Added

• ✨ Update checks for both GUI and CLI, including a popup or console notice when a new release is available; introduce a disable_update_check configuration option.
• ⚙️ Config: Support null/None for boolean options to explicitly represent an unset state.

Changed

• 🚸 Parsing: Further improve handling of missing LC–IM–MS fields in spectrum files.
• 📦 Packaging: Switch to UV for package management and introduce a lockfile to ensure reproducible installations; the version’s single source of truth now resides in pyproject.toml.
• 🐳 Docker: Upgrade base image to python:3.12-slim and use the lockfile to pin dependency versions.
• 📦 Packaging: Move development dependencies into dependency-groups in pyproject.toml.
• 👷 CI: Separate the linting step for faster feedback on code issues.
• 🔧 Tooling: Update pre-commit hook packages.
• ♻️ Types: Improve and correct type annotations.

Fixed

• 🐛 CLI/Config: Prevent command-line defaults (e.g., False) from overriding True values specified in the configuration file.
• 🐛 Parsing: Correct handling of missing precursor data in spectrum files — previously, precursor information was parsed even when not required by the configured feature generators.