Capability composition architecture#931
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rickwierenga merged 31 commits intov1b1from Mar 23, 2026
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Move 18 device module folders (arms, centrifuge, heating_shaking, liquid_handling, microscopes, only_fans, peeling, plate_reading, plate_washing, powder_dispensing, pumps, scales, sealing, shaking, storage, temperature_controlling, thermocycling, tilting) into pylabrobot/legacy/ and update all intra-legacy imports from pylabrobot.<module> to pylabrobot.legacy.<module>. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
Introduce Capability and need_capability_ready decorator in pylabrobot/machines/capability.py. Capabilities are owned by a Machine, share its backend, and track setup state via _on_setup() and _on_stop() lifecycle hooks called by the parent Machine. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
Create pylabrobot/capabilities/temperature_controlling/ with TemperatureControlCapability and TemperatureControllerBackend. Legacy TemperatureController now delegates to the capability, keeping its API fully backwards compatible. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
…y wrappers - Create pylabrobot.inheco module with InhecoCPAC, InhecoCPACBackend, InhecoTemperatureControllerBackend, and InhecoTECControlBox - Make Machine.backend private (_backend) across codebase - Legacy inheco backends use composition: inherit from legacy interface, delegate to new implementation via self._new - Legacy control_box re-exports from new module (no duplication) - Add legacy/__init__.py to fix pytest dual-import issue - Fix bug in MachineBackend.deserialize() accessing popped key - Remove duplicated docstrings from legacy wrappers Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
- Create pylabrobot.capabilities.shaking with ShakerBackend and ShakingCapability - Create pylabrobot.inheco.thermoshake with InhecoThermoshakeBackend, InhecoThermoShake machine, and factory functions (ac, classic, rm) - Legacy thermoshake backend uses composition, delegating to new impl - Legacy ShakerBackend re-exports from new capability module - Legacy Shaker delegates to ShakingCapability Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
…abilities Each BioShake model is its own class composing only the capabilities its hardware supports (shaker, tc, or both). supports_active_cooling is accurate per model. All classes raise NotImplementedError until resource definitions are filled in. Legacy bioshake_backend now delegates to the new implementation. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
SealingCapability covers seal/open/close; temperature uses the existing TemperatureControlCapability. A4SBackend implements both interfaces. Legacy sealer wrappers now delegate to the new implementation. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
Machine.setup() now iterates _capabilities forward calling _on_setup(), and Machine.stop() iterates reversed calling _on_stop(). Removes duplicated boilerplate from BioShake, InhecoThermoShake, InhecoCPAC, A4S. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
Box (USB interface) in separate file. Backend implements TemperatureControllerBackend + ShakerBackend. Machine class composes tc + shaker capabilities. Legacy wrapper delegates to new implementation. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
Move SCILA backend, SiLA interface, and SOAP utilities to pylabrobot/inheco/scila/. SCILABackend now implements TemperatureControllerBackend. Resource definition deferred. Legacy wrappers delegate to new module. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
ScaleBackend with zero/tare/read_weight. MettlerToledoWXS205SDUBackend moved to pylabrobot/mettler_toledo/. Legacy wrappers delegate to new implementation and keep deprecated aliases. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
…Liconic vendor modules New capabilities: - AutomatedRetrievalBackend/Capability for plate fetch/store operations - HumidityControllerBackend/Capability for humidity monitoring and control New vendor modules with multi-capability backends: - pylabrobot.thermo_fisher.cytomat: CytomatBackend, HeraeusCytomatBackend, CytomatChatterbox, Cytomat machine class - pylabrobot.liconic: LiconicBackend, Liconic machine class Legacy support files (constants, errors, schemas, utils, racks) moved to vendor modules; legacy paths re-export via wildcard imports so existing code works with just inserting .legacy. in import paths. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
Barcode scanning is now a capability (not a standalone Machine). The canonical location is pylabrobot/capabilities/barcode_scanning/ with BarcodeScannerBackend and BarcodeScanningCapability. Keyence vendor module implements the backend. Legacy barcode_scanners module provides backward-compatible BarcodeScanner(Machine) wrapper. Liconic frontend now instantiates its own backend from model+port and conditionally creates capabilities based on LiconicType properties: - retrieval: always - tc: all except NC - humidity: only DC2/DR2/AR/DH (independent control) - shaker: opt-in via has_shaker parameter - barcode_scanner: opt-in via BarcodeScanningCapability parameter Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
TiltingCapability tracks absolute angle and provides set_angle/tilt. Hamilton tilt module moved to pylabrobot/hamilton/tilt_module/ with full serial protocol, geometry methods (rotate_coordinate_around_hinge, get_plate_drain_offsets, get_well_drain_offsets), and chatterbox. Legacy tilting module now re-exports from new locations. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
Migrate XPeel from legacy monolithic peeler into capability-based architecture. Legacy peeling module now uses composition wrappers delegating to the new implementation. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
