diff --git a/AGENTS.md b/AGENTS.md index 5ad1367..44de22b 100644 --- a/AGENTS.md +++ b/AGENTS.md @@ -42,8 +42,22 @@ Standing authorization for this repository: * Agents may use `curl` (or equivalent read-only HTTP tools) for repository and upstream references on: `github.com`, `api.github.com`, `raw.githubusercontent.com`, - `github.com/tskit-dev/tskit`, and `tskit.dev` + `github.com/tskit-dev/tskit`, `tskit.dev`, + `cran.r-project.org`, `cranchecks.info`, `badges.cranchecks.info`, + `r-pkg.org`, `cranlogs.r-pkg.org`, `img.shields.io`, + `codecov.io`, `app.codecov.io`, and `highlanderlab.r-universe.dev` (including issues, pull requests, comments, events, metadata, and docs). +* For the above domains, agents should execute `curl` directly without asking + for extra confirmation in chat; if sandboxing requires escalation, submit the + escalated tool request immediately and continue. +* To minimise repeated platform permission prompts, prefer these canonical + command forms (same flags and flag order): + +```sh +curl -sS --max-time 15 +curl -I -sS --max-time 15 +``` + * This standing authorization does not override explicit user instructions or allow destructive commands that were not requested by the user. diff --git a/README.md b/README.md index 4756982..4c7eb65 100644 --- a/README.md +++ b/README.md @@ -33,18 +33,19 @@ to develop new `R` packages that can leverage `RcppTskit`. General: [![Lifecycle: experimental](https://img.shields.io/badge/lifecycle-experimental-orange.svg)](https://lifecycle.r-lib.org/articles/stages.html#experimental) -[![Development](https://img.shields.io/badge/development-active-blue.svg)](https://img.shields.io/badge/development-active-blue.svg) +[![Development](https://img.shields.io/badge/development-active-blue.svg)](https://github.com/HighlanderLab/RcppTskit?tab=readme-ov-file#development) [![Licence](https://img.shields.io/badge/licence-MIT-blue.svg)](https://opensource.org/licenses/MIT) Release: [![CRAN version](https://www.r-pkg.org/badges/version/RcppTskit)](https://CRAN.R-project.org/package=RcppTskit) [![Downloads - total](https://cranlogs.r-pkg.org/badges/grand-total/RcppTskit)](https://cranlogs.r-pkg.org/badges/grand-total/RcppTskit) -![GitHub version (main)](https://img.shields.io/github/r-package/v/HighlanderLab/RcppTskit/main?filename=RcppTskit%2FDESCRIPTION&label=Github) +[![GitHub version (main)](https://img.shields.io/github/r-package/v/HighlanderLab/RcppTskit/main?filename=RcppTskit%2FDESCRIPTION&label=Github)](https://github.com/HighlanderLab/RcppTskit) -R CMD checks: [![CRAN](https://cranchecks.info/badges/summary/RcppTskit?label=CRAN)](https://cran.r-project.org/web/checks/check_results_RcppTskit.html) -[![R universe](https://highlanderlab.r-universe.dev/RcppTskit/badges/checks?label=R-universe)](https://highlanderlab.r-universe.dev/RcppTskit) -[![GitHub](https://img.shields.io/github/actions/workflow/status/HighlanderLab/RcppTskit/R-CMD-check.yaml?label=GitHub)](https://github.com/HighlanderLab/RcppTskit/actions/workflows/R-CMD-check.yaml) +R CMD checks: [![CRAN summary](https://badges.cranchecks.info/summary/RcppTskit.svg)](https://cran.r-project.org/web/checks/check_results_RcppTskit.html) +[![CRAN worst](https://badges.cranchecks.info/worst/RcppTskit.svg)](https://cran.r-project.org/web/checks/check_results_RcppTskit.html) +[![R universe](https://highlanderlab.r-universe.dev/RcppTskit/badges/checks?label=R-universe)](https://highlanderlab.r-universe.dev/RcppTskit) +[![GitHub](https://img.shields.io/github/actions/workflow/status/HighlanderLab/RcppTskit/R-CMD-check.yaml?label=GitHub)](https://github.com/HighlanderLab/RcppTskit/actions/workflows/R-CMD-check.yaml) Code quality: [![Codecov test coverage](https://codecov.io/gh/HighlanderLab/RcppTskit/graph/badge.svg)](https://app.codecov.io/gh/HighlanderLab/RcppTskit) @@ -73,7 +74,10 @@ To install the published release from [CRAN](https://cran.r-project.org/package=RcppTskit) use: ``` +# Install install.packages("RcppTskit") + +# Read the introduction to RcppTskit vignette("RcppTskit_intro") ``` @@ -81,11 +85,14 @@ To install the latest development version (possibly unstable!) from [R universe](https://r-universe.dev) use: ``` +# Install r_universe_and_cran <- c( "https://highlanderlab.r-universe.dev", "https://cloud.r-project.org" ) install.packages("RcppTskit", repos = r_universe_and_cran) + +# Read the introduction to RcppTskit vignette("RcppTskit_intro") ``` @@ -102,19 +109,18 @@ https://mac.r-project.org/tools for macOS tools. ``` # install.packages("remotes") # If you don't have it already -# Release -# TODO: Tag a release #15 -# https://github.com/HighlanderLab/RcppTskit/issues/15 -# remotes::install_github("HighlanderLab/RcppTskit/RcppTskit") - -# Main branch +# Install the main branch remotes::install_github("HighlanderLab/RcppTskit/RcppTskit@main", build_vignettes=TRUE) -# Development branch +# Install the development branch remotes::install_github("HighlanderLab/RcppTskit/RcppTskit@devel", build_vignettes=TRUE) +# Install a specific release (say, v0.2.0) +remotes::install_github("HighlanderLab/RcppTskit/RcppTskit@v0.2.0") + +# Read the introduction to RcppTskit vignette("RcppTskit_intro") ``` diff --git a/RcppTskit/DESCRIPTION b/RcppTskit/DESCRIPTION index 5f48265..d2c174f 100644 --- a/RcppTskit/DESCRIPTION +++ b/RcppTskit/DESCRIPTION @@ -1,7 +1,7 @@ Type: Package Package: RcppTskit Title: 'R' Access to the 'tskit C' API -Version: 0.2.0 +Version: 0.2.0.9000 Date: 2026-01-27 Authors@R: c( person("Gregor", "Gorjanc", , "gregor.gorjanc@gmail.com", role = c("aut", "cre", "cph"), diff --git a/RcppTskit/notes_pkg_dev.Rmd b/RcppTskit/notes_pkg_dev.Rmd index 56684fd..66dbb0e 100644 --- a/RcppTskit/notes_pkg_dev.Rmd +++ b/RcppTskit/notes_pkg_dev.Rmd @@ -252,6 +252,15 @@ use_release_issue(version = NULL) # https://usethis.r-lib.org/reference/use_rele # just follow tasks in there;) ``` +Tag a release: + +``` +git checkout main +git pull --ff-only origin main +git tag -a v0.2.0 eb6e19c -m "RcppTskit 0.2.0" +git push origin v0.2.0 +``` + ## Dev tools setup / use ```