Synergy H1 backend

[Nat-is-coding]

Here is the working backend for the Synergy H1 readers. A work in progress as I was able to verify absorbance reading so far : )

[Nat-is-coding]

Here is my proposal for a BioTekPlateReaderBackend for both CytationBackend and SynergyH1Backend

Modified the following files:

• init.py
• backend.py
• biotek_test.py

Added the following files:

• agilent_biotek_backend.py
• agilent_biotek_cytation_backend.py
• agilent_biotek_synergyh1_backend.py

Deleted the following files:

• biotek_backend.py (replaced by the three files above)

This proposal may not be perfect at first, as I rearranged the code and added some abstract properties in the BioTekPlateReaderBackend. Please feel free to suggest or modify some things, especially CytationBackend, as I do not have one to test it out.

I tested the SynergyH1Backend and all the functions work. Once the coding is finalized, I can work on updating the documentation for the wiki page.

[Copilot]

Pull request overview

This PR introduces support for the Agilent BioTek Synergy H1 plate reader by refactoring the existing Cytation5Backend into a more modular architecture. The refactoring extracts common BioTek plate reader functionality into a new base class BioTekPlateReaderBackend, renames Cytation5Backend to CytationBackend (with backward-compatible deprecation wrappers), and adds the new SynergyH1Backend that inherits from the base class with H1-specific customizations.

Key changes:

• Created BioTekPlateReaderBackend base class containing shared functionality for all BioTek plate readers (FTDI communication, plate management, absorbance/luminescence/fluorescence reading)
• Renamed Cytation5Backend to CytationBackend with deprecation warnings for backward compatibility
• Added SynergyH1Backend with H1-specific features (heating support, custom focal height range, improved read buffer handling with FtdiError retry logic)

Reviewed changes

Copilot reviewed 7 out of 9 changed files in this pull request and generated 5 comments.

Show a summary per file

File	Description
agilent_biotek_backend.py	New base class containing shared BioTek plate reader functionality (594 lines of refactored code from Cytation backend)
agilent_biotek_cytation_backend.py	Refactored Cytation backend to inherit from base class, removing duplicate code and adding deprecation wrappers for old class names
agilent_biotek_synergyh1_backend.py	New backend for Synergy H1 readers with custom _read_until implementation for chunk-based reading and FtdiError handling
__init__.py	Updated exports to include new backends and base class, but missing backward-compatible exports
biotek_tests.py	Updated test import to use new CytationBackend name
molecular_devices_backend.py, imager.py, clario_star_backend.py, chatterbox.py	Minor code formatting improvements (spacing around operators)

Comments suppressed due to low confidence (4)

pylabrobot/plate_reading/agilent_biotek_cytation_backend.py:148

• The stop() method is calling super().stop() first, but then also calls self.stop_shaking() and self.io.stop(), which are already called in the parent class's stop() method (lines 590-592 of agilent_biotek_backend.py). This results in duplicate calls to these methods. Consider removing the duplicate calls here to avoid potential issues:

async def stop(self):
    await super().stop()
    
    if self._acquiring:
        self.stop_acquisition()
    
    self._stop_camera()
    
    self._objectives = None
    self._filters = None
    # _slow_mode is already reset in parent class
    
    self._exposure = None
    # ... rest of the resets

pylabrobot/plate_reading/agilent_biotek_cytation_backend.py:139

• The setup() method duplicates all the code from the parent class's setup() method instead of calling super().setup(). This creates maintainability issues and violates DRY (Don't Repeat Yourself). Consider refactoring to:

async def setup(self, use_cam: bool = False) -> None:
    await super().setup()
    
    if use_cam:
        try:
            await self._set_up_camera()
        except:
            await self.stop()
            raise

pylabrobot/plate_reading/agilent_biotek_cytation_backend.py:944

• Trailing space in the deprecation warning message
  pylabrobot/plate_reading/agilent_biotek_cytation_backend.py:953
• Trailing space in the deprecation warning message

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[rickwierenga]

thank you so much!

[Nat-is-coding]

Of course! And thank you for the review : )

When I'm back in the lab, I'll double check the SynergyH1 Backend and add in the documentation