0.4.0 - 2022-10-06

Added

Load spectra directly from online resources (ProteomeXchange members, metabolomics resources through GNPS) using the Universal Spectrum Identifier mechanism.
Full support of the ProForma 2.0 standard based on a formal context-free grammar.
Retrieve controlled vocabularies used by ProForma from their online sources and (cross-platform) cache locally.
Annotate different ion types: peptide fragments, internal fragment ions, immonium ions, intact precursor ions.
Annotate spectrum peaks that include a neutral loss.
Recommend installing pyteomics.cythonize for faster mass calculations.
Automatic code style enforcement using black.
Added contributing guidelines.
Added code of conduct.
Added .gitignore.
Minimum supported Python version bumped to Python 3.8.
Maximum supported Python version extended to Python 3.10.

Annotate spectrum peaks based on the ProForma 2.0 specification to described (modified) peptides.
Use jitclass instead of multiple jit functions to group the Numba spectrum processing functionality.
Use MyST instead of recommonmark to generate the documentation from MarkDown files.
Update runtime benchmark to the latest versions of all libraries.

annotate_molecule_fragment function to annotate peaks with a molecule string.
annotate_mz_fragment function to annotate peaks with their m/z values. Use the ProForma interface instead.
Global interface to set a static modification; specify modifications using ProForma directly instead.