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PyLabRobot

skills/pylabrobot/SKILL.md

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PyLabRobot

Use PyLabRobot's hardware-agnostic frontends, resource tree, trackers, and device-specific backends to develop laboratory automation. Default to local manifest validation, bookkeeping, and the software-only chatterbox backend.

Verified snapshot

  • PyPI stable: PyLabRobot==0.2.1, released 2026-03-23.
  • Upstream requirement: Python >=3.9. This skill uses Python 3.11 for its reproducible smoke tests.
  • /stable/ documentation identifies itself as 0.2.1. /dev/ and repository main describe unreleased work and must not be assumed available in 0.2.1.
  • Stable liquid-handler backends include STARBackend, VantageBackend, EVOBackend, OpentronsOT2Backend, and the offline LiquidHandlerChatterboxBackend.
  • PyLabRobot's GitHub Releases page has no 0.2.x software release entry; use the PyPI history, v0.2.1 tag, and changelog as release evidence.

Non-negotiable hardware boundary

Never connect to, initialize, home, move, heat, shake, spin, pump, open/close, or otherwise command physical equipment automatically. Do not turn a simulation plan into a live backend merely by changing an environment variable, config value, or import.

Before any separately authorized live run, require a trained human to:

  1. Explicitly confirm the exact backend, device identity, firmware, transport, deck, and protocol revision.
  2. Reconcile the physical deck against the resource tree, including carriers, adapters, lids, plates, tip racks, waste, labware orientation, barcodes, and every occupied coordinate.
  3. Verify calibration, teaching, motion envelopes, collision risks, gripper or channel clearances, and all aspiration/dispense coordinates.
  4. Review source identity and actual fill volume, dead volume, destination capacity, tip type/capacity/filter compatibility, channel mapping, units, heights, rates, liquid class, blowout/mixing, and contamination boundaries.
  5. Confirm guards, doors, waste capacity, containment, emergency stop readiness, PPE, biosafety/chemical controls, and a safe abort/recovery procedure.
  6. Approve a slow dry run or nonhazardous commissioning run when anything is new or changed.

Tracker state is bookkeeping, not sensing. It cannot prove that liquid or a tip is physically present. The Visualizer renders resource/tracker events; it does not model physics. Chatterbox prints planned operations; it does not prove calibration, reachability, collision freedom, liquid behavior, or device state.

Required intake

Do not guess any of these:

  • Exact device model, installed options, firmware, computer/OS, and transport.
  • Stable PyLabRobot version and required extras.
  • Deck/deck origin, carriers, adapters, resource definitions, dimensions, coordinates, orientations, and motion clearances.
  • Plate/tube/reservoir capacities and dead volumes; initial physical volumes.
  • Tip model, filter, fitting, capacity, rack state, channel count, and channel mapping.
  • Transfer units (uL, mm, uL/s, s), heights, rates, mixing, air gaps, blowout, liquid properties, and validated vendor liquid class.
  • Contamination policy, controls, waste handling, operator interventions, acceptance criteria, and recovery procedure.

If information is missing, produce an assumptions/blockers list and an offline draft only.

Reproducible install

For offline API inspection and chatterbox simulation:

bash
uv venv --python 3.11 .venv-pylabrobot
uv pip install --python .venv-pylabrobot/bin/python "PyLabRobot==0.2.1"

On Windows, use .venv-pylabrobot\Scripts\python.exe. Do not install hardware extras until the user names the device and explicitly approves its transport dependencies. Then inspect the matching stable device page before considering a pin such as "PyLabRobot[serial]==0.2.1" or "PyLabRobot[usb]==0.2.1".

