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refactor(dada2): use base R for taxonomy CSV assembly - #61
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Preserve row and column ordering and sample names, update both CI package checks, and add focused join and CSV regression fixtures.
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| library(dada2) | ||
| library(vegan) | ||
| library(dplyr) | ||
| # Retain while installer and CI explicitly verify this package. |
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| # Retain while installer and CI explicitly verify this package. |
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Replaces withdrawn #57. This branch starts directly at upstream main
52feb605and is limited to six files.Replaces the five CSV-assembly joins and row-name conversion with base R. Restores left-row and right-match order, preserves column order and non-syntactic sample names, and uses unique internal names during merging. Repeated suffixing handles collisions such as taxonomy
Speciesalongside samplesSpecies,Species.xandSpecies.x.x.Removes dplyr from the discovery manifest, lockfile, both CI package checks and both installer checks. Keeps tibble in the lockfile AND discovery manifest because the installer and CI still explicitly require it; this does not rely on a claimed transitive dependency. Adds regression checks for joins and exact bytes for all five CSV outputs to the existing CI job.
Validation:
git diff --checkpasses.d9ea982addresses the suffix-collision and tibble-discovery review findings. The new collision regression fails against the previous helper and passes after the fix, alongside all five CSV fixtures, under WebR 0.6.0 / R 4.6.0.Reproduction:
No sequencing algorithm, toolchain pin, frontend, licensing or unrelated fork changes. Related to #36 without closing the broader migration issue.