Version 4.4-beta0

• 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.

Version 4.3.3

• Add pyteomics.electrochem.gravy (#9).

• Fixes and improvements in pyteomics.pepxml.roc_curve (#10).

• Changes in guessing behavior of read functions.

  In modules that implement indexing parsers for non-XML formats (MGF, FASTA, PEFF, ms1/ms2),
  when a parser is instantiated using read, the parser class to instantiate is guessed
  based on the mode of the file object passed to read (text or binary).

  With some file-like objects, mode cannot be easily deduced without consuming some of the data.
  You will now see more warnings in case use_index is not explicitly passed to read and reading mode is not obvious.
  There will also be warnings if use_index is specified but the file is opened in the wrong mode.
  To avoid all of this, you are encouraged to instantiate parser classes directly,
  or explicitly specify use_index to read in all corner cases.

Version 4.3.2

This release addresses the packaging issue #7.

Version 4.3.1

This technical release updates v4.3 by removing references to easy_install.

Version 4.3

First release after the move to Github. Issue and PR numbers in release notes now refer to this
Github repo. Archive of the Bibucket issues and PRs is stored here.

Changes in this release:

• New module pyteomics.openms.idxml.

• Fix #3, #5, and some issues in tandem.