v1b1 changes#1000
Draft
rickwierenga wants to merge 116 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>
Reflow and import sorting only `agilent/biotek/__init__.py` keeps its load-bearing import order via `isort: off` to avoid a circular import.
…e front-ends (#1107) Co-authored-by: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
…traction layers (#1108) Co-authored-by: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
…-recover out-of-range axes (#1118) Co-authored-by: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
…1122) Co-authored-by: Claude Opus 4.8 <noreply@anthropic.com>
Co-authored-by: Claude Opus 4.8 <noreply@anthropic.com>
…mage_size (#1123) Co-authored-by: Claude Opus 4.8 <noreply@anthropic.com>
Co-authored-by: Rick Wierenga <rick_wierenga@icloud.com> Co-authored-by: Claude Opus 4.8 <noreply@anthropic.com>
#1125) Co-authored-by: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
Co-authored-by: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
#1129) Co-authored-by: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
…edRetrieval ` with `RandomAccessRetrieval `) (#1142) Co-authored-by: Claude Opus 4.8 (1M context) <noreply@anthropic.com> Co-authored-by: Rick Wierenga <rick@pylabrobot.org>
…orward from main (#1154)
Co-authored-by: Claude Opus 4.8 <noreply@anthropic.com>
Co-authored-by: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
…1170) Co-authored-by: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
…1171) Co-authored-by: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
…r class (#1172) Co-authored-by: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
…aler drivers (#1173) Co-authored-by: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
Co-authored-by: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
…er (#1176) Co-authored-by: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
Co-authored-by: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
Co-authored-by: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
"measure" describes the operation accurately for balances regardless of whether they have a display, unlike "read". Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
Co-authored-by: Claude Opus 4.8 (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
7 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