v1b1 changes#1000
Draft
rickwierenga wants to merge 79 commits into
Draft
Conversation
Co-authored-by: Claude Opus 4.6 <noreply@anthropic.com>
Co-authored-by: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
Co-authored-by: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
y: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
Notebook autoreload creates new class objects, breaking isinstance checks on backend params (silently falling back to defaults). BackendParams uses a metaclass with __instancecheck__ that falls back to qualname+module comparison, which stays stable across reloads. Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
- DeviceBackend -> Driver (with backward-compat alias) - Device._backend -> Device._driver, param backend -> driver - New CapabilityBackend ABC for capability-specific backend interfaces - All 15 abstract capability backends now extend CapabilityBackend - Concrete backends extend both their capability backend and Driver - Serialization key "backend" -> "driver" (deserialize accepts both) Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
Every monolithic backend that extended both a CapabilityBackend and Driver is now split into: - Driver: owns I/O, connection lifecycle, device-level ops - CapabilityBackend: protocol translation, encodes capability calls into driver commands Devices split: HepaFan, BioShake, Pico, Opentrons TempModule, Hamilton HeaterShaker, Hamilton TiltModule, Keyence BarcodeScanner, XPeel, SCILA, MettlerToledo, A4S, VSpin/Access2, CLARIOstar, SpectraMax 384+/M5. Also: CapabilityBackend gains _on_setup/_on_stop hooks, Capability._on_setup calls backend._on_setup, updated creating-capabilities.md, updated all legacy wrappers. Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
Recording backends and chatterbox backends are now pure CapabilityBackends. Test devices use a _NullDriver for the Device lifecycle. Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
Test capabilities directly via cap._on_setup() instead of wrapping in a fake Device. Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
- Fix import sorting across 10+ files (ruff format --fix) - Fix MolecularDevices legacy backend: reference renamed class, update test mocks to patch at correct level (Driver/Protocol instead of legacy wrapper) - Fix Pico legacy tests: split Driver/MicroscopyBackend usage to match new architecture - Fix Opentrons temp module: add base-type annotations for if/else branches - Fix Liconic: use _on_setup/_on_stop (CapabilityBackend API) - Fix Azenta A4S: type: ignore[safe-super] for abstract Driver methods - Fix Pico backend: self._snap_images() instead of self._driver._snap_images() Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
Co-authored-by: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
Move shaker/tc capabilities into base class with has_shaking, has_temperature, supports_active_cooling flags. Add resource definitions for BioShake3000, BioShake3000Elm, BioShake3000ElmDWP, and BioShakeQ1 from spec sheets. Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
Co-authored-by: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
…nds (#957) Co-authored-by: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
Extract autoload firmware protocol into a standalone class that takes a driver reference and operates on track numbers instead of Carrier objects. The legacy STARBackend and new STAR device can both wire into this class. Includes 36 tests covering all command types. Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
PlateReader now delegates reads through AbsorbanceCapability, LuminescenceCapability, and FluorescenceCapability via adapter backends that wrap the legacy PlateReaderBackend. Extracted _DictBackendParams into pylabrobot/legacy/_backend_params.py for reuse across legacy adapters. Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
