Update nullkomma integration

.Rbuildignore

@@ -4,6 +4,8 @@
 # nullkomma:r:start
 [.]nix$
 ^flake[.]lock$
+^[.]agents$
+^AGENTS[.]md$
 ^[.]envrc$
 ^[.]Renviron$
 ^[.]Rprofile$
@@ -13,9 +15,11 @@
 ^[.]github$
 ^[.]vscode$
 ^[.]nvim[.]lua$
+^[.]nullkomma$
 ^result(-.*)?$
 ^docs$
 ^pkgdown$
 ^coverage[.]xml$
 ^pkg[.]lock$
+^docs$
 # nullkomma:r:end

.github/workflows/push.yml

@@ -9,8 +9,6 @@ concurrency:
 jobs:
   nullkomma:
     uses: dataheld/nullkomma/.github/workflows/ci.yml@main
-    with:
-      visibility: unlisted
     permissions:
       contents: read
       id-token: write

.gitignore

@@ -9,8 +9,11 @@ result
 result-*
 .direnv/
 /.nullkomma/cloudflare/
+/.nullkomma/processes/
 .R/library/
 /.nvim.lua
+/.agents/skills/nullkomma-resolve-file-conflicts
+/.agents/skills/nullkomma-upgrade
 /.vscode/extensions.json
 /.vscode/settings.json
 !man/figures/

AGENTS.md

@@ -0,0 +1,21 @@
+<!-- nullkomma:agents:start -->
+## nullkomma
+
+This project's development environment comes from [nullkomma](https://github.com/dataheld/nullkomma).
+Run commands inside its dev shell:
+`direnv exec . <command>`, or `nix develop --command <command>` without direnv.
+`tasks` lists the project's workflows.
+
+Check your work locally, from fastest to strictest:
+
+1. While you work, run the narrowest task that covers the change,
+   e.g. `check <name>` or a single language task.
+1. Before you report a change as done, run `tasks all`, then `nix flake check`,
+   and fix what fails.
+   `tasks all` formats, regenerates files and runs the checks in the working tree.
+   `nix flake check` runs the checks sandboxed, as CI does,
+   and sees only files that Git tracks: `git add` new files first.
+
+Skills for nullkomma itself are in `.agents/skills/nullkomma-*`;
+if they are missing, run `nk-generate-files`.
+<!-- nullkomma:agents:end -->

README.md

@@ -14,15 +14,15 @@ pak::pak("dataheld/elf")
 <!--
 The block between the nullkomma:r-development markers is generated by
 nullkomma's r-non-nix plugin. Do not edit it directly: `nix develop --command
-write-files` refreshes it. See https://github.com/dataheld/nullkomma#readme
+nk-write-files` refreshes it. See https://github.com/dataheld/nullkomma#readme
 for plugin configuration and development documentation.
 -->
 <!-- nullkomma:r-development:start -->
 ## R development without Nix {.callout-tip}
 
 You do not need Nix or direnv to run or develop this package.
 
-> **Note:**
+> [! NOTE]
 > Developing without nix provides only limited reproducibility of the environment.
 > The PPM date *approximates* the Nix package set:
 > R package versions can differ,

flake.nix

@@ -4,17 +4,21 @@
   inputs = {
     nullkomma.url = "https://flakehub.com/f/dataheld/nullkomma/*";
     nixpkgs.follows = "nullkomma/nixpkgs";
-    brand = {
-      url = "https://flakehub.com/f/dataheld/brand/*";
+    maxheld = {
+      url = "https://flakehub.com/f/dataheld/maxheld/*";
       inputs.nullkomma.follows = "nullkomma";
     };
   };
 
   outputs =
     inputs:
     inputs.nullkomma.lib.mkFlake { inherit inputs; } {
-      nullkomma.r-non-nix.enable = true;
-      nullkomma.brand = inputs.brand;
+      nullkomma.r = {
+        enable = true;
+        nonNix.enable = true;
+        pkgdown.brand.enable = true;
+      };
+      nullkomma.brand = inputs.maxheld;
       nullkomma.cloudflare = {
         enable = true;
         domain = "maxheld.de";

tests/testthat/test-dependencies.R

@@ -1,7 +1,9 @@
 test_that("missing package is identified", {
   withr::local_options(rlib_message_verbosity = "verbose")
-  expect_message(source_pef_elf("dependencies", "is_installed2", "missing"))
-  expect_false(source_pef_elf("dependencies", "is_installed2", "missing"))
+  expect_message(
+    installed <- source_pef_elf("dependencies", "is_installed2", "missing")
+  )
+  expect_false(installed)
 })
 
 test_that("present package is identified", {

tests/testthat/test-options.R

@@ -1,8 +1,9 @@
 test_that("locally setting options works", {
   options::define_option("foo", default = "bar")
   expect_equal(options::opt("foo"), "bar")
-  opt_set_local2("foo", "baz")
-  expect_equal(options::opt("foo"), "baz")
-  withr::deferred_run()
+  local({
+    opt_set_local2("foo", "baz")
+    expect_equal(options::opt("foo"), "baz")
+  })
   expect_equal(options::opt("foo"), "bar")
 })