Bioconductor 3.24 release checklist (25 November 2026)

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Evaluación

Dificultad
5/5
Tiempo estimado
Más de una semana
Aptitud para principiantes
15/100
Tipo de issue
Nueva funcionalidad
Claridad
Bastante claro
Estado de actividad
Activo
Stack tecnológico
r
Área
release

Línea de trabajo

Start with the Bioconductor release schedule and the listed bugphyzz and bugphyzzExports issues, then follow the checklist in release order. Coordinate package checks, data export, NEWS and Zenodo updates, and the DOI change to the import default. Done means the 3.24 release has shipped and every applicable checklist item is complete.

Escrito por el modelo de indexación a partir del texto del issue.

Descripción

Tracking issue for what ships in Bioconductor 3.24. Dates from the release schedule: release candidate 11 November, deadline for packages passing build and check 18 November, release branch 23 November, release 25 November.

Bioconductor's git devel is still at 1.7.1 (29 April); GitHub devel is 1.7.7, 21 commits ahead. The Zenodo deposit is the GitHub archive of the tag, and .downloadZ() reads every file matching "csv" from it, which now includes sources/bacdive/bacdive.csv.gz.

bugphyzz, before the 11 November release candidate
  • Push GitHub devel to git.bioconductor.org devel (1.7.8, 5 November); check the next devel build report
  • .downloadZ() reads only the three bugphyzz_*.csv files from the Zenodo zip
  • #256 bugphyzz: prefix in makeSignatures(), with a NEWS note that signature names change
  • #281 attributes.tsv clean-up (#284; the 56 ungrouped rows stay open)
  • #266, cheap half: \dontrun{} on the physiologies('all') example and skip_if_offline() on download tests; the fixture waits
  • Sheet fixes #260, #261, #262, #273: as overrides in bugphyzzExports (sources/microbe_directory/overrides.tsv, sources/sheet_overrides.tsv, ADR 0005), #273 in the sheet; Bergeys_2026 replaces the 2020 scrape (#274)
bugphyzzExports, data release
  • waldronlab/bugphyzzExports#83 AMR names validated before the rewrite (bugphyzzExports#84, bugphyzz#285)
  • waldronlab/bugphyzzExports#64 family-and-above rows: filtered out (bugphyzzExports#85; deep-node ASR wrong, waldronlab/taxPPro#16)
  • waldronlab/bugphyzzExports#66 point 1 deferred to after the release with points 2 and 3; interim rule in bugphyzzExports ADR 0002 (ties broken alphabetically by source)
  • Dispatch the export after the above; log_file.msg reports no dropped values
  • NEWS.md: date the 2026-11 section as v1.1.0 with the DOI; add #256 and #83
  • .zenodo.json creators (Wokaty, Andres)
  • Tag v1.1.0, GitHub release, Zenodo deposit; confirm the zip holds data, not LFS pointers, and importBugphyzz(version = "<DOI>") works
bugphyzz, after the DOI exists, before 18 November
  • New DOI as the importBugphyzz() default; roxygen, vignette and the pinned-DOI test updated
  • NEWS.md entry for the final 1.7.x and push to Bioconductor again
  • Tick the Zenodo line in waldronlab/bugphyzz-manuscript#10

Not in this release, already filed: waldronlab/bugphyzzExports#66 points 2 and 3, #266 fixture, waldronlab/taxPPro#15, #282, waldronlab/taxPProValidation#2. Close this issue when 3.24 ships.

Drafted with Claude Code.

Lenguaje dominante
R
Estrellas
6
Forks
6
Merge medio
1 h 48 min
PR fusionados (30 d)
13

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