Move autoload, cover, x-arm, wash station, and ~44 generic driver infrastructure methods (firmware queries, EEPROM, area reservation, configuration) into the new STARDriver architecture. Legacy backend methods now delegate to new classes or have deprecation docstrings. - STARAutoload: autoload module control (carrier loading, barcode, LEDs) - STARCover: front cover lock/unlock/enable/disable - STARXArm: left/right X-arm positioning (parameterized by side) - STARWashStation: dual-chamber wash station drain/fill/init - STARDriver: generic instrument operations directly on driver - STARChatterboxDriver: updated with all subsystems - STAR device only exposes capabilities (PIP, Head96, iSWAP) - Subsystems live on the driver, accessed via star._driver - 114 tests across all subsystems - Right X-arm and wash station are conditional on hardware config - X-arm methods use mm (PLR standard), not 0.1mm firmware units - Fixed pre-existing assertion bugs in release_occupied_area and set_instrument_configuration Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
These methods send a command to hardware and wait for a response, so request_ better reflects the I/O semantics. Covers PreciseFlex, capability interfaces (temperature, humidity), and all vendor backends (Azenta, Agilent, BMG, Byonoy, Hamilton, INHECO, Liconic, Molecular Devices, Opentrons, Qinstruments, Thermo Fisher). Legacy public APIs keep get_ names unchanged; only internal delegations are updated. Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
Move 14 multi-channel PIP operations to STARPIPBackend: channel positioning (Y/Z), initialization, spread, z-safety, foil piercing. Parameters use mm (PLR standard) with internal 0.1mm conversion. Key changes: - pierce_foil and step_off_foil on STARPIPBackend with explicit deck param - iSWAP-parked checks on Y-movement methods - Channel min Y spacing queried from firmware in driver setup() - Right X-arm conditional on right_x_drive_large - Wash station conditional on wash_station_*_installed - Legacy backend aliases (left_x_arm, iswap) for PIPBackend compat - Fixed pierce_foil one_by_one bug (z vs z+distance_from_bottom) - Fixed _ensure_can_reach_position dead fallback (is None vs not) - Architecture doc updated Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
Co-authored-by: Claude Opus 4.6 <noreply@anthropic.com>
Co-authored-by: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
Co-authored-by: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
Two new dispensing capabilities under bulk_dispensers/:
- SyringeDispensing: dispense(plate, volumes={col: vol}), prime(plate, volume)
- PeristalticDispensing: dispense(plate, volumes={col: vol}), prime(), purge()
Both use BackendParams for device-specific parameters.
Also adds BackendParams to PlateWashingCapability.
Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
- EL406Driver: FTDI I/O, batch management, device-level ops, queries - EL406PlateWashingBackend: manifold ops (wash, aspirate, dispense, prime) - EL406ShakingBackend: shake/soak - EL406SyringeDispensingBackend: syringe dispense/prime - EL406PeristalticDispensingBackend: peristaltic dispense/prime/purge Legacy code is thin wrappers delegating to new backends. All 385 tests pass. Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
…tecture Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
Move plate washer docs from 00_liquid-handling/plate-washing/ to agilent/biotek/el406/ and heater-shaker docs from 01_material-handling/heating_shaking/ to qinstruments/bioshake/. Add Manufacturers toctree section with manufacturer-level indexes. Include migration guide at repo root for future device migrations. Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
Move device docs from legacy category dirs (00_liquid-handling/, 01_material-handling/, 02_analytical/) to manufacturer-based layout mirroring the codebase. Add Manufacturers toctree section and API reference RST files for all manufacturers with autosummary directives and autoclass for nested BackendParams. Add Sphinx cross-references for BackendParams in notebook markdown cells. Devices migrated: EL406, BioShake, Mettler Toledo WXS205SDU, Azenta a4S, Azenta XPeel, Liconic STX, Inheco ThermoShake, Inheco CPAC, Inheco SCILA, Inheco Incubator Shaker, Inheco ODTC, Thermo Fisher Multidrop Combi. Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
Co-authored-by: Claude Opus 4.6 (1M context) <noreply@anthropic.com> Co-authored-by: Rick Wierenga <rick_wierenga@icloud.com>
