Add BioTek EL406 plate washer backend#878
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tfehlmann wants to merge 12 commits intoPyLabRobot:mainfrom
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Add BioTek EL406 plate washer backend#878tfehlmann wants to merge 12 commits intoPyLabRobot:mainfrom
tfehlmann wants to merge 12 commits intoPyLabRobot:mainfrom
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Add a new plate washing module with a backend for the BioTek EL406 plate washer, communicating via FTDI USB serial interface. Architecture: - PlateWasher resource and PlateWasherBackend base class - BioTekEL406Backend composed from mixins: Communication, Queries, Actions, and Steps (manifold, peristaltic, syringe, shake) - Binary protocol with framed messages, ACK/NAK flow control, and async status polling for long-running operations Features: - Manifold wash/dispense/aspirate/prime/auto-clean operations - Peristaltic pump prime/dispense/purge with column/row selection - Syringe pump dispense/prime with column selection - Plate shaking with configurable intensity and duration - Device queries (manifold type, serial number, sensor status) - Action commands (abort, pause, resume, reset, self-check) - 160+ device error codes with descriptive messages - MockFTDI test double for hardware-free testing 374 tests covering all operations, wire format encoding, parameter validation, communication protocol, and error handling. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
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setup() now resets the instrument and starts batch mode automatically, so users can issue step commands immediately. stop() runs cleanup_after_protocol before disconnecting. Both can be skipped via skip_reset and skip_cleanup flags, following codebase conventions. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
- Extract EL406TestCase base class into mock_tests.py with shared setUp/tearDown, eliminating duplicated boilerplate across all test files - Patch asyncio.sleep in tests so hardware delays don't slow mock tests - Replace hardcoded timeouts (5.0, 2.0) in communication.py with self.timeout so the configured value is used consistently - Timeout-specific tests set backend.timeout = 0.01 to test the path fast Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
Move asyncio.Lock() from __init__ to setup() so it's created inside a running event loop (required on Python 3.9). Increase mock buffer sizes and refill buffer before tearDown's stop() so cleanup commands don't starve. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
Convert all public-facing parameters to PLR standard units (µL for volume, seconds for time) with internal conversion at the API boundary. Add unit suffixes (_ms, _min, _ml) to internal builder params that use wire-format units, so the unit mismatch is always explicit in code. Also add ValueError for minute-resolution params not divisible by 60, and clean up test boundary values and comments. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
Replace manual bytes([...]) construction, bit manipulation (value & 0xFF, (value >> 8) & 0xFF), and helpers (encode_volume_16bit, encode_signed_byte) with Writer's fluent API (w.u8().u16().i8().finish()) across all 9 command builders and build_framed_message. Absorb _encode_wash_byte_values into _build_wash_composite_command. Remove now-dead encode_volume_16bit and encode_signed_byte helpers. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
Replace manual LE u16 parsing (data[i] | (data[i+1] << 8)) with Reader.u16() in communication.py for header data-length, command echo, and poll state fields. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
Validation functions that were only used in one file now live there instead of in helpers.py. Wire-format range checks (offset_xy, offset_z, num_pre_dispenses) removed — the binary Writer will enforce those. validate_volume inlined at call sites. validate_intensity moved to _shake.py since intensity is a shake concept. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
The build command methods already document wire format and byte layout. Strip repeated protocol specs from test class/method docstrings and inline comments across all test files. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
- Inline single-use command codes with keyword arguments across all files - Move LONG_READ_TIMEOUT to communication.py (used by communication, queries, actions) - Inline DEFAULT_READ_TIMEOUT (15.0) in backend.py - Inline ACK_BYTE/NAK_BYTE as 0x06/0x15 in communication.py - Inline MSG_* protocol constants in protocol.py - Inline VALID_* sets into their validation functions - Inline syringe limit constants into validators - Remove constants re-exports from __init__.py Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
- syringe_to_byte → _syringe.py - cassette_to_byte, encode_quadrant_mask_inverted → _peristaltic.py - columns_to_column_mask, encode_column_mask → protocol.py - TRAVEL_RATE_TO_BYTE, travel_rate_to_byte → _manifold.py - INTENSITY_TO_BYTE → _shake.py (manifold imports from there) - get_plate_type_wash_defaults → _manifold.py - helpers.py now only has plate type defaults and lookup functions Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
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Summary
pylabrobot.plate_washingmodule withPlateWasherresource andPlateWasherBackendbase classBioTekEL406Backendfor the BioTek EL406 plate washer, communicating via FTDI USB serialSupported operations
Architecture
MockFTDItest double enables hardware-free testingPlateReader/PlateReaderBackendhierarchy)Test plan
pytest pylabrobot/plate_washing/biotek/)🤖 Generated with Claude Code