BigDataBiology/SemiBin: Version 2.2.0

RLS Version 2.2.0

This is a maintenance release with many small improvement rather than a single big new feature. Upgrading is recommended, but not crucial.

User-visible changes

• Remove SemiBin command. Only SemiBin1 and SemiBin2 are available (and SemiBin1 is deprecated). The only reason to use SemiBin1 is if you have old scripts that use it. It will be removed in the next release.
• Better logging: Always log to file in DEBUG level and log command-line arguments. Print version number in logs.
• Better error messages in several instances
• check_install: Prints out information on the GPU

Deprecations

• SemiBin: Deprecate --prodigal-output-faa argument
• No longer check for mmseqs in check_install (it is not a hard requirement)

Internal improvements and bugfixes

• Respect the number of threads requested better (#140)
• SemiBin: Better method to save the model which is more compatible with newer versions of PyTorch. Added a subcommand to update old models to the new format (update_model)
• SemiBin: Switch to pixi for testing (and recommend it in the README/installation instructions)
• Convert to pyproject.toml instead of setup.py
• Do not fail if no bins are produced (#170 & #173)