Casanovo v3.0.0

3.0.0 - 2022-10-10

Added

• The first PyPI release! 🎉
• Tests are run on every PR automatically.
• Test code coverage must be maintained or improved with each change.
• Log the active Casanovo configuration.
• Log to both the console and a log file.
• Use all available hardware resources (GPU and CPU).
• Add ICML paper citation info.
• Document GPU out of memory error in the README.
• Allow mzML and mzXML peak files as input during predicting.
• Ability to reuse an existing HDF5 index during training.
• Move the changelog information from the README to CHANGELOG.

Changed

• Consistent code formatting using black.
• Assign a negative score to peptide predictions that don't fit the precursor m/z tolerance.
• Faster empty token detection during decoding.
• Consistently set the random seed to get reproducible results.
• Spectrum indexes are written to temporary HDF5 files.
• Use spectrum_utils for spectrum preprocessing.
• Rename the mode to predict peptides for unknown spectra from test to predict.
• Export spectrum predictions to mzTab files.
• Update the residue alphabet to include N-terminal modifications (acetylation, carbamidomethylation, NH3 loss).
• Specify input peak files as a shell pattern rather than by their directory.
• Make the config file optional to specify.

Removed

• Always preprocess spectra, rather than having this as a user option.

Fixed

• Don't log overly detailed messages from dependencies.
• Don't crash on invalid spectrum preprocessing.
• Ensure that config values have the correct type.
• Don't crash when an invalid residue is encountered during predicting (i.e. an N-terminal modification in another position).
• Don't penalize peptide scores if the precursor m/z fits a C13 difference.

v2.1.1

Update tutorial.

v2.1.0

Import latest depthcharge version with stable memory usage and fix to positional encoding for amino acids.

v2.0.1

Release notes added.

v2.0.0

Added additional CLI functionality, changed config file format, added pytest functionality, tutorial added, documentation with sphinx/ReadTheDocs added.

v1.2.0

Add peptide and amino acid confidence scores to output file.

v1.1.2

Add support for multiple MGF files in a directory.

v1.1.1

Add more CLI options and specify custom config file.

v1.1.0

Add data infrastructure, model and training/testing functionality.