Pyteomics

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- Further tweaked behavior of :py:func:`pyteomics.auxiliary.file_helpers._check_use_index`, which is responsible for
handling of `use_index` in :py:func:`read` functions in parser modules.

- Fix indexing when element identifiers contain XML-escaped characters
(`20 <https://github.com/levitsky/pyteomics/pull/20>`_ by Joshua Klein).

- Add support for MzTab 2.0 (`22 <https://github.com/levitsky/pyteomics/pull/22>`_ by annalefarova).

- Also, check out the `Pyteomics Discussions page <https://github.com/levitsky/pyteomics/discussions>`_!
You can use it to share your thoughts, ask questions, discuss coding practices, etc.

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- New module :py:mod:`pyteomics.usi` implements a minimal Universal Spectrum Identifier parser and PROXI client
(`11 <https://github.com/levitsky/pyteomics/pull/11>`_ by Joshua Klein).

- Support peak annotations in MGF (`12 <https://github.com/levitsky/pyteomics/pull/12>`_ by Julian Müller).

- Provide version information in :py:mod:`pyteomics.version` (`14 <https://github.com/levitsky/pyteomics/pull/14>`_).

- Make the order of isoforms reproducible in :py:func:`pyteomics.parser.isoforms`
(`15 <https://github.com/levitsky/pyteomics/issues/15>`_).

- Rename `types` keyword argument to `ion_types` in :py:func:`pyteomics.pylab_aux.annotate_spectrum`.

- Fix `16 <https://github.com/levitsky/pyteomics/issues/16>`_, a bug introduced in 4.3.3.

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- Add :py:func:`pyteomics.electrochem.gravy` (`9 <https://github.com/levitsky/pyteomics/pull/9>`_ by Vladimir Gorshkov).

- Fixes and improvements in :py:func:`pyteomics.pepxml.roc_curve` (`10 <https://github.com/levitsky/pyteomics/pull/10>`_
by Andrey Rozenberg).

- Changes in guessing behavior of :py:func:`read` functions.

In modules that implement :ref:`indexing parsers <indexing>` for non-XML formats (MGF, FASTA, PEFF, ms1/ms2),
when a parser is instantiated using :py:func:`read`, the parser class to instantiate is guessed
based on the mode of the file object passed to :py:func:`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 :py:func:`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 :py:func:`read` in all corner cases.

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Fix `7 <https://github.com/levitsky/pyteomics/issues/7>`_.

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Technical release.

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First release after the move to Github. Issue and PR numbers from now on refer to the
`Github repo <https://github.com/levitsky/pyteomics>`_. Archive of the Bibucket issues and PRs is stored
`here <https://levitsky.github.io/bitbucket_backup/#!/levitsky/pyteomics>`_.

Changes in this release:

- New module :py:mod:`pyteomics.openms.idxml`.

- Fix `3 <https://github.com/levitsky/pyteomics/issues/3>`_, `#5 <https://github.com/levitsky/pyteomics/issues/5>`_,
and some issues in :py:mod:`tandem`.