feat: Debug for Opentrons Simulate

[ChrisTwig]

Overview

As part of developing a complex protocol, I would like add break points on the protocol when running opentrons.simulate() to understand the current states.

Implementation details

No response

Design

No response

Acceptance criteria

No response

[ecormany]

For inspecting the state of the robot at a certain step or breakpoint, would it be more useful for you to have a text or visual representation?

[ChrisTwig]

Hi @ecormany - Thanks for the reply!

Just to be clear, for our protocols we import in custom objects to add more dynamic capabilities to our protocol (e.g from LIMS).
For example - this is one that I am currently working on.

from opentrons import protocol_api
from opentrons.protocol_api.labware import Labware
from opentrons.protocol_api import PARTIAL_COLUMN, SINGLE

# Appends path in OT2 Raspberry Pi
REMOTE_BASE_DIRECTORY = "/data/user_storage/opentrons-protocols"
if REMOTE_BASE_DIRECTORY:
    sys.path.append(REMOTE_BASE_DIRECTORY)

from rw_ot_controller.protocol_helpers import (  # noqa: E402
    load_labware_and_instrument_from_pydantic_model,
    add_stage_break,
    idx_to_char,
    load_labware_barcode_plate,
    get_row_col_end_partial_pipette,
)
from rw_ot_controller.schemas import (
    ChemicalTransformationProtocolConfig,
    TiprackType,
    Barcode,
    Well,
)  # noqa: E402

metadata = {"apiLevel": "2.23"}

def run(ctx: protocol_api.ProtocolContext):
    with open(
        f"{REMOTE_BASE_DIRECTORY}/rw_ot_controller/config_storage/{{config_id}}.json",
        "rb",
    ) as f:
        config = ChemicalTransformationProtocolConfig.model_validate_json(f.read())

    tipracks_20 = ctx.load_labware(
        load_name=TiprackType.TIPRACK_20,
        location="3",
    )
    multi_20 = ctx.load_instrument(
        config.mount_instruments[0].instrument,
        config.mount_instruments[0].mount,
        [tipracks_20],
    )
    tipracks_300 = ctx.load_labware(
        load_name=TiprackType.TIPRACK_300,
        location="6",
    )
    multi_300 = ctx.load_instrument(
        config.mount_instruments[1].instrument,
        config.mount_instruments[1].mount,
        [tipracks_300],
    )

    ### Stage 1  - Transformation Setup

    lvl_0_plates = load_labware_barcode_plate(
        ctx=ctx, barcode_plate=config.lvl_0_plates, possible_locations=["1", "4", "7"]
    )
    transformation_plates = load_labware_barcode_plate(
        ctx=ctx,
        barcode_plate=config.transformation_plates,
        possible_locations=["2", "5", "8"],
    )
    barcode_col_ends = get_row_col_end_partial_pipette(
        [o.lvl_0_barcode_wells for o in config.lvl_0_outputs]
    )

    ## Transfer from a cell plate column matching the lvl0 Layout
    for barcode_col_end, transformation_plate in zip(
        barcode_col_ends.values(), transformation_plates.values(), strict=True
    ):
        for col, end_dest in barcode_col_end.items():
            if end_dest["end"] != "H1":
                multi_20.configure_nozzle_layout(
                    style=PARTIAL_COLUMN,
                    start="H1",
                    end=end_dest["end"],
                    tip_racks=[tipracks_20],
                )
            else:
                multi_20.configure_nozzle_layout(
                    style=SINGLE, start="H1", tip_racks=[tipracks_20]
                )

            multi_20.transfer(
                source=transformation_plate.wells_by_name()[end_dest["dest"]],
                dest=transformation_plate.wells_by_name()[end_dest["dest"]],
                volume=10,
                new_tip=False,
            )

As part of our development process, we are creating tests on the output of opentrons simulate. I mainly want to run debug with opentrons.simulate() on this protocol and add breakpoints on the protocol file itself so that I can inspect the different steps.

Your suggestion on a visual rep by step would also be great.