Co-authored-by: Claude Opus 4.6 (1M context) <noreply@anthropic.com> Co-authored-by: Rick Wierenga <rick_wierenga@icloud.com>
Each of the 4 drawers is now a LoadingTray keyed by drawer_id in `scila.drawers`. Command sequences (PrepareForInput/OpenDoor, PrepareForOutput/CloseDoor) and drawer_id validation move from the driver into SCILADrawerLoadingTrayBackend. Re-add CO2-flow warning suppression (log + continue) that had been lost in the rewrite. Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
…re (#989) Co-authored-by: Claude Opus 4.6 (1M context) <noreply@anthropic.com> Co-authored-by: Hazlam Shamin <69739427+hazlamshamin@users.noreply.github.com>
Co-authored-by: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
…imbus Deck is now passed into the driver at __init__ time (not through setup), so the driver can construct backends with deck as a required arg. PIP/Head96 capabilities also take deck required on __init__. Legacy STARBackend still receives deck via set_deck (legacy flow) and forwards it to the already-built STARDriver. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
rickwierenga
force-pushed
the
v1b1
branch
2 times, most recently
from
feee0ba to
162dd2c
Compare
Makes gripper_length and gripper_z_offset required on PreciseFlexArmBackend (no sensible backend-level defaults — they depend on the mounted gripper) and moves the per-model defaults (162 mm length, 0 mm z offset) to the PreciseFlex400 Device wrapper so users can override them when installing a non-stock gripper. Also renames PF400Params.z_tool_offset to gripper_z_offset for naming consistency with the user-facing parameter. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
Co-authored-by: Rick Wierenga <rick_wierenga@icloud.com> Co-authored-by: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
BioCam
reviewed
Apr 27, 2026
…ding invalid C0 RA pn= (#1012)
PIPChannel.request_firmware_version and STARDriver.request_firmware_version now parse the RF response through parse_star_firmware_version_date and return a datetime.date, matching what STARHead96Backend already did. ztouch_probe_z_height uses version.year < 2022 directly instead of regex re-parsing the raw string. Drop the chatterbox-None fallback from STARHead96Backend.request_firmware_version: chatterbox paths should explicitly override the method (or accept the ValueError) rather than silently advertising a fabricated date. Legacy STARBackend.request_pip_channel_version keeps its str return type by inlining the raw RF query — the new PIPChannel method now returns datetime so direct delegation would have broken the legacy contract. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
Move the read-window from a backend/device-construction parameter to a per-call argument on BarcodeScanner.scan(read_time=...). Backends for scanners without a configurable window (chatterbox, Keyence) accept and ignore.
scan() / scan_barcode() now return None when the read window elapses with no successful decode. Reserved for the "nothing seen" case; hardware faults still raise BarcodeScannerError. Liconic propagates the Optional through read_barcode_inline / scan_barcode.
…0-100, PF400 park override
- GripperLocation → CartesianPose; add JointPose=Dict[int,float] alias
- PreciseFlexGripperLocation → PreciseFlexCartesianPose; PFAxis → Axis
- Cart.rail field → rail_position; consistent rail_position kwarg naming
- Percentage params suffixed _pct (speed_pct, acceleration_pct, finger_speed_pct, etc.)
with 0-100 ValueError validation across set_profile_*, set_motion_profile_values,
set_monitor_speed (lower bound relaxed from 1 to 0), and _set_grasp_data
- park() consolidates the firmware "movetosafe" call (move_to_safe removed)
- New PreciseFlex400Backend overrides park() with explicit joint pose
{BASE:170, SHOULDER:0, ELBOW:180, WRIST:-180}; PreciseFlex400 device wires it up
- Legacy shim updated to delegate to renamed new-module API; legacy public API preserved
The method returns a CartesianPose (location + rotation), so 'location' was a misnomer. Renamed across the ABC, the Arm wrapper, and all backends (xArm6, Hamilton STAR/iSwap/core, Brooks PreciseFlex, legacy adapters), plus user-guide notebooks/markdown.
