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Material handling, pumps, and environmental devices

skills/pylabrobot/references/material-handling.md

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Material handling, pumps, and environmental devices

Verified against PyLabRobot 0.2.1 on 2026-07-23. Every operation in this domain can create physical motion, pressure, heat, or stored energy. The snippets below identify APIs only; they do not connect to devices.

Pumps

Stable frontend and one stable backend export:

python
from pylabrobot.pumps import MasterflexBackend, Pump

Verified Pump methods:

text
run_revolutions(num_revolutions)
run_continuously(speed)
run_for_duration(speed, duration)
halt()

The stale methods start, stop as a pumping command, pump_volume, and calibrate(duration=..., speed=..., volume=...) are not the verified universal 0.2.1 frontend shown above. stop() belongs to machine lifecycle; halt() is the pump-motion command.

MasterflexBackend(com_port) is transport-specific. Do not instantiate it during discovery. Stable supported machines labels Cole-Parmer Masterflex L/S listed models and Agrowtek Pump Array as Full.

Pump safety

Before a separately authorized run, verify:

  • exact pump/head/tubing model, material, inner diameter, direction, occlusion, fittings, valves, clamps, and destination;
  • calibrated relationship among command speed/revolutions/time and delivered volume for the current fluid, tubing age, backpressure, and temperature;
  • prime/purge route, bubbles, siphoning, dead volume, residual volume, maximum pressure/flow, leak containment, and waste capacity;
  • chemical/biological compatibility, cross-contamination controls, and tubing change policy;
  • an accessible stop and safe behavior on disconnect, timeout, or partial delivery.

A time/speed command is not a measured volume. Record the calibration and uncertainty; use a validated scale/flow sensor if closed-loop confirmation is required.

Heater shakers and shakers

Stable frontend imports:

python
from pylabrobot.heating_shaking import (
    HamiltonHeaterShakerBackend,
    HeaterShaker,
    InhecoThermoshakeBackend,
)
from pylabrobot.shaking import Shaker

The stable class is InhecoThermoshakeBackend (lowercase s in Thermoshake), not the stale InhecoThermoShakeBackend.

Verified HeaterShaker methods:

text
set_temperature(temperature, passive=False)
get_temperature()
shake(speed, duration=None, **backend_kwargs)
stop_shaking(**backend_kwargs)
lock_plate(**backend_kwargs)
unlock_plate(**backend_kwargs)

The old names set_shake_rate and set_temperature(None) are not the verified 0.2.1 frontend signatures. Use the exact device page for deactivation/cooling and do not substitute zero/None unless documented for that backend.

HeaterShaker construction requires name, dimensions, backend, and a child_location. Backend construction is also device topology-specific: HamiltonHeaterShakerBackend(index, interface) and InhecoThermoshakeBackend(index, control_box) require approved shared interfaces/controllers.

Stable supported machines lists:

  • Inheco Thermoshake and Thermoshake AC: Full
  • Opentrons Thermoshake: Full
  • Hamilton Heater Shaker: Full
  • QInstruments BioShake: Full

Heater/shaker safety

Confirm plate compatibility, mass, balance, lid/seal, locking, condensation, spillage containment, orbit/speed limits, thermal limits, ramp/equilibration, sensor calibration, and safe unlock temperature. Never unlock or move a plate while shaking. Treat a requested setpoint as a command, not proof that the sample has reached that temperature.

Temperature controllers

Stable frontend:

python
from pylabrobot.temperature_controlling import TemperatureController

Verified methods:

text
set_temperature(temperature, passive=False)
get_temperature()
deactivate()

Stable support includes Inheco CPAC (Full) and Opentrons Temperature Module (Mostly in the complete stable table). Validate active cooling, condensation, plate/adapter contact, setpoint range, ramp, sensor placement, overshoot, and sample-versus-block temperature.

Centrifuges

Stable imports:

python
from pylabrobot.centrifuge import Access2Backend, Centrifuge, VSpinBackend

Verified frontend:

text
open_door()
close_door()
lock_door()
unlock_door()
spin(g, duration, **backend_kwargs)

The stable method takes relative centrifugal force g, not the stale speed=... RPM argument. Converting RPM to RCF requires the correct rotor radius; never guess it.

Stable supported machines labels:

  • Agilent VSpin: Mostly
  • Agilent VSpin Access2 Loader: Full

VSpinBackend(device_id=None) and Access2Backend(device_id, timeout=60) are device-specific. Do not use placeholder IDs in a live script.

The current changelog lists HighRes Biosolutions MicroSpin under Unreleased. Although development main may expose MicroSpin, it is not a stable 0.2.1 API and must not be imported in pinned examples.

Centrifuge safety

Require human verification of rotor/bucket/adapter model, plate rating, orientation, balance, maximum RCF, duration, acceleration/deceleration, lid/door interlocks, loading position, clearance, maintenance, and emergency procedure. Never open/unlock while rotating or issue movement merely to test a connection. On timeout or disconnect, assume the rotor may still be moving until physically verified safe.

Storage/incubation

The stable machine inventory includes multiple Thermo Fisher/Heraeus Cytomat models as Full, and Inheco Incubator Shaker/SCILA as Mostly. Their APIs are model-specific; do not use stale generic examples such as from pylabrobot.incubation import Incubator without verifying that exact symbol in the pinned wheel.

Storage moves require explicit plate identity, slot mapping, occupancy state, door/hatch/interlock state, orientation, environmental setpoints, and recovery from an interrupted handoff. Software occupancy is not physical detection.

Multi-device orchestration

Do not independently gather() hardware operations just because frontends are async. Safe concurrency requires approved workcell interlocks and a scheduler that owns:

  • device and plate state;
  • collision zones and transfer ownership;
  • door/tray/bucket/lock preconditions;
  • timeouts, retries, idempotency, and partial-completion handling;
  • emergency stop and restart/reconciliation behavior.

Default sequence:

  1. Validate manifests and transfers offline.
  2. Generate a non-executable simulation plan.
  3. Exercise software-only frontends where available.
  4. Review every handoff with the operator.
  5. Obtain explicit confirmation for the exact live protocol.
  6. Commission one device/move at a time under site procedures.

No-connection inspection

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

This checks a fixed set of frontend symbols and methods without constructing devices or calling setup().

Sources

Checked 2026-07-23: