v1.5.0

Added

• ✨ io: Read/write support for JSON and CBOR formats. (#129)
• ✨ io.percolator: Added support for Comet-style N- and C-terminal modifications (#121 and #131 by @ATPs)

Changed

• ♻️ stats.qvalues: Set the regular target–decoy formula explicitly in Pyteomics when remove_decoy=False and apply the +1 correction (probability that the first excluded decoy out-scores the threshold PSM). This produces less overly conservative q-values (e.g., on example_files/msms.txt). (#128)
• ♻️ io.pepxml: Refactor spectrum naming logic to prefer spectrumNativeID when available (#122 by @julianu)
• 🏷️ Typing: Adopted full MyPy typing across the codebase. (#125)
• 👷 CI: Replaced file-hash–based tests for io.idxml with unit tests; added formatting checks. (#125)

Removed

• 💥 Dropped support for Python 3.9. (#125)

Fixed

• 🐛 io.mzid: Treat MS:1001460 “unknown modification” as a delta-mass–designated modification in peptidoforms so mass calculations remain possible. Previously rendered as [unknown modification]. (#126 by @levitsky)
• 🐛 io.fragpipe: Build more comprehensive ProForma strings using “Assigned Modifications” from FragPipe output. (fixes #123; #124 by @levitsky)
• 🐛 peptidoform: Allow residue X with a MassModification to indicate a gap of known mass per ProForma §4.2.7; resolves failures computing theoretical mass for non-natural residues (fixes #127). (#130)

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Full Changelog: v1.4.1...v1.5.0