Handle None in psm_list['rescoring_features']

[rodvrees]

At the moment, psm_utils' PepXMLReader reader passes by default:
rescoring_features = None

This gives the following error in MS2Rescore:

  File "/home/robbe/miniconda3/envs/rescore/lib/python3.10/site-packages/ms2rescore/__main__.py", line 237, in main
    rescore(configuration=config)
  File "/home/robbe/miniconda3/envs/rescore/lib/python3.10/site-packages/ms2rescore/core.py", line 55, in rescore
    psm_list_feature_names = {
  File "/home/robbe/miniconda3/envs/rescore/lib/python3.10/site-packages/ms2rescore/core.py", line 58, in <setcomp>
    for feature_name in psm_list_features.keys()
AttributeError: 'NoneType' object has no attribute 'keys'

None values should thus handle None values as empty lists for correct processing.

[RalfG]

To be fixed in PepXMLReader:

psm_utils/psm_utils/io/pepxml.py

Line 156 in 0ba376d

rescoring_features=None,

However, ideally, this should also be validated by PSM. The current implementation is a bit ambiguous. The default is dict(), but the type hint Optional allows None:

psm_utils/psm_utils/psm.py

Lines 28 to 30 in 0ba376d

	provenance_data: Optional[Dict[str, str]] = dict()
	metadata: Optional[Dict[str, str]] = dict()
	rescoring_features: Optional[Dict[str, float]] = dict()

We can change the type hints to remove optional, which might break things downstream that assumed None is an allowed value... What do you think, @paretje?