Pyteomics

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Fix for a memory leak in :py:func:`pyteomics.mzid.get_by_id`, which affects
:py:func:`pyteomics.mzid.read` with ``retrieve_refs=True``.

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- New functions :py:func:`local_fdr` in :py:mod:`pepxml`, :py:mod:`mzid`, and
:py:mod:`tandem`. The function returns a NumPy array with PSM scores and
corresponding values of local FDR.

- New parameter `iterative` in :py:func:`read` functions of XML parsing
modules. Parsing of mzIdentML files with ``retrieve_refs=True`` got
significantly faster.

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- Universally applicable modifications are now allowed in
:py:func:`pyteomics.parser.isoforms`.

- It is now also possible to specify non-terminal modifications which are
only applicable to terminal residues.

- Fix in :py:func:`pyteomics.parser.parse`: if the `labels` argument is
provided, it needs to contain standard terminal groups if they are present
in the sequence or if `show_unmodified_termini` is set to :py:const:`True`.

- :py:class:`pyteomics.mass.Composition` instances are now pickleable.

- Performance improvements.

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- New parameter `reverse` in all :py:func:`!filter` functions.

- New function :py:func:`pyteomics.mass.fast_mass2`, which is analogous to
:py:func:`pyteomicsmass.fast_mass`, but supports full *modX* notation and
is several times slower.

- Fix in :py:func:`pyteomics.pepxml.read` for compatibility with files
produced with Mascot2XML utility.

- Unknown labels now allowed in :py:mod:`pyteomics.electrochem` and
:py:mod:`pyteomics.achrom` functions in accordance with new general policy.

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

- handling of the `labels` argument is now in accordance with new policy
- solved memory problems when using `max_mods`

- :py:func:`pyteomics.parser.cleave` does not require a valid *modX* sequence
by default.

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- :py:func:`pyteomics.parser.amino_acid_composition` now accepts "split"
parsed sequences.

- Cleavage rules in :py:data:`pyteomics.parser.expasy_rules` updated.

- Helper function :py:func:`pyteomics.parser.num_sites` counts the number
of cleavage sites in a sequence.

- Helper function :py:func:`pyteomics.parser.match_modX` does essentially
the same as :py:func:`pyteomics.parser.is_modX`, but returns a
:py:class:`re.match` object or :py:const:`None` instead of a :py:class:`bool`.

- Bugfix in :py:func:`pyteomics.auxiliary.filter`, which didn't work correctly
with iterators.

- Added a new parameter ``max_mods`` in :py:func:`pyteomics.parser.isoforms`.

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

- The boolean ``overlap`` parameter in :py:func:`pyteomics.parser.cleave` is
replaced with an integer ``min_length``. Since ``min_length`` uses
:py:func:`pyteomics.parser.length`, the ``labels`` keyword argument is now
accepted by :py:func:`cleave` and :py:func:`num_sites`, if needed. With
carefully designed cleavage rules, all cleavage functions work
with *modX* sequences.

- The ``labels`` argument in :py:func:`pyteomics.parser.parse` and related
functions has changed its meaning. :py:func:`parse` won't raise an exception
for non-standard labels in sequences if the ``labels`` keyword argument is
not given.

- The *modX* notation specification is now more strict to avoid ambiguity:
only zero or two terminal groups can be present in a *modX* sequence.
Sequences with one terminal group specified will be supported where possible,
but be advised that sequences such as "H-OH" are intrinsically ambiguous.