{"a6ef8103-01f5-4b11-987a-a0ee157c9db8":"left"},"moduleLocationUpdate":{},"trashBinLocationUpdate":{"07d18bcf-d000-43e6-9efc-5e744bc02ae0:trashBin":"cutoutA3"},"wasteChuteLocationUpdate":{},"stagingAreaLocationUpdate":{},"gripperLocationUpdate":{}},"447a44fa-088f-405d-8f2d-197791e7368e":{"id":"447a44fa-088f-405d-8f2d-197791e7368e","stepType":"moveLiquid","stepName":"transfer","stepDetails":"","stepNumber":0,"aspirate_airGap_checkbox":false,"aspirate_airGap_volume":null,"aspirate_delay_checkbox":true,"aspirate_delay_mmFromBottom":null,"aspirate_delay_seconds":"0.2","aspirate_flowRate":"32.2","aspirate_labware":"8ae752f6-c1db-4961-919f-2263bb8c5ede:opentrons/biorad_96_wellplate_200ul_pcr/3","aspirate_mix_checkbox":false,"aspirate_mix_times":"1","aspirate_mix_volume":"50","aspirate_mmFromBottom":2,"aspirate_position_reference":"well-bottom","aspirate_retract_delay_seconds":"0","aspirate_retract_mmFromBottom":2,"aspirate_retract_speed":"50","aspirate_retract_x_position":0,"aspirate_retract_y_position":0,"aspirate_retract_position_reference":"well-top","aspirate_submerge_delay_seconds":"0","aspirate_submerge_speed":"100","aspirate_submerge_mmFromBottom":2,"aspirate_submerge_x_position":0,"aspirate_submerge_y_position":0,"aspirate_submerge_position_reference":"well-top","aspirate_touchTip_checkbox":false,"aspirate_touchTip_mmFromTop":-1,"aspirate_touchTip_speed":"30","aspirate_touchTip_mmFromEdge":"0.5","aspirate_wellOrder_first":"t2b","aspirate_wellOrder_second":"l2r","aspirate_wells_grouped":false,"aspirate_wells":["A1"],"aspirate_x_position":0,"aspirate_y_position":0,"blowout_checkbox":false,"blowout_flowRate":"50","blowout_location":"07d18bcf-d000-43e6-9efc-5e744bc02ae0:trashBin","blowout_z_offset":0,"changeTip":"once","conditioning_checkbox":true,"conditioning_volume":"5","dispense_airGap_checkbox":false,"dispense_airGap_volume":"","dispense_delay_checkbox":true,"dispense_delay_mmFromBottom":null,"dispense_delay_seconds":"0.2","dispense_flowRate":"50","dispense_labware":"8ae752f6-c1db-4961-919f-2263bb8c5ede:opentrons/biorad_96_wellplate_200ul_pcr/3","dispense_mix_checkbox":false,"dispense_mix_times":null,"dispense_mix_volume":null,"dispense_mmFromBottom":2,"dispense_position_reference":"well-bottom","dispense_retract_delay_seconds":"0","dispense_retract_mmFromBottom":2,"dispense_retract_speed":"50","dispense_retract_x_position":0,"dispense_retract_y_position":0,"dispense_retract_position_reference":"well-top","dispense_submerge_delay_seconds":"0","dispense_submerge_speed":"100","dispense_submerge_mmFromBottom":2,"dispense_submerge_x_position":0,"dispense_submerge_y_position":0,"dispense_submerge_position_reference":"well-top","dispense_touchTip_checkbox":false,"dispense_touchTip_mmFromTop":-1,"dispense_touchTip_speed":"30","dispense_touchTip_mmFromEdge":"0.5","dispense_wellOrder_first":"t2b","dispense_wellOrder_second":"l2r","dispense_wells":["F12","G12","H12"],"dispense_x_position":0,"dispense_y_position":0,"disposalVolume_checkbox":true,"disposalVolume_volume":"5","dropTip_location":"07d18bcf-d000-43e6-9efc-5e744bc02ae0:trashBin","liquidClassesSupported":true,"liquidClass":"waterV1","nozzles":null,"path":"multiDispense","pipette":"a6ef8103-01f5-4b11-987a-a0ee157c9db8","preWetTip":false,"pushOut_checkbox":true,"pushOut_volume":"2","tipRack":"opentrons/opentrons_flex_96_tiprack_50ul/1","volume":"10"}},"orderedStepIds":["447a44fa-088f-405d-8f2d-197791e7368e"],"pipettes":{"a6ef8103-01f5-4b11-987a-a0ee157c9db8":{"pipetteName":"p50_single_flex"}},"modules":{},"labware":{"5078453b-c146-4f7e-ae1e-ed3633312d16:opentrons/opentrons_flex_96_tiprack_50ul/1":{"displayName":"Opentrons Flex 96 Tip Rack 50 µL","labwareDefURI":"opentrons/opentrons_flex_96_tiprack_50ul/1"},"8ae752f6-c1db-4961-919f-2263bb8c5ede:opentrons/biorad_96_wellplate_200ul_pcr/3":{"displayName":"Bio-Rad 96 Well Plate 200 µL PCR","labwareDefURI":"opentrons/biorad_96_wellplate_200ul_pcr/3"}}}},"metadata":{"protocolName":"","author":"","description":"","source":"Protocol Designer","created":1749659087170,"lastModified":1749659137105}}"""

