From 9c2eaf2cb0bd928492f76e29814d7b953a0fd5c8 Mon Sep 17 00:00:00 2001 From: jakeberv Date: Sat, 17 Oct 2026 03:13:59 -0400 Subject: [PATCH] Document CRAN publication of bifrost 0.2.2 --- README.md | 6 +-- tools/releases/0.2.2.md | 61 +++++++++++++---------- vignettes/articles/development-status.Rmd | 16 +++--- 3 files changed, 47 insertions(+), 36 deletions(-) diff --git a/README.md b/README.md index 8a94280..3f954cf 100644 --- a/README.md +++ b/README.md @@ -53,7 +53,7 @@ The method works with fossil tip-dated trees and with a wide range of multivaria ## Installation -### CRAN release (0.2.0) +### CRAN release (0.2.2) ```r install.packages("bifrost") @@ -83,8 +83,8 @@ also apply when Zenodo captures a GitHub release. ## Development status -Version 0.2.2 is being prepared for release on GitHub; the latest published -GitHub release is 0.2.1 and CRAN currently distributes 0.2.0. All require +Version 0.2.2 is available on CRAN. The latest published GitHub release is +0.2.1; the 0.2.2 GitHub release is still being prepared. All require R 4.2 or newer. The 0.2.2 update makes search initialization explicit and corrects progress-related random-stream and numerical-thread handling, with console-display refinements. These changes can affect results relative to diff --git a/tools/releases/0.2.2.md b/tools/releases/0.2.2.md index da145de..f0030da 100644 --- a/tools/releases/0.2.2.md +++ b/tools/releases/0.2.2.md @@ -1,9 +1,21 @@ -# bifrost 0.2.2 publication preparation +# bifrost 0.2.2 publication record and GitHub preparation -Maintainer draft only: the checked source archive and results are recorded -below; publication is still pending. Keep 0.2.2 described as planned until -publication. This file is excluded from package and GitHub source archives -by the existing `tools/` rules. +CRAN published 0.2.2 on October 17, 2026. The GitHub release remains pending; +its draft body and remaining steps are recorded below. This file is excluded +from package and GitHub source archives by the existing `tools/` rules. + +## CRAN publication + +The [CRAN source index](https://cran.r-project.org/src/contrib/PACKAGES.gz) +records version 0.2.2 as published at `2026-10-17 07:10:02 UTC` +(3:10 a.m. EDT). The [source archive](https://cran.r-project.org/src/contrib/bifrost_0.2.2.tar.gz) +was verified downloadable; its index MD5 is `69050a80fb436cfc2e93ede8967729b7`. +The maintainer submitted a fresh rebuild, so this published archive is separate +from the locally checked archive recorded below. `cran-comments.md` retains +the submitted comments as a historical record. + +The latest published GitHub release remains v0.2.1. No v0.2.2 GitHub release +or Zenodo version archive is claimed here. ## Draft GitHub release body @@ -68,21 +80,22 @@ for details. GitHub publication does not update CRAN automatically. - [x] Rebuild and check the PR #255 author-metadata correction, including both manuals, in an isolated library. - [x] PR #255 merged as `ff805582`; the author-metadata correction is on main. -- [ ] Confirm PR #255 post-merge CI and merge the follow-up check-evidence PR - through normal review. Select the exact release commit and use the verified - submission archive recorded below. -- [ ] Retain the documented deferral of #231; this preparation does not fix it. +- [x] PR #256 merged as `8e0aceef`; all post-merge checks passed, including + exactly 100% coverage with zero uncovered rows and a clean Windows check. +- [x] The maintainer submitted 0.2.2; CRAN publication is verified above. +- [x] Update README and the release-status page to show CRAN 0.2.2 while + retaining the pending GitHub release. +- [x] Retain the documented deferral of #231; this preparation does not fix it. Keep the initialization/convergence follow-up (#242) and RRphylo dependency work (#247) separate from this release. - [ ] Review the remaining advisory findings and final check notes before - CRAN submission. The advisory job's success is not a clean-audit claim. -- [ ] Obtain explicit approval to publish. Do not create a tag, GitHub release, - or CRAN submission as part of preparation. -- [ ] At approved publication, use the verified commit for `v0.2.2` and the - release body above. Verify the GitHub archive and any Zenodo record after + GitHub publication. The advisory job's success is not a clean-audit claim. +- [ ] Obtain explicit approval before creating a tag or publishing the + GitHub release. CRAN publication does not authorize either action. +- [ ] At approved GitHub publication, select and verify the commit for `v0.2.2` + and use the release body above. Verify the GitHub archive and any Zenodo record after publication; never describe an unverified archive/DOI as available. -- [ ] Apply the publication-time documentation edits below through a PR. - Update CRAN availability separately, only after CRAN actually publishes it. +- [ ] Apply the GitHub publication-time documentation edits below through a PR. ## Latest check: PR #255 author-metadata correction @@ -104,9 +117,9 @@ paper citations remain unchanged. No package code or tests changed. Evidence: `output/release-0.2.2-author-check/run-wbvv4gjx/`, including the archive, `SHA256SUMS`, `final-summary.txt`, `bifrost.Rcheck/00check.log`, and the manual. -Confirm post-merge CI for `ff805582` before submission. -This archive supersedes the earlier archives recorded below; -use its path and checksum for any later authorized submission. +This is the final locally checked archive, superseding the earlier local +archives below. The maintainer subsequently rebuilt for CRAN submission; +the published archive is identified separately above. ## Earlier check: PR #254 Zenodo concept DOI update @@ -202,13 +215,13 @@ These local artifacts are not committed or published. V8 was subsequently reinstalled in the maintainer's user library as a separate authorized environment repair; it did not change this archive or the check results. -## Publication-time documentation edits (staged text, not applied) +## GitHub publication-time documentation edits (staged text, not applied) After GitHub 0.2.2 is published, replace the opening two sentences under `README.md`'s **Development status** with: > Version 0.2.2 is the latest published GitHub release; CRAN currently distributes -> 0.2.0. All require R 4.2 or newer. +> 0.2.2. All require R 4.2 or newer. Recheck the CRAN version at that time. Leave the remaining initialization and reproducibility text in place. @@ -229,9 +242,7 @@ In `vignettes/articles/development-status.Rmd`: > published on GitHub. Publishing a GitHub release does not change the version > installed from CRAN. -- Change “planned 0.2.2 release” in the Gumbel caveat to “0.2.2 release”. - Retain the historical 0.2.1 and 0.2.0 change summaries and current caveats. -Before a CRAN submission, finish `cran-comments.md` with the final evidence and -remove its draft/pending language. After CRAN publication, update the CRAN -version in README and the release-status page to the version actually available. +CRAN submission and publication are complete. Preserve `cran-comments.md` +as the submitted record; do not resubmit as part of GitHub release preparation. diff --git a/vignettes/articles/development-status.Rmd b/vignettes/articles/development-status.Rmd index ee398c1..212cc19 100644 --- a/vignettes/articles/development-status.Rmd +++ b/vignettes/articles/development-status.Rmd @@ -3,22 +3,22 @@ title: "Release Status" description: "CRAN availability and GitHub release preparation for bifrost 0.2.2." --- -This page describes the published CRAN version of `bifrost`, the planned -0.2.2 GitHub release, and the relationship between package source archives -and the fuller documentation maintained in the repository. +This page describes `bifrost` 0.2.2, published on CRAN on October 17, 2026, +the planned 0.2.2 GitHub release, and the relationship between package source +archives and the fuller documentation maintained in the repository. ## At a glance | Distribution | Version | Installation | Best for | |---|---:|---|---| -| [CRAN](https://CRAN.R-project.org/package=bifrost) | 0.2.0 | `install.packages("bifrost")` | Current published CRAN release | +| [CRAN](https://CRAN.R-project.org/package=bifrost) | 0.2.2 | `install.packages("bifrost")` | Current published CRAN release | | [GitHub](https://github.com/jakeberv/bifrost/releases/tag/v0.2.1), published release | 0.2.1 | `remotes::install_github("jakeberv/bifrost@v0.2.1")` | Citation, documentation, and archive updates | | [GitHub](https://github.com/jakeberv/bifrost), planned release | 0.2.2 | `remotes::install_github("jakeberv/bifrost@v0.2.2")`, after the tag is published | Explicit initialization and reproducibility corrections | | [GitHub](https://github.com/jakeberv/bifrost), development source | Version on `main` | `remotes::install_github("jakeberv/bifrost")` | Latest merged development source | -Versions 0.2.0, 0.2.1, and 0.2.2 require R 4.2 or newer. Version 0.2.2 is being -prepared for GitHub publication; its tag is not yet available. Publishing a -GitHub release does not change the version installed from CRAN. +Versions 0.2.0, 0.2.1, and 0.2.2 require R 4.2 or newer. Version 0.2.2 is +available on CRAN; its GitHub release and tag are still pending. CRAN and +GitHub releases are published separately. ## What 0.2.2 adds @@ -103,7 +103,7 @@ or underflow can discard valid large draws and make its confidence interval understate uncertainty. Do not rely on the affected interval as a dependable uncertainty estimate. The correction is deferred in [issue #231](https://github.com/jakeberv/bifrost/issues/231) and is not included -in the planned 0.2.2 release. +in the 0.2.2 release. Some repository workflows and their methodological guidance remain under active development, especially pGLS-style uses of `bifrost` with hidden