Pyteomics

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- Update parsers for FASTA headers.

- NamedTuple for FASTA entries is now defined globally, which should solve
pickling problems.

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- New module :py:mod:`pyteomics.tandem` for reading output files of X!Tandem
search engine.

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- Fix in :py:mod:`pyteomics.pepxml`. pepXML files generated by TPP are now
processed without errors.

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- Fix in :py:mod:`pyteomics.pepxml`. 'modified_peptide' is now always available.

- Fix in :py:mod:`pyteomics.mass` (issue 2 in the bug tracker).

- Improved arithmetics for :py:class:`Composition` objects.

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- In :py:mod:`fasta`, :py:func:`decoy_db` now doesn't write to file, but returns
an iterator over FASTA records. The old :py:func:`decoy_db` is now called
:py:func:`write_decoy_db`, which is equivalent to :py:func:`decoy_db` combined
with :py:func:`write`.

Bugfixes:

- In :py:func:`pyteomics.mgf.read`, the charges, if present, are returned as a
masked array now. Previously, an exception occurred if charges were missing
for some of the fragments.

- Values in :py:data:`mass.nist_mass` corrected.

- Other minor corrections.

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- Adjust the behavior affected by the bug fixed in 2.1.2. `name` attributes
of `<cvParam>` elements in the absence of `value` attributes are now collected
in a list under the `'name'` key.

- Add support for overlapping matches in :py:func:`parser.cleave`.