# NEWS file for singIST

## Version 0.99.1 (2025-06-18)
Initial submission to Bioconductor

## Version 0.99.7 (2025-12-12)
First review round

## Version 0.99.82 (2026-01-05)
Second review round minor points

## Version 1.0.0 (2026-04-29)
Released in Bioconductor 3.23

## Version 1.1.0 (2026-04-29)
devel branch (Bioconductor 3.24) opened

## Version 1.1.1 (2026-08-04)
Removed large data file (data/OXA.rda, ~229MB) from git history to comply
with GitHub's 100MB file size limit ahead of Bioconductor's migration to
GitHub-hosted repositories. Data now hosted in inst/extdata in reduced form;
git history cleaned accordingly.
Migrated BioMart orthology retrieval to biomaRt::useEnsembl() with automatic
mirror fallback (www, useast, asia) and retries with exponential backoff
(.connect_ensembl).

## Version 1.1.2 (2026-08-20)
Reviewer 2, second review round:
* Wrapped every BioMart step in informative error handling (.biomart_step)
  reporting which step and dataset failed, with remediation guidance.
* Added orthology_cache argument to orthology_mapping(),
  singISTrecapitulations(), and multiple_singISTrecapitulations() to skip
  live Ensembl queries when a cached mapping is supplied.
* Shipped example_orthology_mapping.rda (human->mouse 1:1 orthologs, 17066
  pairs) in inst/extdata for offline vignette reproducibility.
* Wrapped Ensembl-dependent examples in \dontrun{} so R CMD check passes
  without network access.
* Vignette: added version/reproducibility section, dynamic version chunk,
  automatic offline fallback to shipped orthology cache, and sessionInfo().