Offline-first workflow

Run from the repository root. Every bundled CLI uses strict, bounded UTF-8 JSON/CSV, local non-symlink paths, fixed allowlists, and JSON output. None can select a live backend.

bash
python3 skills/pylabrobot/scripts/validate_manifest.py \
  --input skills/pylabrobot/tests/fixtures/protocol_manifest.json

python3 skills/pylabrobot/scripts/check_deck_geometry.py \
  --input skills/pylabrobot/tests/fixtures/protocol_manifest.json

python3 skills/pylabrobot/scripts/plan_transfers.py \
  --manifest skills/pylabrobot/tests/fixtures/protocol_manifest.json \
  --transfers skills/pylabrobot/tests/fixtures/transfers.csv

python3 skills/pylabrobot/scripts/generate_simulation_plan.py \
  --manifest skills/pylabrobot/tests/fixtures/protocol_manifest.json \
  --transfers skills/pylabrobot/tests/fixtures/transfers.csv

python3 skills/pylabrobot/scripts/inspect_backends.py \
  --expected-version 0.2.1 --strict

The geometry checker uses conservative static axis-aligned boxes; it is not a motion planner. The transfer planner requires one new tip per row and checks source/dead/destination volumes, tip capacity, wells, channels, heights, rates, units, and allowlists. Review assets/protocol-manifest.schema.json and the synthetic fixtures before making a project-specific manifest.

Verified software-only example

The exact backend below is software-only. Do not substitute a hardware backend.

python
from pylabrobot.liquid_handling import LiquidHandler
from pylabrobot.liquid_handling.backends import LiquidHandlerChatterboxBackend
from pylabrobot.resources import (
    Cor_96_wellplate_360ul_Fb,
    PLT_CAR_L5AC_A00,
    TIP_CAR_480_A00,
    hamilton_96_tiprack_1000uL_filter,
    set_tip_tracking,
    set_volume_tracking,
)
from pylabrobot.resources.hamilton import STARLetDeck

set_tip_tracking(True)
set_volume_tracking(True)

deck = STARLetDeck()
tip_carrier = TIP_CAR_480_A00(name="tip_carrier")
tips = hamilton_96_tiprack_1000uL_filter(name="tips")
tip_carrier[0] = tips
plate_carrier = PLT_CAR_L5AC_A00(name="plate_carrier")
source = Cor_96_wellplate_360ul_Fb(name="source")
destination = Cor_96_wellplate_360ul_Fb(name="destination")
plate_carrier[0] = source
plate_carrier[1] = destination
deck.assign_child_resource(tip_carrier, rails=3)
deck.assign_child_resource(plate_carrier, rails=15)
source.get_well("A1").tracker.set_volume(100.0)  # planned state, not sensing

lh = LiquidHandler(backend=LiquidHandlerChatterboxBackend(), deck=deck)
await lh.setup()  # safe here only because the backend above is software-only
try:
    await lh.pick_up_tips(tips["A1"])
    await lh.aspirate(source["A1"], vols=[10.0])
    await lh.dispense(destination["A1"], vols=[10.0])
    await lh.return_tips()
finally:
    await lh.stop()

API rules that prevent stale code

  • Current names are STARBackend, VantageBackend, EVOBackend, and OpentronsOT2Backend; do not use stale STAR, TecanBackend, OpentronsBackend, or ChatterboxBackend imports.
  • Use LiquidHandlerChatterboxBackend for generic offline liquid-handler testing. ChatterBoxBackend is a separate legacy-named export; do not conflate the two.
  • Visualizer(resource=...) is valid, followed by await vis.setup() and await vis.stop(); it starts localhost HTTP/WebSocket servers and may open a browser.
  • There is no generic from pylabrobot.liquid_handling import LiquidClass in 0.2.1. Stable liquid classes are vendor-specific, for example pylabrobot.liquid_handling.liquid_classes.hamilton.HamiltonLiquidClass.
  • Most frontend methods are async. Backend kwargs and capabilities are vendor/model specific; a shared frontend does not imply identical behavior.

References

  • Liquid handling — operations, tips, tracking, liquid classes, units, and validation.
  • Resources — decks, coordinates, plates, tip racks, collisions, state, and serialization.
  • Hardware backends — verified names, support levels, capabilities, and live-run gate.
  • Analytical equipment — plate readers and scales.
  • Material handling — pumps, heaters, shakers, temperature control, storage, and centrifuges.
  • Visualization — chatterbox, Visualizer, localhost services, and simulation limits.

Dated upstream sources

Checked 2026-07-23: