(v3.1.0.9002) Add a release checklist (release.md) with all steps of a regular CRAN release

.Rbuildignore

@@ -12,6 +12,7 @@
 ^CLAUDE\.md$
 ^\.claude$
 ^cran-comments\.md$
+^release\.md$
 ^CRAN-RELEASE$
 index\.html
 README\.html

DESCRIPTION

@@ -1,5 +1,5 @@
 Package: AMR
-Version: 3.1.0.9001
+Version: 3.1.0.9002
 Date: 2026-10-16
 Title: Antimicrobial Resistance Data Analysis
 Description: Functions to simplify and standardise antimicrobial resistance (AMR)

NEWS.md

@@ -1,4 +1,4 @@
-# AMR 3.1.0.9001
+# AMR 3.1.0.9002
 
 # AMR 3.1.0
 

release.md

@@ -0,0 +1,56 @@
+# 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:
+
+  ```bash
+  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