Fix spatial analysis bugs from adversarial review

.Rbuildignore

@@ -19,3 +19,8 @@
 (^|/)Rplots\.pdf$
 \.DS_Store$
 ^Claude outputs$
+# Local files a build from a working tree would otherwise ship: the internal
+# review notes (kept out of git by .gitignore) and the .claude/ directory of
+# assistant settings and worktrees.
+^CODE_REVIEW\.md$
+^\.claude$

.github/workflows/R-CMD-check.yaml

@@ -43,26 +43,32 @@ jobs:
           http-user-agent: ${{ matrix.config.http-user-agent }}
           use-public-rspm: true
 
-      # Hard dependencies only.  Installing Suggests here pulled the entire
-      # Stan toolchain into every matrix job -- slow everywhere, and fatal on
-      # r-devel, where nothing arrives as a binary.  There CRAN's rstan 2.32.7
-      # was compiled against StanHeaders 2.39.0.9000 from the stan-dev
-      # universe and died with "'ecuyer1988' is not a member of 'boost'":
-      # Stan dropped that typedef after 2.32.  The optional backends are the
-      # job of the `backends` job below and of check-brms.yaml.
+      # Hard dependencies and a short list of Suggests.  Installing all of
+      # Suggests here pulled the entire Stan toolchain into every matrix job --
+      # slow everywhere, and fatal on r-devel, where nothing arrives as a
+      # binary.  There CRAN's rstan 2.32.7 was compiled against StanHeaders
+      # 2.39.0.9000 from the stan-dev universe and died with "'ecuyer1988' is
+      # not a member of 'boost'": Stan dropped that typedef after 2.32.  The
+      # optional backends are the job of the `backends` job below and of
+      # check-brms.yaml.
       #
       # Three Suggests are not optional in practice.  knitr and rmarkdown build
-      # the vignette during R CMD build, and tests/testthat.R opens with
+      # the vignettes during R CMD build, and tests/testthat.R opens with
       # library(testthat), so without it the test stage errors rather than
       # skipping.  _R_CHECK_FORCE_SUGGESTS_ = false does not cover this -- it
       # only downgrades the complaint about absent Suggests, it does not stop
       # check from running the test file.
       #
-      # ggplot2 is installed by choice rather than necessity.  The vignette
-      # gates every chunk on requireNamespace("ggplot2") in its setup chunk, so
-      # R CMD build succeeds without it -- but then the vignette renders as code
-      # with no output and none of the plotting code runs anywhere in this
-      # matrix.  It is a cheap pure-R install; keep it.
+      # ggplot2 and gstat are installed by choice rather than necessity.  Every
+      # vignette gates its chunks on requireNamespace() in its setup chunk, so
+      # R CMD build succeeds without them -- but then the North Carolina demo
+      # (gated on ggplot2) and the resolution, diagnostics and spatial
+      # cross-validation vignettes (gated on gstat and ggplot2) render as code
+      # with no output, and the tests behind skip_if_not_installed("gstat")
+      # skip.  Without these two, that code would run only on ubuntu, in the
+      # `backends` job below.  gstat brings sp, FNN, zoo, xts, intervals,
+      # spacetime, sftime and stars with it; none declares a system
+      # requirement, but on r-devel they build from source, which is slower.
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
           dependencies: '"hard"'
@@ -71,6 +77,7 @@ jobs:
             any::knitr
             any::rmarkdown
             any::ggplot2
+            any::gstat
             any::testthat
           needs: check
 
@@ -145,7 +152,7 @@ jobs:
       - name: Confirm optional backends are installed
         run: |
           for (p in c("sp", "GWmodel", "gstat", "FNN", "Matrix", "geometry",
-                      "ranger", "tibble")) {
+                      "ranger", "tibble", "spdep")) {
             if (!requireNamespace(p, quietly = TRUE))
               stop("Backend package not installed: ", p)
           }

.github/workflows/pkgdown.yaml

@@ -4,7 +4,8 @@
 # Builds the pkgdown site and pushes it to the gh-pages branch, from which
 # GitHub Pages serves https://elkronos.github.io/gis_modeling_toolkit/.
 # Pull requests build the site (so a broken _pkgdown.yml or vignette fails
-# the check) but do not deploy it.
+# the check) but do not deploy it, and neither does a manual run from any
+# branch but main.
 on:
   push:
     branches: [main, master]
@@ -36,7 +37,7 @@ jobs:
         with:
           use-public-rspm: true
 
-      # Hard dependencies plus the optional packages the five vignettes gate
+      # Hard dependencies plus the optional packages the six vignettes gate
       # their chunks on: ggplot2, gstat, sp and GWmodel, geometry, ranger and
       # patchwork.  Every gate is requireNamespace()-guarded, so a missing
       # package does not fail the build -- it silently renders that article
@@ -80,8 +81,15 @@ jobs:
         run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)
         shell: Rscript {0}
 
+      # Publish from main, and from a published release as the r-lib template
+      # does.  A pull request builds the site without publishing it, and so
+      # does a manual run started from any other branch: without the ref test
+      # a workflow_dispatch on an unmerged branch would replace the live site.
+      # The job-level `contents: write` above exists for this step.  Pull
+      # requests from forks get a read-only token whatever it says, and the
+      # deploy action is pinned to a commit rather than a tag.
       - name: Deploy to GitHub pages 🚀
-        if: github.event_name != 'pull_request'
+        if: github.event_name == 'release' || (github.event_name != 'pull_request' && github.ref == 'refs/heads/main')
         uses: JamesIves/github-pages-deploy-action@d92aa235d04922e8f08b40ce78cc5442fcfbfa2f # v4.8.0
         with:
           clean: false

DESCRIPTION

@@ -52,15 +52,18 @@ Suggests:
     tibble,
     geometry,
     gstat,
-    ggplot2,
+    ggplot2 (>= 3.4.0),
     patchwork,
     FNN,
     Matrix,
     nlme,
     spdep,
-    testthat (>= 3.1.5),
+    testthat (>= 3.1.7),
     knitr,
-    rmarkdown
+    rmarkdown,
+    units,
+    vctrs,
+    withr
 Additional_repositories: https://stan-dev.r-universe.dev
 Config/testthat/edition: 3
 VignetteBuilder: knitr

NAMESPACE

@@ -64,10 +64,10 @@ export(fit_gwr_model)
 export(fit_rf_model)
 export(fold_separation)
 export(get_voronoi_seeds)
-export(kriging_adequacy)
 export(gp_lengthscale_bounds)
 export(gwr_model_selection)
 export(harmonize_crs)
+export(kriging_adequacy)
 export(make_folds)
 export(model_metrics)
 export(new_spatial_fit)