Pyteomics

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- Fix pickling of resolved ProForma modifications (`144 <https://github.com/levitsky/pyteomics/pull/144>`_
by Joshua Klein).
- Fix a deprecation warning in :py:mod:`pyteomics.mass.unimod` (`126 <https://github.com/levitsky/pyteomics/pull/126>`_
by Ralf Gabriels).
- Add caching for modifications resolvers in :py:mod:`pyteomics.proforma`
(`148 <https://github.com/levitsky/pyteomics/pull/148>`_ by Joshua Klein).
- Add support for constant terminal modifications in :py:mod:`pyteomics.proforma`
(`148 <https://github.com/levitsky/pyteomics/pull/148>`_ by Joshua Klein).
- Fix an exception in :py:mod:`pyteomics.ms1` when an information string has only one token
(`149 <https://github.com/levitsky/pyteomics/issues/149>`_).

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- Fix issue with :py:func:`calculate_mass` with a `composition` keyword argument.

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- Make :py:class:`proforma.MassModification` objects hashable
(`130 <https://github.com/levitsky/pyteomics/pull/130>`_ by Joshua Klein).
- Fix `132 <https://github.com/levitsky/pyteomics/issues/132>`_
(`133 <https://github.com/levitsky/pyteomics/pull/133>`_ by Joshua Klein).
- Fix thermolysin cleavage rule (`135 <https://github.com/levitsky/pyteomics/issues/135>`_).
- Fix `136 <https://github.com/levitsky/pyteomics/issues/136>`_.
- :py:func:`pyteomics.mass.mass.calculate_mass` now supports `ProForma <https://www.psidev.info/proforma>`_.
A sequence or a :py:class:`proforma.ProForma` object can be passed with the `proforma` keyword argument
(`137 <https://github.com/levitsky/pyteomics/pull/137>`_).
- Fix: restored the ability of :py:class:`IndexedTextReader` parsers (:py:class:`pyteomics.mgf.IndexedMGF`,
:py:class:`pyteomics.fasta.IndexedFASTA`, etc.) to load the byte offset index from a previously saved byte offset file
(created with :py:meth:`cls.prebuild_byte_offset_file` or :py:meth:`reader.write_byte_offsets`)
(`142 <https://github.com/levitsky/pyteomics/pull/142>`_).
- API change: uncodumented method :py:meth:`_build_index` of indexing XML parsers renamed to :py:meth:`build_byte_index`
(`142 <https://github.com/levitsky/pyteomics/pull/142>`_).
- Add a warning when creating an :py:class:`IndexedTextReader` instance with an empty offset index.
This warning can be disabled by passing `warn_if_empty=False`
(`138 <https://github.com/levitsky/pyteomics/pull/138>`_).

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- Fix `122 <https://github.com/levitsky/pyteomics/issues/122>`_.
- Fix `124 <https://github.com/levitsky/pyteomics/issues/124>`_
(in `125 <https://github.com/levitsky/pyteomics/pull/125>`_ by Seth Just).
- Fix `128 <https://github.com/levitsky/pyteomics/issues/128>`_
(in `129 <https://github.com/levitsky/pyteomics/pull/129>`_ by Joshua Klein).

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- :py:func:`pyteomics.fasta.write` can now write entries with parsed sequences
(`120 <https://github.com/levitsky/pyteomics/pull/120>`_ by Vladimir Gorshkov, Joshua Klein and Lev Levitsky).
- Fix `119 <https://github.com/levitsky/pyteomics/issues/119>`_.
- Fix import issue with :py:mod:`pyteomics.pylab_aux`.

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- Make :py:func:`pyteomics.mgf.write` work with a regular list of ints as "charge" param.
- Add mean absolute error (MAE) regression in :py:mod:`pyteomics.achrom`
(`117 <https://github.com/levitsky/pyteomics/pull/117>`_ by Mark Ivanov).
- Fix `115 <https://github.com/levitsky/pyteomics/issues/115>`_ and `#118 <https://github.com/levitsky/pyteomics/issues/118>`_.
- Remove :py:class:`auxiliary.Version`. :py:class:`pyteomics.version.VersionInfo` can be used instead.
- For target-decoy calculations, :py:mod:`pandas` is assumed to be 0.17 or newer.