Pyteomics

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- Fix issue 74.
- In :func:`pyteomics.auxiliary.fdr`, raise :exc:`PyteomicsError` instead of :exc:`ZeroDivisionError` when
using formula 1 on input without any target PSMs.
- Provide more accurate amino acid masses in :py:data:`mass.std_aa_mass`.
- Fix SyntaxError in :py:mod:`pyteomics.pylab_aux` on Python 2.7.

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- Fix ThreadPool shutdown and add new parameter `ephemeral_pool` in :py:class:`pyteomics.usi.PROXIAggregator`
(`67 <https://github.com/levitsky/pyteomics/pull/67>`_ by Joshua Klein).
- Bugfix in `pyteomics.proforma.GenericModificationResolver` (`68 <https://github.com/levitsky/pyteomics/issues/68>`_ by Joshua Klein).
- New helper function :py:func:`pyteomics.fasta.decoy_entries`.
- New arguments `charge_carrier`, `absolute` in :py:func:`mass.calculate_mass` and
:py:meth:`mass.Composition.mass` (`61 <https://github.com/levitsky/pyteomics/pull/61>`_).
Charge is now only handled in :py:meth:`Composition.mass` and not :py:meth:`Composition.__init__`.
- Bugfix in :py:mod:`pyteomics.tandem` (`71 <https://github.com/levitsky/pyteomics/pull/71>`_ by superrino130).

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- Support Python 3.10.

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- Add `max_length` parameter in :py:func:`pyteomics.parser.cleave`.
- Bugfix in :py:func:`pyteomics.parser.cleave` for `semi=True`.
- Add `regex` parameter in :py:func:`pyteomics.parser.cleave` and warn for possible typos in cleavage rule names.
- Add functions :py:func:`parser.icleave` (generator) and :py:func:`parser.xcleave` (list) to produce
peptide sequences with indices and possible repetitions.
- Bugfixes (`63 <https://github.com/levitsky/pyteomics/pull/63>`_ and `#64 <https://github.com/levitsky/pyteomics/pull/64>`_
by Joshua Klein).

---

- Add support for `mzMLb <https://www.biorxiv.org/content/10.1101/2020.02.13.947218v3>`_
(`35 <https://github.com/levitsky/pyteomics/pull/35>`_
and `38 <https://github.com/levitsky/pyteomics/pull/38>`_ by Joshua Klein)
with new module :py:mod:`pyteomics.mzmlb`.

- Add ProteomeExchange backend for PROXI requests and implement an aggregator for responses from all backends
(`36 <https://github.com/levitsky/pyteomics/pull/36>`_,
`45 <https://github.com/levitsky/pyteomics/pull/45>`_, and
`55 <https://github.com/levitsky/pyteomics/pull/55>`_ by Joshua Klein)
in :py:mod:`pyteomics.usi`.

- Add support for `ProForma <https://www.psidev.info/proforma>`_
(`37 <https://github.com/levitsky/pyteomics/pull/37>`_ by Joshua Klein)
in new module :py:mod:`pyteomics.proforma`.

- New arguments `keep_nterm_M` and `fix_aa` in :py:func:`pyteomics.fasta.shuffle`
(`54 <https://github.com/levitsky/pyteomics/pull/54>`_ by Vladimir Gorshkov).

- Fix for unwanted warnings in :py:func:`pyteomics.auxiliary.file_helpers._check_use_index` when
`use_index` is explicitly passed (`52 <https://github.com/levitsky/pyteomics/issues/52>`_).

- Update the default XML schema for featureXML and fix issues with incorrectly specified data types
(`53 <https://github.com/levitsky/pyteomics/pull/53>`_).

- Add a new backend for spectrum annotation and plotting. :py:func:`pyteomics.pylab_aux.plot_spectrum` and
:py:func:`pyteomics.pylab_aux.annotate_spectrum` can now use
`spectrum_utils <https://github.com/bittremieux/spectrum_utils>`_ under the hood
(`43 <https://github.com/levitsky/pyteomics/pull/43>`_).

See new `Example 4 <examples/example_annotation.html>`_ for demonstration.

- New function :py:func:`pyteomics.pylab_aux.mirror` for making a
`spectrum_utils <https://github.com/bittremieux/spectrum_utils>`_ mirror plot.

- :py:func:`pyteomics.pylab_aux.plot_spectrum` and :py:func:`pyteomics.pylab_aux.annotate_spectrum` now
always return :py:class:`matplotlib.pyplot.Axes`.

- Add a warning when passing an existing file by name in writing functions.
The default mode for output files will change from `'a'` to `'w'` in a future version.

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- Add cleavage rules from `MS ontology <http://purl.obolibrary.org/obo/MS_1001045>`_ as
:py:data:`pyteomics.parser.psims_rules`. :py:func:`pyteomics.parser.cleave` now understands keys and accessions from
:py:data:`psims_rules` as rules.

- Improve mzIdentML parser performance (and possibly others in some cases) by relying more on offset indexes
(`34 <https://github.com/levitsky/pyteomics/pull/34>`_ by Joshua Klein).

- Extend the :py:class:`pyteomics.mztab.MzTab` parser with auto-generated properties. Almost all metadata entities are
now exposed as properties on the parser object (`23 <https://github.com/levitsky/pyteomics/pull/23>`_ by Joshua Klein).

- Fix the version parsing in :py:mod:`pyteomics.mztab` to support shorter vMzTab version strings
(`24 <https://github.com/levitsky/pyteomics/pull/24>`_ by Donavan See).

- Tweak the :py:class:`pyteomics.pepxml.PepXML` parser to present some values that were previously reported as None.

- Fix compatibility with :py:mod:`SQLAlchemy` 1.4 (`32 <https://github.com/levitsky/pyteomics/pull/32>`_ by Joshua Klein).