Tecan spark #798

xbtu2 · 2025-12-21T01:33:06Z

tecan spark WIP. luminescence coming up soon. i had a hard time to get io.usb to work with this, so i'm directly using libusb for now

hazlamshamin · 2025-12-21T05:56:39Z

CRAZY COOOOL! this is VERY complete

Copilot

Pull request overview

This PR adds support for the Tecan Spark plate reader by implementing a comprehensive async backend with USB communication, packet parsing, and data processing capabilities. The implementation includes controls for various instrument subsystems and processors for absorbance and fluorescence measurements.

Key Changes

New async USB reader with packet parsing for Tecan Spark devices
Absorbance and fluorescence data processors with real-world test coverage
Comprehensive control modules for plate transport, optics, sensors, measurements, and system configuration
Utility function for calculating non-overlapping well rectangles

Reviewed changes

Copilot reviewed 23 out of 24 changed files in this pull request and generated 2 comments.

Show a summary per file

File	Description
pylabrobot/plate_reading/utils.py	Adds helper to find non-overlapping rectangles covering plate wells
pylabrobot/plate_reading/tecan/spark20m/spark_reader_async.py	Implements async USB communication layer for Spark devices
pylabrobot/plate_reading/tecan/spark20m/spark_packet_parser.py	Parses binary measurement data packets from the device
pylabrobot/plate_reading/tecan/spark20m/spark_processor.py	Processes raw measurement data into absorbance/fluorescence values
pylabrobot/plate_reading/tecan/spark20m/spark_backend.py	Main backend integrating all components for plate reading operations
pylabrobot/plate_reading/tecan/spark20m/controls/*.py	Control modules for device subsystems (optics, sensors, movement, etc.)
pylabrobot/plate_reading/tecan/spark20m/*_tests.py	Unit tests for reader, processor, and backend components

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pylabrobot/plate_reading/tecan/spark20m/controls/system_control.py

pylabrobot/plate_reading/tecan/spark20m/spark_reader_async.py

Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>

rickwierenga · 2026-01-21T00:30:42Z

is this ready for review?

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

- Remove AutoReaderProxy, integrate reading into send_command - Remove reading context manager (no longer needed) - Rename control classes to follow PEP8 (BaseControl, PlateControl, etc.) - BaseControl now takes send_command directly instead of reader - Make init_read and get_response private methods - Add io.binary.Reader utility class Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

rickwierenga · 2026-01-31T18:49:05Z

Code review changes

Simplified the Spark control architecture:

Removed AutoReaderProxy - This was a magic proxy that wrapped every async method call with a reading context. Instead, the reading logic is now integrated directly into send_command(), making the flow more explicit and easier to follow.
Removed reading() context manager - No longer needed since send_command() handles read setup internally.
Renamed control classes to follow PEP8 - baseControl → BaseControl, plateControl → PlateControl, measurement_control → MeasurementControl, etc.
Simplified BaseControl - Now takes send_command function directly instead of the entire reader object, since that's all it uses.
Made internal methods private - init_read() → _init_read(), get_response() → _get_response() since they're only used internally by send_command().
Added io.binary.Reader - Utility class for binary parsing, used to replace the custom _read_u8, _read_u16, etc. helper functions in the packet parser.

# Conflicts: # pylabrobot/io/binary.py # pylabrobot/io/usb.py

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

Replace custom byte parsing helpers (_read_bytes, _read_u8, _read_u16, _read_u32, _read_string) with the Reader class from pylabrobot.io.binary. Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

Use pytest.approx() instead of exact equality for float comparisons in test_process_real_data tests. Compare row by row since pytest.approx does not support nested data structures. Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

Add max_workers parameter to USB class constructor with default of 1 to maintain backward compatibility. SparkReaderAsync passes max_workers=16 for its specific needs. Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

The PR fixed the timeout conversion for the main write but missed the zero-length packet write. PyUSB expects timeout in milliseconds, so timeout must be multiplied by 1000. Also add max_workers parameter to USBValidator for signature compatibility. Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

Replace manual calculation of well spacing with the new item_dx and item_dy properties from ItemizedResource. Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

pylabrobot/plate_reading/tecan/spark20m/spark_reader_async.py

rickwierenga · 2026-02-01T04:09:26Z

instead of returning False on error, can we raise the error in send command? this is a more pythonic way of dealing with errors

Extracts SparkDevice, SparkEndpoint, and VENDOR_ID from spark_reader_async.py to a separate enums.py file for better organization. These are USB protocol constants, not control logic. Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

xbtu2 added 5 commits December 20, 2025 12:23

tecan spark backend

b132be7

use enum for endpoints

fbec36f

add time

16edc58

format

ad9843d

fix typo

a799855

BioCam requested a review from Copilot December 21, 2025 07:33

Copilot AI reviewed Dec 21, 2025

View reviewed changes

pylabrobot/plate_reading/tecan/spark20m/controls/system_control.py Outdated Show resolved Hide resolved

pylabrobot/plate_reading/tecan/spark20m/spark_reader_async.py Outdated Show resolved Hide resolved

xbtu2 and others added 6 commits December 21, 2025 11:24

Update pylabrobot/plate_reading/tecan/spark20m/spark_reader_async.py

4190426

Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>

remove unused method

c937c24

use plr usb io

7560ed3

Merge branch 'main' into tecan_spark

1e2c30a

fix test

0c99649

Merge branch 'main' into tecan_spark

eaf2f3b

rickwierenga and others added 2 commits January 31, 2026 10:18

Use io.binary.Reader in spark_packet_parser

24ec263

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

Merge remote-tracking branch 'origin/main' into tecan_spark

b56ffdd

# Conflicts: # pylabrobot/io/binary.py # pylabrobot/io/usb.py

rickwierenga force-pushed the tecan_spark branch from fc9cf36 to b56ffdd Compare January 31, 2026 19:20

rickwierenga and others added 7 commits January 31, 2026 11:27

Rename control attributes to include _control suffix

aaa6fae

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

Refactor spark_packet_parser.py to use binary.py Reader

9747549

Replace custom byte parsing helpers (_read_bytes, _read_u8, _read_u16, _read_u32, _read_string) with the Reader class from pylabrobot.io.binary. Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

Make USB max_workers configurable per-instance

2e1db3c

Add max_workers parameter to USB class constructor with default of 1 to maintain backward compatibility. SparkReaderAsync passes max_workers=16 for its specific needs. Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

Merge remote-tracking branch 'origin/main' into tecan_spark

31949fa

Use item_dx and item_dy properties in SparkBackend

847d895

Replace manual calculation of well spacing with the new item_dx and item_dy properties from ItemizedResource. Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

rickwierenga reviewed Jan 31, 2026

View reviewed changes

pylabrobot/plate_reading/tecan/spark20m/spark_reader_async.py Outdated Show resolved Hide resolved

fix send_commend and tests

e95d88d

xbtu2 and others added 3 commits January 31, 2026 20:53

fix send_command error handling

a0da054

Move Spark enums to dedicated enums.py module

d9e4c4e

Extracts SparkDevice, SparkEndpoint, and VENDOR_ID from spark_reader_async.py to a separate enums.py file for better organization. These are USB protocol constants, not control logic. Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

Add type annotations to spark20m module for mypy --strict

d6e76aa

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

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Tecan spark #798

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Pull request overview

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rickwierenga commented Jan 21, 2026

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rickwierenga commented Jan 31, 2026

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