Migrate fan control from legacy monolithic Fan into capability-based architecture. Legacy only_fans module now uses composition wrappers delegating to the new implementation. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
Add pylabrobot/device.py with Device and DeviceBackend base classes for the new capability architecture. Move Capability from pylabrobot/machines/ to pylabrobot/capabilities/capability.py. Move Machine and MachineBackend to pylabrobot/legacy/machines/ as independent copies. Delete pylabrobot/machines/. Update all capability backends and vendor modules to import DeviceBackend from pylabrobot.device. Update all legacy modules to import from pylabrobot.legacy.machines. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
Migrate Pico microscope from legacy monolithic imager into capability-based architecture. Legacy imaging module now delegates to MicroscopyCapability via an adapter backend. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
…y vendor module Three separate plate reading capabilities with typed result dataclasses, replacing the legacy monolithic PlateReaderBackend. Each capability has its own backend ABC, chatterbox, and tests. Shared well-masking logic lives in plate_reading/utils.py. New pylabrobot/byonoy/ vendor module extracts the real HID backends from legacy, with resource definitions and factory functions. Legacy Byonoy module delegates to the new backends via self._new wrappers, preserving full PlateReader API compatibility. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
Create pylabrobot/agilent/biotek/ with BioTekBackend base, CytationBackend (with MicroscopyBackend), SynergyH1Backend, and Device classes (Cytation5, Cytation1, SynergyH1) with PlateHolder resources. Legacy wrappers delegate to new backends; deprecated aliases (Cytation5Backend, Cytation5ImagingConfig) and re-export shims removed. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
Move Molecular Devices SpectraMax serial protocol code to pylabrobot/molecular_devices/spectramax/ with capability-based backends (AbsorbanceBackend, FluorescenceBackend, LuminescenceBackend, TemperatureControllerBackend). Legacy wrappers delegate to _new backend and convert typed results back to List[Dict]. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
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# Conflicts: # pylabrobot/agilent/biotek/biotek_tests.py # pylabrobot/azenta/a4s.py # pylabrobot/azenta/xpeel.py # pylabrobot/legacy/liquid_handling/backends/opentrons_backend_tests.py # pylabrobot/legacy/liquid_handling/backends/opentrons_simulator.py # pylabrobot/legacy/plate_reading/tecan/__init__.py # pylabrobot/legacy/plate_reading/tecan/infinite_backend.py # pylabrobot/legacy/plate_reading/tecan/infinite_backend_tests.py # pylabrobot/legacy/plate_reading/tecan/spark20m/__init__.py # pylabrobot/legacy/plate_reading/tecan/spark20m/controls/__init__.py # pylabrobot/legacy/plate_reading/tecan/spark20m/controls/base_control.py # pylabrobot/legacy/plate_reading/tecan/spark20m/controls/camera_control.py # pylabrobot/legacy/plate_reading/tecan/spark20m/controls/config_control.py # pylabrobot/legacy/plate_reading/tecan/spark20m/controls/data_control.py # pylabrobot/legacy/plate_reading/tecan/spark20m/controls/gas_control.py # pylabrobot/legacy/plate_reading/tecan/spark20m/controls/injector_control.py # pylabrobot/legacy/plate_reading/tecan/spark20m/controls/measurement_control.py # pylabrobot/legacy/plate_reading/tecan/spark20m/controls/movement_control.py # pylabrobot/legacy/plate_reading/tecan/spark20m/controls/optics_control.py # pylabrobot/legacy/plate_reading/tecan/spark20m/controls/plate_transport_control.py # pylabrobot/legacy/plate_reading/tecan/spark20m/controls/sensor_control.py # pylabrobot/legacy/plate_reading/tecan/spark20m/controls/spark_enums.py # pylabrobot/legacy/plate_reading/tecan/spark20m/controls/system_control.py # pylabrobot/legacy/plate_reading/tecan/spark20m/enums.py # pylabrobot/legacy/plate_reading/tecan/spark20m/spark_backend.py # pylabrobot/legacy/plate_reading/tecan/spark20m/spark_backend_tests.py # pylabrobot/legacy/plate_reading/tecan/spark20m/spark_packet_parser.py # pylabrobot/legacy/plate_reading/tecan/spark20m/spark_processor.py # pylabrobot/legacy/plate_reading/tecan/spark20m/spark_processor_tests.py # pylabrobot/legacy/plate_reading/tecan/spark20m/spark_reader_async.py # pylabrobot/legacy/plate_reading/tecan/spark20m/spark_reader_async_tests.py # pylabrobot/legacy/plate_reading/utils.py # pylabrobot/plate_reading/agilent/biotek_synergyh1_backend.py
…ppers - Restore legacy backends to original MachineBackend definitions (shaking, temperature_controlling, tilting, scales, barcode_scanners) - Add adapters in legacy frontends to bridge between MachineBackend and DeviceBackend when delegating to capabilities - Fix IO constructor calls missing human_readable_device_name - Fix broken import paths in legacy modules (plate_reading, liquid_handling, microscopes) - Fix Liconic legacy wrapper barcode read ordering to match original hardware command sequence - Restore SiLAError class dropped during migration - Add class-level type annotations for Cytomat unreachable __init__ - Narrow CytationBackend._new type annotation - Fix test type annotations for plate reading results - Add creating-capabilities.md documenting the migration pattern Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
…ectly Update installation docs to match new extra names. Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
…scopy The time.time patch cleanup was calling stop() on the mock object instead of the patcher, causing time.time to remain frozen for all subsequent tests. This made the Hamilton reader thread timeout check never fire, hanging the STAR USB comms tests. 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>
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See http://discuss.pylabrobot.org/t/updating-plr-api-for-machine-interfaces-discussion/445/
for v1.0.0b1