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CHANGELOG.md

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Changelog

Follow the changelog format from https://keepachangelog.com/en/1.0.0/.

1.1.0 - 2023.xx.xx

Added

  • Separate library_reader_base in psm_reader.yaml config for LibraryReaderBase.

Changed

  • mod@Any N-term and mod@Any_N-term are both supported, Any_N-term is prefered as there are no spaces and hence better for command line tools. The same for mod@Protein N-term, mod@Any C-term, and mod@Protein C-term.
  • Enable customizing dtypes of peak mz and intensty values.
  • SWATHLibraryReader to LibraryBaseReader in alphabase.spectral_library.reader.
  • New LibraryReaderBase._get_fragment_intensity implementation which is called at the end of the parsing process in PSMReaderBase._post_process. This allows it to operate only on the translated column names. By default, all non-fragment columns will be grouped and part of the final output.
  • SpecLibBase.copy() for copying spectral libraries including all attributes.
  • SpecLibBase.append() for appending spectral libraries while maintaining the fragment index mapping.

1.0.2 - 2023.02.10

Changed

  • Use flat_frag_start/stop_idxes for SpecLibFlat.
  • Check if group name is *_df for DataFrame in hdf files; remove is_pd_dataframe attr.

1.0.1 - 2023.01.15

Added

  • 'protein_reverse' decoy added in alphabase.protein.protein_level_decoy.py.

1.0.0 - 2023.01.10

Added

  • Percolator and SupervisedPercolator (alphabase.scoring.ml_scoring.py).
  • SpecLibFat for flat fragment dataframes from SpecLibBase (alphabase.spectral_library.flat.py).
  • SpecLibBase from TSV library (alphabase.spectral_library.reader.py)
  • LOESSRegression for recalibration stuffs (alphabase.statistics.regression.py)
  • Auto include contaminants.fasta with include_contaminants in alphabase.protein.fasta.SpecLibFasta.

0.4.0 - 2022.12.28

Changed

  • frag_end_idx -> frag_stop_idx

0.3.0 - 2022.12.27

Added

  • alphabase.protein.fasta.SpecLibFasta.add_peptide_labeling() supports mDIA.
  • Move alphabase.spectral_library.translate module (.py) from alphapeptdeep to alphabase.
  • alphabase.constants.modification.add_new_modifications() to add user-defined modifications that are not in UniMod.
  • alphabase.psm_reader.psm_reader.PSMReaderBase.add_modification_mapping() to support arbitrary modifications of different search engines.

Changed

  • Use sphinx and readthedocs for documentation. nbdev is no longer for documentation, it is only used for unit testing (nbdev_test).
  • FastaLib to SpecLibFasta.
  • Protease: trypsin==trypsin/p, add trypsin_not_p will not cleave peptides before N-term of P.

0.2.0

First official release.

0.0.1

FEAT: Initial creation of AlphaBase.