v3.10.0 - Githubissues

New argument spectrum_id_pattern: Regular expression pattern to apply to spectrum titles before matching to peptide file entries.
When using MS²PIP as class instance, the resulting pred_and_emp dataframe can also be returned (instead of writing to a file) when setting return_results to True.
If requested, retention time prediction with DeepLC is now also enabled if spectrum file is given. This feature was previously only enabled if only a peptide file was given.

Improved logging: Use Rich library for logging, show time stamps and message log levels.
MS²PIP now shows a progress bar instead of a wall of text to display prediction progress.
fasta2speclib: Improved algorithm for variable modification assignment. Combinatorial explosion from variable modifications is now reduced by setting a maximum of modified residues per peptide, instead of arbitrarily selecting a maximum of potentially modified sites per peptide.
Update README.md (Switch from BadGen to Shields.io)

Vastly improved computational speed and reduced memory usage when using XGBoost model files for prediction in combination with providing a spectrum file (XGB prediction step is now moved out of multiprocessing).
For optimal performance, feature vectors for predictions from XGBoost model files now also uses the traditional ms2pipC.py multiprocessing system.
fasta2speclib: Fixed issue where modified versions of peptide were duplicated.
spectrum_output: Various fixes in MSP spectral library file writing for DIA-NN compatibility: Write m/z error of 0.0 for each predicted peak in peak annotation string, ensure modifications in MSP Mods field are sorted by position, use RetentionTime instead of RTINSECONDS in comments field.
Fix typo in write_amino_acid_masses function name

compomics / ms2pip