diff --git a/CITATION.cff b/CITATION.cff index a3961d7..af84a05 100644 --- a/CITATION.cff +++ b/CITATION.cff @@ -10,6 +10,10 @@ license: GPL-2.0-or-later title: 'bifrost: Branch-Level Inference Framework for Recognizing Optimal Shifts in Traits' version: 0.2.2 +identifiers: +- type: doi + value: 10.5281/zenodo.23268805 + description: Zenodo concept DOI for all archived versions of bifrost. abstract: Methods for detecting, visualizing, and evaluating cladogenic shifts in multivariate trait data on phylogenies. Implements penalized-likelihood multivariate generalized least squares models and a greedy step-wise shift search for high-dimensional diff --git a/README.md b/README.md index c534b3a..8a94280 100644 --- a/README.md +++ b/README.md @@ -5,6 +5,7 @@ [![Codecov test coverage](https://codecov.io/gh/jakeberv/bifrost/graph/badge.svg)](https://app.codecov.io/gh/jakeberv/bifrost) [![CRAN status](https://www.r-pkg.org/badges/version/bifrost)](https://CRAN.R-project.org/package=bifrost) [![CRAN downloads](https://cranlogs.r-pkg.org/badges/grand-total/bifrost)](https://cran.r-project.org/package=bifrost) +[![Zenodo concept DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.23268805.svg)](https://doi.org/10.5281/zenodo.23268805) [![Package paper: Methods in Ecology and Evolution (in press)](https://img.shields.io/badge/package%20paper-MEE%20(in%20press)-005a70.svg)](#citation) [![Paper: Nature Ecology & Evolution](https://img.shields.io/badge/paper-Nature%20Ecology%20%26%20Evolution-000000.svg)](https://www.nature.com/articles/s41559-026-03110-5.epdf?sharing_token=PNALt0fkwK7zWng8AcHUw9RgN0jAjWel9jnR3ZoTv0MY7RbzUNNAnMQsco3ST9ehysSF4OiMNSc7ku-ywR1G5HC7BVOhY0inuNGDXiP16Z26oaZtwiblA-f61S2M-2llNRsRbegpuTeyhziEWzMipUgtyZKBEe3dsZlBVa67S4c%3D) [![bioRxiv preprint](https://img.shields.io/endpoint?url=https%3A%2F%2Fjakeberv.github.io%2Fbiorxiv-badge%2Fbadges%2F10.64898__2026.04.12.718036.json)](https://doi.org/10.64898/2026.04.12.718036) @@ -187,6 +188,8 @@ If you use `bifrost`, please cite the package paper first listed below and the o citation("bifrost") ``` +Software releases are archived on Zenodo under the concept DOI [10.5281/zenodo.23268805](https://doi.org/10.5281/zenodo.23268805), which covers all archived versions of `bifrost`. + ### Recommended citations 1. `bifrost` methods / package paper\ diff --git a/cran-comments.md b/cran-comments.md index 588da40..85949ed 100644 --- a/cran-comments.md +++ b/cran-comments.md @@ -23,7 +23,7 @@ timestamp check. Installation, examples and tests passed, with 2,980 passing test assertions and no test warnings or failures. The RNG chunk-invariance test now exercises two and three chunks using at most two worker processes. -[CI](https://github.com/jakeberv/bifrost/pull/252/checks) +[CI](https://github.com/jakeberv/bifrost/pull/254/checks) also checks macOS and Windows R release, and Ubuntu R release, devel and oldrel-1 (`--as-cran --run-donttest --no-manual`). A Windows temporary-file note was traced to the worker-cancellation test; its worker files now use a diff --git a/tools/releases/0.2.2.md b/tools/releases/0.2.2.md index 316f175..9985598 100644 --- a/tools/releases/0.2.2.md +++ b/tools/releases/0.2.2.md @@ -59,7 +59,11 @@ for details. GitHub publication does not update CRAN automatically. complete the package and manual check with zero test warnings or failures. - [x] Preserve the two-versus-three-chunk RNG comparison using at most two real workers; also verify identical final caller RNG state. -- [ ] Merge PR #252 through normal review and confirm its CI. Select the exact +- [x] PR #252 merged as `f25e05cf`; all post-merge checks passed, including a + clean Windows check and exactly 100% coverage with zero uncovered rows. +- [x] Rebuild and check the PR #254 source archive with the Zenodo README update, + including both manuals, in an isolated library. +- [ ] Merge PR #254 through normal review and confirm its CI. 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. Keep the initialization/convergence follow-up (#242) and RRphylo dependency @@ -74,7 +78,30 @@ for details. GitHub publication does not update CRAN automatically. - [ ] Apply the publication-time documentation edits below through a PR. Update CRAN availability separately, only after CRAN actually publishes it. -## Latest check: PR #252 Windows cancellation-test cleanup +## Latest check: PR #254 Zenodo concept DOI update + +Source commit: `b3940d7c3cd2c8dec9392433358ea6823832b7bb`; checked on 2026-10-17 UTC. +Archive SHA-256: `846b0c6b9c97c51f16f8937919c687959eb28a6fd7a2a2dd35a3249348dc1c70`. + +`R CMD check --as-cran --run-donttest`, including PDF and HTML manuals, +returned **0 errors, 0 warnings, 1 note** (`unable to verify current time`). +All **2,980 assertions passed**, with zero test warnings/failures and 138 +expected skips. The 101-page PDF also passed `qpdf --check`. + +Validation used a fresh isolated library with existing dependencies accessed +read-only, two advertised cores, and one numerical thread per worker. +Dependency DESCRIPTION hashes remained unchanged. Compared with the previous +checked archive, only `README.md` and the generated packaging timestamp differ. +The README contains the concept DOI badge/link; `CITATION.cff` is excluded from +the CRAN archive as intended. No package code or tests changed. + +Evidence: `output/release-0.2.2-pr254-check/run-lnj56l9_/`, including the archive, +`SHA256SUMS`, `final-summary.txt`, `bifrost.Rcheck/00check.log`, and the manual. +Check the latest [PR #254 CI](https://github.com/jakeberv/bifrost/pull/254/checks) +before merging. This archive supersedes the earlier archives recorded below; +use its path and checksum for any later authorized submission. + +## Earlier check: PR #252 Windows cancellation-test cleanup Source commit: `87b6d31444424a90f823aebcbcbd291bbf80b5d6`; checked on 2026-10-17 UTC. Archive SHA-256: `4a817a3ab4e3f6c98efc01342ebaf8fb0b47b61287a05294d943c596a78a00dc`.