AMR/release.md

Release checklist

The steps of a regular CRAN release of the AMR package, as followed for v3.1.0 (October 2026). Replace X.Y.Z with the new version number. Copy this list into an issue or a note per release, or tick the boxes in a local copy.

1. Preparation (on the development version)

• All intended issues and pull requests for this release are merged into main
• All GitHub Actions on main succeed, including check-revdeps (it runs on every push to main and can also be started manually from the Actions tab)
• Reverse dependencies are checked against this version; if a package breaks, its maintainer is informed in advance through an issue in its repository (e.g., https://github.com/agerada/MIC/issues/15 for v3.1.0)
• vignettes/welcome_to_AMR.Rmd is reviewed, since it is the only vignette that goes to CRAN (all other vignettes are in .Rbuildignore): check the text, the links, and the outcome of its inline R code (number of species and drugs, guideline years, languages, taxonomy date)
• index.Rmd (website home page) and README.Rmd are up to date with the new version
• inst/CITATION is up to date

2. Version and documentation

• DESCRIPTION: Version: X.Y.Z and Date: set to the submission date
• NEWS.md: line 1 replaced by # AMR X.Y.Z, the line about the planned release removed, and the intro paragraph written in past tense, summarising the main changes (see NEWS.md style in CLAUDE.md)
• NEWS.md: the Breaking section mentions every change that can alter results or break code, with how to get the old behaviour
• cran-comments.md rewritten for this release: type of release, main changes, reverse dependency results (with links to the issues of affected packages), and the note on the installation size
• devtools::document() is run, so that man/, NAMESPACE and R/sysdata.rda are current (the pre-commit hook does this on commits with the hooks active)

3. Checks

• R CMD build and R CMD check --as-cran on the tarball: no errors or warnings, and only the known note on the installation size
• devtools::check_win_devel() (win-builder, R-devel); wait for the e-mail
• Optionally R-hub (rhub::rhub_check()) for other platforms
• urlchecker::url_check() reports no broken or redirected URLs

4. Submission

• devtools::submit_cran(); this also updates CRAN-SUBMISSION (version, date and SHA)
• Confirm the submission through the link in the e-mail from CRAN
• Wait for acceptance; answer any questions from the CRAN team and resubmit if needed (keep the version number unless CRAN asks otherwise)

5. After acceptance by CRAN

The pre-commit hook in .github/prehooks/ sets the version to X.Y.Z.9NNN and rewrites line 1 of NEWS.md on every commit to main. The release commit must therefore skip the hooks.

• git status: only the intended files are changed, with no build leftovers (e.g., AMR_X.Y.Z.tar.gz, AMR.Rcheck/)

• Commit the release without hooks, with only the version as message: git add -u && git commit -n -m "vX.Y.Z"

• git push origin main (this also rebuilds the website and publishes the Python package to PyPI)

• Create the tag through a GitHub release, with the NEWS.md section of this version without its # AMR X.Y.Z heading as release notes:

  awk 'NR==1 {next} /^# AMR /{exit} 1' NEWS.md > notes.md
  gh release create vX.Y.Z --target main --title "AMR vX.Y.Z" --notes-file notes.md --latest
  rm notes.md
  

• git fetch --tags and check that vX.Y.Z points at the release commit

• Run source("data-raw/microorganisms_files/build_mo_code_registry.R") from the root of the repository (takes a few minutes; the tag must exist), then review the diff of mo_code_registry.csv: only new codes may be added, existing codes may only get a later last_release, and renamed codes must have their old name in previous_names (see data-raw/microorganisms_files/README.md)

• .github/ISSUE_TEMPLATE/1-bug-report.yml: set the versions to Latest CRAN version (X.Y.Z) and One of the latest GitHub versions (X.Y.Z.9xxx)

• NEWS.md: put a new line 1 # AMR X.Y.Z.9001, followed by an empty line, above # AMR X.Y.Z; without this, the hook overwrites the heading of the released section

• Commit with the hooks active (the version becomes X.Y.Z.9001) and push to main

• Check that the GitHub Actions succeed, the website (https://amr-for-r.org) shows the new version, and the package is available on PyPI

• Check the CRAN page (https://cran.r-project.org/package=AMR) and the CRAN check results some days later