makeSignatures() names discrete signatures "bugphyz:" (missing z)
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Assessment
- Difficulty
- 2/5
- Estimated time
- 1-3 hours
- Newbie friendliness
- 76/100
Research direction
Read makeSignatures() in R/bugphyzz.R, especially the discrete-signature branch and the range branches cited in the issue. Change the discrete prefix to match the range prefixes and add a NEWS.md entry explaining the changed names and compatibility impact. Done when discrete and range signatures use the same prefix and the release note describes the change.
Written by the indexing model from the issue text.
Description
makeSignatures() prefixes discrete signature names with "bugphyz:" (R/bugphyzz.R#L237), but the range branches at lines 265 and 287 use "bugphyzz:". Every GMT file mixes the two. For example, bugphyzz-genus-NCBI_ID.gmt in bugphyzzExports v1.0.3 (Zenodo 12574596) has 48 bugphyz: signatures and 16 bugphyzz:.
The Python port (bugphyzz-py) already uses bugphyzz:, so R and Python now give different names for the same signatures.
Proposed fix: change line 237 to "bugphyzz:", add a NEWS.md entry noting that discrete signature names changed, and use the corrected prefix in the next bugphyzzExports release. Code that matches signature names against the current exports will need updating, which the NEWS entry should say.
Drafted with Claude Code
- Dominant language
- R
- Stars
- 6
- Forks
- 6
- PR merge metrics
- No merged PRs in 30d
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