Spectrum-utils

Added

- Bubble plot for mass errors by RalfG.
- Speedup of peptide parsing and annotation by jspaezp.
- Generate theoretical fragments for non-monoisotopic peaks.

Fixed

- Support Python 3.11.
- Ensure proper version number is set when installed using Conda.
- XLMOD location changed from the mzIdentML repository to a dedicated repository.
- Metabolomics USI resolver moved from GNPS to GNPS2.
- Replace deprecated appdirs dependency by platformdirs.

Added

- Verify that the given mass tolerance unit is always "Da" or "ppm".

Changed

- Update to matplotlib version 3.5 and above.

Fixed

- Plot spectra without a ProForma peptide annotation.

Added

- Load spectra directly from online resources (ProteomeXchange members, metabolomics resources through GNPS) using the [Universal Spectrum Identifier](https://www.psidev.info/usi) mechanism.
- Full support of the [ProForma 2.0](https://www.psidev.info/proforma) 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](https://pypi.org/project/pyteomics.cythonize/) for faster mass calculations.
- Automatic code style enforcement using [black](https://github.com/psf/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.

Changed

- Annotate spectrum peaks based on the [ProForma 2.0 specification](https://www.psidev.info/proforma) to described (modified) peptides.
- Use `jitclass` instead of multiple `jit` functions to group the Numba spectrum processing functionality.
- Use [MyST](https://myst-parser.readthedocs.io/) instead of recommonmark to generate the documentation from MarkDown files.
- Update runtime benchmark to the latest versions of all libraries.

Removed

- `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.

Fixed

- Don't crash when plotting empty spectra.
- Use the correct 13C mass difference for isotope precursor removal.

- Remove RDKit as a dependency.