…convention so 0°=+X (#1034) Co-authored-by: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
Co-authored-by: Rick Wierenga <rick_wierenga@icloud.com> Co-authored-by: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
…hy refactor (#1044) Co-authored-by: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
rickwierenga
added a commit
to c-reiter/pylabrobot
that referenced
this pull request
May 19, 2026
Hold off on the agilent/ subpackage split (and its deprecation shims) until the broader machine-interface architecture lands (see PyLabRobot#1000). This PR now only adds the new HighRes MicroSpin files; existing VSpin imports are unchanged. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
…1b1 refactor Surfaced by a firmware-level audit of v1b1 vs main; restores effective parity for defaults and call surfaces without changing the new Device/Driver/Capability architecture. - iSWAP: MoveToLocationParams.minimum_traverse_height 360.0 → 280.0 to match main's _iswap_traversal_height; move_gripper(width=None) picks 91/132 mm by firmware vintage. - 96-head: slave-timeout polling (_is_slave_timeout / _wait_for_idle) wraps aspirate96/dispense96; read_timeout=max(300, driver.read_timeout) restored; _check_96_position_legal envelope check at pickup/drop/asp/disp; drop-z 216.4 sanity warn. - CoRe: reject negative y/z; range checks for grip_strength, y_gripping_speed, z_speed, z_press_on_distance, acceleration_index; back/front_y ordering + left_arm_min_y assertions in core_grippers(); add core_read_barcode (C0 ZB) and CoreGripper.check_resource_exists_at_location_center. - X-arm: restore x_arm_request_firmware_version (X0 RF) and experimental_x_arm_move (X0 XP). - Probing: real probe_liquid_heights / probe_liquid_volumes / empty_tips on STARDriver (were NotImplementedError stubs); aspirate(probe_liquid_height=True) now works. - PIP: PIPChannel.move_x / move_x_relative / move_y_relative / move_tool_z_relative; STARPIPBackend.request_tadm_status batch query; get_channel_spacings; or → is None traversal-height fallback semantics. - Setup: skip_pip / skip_iswap / skip_core96_head / skip_autoload kwargs; num_channels from RT count (kp fallback); _channels_minimum_y_spacing pre-fill restored to [9.0] * 8. - Top-level: set_minimum_channel_traversal_height / set_minimum_iswap_traversal_height setters + iswap_minimum_traversal_height context manager on _HamiltonSTAR; deprecated set_minimum_traversal_height shim raises with migration message. - Autoload: set_barcode_type legacy 7-bool shim restored as deprecation. - Errors: tighten skip condition to (error_code == 0 AND trace_information == 0) so master-side trace-only faults aren't silently dropped; fw_parsing date regexes re-anchored with \b. - Misc: dedup DEFAULT_TIP_FITTING_DEPTH; y_drive_mm_per_increment typo 0.046302082 → 0.046302083. All 117 existing STAR tests pass. Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com>
…lidate_tip_inventory from legacy Byte-equivalent move into the v1b1 PIP capability. STAR-specific z kwargs (minimum_traverse_height_at_beginning_of_a_command, z_position_at_end_of_a_command) are now passed via pick_up_backend_params / drop_backend_params instead of being named kwargs on pick_up_tips / drop_tips. Legacy use_channels default (list(range(num_channels_available))) preserved verbatim in consolidate. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
When the SCILA is operated without an external gas mixer, drawer open/close emits a non-fatal CO2-flow warning. Until now this was always swallowed-and- logged via an unconditional substring match. The new flag (default True) makes the swallow deliberate: with no mixer connected, the warning is expected and silenced; with a mixer connected, the warning is surfaced via logger.warning so a real CO2 problem isn't hidden. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
The legacy stubs forwarded to pylabrobot.brooks, but the new brooks API has diverged enough (renamed poses/axes, *_pct units, new access types) that the forwarders are brittle. Drop the forwarders and keep a verbatim copy of main's pylabrobot/arms/precise_flex/ under pylabrobot/legacy/arms/precise_flex/, with only the pylabrobot.arms.* -> pylabrobot.legacy.arms.* import path rewritten. The new pylabrobot/brooks/ implementation is unchanged. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
5 participants
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
https://discuss.pylabrobot.org/t/updating-plr-api-for-machine-interfaces-discussion/445