v1.2.0 - Site and proteoform views, DuckDB 2.0 and faster conversion

QPX 1.2.0 writes files with specification version 1.2 (qpx_version 1.2). Nothing is removed or retyped, so 1.1 files are valid 1.2 files; see Versioning.

Highlights

• site and proteoform views, the optional modification_candidates column of psm and feature, and the optional sequence_edits column of pepmap.
• Works with DuckDB 2.0; DuckDB 1.5.0 or later is required (#356).
• Run, mz and PSM files may leave out the columns the specification does not require (#356).
• Faster conversion, transforms, validation and MuData export, most with less memory; outputs are unchanged.
• CLI options that had no effect are removed, so passing them is now an error: convert diann --protein-file/--partitions/--batch-size/--standardized-intensities, convert maxquant --protein-file/--standardized-intensities/--fixed-mod-only, and --batch-size of convert cdap, fragpipe, maxquant and quantms-msstats. Feature files whose intensities are keyed by channel (the quantms.io layout) and qpx.open() are no longer supported.

See CHANGELOG.md for every change.

What's Changed

• Speed up converters, remove dead code and no-op options, write null for missing values by @Shen-YuFei in #350
• Enhance performance, clean up code, and handle missing values by @ypriverol in #351
• Add site and proteoform views by @ypriverol in #352
• Competing modification interpretations and sequence edits by @ypriverol in #353
• Add site and proteoform views with validation and documentation by @ypriverol in #357
• Faster transforms and validation, optional run/mz/PSM columns, cleanup and module splits by @Shen-YuFei in #358
• Improve performance and validation in quantify and feature processing by @ypriverol in #359

Full Changelog: v1.1.6...v1.2.0