fix: handle GlycoCT alditol residues

[fubin1999]

Summary

Adds GlycoCT alditol support to parse_glycoct() by normalizing open-chain alditol residues to regular reducing-end glycans with unknown anomer configurations.

Details

• Detects GlycoCT alditol residues encoded as open-chain o-...-0:0|1:aldi monosaccharides.
• Uses converter-derived GlycoCT alditol mappings so supported monosaccharides parse to the same names as regular glycans where GlycoCT has distinct descriptors.
• Uses glyrepr::get_anomer_pos() to return unknown reducing-end anomers such as ?1 for GlcNAc-ol.
• Emits a warning when GlycoCT alditol residues are normalized this way.
• Adds GlycoCT regression coverage for GlcNAc-ol, a linked alditol glycan, and all distinct converter-derived alditol descriptors available from the local converter.
• Regenerates parse_glycoct() documentation and adds a development NEWS entry for fix: handle GlycoCT alditol residues #22.

Verification

• Rscript -e 'devtools::document()' -> updated parse_glycoct.Rd
• Rscript -e 'devtools::test(filter = "parse-glycoct")' -> 298 passed
• air format R/parse-glycoct.R tests/testthat/test-parse-glycoct.R
• Rscript -e 'devtools::test()' -> 922 passed
• git diff --check -> clean

[codacy-production]

Up to standards ✅

🟢 Issues 0 issues

Results:
0 new issues

View in Codacy

_{NEW Get contextual insights on your PRs based on Codacy's metrics, along with PR and Jira context, without leaving GitHub. Enable AI reviewer
TIP This summary will be updated as you push new changes.}

[Copilot]

Copilot was unable to review this pull request because the user who requested the review has reached their quota limit.

[fubin1999]

@codex review

[chatgpt-codex-connector]

Codex Review: Didn't find any major issues. Already looking forward to the next diff.

Reviewed commit: ed5ed275ad

ℹ️ About Codex in GitHub

Your team has set up Codex to review pull requests in this repo. Reviews are triggered when you

• Open a pull request for review
• Mark a draft as ready
• Comment "@codex review".

If Codex has suggestions, it will comment; otherwise it will react with 👍.

Codex can also answer questions or update the PR. Try commenting "@codex address that feedback".