feat: support mixed residue types - #50
Conversation
Preserve generic and concrete residues in the same parsed graph and result vector. Remove the unreleased drop_generic argument, refresh documentation, and add cross-format regression coverage.
Up to standards ✅🟢 Issues
|
|
@codex review |
![chatgpt-codex-connector[bot]](https://avatars.githubusercontent.com/in/1144995?s=60&v=4){kind=small}
There was a problem hiding this comment.
💡 Codex Review
Here are some automated review suggestions for this pull request.
Reviewed commit: 576047be0b
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".
| * Parsers now preserve unusual monosaccharide configurations using `glyrepr` names such as `D-Fuc`, `L-Gul`, and `D-Fucf`, while unprefixed names retain their natural configurations. (#43, #44) | ||
| * Parsers now preserve explicit furanose forms as `glyrepr` monosaccharide names such as `Galf`, `GlcfNAc`, and `Neuf5Ac` across IUPAC, GlyCAM IUPAC, GlycoCT, WURCS, LINUCS, Linear Code, and KCF inputs. (#41) | ||
| * `auto_parse()` and all format-specific parsers gain `drop_generic` to replace generic glycans with `NA` when generic and concrete glycans coexist, with a message reporting the number dropped. (#39) | ||
| * `auto_parse()` and all format-specific parsers now preserve generic and concrete residues mixed within a glycan and across parsed vectors. (#50) |
There was a problem hiding this comment.
When this package is installed with a pre-glyrepr#90 glyrepr 0.14.0.9000 snapshot, that dependency still satisfies the unchanged Imports requirement even though its constructors reject mixed monosaccharide types. Consequently, the newly advertised mixed inputs continue to error in both wrapper paths. Bump glyrepr's development version and require that version here, or pin a compatible remote revision.
Useful? React with 👍 / 👎.
1 participant
Summary
drop_genericargument and filtering path from all parsersThis aligns glyparse with glycoverse/glyrepr#90.
Verification
devtools::test()— 1,658 expectations passedpkgdown::check_pkgdown()— passeddevtools::check(document = FALSE)— 0 errors, 0 warnings, 1 environment-only clock note