Merge branch 'main' into mon_popparams

Author: d-morrison

.github/workflows/claude.yml

@@ -21,7 +21,7 @@ jobs:
     permissions:
       contents: read
       pull-requests: write
-      issues: read
+      issues: write # so Claude can open follow-up issues for deferred work
       id-token: write
       actions: read # Required for Claude to read CI results on PRs
     steps:
@@ -30,6 +30,48 @@ jobs:
         with:
           fetch-depth: 1
 
+      # R toolchain so Claude can run common package-maintenance commands
+      # (e.g. devtools::document(), styler::style_pkg(), pkgdown builds,
+      # spelling::spell_check_package(), lintr, R CMD check).
+      # Adds ~1–3 min when the dependency cache is warm; the first run after
+      # a lockfile change is slower. JAGS is required because `runjags` is in
+      # Imports and load-all/document needs the package to be loadable.
+      # System libs mirror copilot-setup-steps.yml so packages that source-
+      # build (textshaping, ragg, curl, xml2, ...) don't fail unpredictably.
+      - name: Install system dependencies (Ubuntu)
+        run: |
+          sudo apt-get update
+          sudo apt-get install -y \
+            jags \
+            libcurl4-openssl-dev \
+            libssl-dev \
+            libxml2-dev \
+            libfontconfig1-dev \
+            libharfbuzz-dev \
+            libfribidi-dev \
+            libfreetype6-dev \
+            libpng-dev \
+            libtiff5-dev \
+            libjpeg-dev
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: |
+            any::devtools
+            any::roxygen2
+            any::rjags
+            any::rmarkdown
+            any::lintr
+            any::spelling
+            any::rcmdcheck
+          needs: check
+
       - name: Resolve PR number (if any)
         id: pr
         env:
@@ -86,10 +128,12 @@ jobs:
           # Optional: Give a custom prompt to Claude. If this is not specified, Claude will perform the instructions specified in the comment that tagged it.
           # prompt: 'Update the pull request description to include a summary of changes.'
 
-          # Optional: Add claude_args to customize behavior and configuration
-          # See https://github.com/anthropics/claude-code-action/blob/main/docs/usage.md
-          # or https://code.claude.com/docs/en/cli-reference for available options
-          # claude_args: '--allowed-tools Bash(gh pr *)'
+          # Extend the Bash allowlist so Claude can:
+          #   * run package-maintenance R commands (devtools::document(),
+          #     styler::style_pkg(), R CMD ...) — toolchain is installed above;
+          #   * file follow-up issues for work deferred out of the current PR
+          #     (gh issue create / comment / edit / view / list).
+          claude_args: '--allowed-tools "Bash(Rscript:*)" "Bash(R:*)" "Bash(R CMD:*)" "Bash(gh issue:*)"'
 
       - name: Re-assign reviewers after Claude finishes
         if: always() && steps.stash.outcome == 'success' && steps.pr.outputs.number != ''

.github/workflows/copilot-setup-steps.yml

@@ -102,7 +102,7 @@ jobs:
           withr::local_options(warn = 2)
           library(rjags)
           library(runjags)
-          runjags::findJAGS()
+          runjags::findjags()
           runjags::testjags()
         shell: Rscript {0}
 
@@ -119,7 +119,7 @@ jobs:
           Rscript -e 'cat("runjags version:", as.character(packageVersion("runjags")), "\n")'
           echo ""
           echo "JAGS location (from runjags):"
-          Rscript -e 'print(runjags::findJAGS())'
+          Rscript -e 'print(runjags::findjags())'
           echo ""
           echo "Running JAGS test:"
           Rscript -e 'runjags::testjags()'

.github/workflows/test-coverage.yaml

@@ -57,7 +57,7 @@ jobs:
            withr::local_options(warn = 2)
            library(rjags)
            library(runjags)
-           runjags::findJAGS()
+           runjags::findjags()
            runjags::testjags()
         shell: Rscript {0}
 

NEWS.md

@@ -1,5 +1,19 @@
 # serodynamics (development version)
 
+* Expanded what the `Claude Code` (`@claude`) workflow can do:
+  - Install the full R toolchain (R, JAGS, pandoc, the apt system libs
+    mirrored from `copilot-setup-steps.yml`, plus `devtools`, `roxygen2`,
+    `rmarkdown`, `lintr`, `spelling`, `rcmdcheck`) and allow `Rscript`,
+    `R`, and `R CMD` invocations, so requests that need package-
+    maintenance commands (`devtools::document()`,
+    `spelling::spell_check_package()`, `R CMD check`, vignette rebuilds)
+    succeed instead of being patched by hand.
+  - Grant `issues: write` and allow `gh issue` invocations so Claude
+    can file follow-up issues for work deferred out of the current PR
+    instead of burying it in a comment.
+* Standardized `runjags::findjags()` casing across `test-coverage.yaml`
+  and `copilot-setup-steps.yml` to match the `R-CMD-check.yaml` form
+  arriving with the 0.1.0 release (#207 advisory).
 * Re-assign reviewers to a PR's human assignees (filtered via
   `type == "User"`) when Claude pushes commits during a `@claude` or
   `Claude Code Review` run; if Claude makes no commits, the original

inst/WORDLIST

@@ -17,6 +17,7 @@ SHA
 TSI
 Vectorization
 Wasserstein
+allowlist
 assignees
 behaviour
 biomarker
@@ -38,12 +39,14 @@ iso
 isotype
 isotypes
 libm
+libs
 linux
 mcmc
 mitre
 newperson
 nmc
 onwards
+pandoc
 params
 pkgdown
 prec
@@ -58,6 +61,7 @@ stratifications
 tbl
 testthat
 tibble
+toolchain
 unstratified
 vh
 wishdf