Version 4.5.6

• New function pyteomics.proforma.set_unimod_path allowing the ProForma parsing machinery to work with a local Unimod copy (#85 by @mobiusklein). See documentation for a usage example.
• New method pyteomics.proforma.Proforma.fragments to generate m/z for an ion series (#85 by @mobiusklein).
• New function pyteomics.parser.to_proforma helps convert modX sequences to ProForma.
• Fix: prevent pyteomics.mass.fast_mass2 from changing aa_mass.
• Update pyteomics.pylab_aux.annotate_spectrum for compatibility with latest spectrum_utils. Pyteomics is now compatible with spectrum_utils 0.4.0 and newer.

Version 4.5.5

• Fix #77 (fix by @mobiusklein).

Version 4.5.4

• Fix issue #74.
• In pyteomics.auxiliary.fdr, raise PyteomicsError instead of ZeroDivisionError when using formula 1 on input without any target PSMs.
• Provide more accurate amino acid masses in mass.std_aa_mass.
• Fix SyntaxError in pyteomics.pylab_aux on Python 2.7.

Version 4.5.3

• Fix ThreadPool shutdown and add new parameter ephemeral_pool in pyteomics.usi.PROXIAggregator (#67 by @mobiusklein).
• Bugfix in pyteomics.proforma.GenericModificationResolver (#68) by @mobiusklein.
• New helper function pyteomics.fasta.decoy_entries.
• New arguments charge_carrier, absolute in mass.calculate_mass and mass.Composition.mass (#61).
  Charge is now only handled in Composition.mass and not Composition.__init__.
• Bugfix in pyteomics.tandem (#71 by @superrino130).

Version 4.5.2

• Support Python 3.10.

Version 4.5.1

• Add max_length parameter in pyteomics.parser.cleave.
• Bugfix in pyteomics.parser.cleave for semi=True.
• Add regex parameter in pyteomics.parser.cleave and warn for possible typos in cleavage rule names.
• Add functions parser.icleave (generator) and parser.xcleave (list) to produce peptide sequences with indices and possible repetitions.
• Bugfixes (#63 and #64 by @mobiusklein).

Version 4.5

• Add support for mzMLb (#35 and #38 by @mobiusklein) with new module pyteomics.mzmlb.

• Add ProteomeExchange backend for PROXI requests and implement an aggregator for responses from all backends (#36, #45 and #55 by @mobiusklein) in pyteomics.usi.

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

• New arguments keep_nterm_M and fix_aa in pyteomics.fasta.shuffle (#54 by @caetera).

• Fx for unwanted warnings in pyteomics.auxiliary.file_helpers._check_use_index when use_index is explicitly passed (#52).

• Update the default XML schema for featureXML and fix issues with incorrectly specified data types (#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 (#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.

Version 4.4.2

• Add cleavage rules from MS ontology as pyteomics.parser.psims_rules. parser.cleave now understands keys and accessions from psims_rules as rules.

• Improve mzIdentML parser performance (and possibly others in some cases) by relying more on offset indexes (#34 by @mobiusklein).

• Extend the pyteomics.mztab.MzTab parser with auto-generated properties. Almost all metadata entities are now exposed as properties on the parser object (#23 by @mobiusklein).

• Fix the version parsing in pyteomics.mztab to support shorter MzTab version strings (#24 by @donnyyy777).

• Tweak the pyteomics.pepxml.PepXML parser to present some values that were previously reported as None.

• Fix compatibility with SQLAlchemy 1.4 (#32 by @mobiusklein).

Version 4.4.1

• Further tweaked behavior of pyteomics.auxiliary.file_helpers._check_use_index, which is responsible for handling of use_index in read functions in parser modules.

• Fix indexing when element identifiers contain XML-escaped characters (#20 by @mobiusklein).

• Add support for MzTab 2.0 (#22 by @annalefarova).

• Also, check out the Pyteomics Discussions page!
  You can use it to share your thoughts, ask questions, discuss coding practices, etc.

Version 4.4

• New module pyteomics.usi implements a minimal Universal Spectrum Identifier parser and PROXI client (#11 by Joshua Klein).
• Support peak annotations in MGF (#12 by Julian Müller).
• Provide version information in pyteomics.version (#14).
• Make the order of isoforms reproducible in pyteomics.parser.isoforms (#15).
• Rename types keyword argument to ion_types in pyteomics.pylab_aux.annotate_spectrum.
• Fix #16, a bug introduced in 4.3.3.