Pyteomics

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- Added :py:mod:`mzid` module for parsing of mzIdentML files.

- Fixed bugs, improved tests.

API changes
...........

- top-module functions in :py:mod:`fasta`, :py:mod:`mgf`, :py:mod:`mzml`,
:py:mod:`pepxml`, as well as :py:mod:`mzid`, are now called :py:func:`read`.

- in :py:mod:`parser`, :py:func:`parse_sequence` renamed to :py:func:`parse`.
It now accepts an optional parameter `allow_unknown_modifications`.

- :py:func:`mgf.write_mgf` and :py:func:`fasta.write_fasta` renamed to
:py:func:`write`.

- the output format of all :py:func:`read` functions has changed.

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- Include Apache license version 2.0:
http://www.opensource.org/licenses/Apache-2.0

- Minor bugfix in :py:mod:`pyteomics.fasta`.

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- Changes in :py:mod:`pyteomics.mass`.

API changes
...........

- :py:class:`Composition` objects can be created using positional first
argument, which will be treated as a sequence or (upon failure) as a formula.
This means that all functions relying on Composition
(:py:func:`calculate_mass`, :py:func:`most_probable_isotopic_composition`,
:py:func:`isotopic_composition_abundance`) allow that as well. However, it's
of no use for the latter.

- :py:class:`Composition` entries for modifications can be added to *aa_comp*
and used in composition and mass calculations. This way the specified group
will be added to any residue bearing this modification.

- That being said, the :py:func:`add_modifications` function is not needed
anymore and has been removed.

- Addition and subtraction of :py:class:`Composition` objects now produces a
:py:class:`Composition` object, allowing addition/subtraction of multiple
objects.

- :py:class:`Composition` is now a subclass of
:py:class:`collections.defaultdict` so one can safely retrieve values
without checking if a key exists.

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- :py:func:`pyteomics.parser.isoforms` now allows terminal modifications.

- Bugfixes in :py:func:`pyteomics.parser.parse_sequence`.

- New function :py:func:`pyteomics.parser.tostring` converts parsed sequences
to strings.

- Helper function :py:func:`pyteomics.parser.is_modX` added to check *modX* labels.

API changes
...........

- :py:func:`pyteomics.parser.isoforms` now returns a generator object

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- Bugfix in :py:mod:`pyteomics.pepxml`: modification info is now extracted.

- New optional boolean argument 'split' in :py:func:`pyteomics.parser.parse_sequence()`
allows to generate a list of tuples where modifications are separated from the
residues instead of a regular list of labels. In *labels* not only *modX* labels
are now allowed, but also separate *mod* prefixes. Such modifications are
assumed to be applicable to any residue.

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- Memory usage **significantly** decreased when parsing large mzML and pepXML
files.