io.Socket refactor

[rickwierenga]

• don't have read_once in read, instead split into read and read_until_eof (not all higher level protocols require/support this)
• add read_until and readline
• write and read work with bytes, not strings
• save validation data in hex format
• update Proflex backend to new api

[Copilot]

Pull Request Overview

This PR refactors the io.Socket class to improve the API design by distinguishing between different read patterns and switching from string-based to bytes-based I/O operations.

Key Changes:

• Split read operations into specialized methods: read(), readline(), readuntil(), and read_until_eof() instead of a single read() method with flags
• Changed write and read methods to work with bytes instead of strings, requiring explicit encoding/decoding at call sites
• Updated validation data storage to use hex format for binary safety

Reviewed Changes

Copilot reviewed 4 out of 4 changed files in this pull request and generated 9 comments.

File	Description
pylabrobot/io/io.py	Updated abstract base interface to specify bytes type for write data parameter and read return type
pylabrobot/io/socket.py	Major refactor: removed read_once parameter, added new read methods (readline, readuntil, read_until_eof), changed I/O to use bytes, updated logging/capture to use hex encoding, added read/write locks
pylabrobot/thermocycling/thermo_fisher/thermo_fisher_thermocycler.py	Adapted to new Socket API by encoding writes to bytes, decoding reads from bytes, and using read_until_eof() instead of read(read_once=False)
pylabrobot/thermocycling/thermo_fisher/proflex_tests.py	Updated test mocks to return bytes instead of strings, added separate mock for read_until_eof(), updated expected write calls to use bytes

Comments suppressed due to low confidence (1)

pylabrobot/thermocycling/thermo_fisher/thermo_fisher_thermocycler.py:370

• The exception handling on line 369 catches TimeoutError, but with the new Socket implementation, read operations raise asyncio.TimeoutError instead of TimeoutError. This means timeouts will not be caught by this except block and will propagate as unhandled exceptions. Either update the Socket methods to raise TimeoutError, or update this handler to catch asyncio.TimeoutError.

    except TimeoutError:
      return ""

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[xbtu2]

lgtm

[rickwierenga]

Thanks Bo