glyenzy 0.7.0

Breaking changes

• path_biosynthesis() and trace_biosynthesis() no longer support paucimannose N-glycans; use glyenzy 0.6.3 if you need to analyze those structures. (#25)

New features

• Add first-class sulfotransferases (ST) with 12 human N- and O-glycan enzymes, sulfate-aware inference and biosynthesis, and virtual sulfation steps. (#20, #33)
• path_biosynthesis() and trace_biosynthesis() gain max_virtual_steps to bridge a bounded number of unsupported, target-directed transitions before resuming concrete enzyme tracing; fallback edges are marked by is_virtual. (#32)
• New trace_biosynthesis_virtual() and path_biosynthesis_virtual() build enzyme-agnostic networks by trimming targets backward; annotate_enzymes = TRUE adds exact rule-matched candidates in concrete_enzymes. (#22, #28, #30)
• Add support for non-intact glycan structures by using lenient motif matching with a warning about reduced reliability. (#25)

Minor improvements and fixes

• path_biosynthesis() and trace_biosynthesis() now scale better to large and multi-target searches by keeping intermediates as graphs, sharing prepared graph and rule work, vectorizing and batching frontier matching, caching graph products, pruning irreversible pre-MGAT2 decorations and occupied acceptor carbons, prioritizing inclusive targets, and using one multi-target reachability traversal. (#26, #29, #34)