Changelog

update getCustomLiquidClassProperties to account for the distribute args disposalVolume and conditioningVolume
wire up distribute_with_liquid_class in distribute
add some unit tests to test the different args
fix for quick transfer

Risk assessment

low, behind ff

closes AUTH-1098

closes AUTH-1099

codecov · 2025-06-11T16:35:27Z

Codecov Report

Attention: Patch coverage is 88.81119% with 16 lines in your changes missing coverage. Please review.

Project coverage is 23.74%. Comparing base (71e6b93) to head (616114b).
Report is 1 commits behind head on chore_release-pd-8.5.0.

Files with missing lines	Patch %	Lines
...eration/src/commandCreators/compound/distribute.ts	87.39%	15 Missing ⚠️
...organisms/ODD/QuickTransferFlow/utils/pythonDef.ts	0.00%	1 Missing ⚠️

Additional details and impacted files

@@                    Coverage Diff                     @@
##           chore_release-pd-8.5.0   #18603      +/-   ##
==========================================================
- Coverage                   25.88%   23.74%   -2.14%     
==========================================================
  Files                        3279     3233      -46     
  Lines                      284277   279751    -4526     
  Branches                    28648    28095     -553     
==========================================================
- Hits                        73579    66440    -7139     
- Misses                     210671   213284    +2613     
  Partials                       27       27

Flag	Coverage Δ
protocol-designer	`19.11% <78.32%> (-0.14%)`	⬇️
step-generation	`5.17% <87.41%> (+0.28%)`	⬆️

Flags with carried forward coverage won't be shown. Click here to find out more.

Files with missing lines	Coverage Δ
...c/timelineMiddleware/generateRobotStateTimeline.ts	`78.30% <100.00%> (+3.30%)`	⬆️
step-generation/src/utils/liquidClassUtils.ts	`99.51% <100.00%> (-0.49%)`	⬇️
...organisms/ODD/QuickTransferFlow/utils/pythonDef.ts	`0.00% <0.00%> (ø)`
...eration/src/commandCreators/compound/distribute.ts	`73.46% <87.39%> (+15.70%)`	⬆️

... and 258 files with indirect coverage changes

🚀 New features to boost your workflow:

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📦 JS Bundle Analysis: Save yourself from yourself by tracking and limiting bundle sizes in JS merges.

ddcc4 · 2025-06-13T22:59:17Z

app/src/organisms/ODD/QuickTransferFlow/__tests__/utils/quickTransferStepCommands.test.ts

+                            "x": 0,
+                            "y": 0,
+                            "z": 0,
+                        },


You might have to update your test after I checked in the change to generate more compact code. (This line would probably be something like "offset": {"x": 0, "y": 0, "z": 0},

ddcc4 · 2025-06-13T23:00:48Z

app/src/organisms/ODD/QuickTransferFlow/utils/pythonDef.ts

-    `# ${upperCase(stepArgs?.commandCreatorFnName)} STEP\n\n` +
-    nonLoadCommands +
-    `\n` +
-    finalDropTipCommand


So after this change, the drop tip will always be handled by transfer/consolidate/distribute_with_liquid_class() now?

correct! since QT does not support mix()

jerader added 5 commits June 11, 2025 08:47

consolidate with liquid class support

659505b

feat(step-generation, app): emit consolidate_with_liquid_class in python

40ab32c

closes AUTH-1098

fix arg name

57ba773

add comment and fix typo

5641d95

feat(step-generation, app): emit distribute_with_liquid_class for python

65a3dea

closes AUTH-1099

jerader added the DO NOT MERGE Indicates a PR should not be merged, even if there's a shiny green merge button available label Jun 11, 2025

jerader added 2 commits June 11, 2025 12:37

show mix enabled for dispense in distribute

c48f232

Merge branch 'chore_release-pd-8.5.0' into sg_distribute-liquid-class

32ce693

jerader removed the DO NOT MERGE Indicates a PR should not be merged, even if there's a shiny green merge button available label Jun 13, 2025

clean up

1085159

jerader marked this pull request as ready for review June 13, 2025 15:57

jerader requested review from a team as code owners June 13, 2025 15:57

jerader requested review from TamarZanzouri and ddcc4 and removed request for a team June 13, 2025 15:57

ddcc4 approved these changes Jun 13, 2025

View reviewed changes

jerader added 2 commits June 16, 2025 08:11

Merge branch 'chore_release-pd-8.5.0' into sg_distribute-liquid-class

1c919cb

fix py formatting

616114b

jerader merged commit 237544a into chore_release-pd-8.5.0 Jun 16, 2025
44 checks passed

jerader deleted the sg_distribute-liquid-class branch June 16, 2025 12:50

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Overview

Test Plan and Hands on Testing

Changelog

Risk assessment

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