v2024.2.0 - Dorado >= 7.3.9 support

What's new

Dorado 7.3.9 support

As discussed in #347, due to the move to ont_pybasecall_client_lib by ONT with the release of Dorado 7.3.9, readfish was unable to connect to the basecall socket, as it was using ont_pyguppy_client_lib.

This release supports both connections to dorado 7.3.9 and upwards with the dorado plugin, (which also handles the new parameter sample_rate on package_reads smartly) and dorado < 7.3.9 with the guppy plugin.

To use the new plugin, simply switch the caller_settings table in your toml from .guppy to .dorado, leaving other parameters the same, like so:

[caller_settings.dorado]

MinKNOW version checking

Readfish also now lists a tested MinKNOW version range, and will raise a warning if the MinKNOW version being connected to is outside the range for the given version of readfish.
However, readfish will still attempt to run adaptive sampling, and will most likely succeed!
As recommended in the logged warning, if a newer version of readfish doesn't exist, we recommend opening an issue on the github.

Warning

The Guppy plugin will likely be deprecated in the next major release of readfish.

What's Changed

• Dorado plugin by @mattloose and @Adoni5 in #344
• Minknow version checking by @mattloose and @Adoni5 #351

Full Changelog: 2024.1.0...2024.2.0