feat: add GlyCAM IUPAC parser

[fubin1999]

Summary

Add parse_glycam_iupac() for GlyCAM IUPAC strings and export it from glyparse.

Details

• Normalize GlyCAM IUPAC residue tokens into IUPAC-condensed notation, including D/L configuration markers, pyranose/furanose ring markers, terminal -OH, and residue modifiers such as [6S] and [9A].
• Delegate graph construction to the existing IUPAC-condensed parser after normalization.
• Accept explicit alphabetic reducing-end caps such as -OME; these are normalized to the regular reducing-end form because glyrepr does not represent the terminal moiety separately.
• Accept comma-separated modifier lists inside one GlyCAM bracket, such as [2NAc,6S], and normalize them into IUPAC-condensed modifier suffixes.
• Add focused parser tests for simple, branched, modified, representative corpus-derived examples, and NA behavior.
• Use only successful GlyCAM test sequences that have exact non-NA reference answers in docs/glycan_sequences_iupac_condensed.csv.
• Add representative fixed test cases for sialylated LacNAc, core fucose, uronic acid, pyranose Xyl, polysialic branching, Xyl chains, GlcNAc-7-linked Neu5Ac, and Gal-8/Gal-9-linked Neu5Ac patterns.
• Add a NEWS.md entry for the new parser.

Verification

• Rscript -e 'devtools::document()'
• Local provenance audit against docs/glycan_sequences_glycam_iupac.csv and docs/glycan_sequences_iupac_condensed.csv -> all 15 successful GlyCAM test sequences have exact non-NA IUPAC-condensed references
• Local manual syntax check for review-only forms absent from the CSVs: DGlcpb1-4DGlcpb1-OME, DGlcp[2NAc,6S]b1-OH, and DGalpNAc[4S,6S]b1-OH
• air format R/parse-glycam-iupac.R tests/testthat/test-parse-glycam-iupac.R
• Rscript -e 'devtools::test(filter = "parse-glycam-iupac")' -> 7 passed, 0 failed, 0 warnings, 0 skipped
• Rscript -e 'devtools::test()' -> 953 passed, 0 failed, 0 warnings, 0 skipped

[codacy-production]

Up to standards ✅

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[Copilot]

Pull request overview

Adds first-class support for parsing GlyCAM IUPAC glycan strings by normalizing them into IUPAC-condensed notation and then reusing the existing IUPAC-condensed parser, with accompanying documentation and regression tests against the published GlyCAM corpus.

Changes:

• Introduces parse_glycam_iupac() (plus internal conversion helpers) that converts GlyCAM residue tokens/modifiers and delegates graph construction to parse_iupac_condensed().
• Adds unit tests for simple/branched/modified glycans and corpus-level regression coverage including NA and on_failure semantics.
• Exports the new API and ships generated Rd docs and an initial (header-only) parse-failures report CSV.

Reviewed changes

Copilot reviewed 5 out of 6 changed files in this pull request and generated no comments.

Show a summary per file

File	Description
tests/testthat/test-parse-glycam-iupac.R	Adds focused unit tests plus a chunked corpus regression test ensuring GlyCAM parses and matches IUPAC-condensed references.
R/parse-glycam-iupac.R	Implements parse_glycam_iupac() and normalization from GlyCAM IUPAC to IUPAC-condensed prior to parsing.
NAMESPACE	Exports parse_glycam_iupac.
man/parse_glycam_iupac.Rd	Generated documentation for the new exported function.
docs/glycam_iupac_parse_failures.csv	Adds the expected parse-failures report file (currently header-only).

Files not reviewed (1)

• man/parse_glycam_iupac.Rd: Generated file

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[fubin1999]

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