Nova version 1.1.0

Release candidate for v1.1.0, built from main @
4b1f007.

Nova 1.1.0

Nova and Nova.IO ship together; both are 1.1.0.

Breaking

• Nova targets netstandard2.0 instead of .NET Framework 4.8. One build now serves .NET Framework 4.8 and .NET 8+ consumers.
• The named-pipe wire format changed: Spectrum serialization now includes ScanDescription. Upgrade both ends of a pipe together; 1.1.0 cannot talk to 1.0.0.18.
• FramentationType and PrecursorIon.FramentationMethod are renamed FragmentationType and FragmentationMethod.
• Files that cannot be opened or indexed throw SpectrumFileOpenException instead of returning a reader that yields empty spectra. Affects SpectrumFileReaderFactory.GetReader, and FileReader.ReadSpectrum / ReadSpectrumEx / ReadChromatogram when given a new file name.
• ThermoRawReader is internal, like the other format readers. Obtain readers through FileReader or SpectrumFileReaderFactory.GetReader.
• ISpectrumFileReader gained ChromatCount, surfaced by FileReader. Breaking only for external implementers of the interface.
• MzMLWriter.Write returns void. It only ever returned true; failures throw.

New

• MGF reading. It was previously a stub that returned empty spectra. A CHARGE= line listing several states yields one precursor per state.
• mzML and mzXML files larger than 2 GiB read correctly; byte offsets are 64-bit. Earlier versions silently returned zero peaks for every scan in such files.
• IChromatogram and IChromatDataPoint are public.
• MzMLWriter.Write takes optional validateSchema and schemaPath. Validation is off by default and no longer uses a hardcoded path.
• XML documentation ships in both packages, so IntelliSense shows the API comments.

Fixed

• PipeIO.Read handles partial stream reads; larger messages could be truncated.
• Deserialize appended precursors to those already on the spectrum instead of replacing them.
• PrecursorIon's copy constructor and Clear skipped CollisionEnergy, FragmentationMethod, and IsolationSpecificity.
• The mzML and mzXML readers shared one PrecursorIon object across every precursor and spectrum read; each spectrum now owns its own.
• Switching files with FileReader leaked a handle to the previous mzML or mzXML file, leaving it locked.
• MzMLReader set Analyzer to "OTMS" instead of "ITMS" for ion-trap filters.
• FileReader.OpenSpectrumFile returned true on a failed open, and FileReader.Format stayed Unknown.

Dependencies

• ThermoFisher.CommonCore.* pinned to 8.0.37. The matching packages are included in the release bundle.

New Contributors

• @ChrisMcGann made their first contribution in #17

Full Changelog: v1.0.0.18...v1.1.0