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Casanovo v3.0.0
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@wfondrie wfondrie released this 10 Oct 22:19
· 97 commits to main since this release
v3.0.0
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Learn about vigilant mode.

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.
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