
# Aerith 1.1.3

* Avoid a Windows OpenMP runtime crash during PSM feature extraction by no
  longer enabling unused nested parallelism.

# Aerith 1.1.2

* Use release-compatible version numbering and exclude local build artifacts
  and development configuration from package builds and Git status.

# Aerith 1.1.1

* Remove precursor_peak_calculator_DIY_averagine and its native entry point.
  Use precursor_peak_calculator_DIY; no compatibility alias is provided.
  Rename the remaining exact-composition helper to PeptideIsotopeCalculator.

* Store compiled peptide chemistry in AerithParameters with
  three atom sources: biosynthetic, reagent-natural, and digestion solvent.
* Remove the bundled SiprosConfig.cfg, its parser, and generateOneCFG/generateCFGs.
  All peptide calculations initialize compiled parameters without file fallback.
* Add getAerithParameters and reagent/solvent pools to calPepAtomCount.
* Keep fixed IAA, oxidation/deamidation reagent atoms, and terminal water natural;
  use real phosphorus and proportional O/S isotope rescaling.
* Reject unsupported isotopes and invalid abundances instead of returning defaults.
* Use actual sourced formulas for precursor and B/Y spectra, including PTM losses,
  and estimate precursor mass from the modal isotope shift.
* Guard scan boundaries when annotating precursor and fragment isotope peaks.

* Add a compact show method for AAspectra objects.
* Fix invalid phosphorus isotope access and guard peak-array boundaries during
  PSM feature extraction, including missing precursor scans and empty matches.
* Retain the first peak when reading FT scans and support single-peak MGF files.
* Avoid reading past peak arrays when denoising spectra.
* Handle empty target or decoy protein-name lists without invalid string access.

# Aerith 0.99.0

* Initial submission to Bioconductor
