Pyteomics

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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.

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- When passing an existing file (by name) to :py:func:`pyteomics.mgf.write` or :py:func:`pyteomics.fasta.write` and
other writing functions, **the file will be opened for writing by default**. Previously, it would be opened for
appending with a warning about the upcoming change. Please be aware that existing files will be overwritten
if passed by name. The rationale for this is better reproducibility if the same code is run multiple
times. You can use the `file_mode` argument of the writing functions to override this behaviour, or pass your own
file objects.
- Add a special warning when trying to write a single spectrum with :py:func:`pyteomics.mgf.write`.
See also: `Writing one or more MGF spectra to a file <https://github.com/levitsky/pyteomics/discussions/109>`_.
- In :py:func:`pyteomics.mass.mass.calculate_mass`, the `absolute` parameter is now `True` by default.
When calculating *m/z* for negative charges, the returned value will be positive by default.
- Fix issue 98 (`99 <https://github.com/levitsky/pyteomics/pull/99>`_ and
`101 <https://github.com/levitsky/pyteomics/pull/101>`_ by Joshua Klein).
- Fix issue 91 (`92 <https://github.com/levitsky/pyteomics/pull/92>`_ by Joshua Klein).
- Fix issue 96.
- Update the UniProt header pattern (fix rare parsing errors with
:py:class:`pyteomics.fasta.UniProt` and :py:class:`pyteomics.fasta.IndexedUniProt`) in
`93 <https://github.com/levitsky/pyteomics/pull/93>`_.
- Update the UniRef header pattern (fix parsing errors with
:py:class:`pyteomics.fasta.UniRef` and :py:class:`pyteomics.fasta.IndexedUniRef`) in
`102 <https://github.com/levitsky/pyteomics/pull/102>`_. Some keys are removed from the output.
- Fix pickling issues with :py:class:`pyteomics.mgf.IndexedMGF`, :py:class:`pyteomics.ms1.IndexedMS1`,
:py:class:`pyteomics.ms2.IndexedMS2` (108).
- Add "charge array" and "resolution array" to the output of MS2 parsers (108). Add new arguments `read_charges`
and `read_resolutions` to disable parsing, and `convert_arrays` to govern the creation of NumPy arrays
(and masked arrays).

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- New function :py:func:`pyteomics.proforma.set_unimod_path` allowing the ProForma parsing machinery
to work with a local Unimod copy (`85 <https://github.com/levitsky/pyteomics/pull/85>`_ by Joshua Klein).
See `documentation <https://pyteomics.readthedocs.io/en/latest/api/proforma.html#cv-disk-caching>`_ for a usage example.
- New method :py:meth:`pyteomics.proforma.Proforma.fragments` to generate m/z for an ion series
(`85 <https://github.com/levitsky/pyteomics/pull/85>`_ by Joshua Klein).
- New function :py:func:`pyteomics.parser.to_proforma` helps convert *modX* sequences to ProForma.
- Fix: prevent :func:`pyteomics.mass.mass.fast_mass2` from changing `aa_mass`.
- Update :py:func:`pyteomics.pylab_aux.annotate_spectrum` for compatibility with latest :py:mod:`spectrum_utils`.
Pyteomics is now compatible with :py:mod:`spectrum_utils` 0.4.0 and newer.

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- Fix issue 77.