Doc updates; version bump

Author: RalfG

README.rst

@@ -59,6 +59,7 @@ The MS³PIP Python application can perform the following tasks:
 - ``correlate``: Compare predicted and observed intensities and optionally compute correlations.
 - ``get-training-data``: Extract feature vectors and target intensities from observed spectra for
   training.
+- ``annotate-spectra``: Annotate peaks in observed spectra.
 
 MS²PIP supports a wide range of PSM input formats and spectrum output formats, and includes
 pre-trained models for multiple fragmentation methods, instruments and labeling techniques. See

ms2pip/__init__.py

@@ -1,7 +1,7 @@
 # isort: skip_file
 """MS2PIP: Accurate and versatile peptide fragmentation spectrum prediction."""
 
-__version__ = "4.0.0-dev12"
+__version__ = "4.0.0-dev13"
 
 from warnings import filterwarnings
 

ms2pip/search_space.py

@@ -40,6 +40,10 @@
 result in a cleavage rule that allows cleavage after any amino acid with an unlimited number of
 allowed missed cleavages.
 
+To disable protein digestion when the FASTA file contains peptides, set the cleavage rule to
+``-``. This will treat each line in the FASTA file as a separate peptide sequence, but still
+allow for modifications and charges to be added.
+
 
 Examples
 --------