Pyteomics

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- Fix `159 <https://github.com/levitsky/pyteomics/issues/159>`_.

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- Fix call signature for :py:func:`pepxml.read` and make it a full alias to :py:class:`pepxml.PepXML`.
- Disable indexing of pepXML in :py:func:`pepxml.DataFrame`, which fixes creation of dataframes from files
with non-unique spectrum IDs.
- Allow iteration over search hits instead of spectrum queries with :py:meth:`pyteomics.pepxml.PepXML.search_hits`.
:py:func:`pyteomics.pepxml.DataFrame` has a new argument `by`, which accepts values "spectrum_query" (default)
and "search_hit" (new).
- Fix `156 <https://github.com/levitsky/pyteomics/issues/156>`_.
- Fix `157 <https://github.com/levitsky/pyteomics/issues/157>`_
(`158 <https://github.com/levitsky/pyteomics/pull/158>`_ by Joshua Klein).

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- Add compatibility with NumPy 2.0.
- Fix `153 <https://github.com/levitsky/pyteomics/issues/153>`_. MGF parser now recognizes precursor charge specified
on the PEPMASS line. If CHARGE is also specified, it is ignored.

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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>`_).