Bio.Application Modules Have Been Deprecated

[emarinier]

It looks like Bio.Applications (notably Bio.Blast.Applications in staramr.blast.JobHandler.py) have been deprecated and will need to be called directly using the subprocess module.

/home/eric/miniforge3/envs/staramr/bin/staramr:4: DeprecationWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html
  __import__('pkg_resources').require('staramr==0.11.0.dev0')
/home/eric/miniforge3/envs/staramr/lib/python3.12/site-packages/Bio/Application/__init__.py:39: BiopythonDeprecationWarning: The Bio.Application modules and modules relying on it have been deprecated.

Due to the on going maintenance burden of keeping command line application
wrappers up to date, we have decided to deprecate and eventually remove these
modules.

We instead now recommend building your command line and invoking it directly
with the subprocess module.