Release Casanovo v5.0.0 · Noble-Lab/casanovo

5.0.0 - 2025-07-09

Casanovo-DB mode (casanovo db_search) to use Casanovo as a learned score function for sequence database searching (given a FASTA protein database).
During training, model checkpoints will be saved at the end of each training epoch in addition to the checkpoints saved at the end of every validation run.
Besides as a local file, model weights can be specified from a URL. Upon initial download, the weights file is cached for future re-use.
Training and optimizer metrics can be logged to a CSV file by setting the log_metrics config file option to true. The CSV file will be written to under a sub-directory of the output directory named csv_logs.
New configuration options for detailed control of the gradients during training (gradient accumulation, clipping).
New configuration option min_peaks to discard low-quality spectra with too few peaks.

Removed the evaluate sub-command, and all model evaluation functionality has been moved to the sequence command using the new --evaluate flag.
The --output option has been split into two options, --output_dir and --output_root.
The path suffix (extension) of --output_root will no longer be removed as it was with the old --output option.
The --validation_peak_path is now optional when training; if --validation_peak_path is not set then the train_peak_path will also be used for validation.
The tb_summarywriter config option is now a boolean config option, and if set to true the TensorBoard summary will be written to a sub-directory of the output directory named tensorboard.
Input peak files can now be specified as both individual file(s) and a directory.
Peptidoforms are specified using ProForma 2.0 notation by default.
DepthCharge is upgraded to the latest version 0.4.8.
The product of the raw amino acid scores is used as the peptide score, rather then the arithmetic mean.
Amino acid scores are directly reported, rather than averaged with the peptide score.
The amino acid-level score of stand-alone N-terminal modifications is combined with that of the leading N-terminal residue.
Renamed the n_peaks configuration option of the maximum number of peaks to retain in a spectrum to max_peaks.
Beam search decoding has been optimized for computational efficiency, achieving increased prediction speed.

Precursor charges are exported as integers instead of floats in the mzTab output file, in compliance with the mzTab specification.
Fixed log entries written to the config file instead of the log file when running the configure command.

Removed the save_top_k option from the Casanovo config, the model with the lowest validation loss during training will now be saved to a fixed filename <output_root>.best.ckpt.
The model_save_folder_path config option has been removed; model checkpoints will now be saved to --output_dir during training.