Version 4.5

[levitsky]

• Add support for mzMLb (Draft mzmlb implementation #35 and Improve mzMLb read performance with array cache #38 by @mobiusklein) with new module pyteomics.mzmlb.

• Add ProteomeExchange backend for PROXI requests and implement an aggregator for responses from all backends (Add USI PROXI backend for ProteomeExchange #36, PROXIAggregator may also return tagged responses instead of merging #45 and Handle cases where the PROXI server responds with properly typed numerical values for attributes #55 by @mobiusklein) in pyteomics.usi.

• Add support for ProForma (Draft ProForma implementation #37 by @mobiusklein) in new module pyteomics.proforma.

• New arguments keep_nterm_M and fix_aa in pyteomics.fasta.shuffle (Shuffling that preserves some amino acids #54 by @caetera).

• Fx for unwanted warnings in pyteomics.auxiliary.file_helpers._check_use_index when use_index is explicitly passed (Warning is triggered even with use_index=False #52).

• Update the default XML schema for featureXML and fix issues with incorrectly specified data types (Update default featureXML schema_info and version, add overrides #53).

• Add a new backend for spectrum annotation and plotting. pyteomics.pylab_aux.plot_spectrum and pyteomics.pylab_aux.annotate_spectrum can now use spectrum_utils under the hood (Addition of spectrum_utils backend #43).

  See new Example 4 for demonstration.

• New function pyteomics.pylab_aux.mirror for making a spectrum_utils mirror plot.

• pyteomics.pylab_aux.plot_spectrum and pyteomics.pylab_aux.annotate_spectrum now always return matplotlib.pyplot.Axes.

• Add a warning when passing an existing file by name in file-writing functions (mgf.write, fasta.write, fasta.write_decoy_db). The default mode for output files will change from 'a' to 'w' in a future version.

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This discussion was created from the release Version 4.5.