Merge commit '81e4f99285cfa886d83c93265d79efd10e635213'

Author: hadley

.Rbuildignore

@@ -20,3 +20,8 @@
 ^\.github/workflows/R\.yaml$
 ^\.github/workflows/pr-commands\.yaml$
 ^CRAN-SUBMISSION$
+^[\.]?air\.toml$
+^\.vscode$
+^\.git-blame-ignore-rev$
+^CLAUDE\.md$
+^\.claude$

.claude/settings.local.json

@@ -0,0 +1,15 @@
+{
+  "$schema": "https://json.schemastore.org/claude-code-settings.json",
+  "permissions": {
+    "allow": [
+      "Bash(find:*)",
+      "Bash(R:*)",
+      "Bash(rm:*)",
+      "Bash(air format:*)",
+      "Edit(R/**)",
+      "Edit(tests/**)",
+      "Edit(vignettes/**)"
+    ],
+    "deny": []
+  }
+}

.git-blame-ignore-rev

@@ -0,0 +1,8 @@
+# This file lists revisions of large-scale formatting/style changes so that
+# they can be excluded from git blame results.
+#
+# To set this file as the default ignore file for git blame, run:
+#   $ git config blame.ignoreRevsFile .git-blame-ignore-revs
+
+# https://github.com/r-lib/testthat/pull/2121
+13d17788e5d3a54fa83beed25e325703608f8b9f

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

@@ -8,9 +8,10 @@ on:
   push:
     branches: [main, master]
   pull_request:
-    branches: [main, master]
 
-name: R-CMD-check
+name: R-CMD-check.yaml
+
+permissions: read-all
 
 jobs:
   R-CMD-check:
@@ -25,24 +26,22 @@ jobs:
           - {os: macos-latest,   r: 'release'}
 
           - {os: windows-latest, r: 'release'}
-          # Use 3.6 to trigger usage of RTools35
-          - {os: windows-latest, r: '3.6'}
-          # use 4.1 to check with rtools40's older compiler
-          - {os: windows-latest, r: '4.1'}
+          # use 4.0 or 4.1 to check with rtools40's older compiler
+          - {os: windows-latest, r: 'oldrel-4'}
 
-          - {os: ubuntu-latest,   r: 'devel', http-user-agent: 'release'}
-          - {os: ubuntu-latest,   r: 'release'}
-          - {os: ubuntu-latest,   r: 'oldrel-1'}
-          - {os: ubuntu-latest,   r: 'oldrel-2'}
-          - {os: ubuntu-latest,   r: 'oldrel-3'}
-          - {os: ubuntu-latest,   r: 'oldrel-4'}
+          - {os: ubuntu-latest,  r: 'devel', http-user-agent: 'release'}
+          - {os: ubuntu-latest,  r: 'release'}
+          - {os: ubuntu-latest,  r: 'oldrel-1'}
+          - {os: ubuntu-latest,  r: 'oldrel-2'}
+          - {os: ubuntu-latest,  r: 'oldrel-3'}
+          - {os: ubuntu-latest,  r: 'oldrel-4'}
 
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
       R_KEEP_PKG_SOURCE: yes
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-pandoc@v2
 
@@ -65,3 +64,4 @@ jobs:
       - uses: r-lib/actions/check-r-package@v2
         with:
           upload-snapshots: true
+          build_args: 'c("--no-manual","--compact-vignettes=gs+qpdf")'

.github/workflows/claude-code-review.yml

@@ -0,0 +1,59 @@
+name: Claude Code Review
+
+on:
+  pull_request:
+    types: [opened]
+    # Optional: Only run on specific file changes
+    # paths:
+    #   - "src/**/*.ts"
+    #   - "src/**/*.tsx"
+    #   - "src/**/*.js"
+    #   - "src/**/*.jsx"
+
+jobs:
+  claude-review:
+    # Optional: Filter by PR author
+    # if: |
+    #   github.event.pull_request.user.login == 'external-contributor' ||
+    #   github.event.pull_request.user.login == 'new-developer' ||
+    #   github.event.pull_request.author_association == 'FIRST_TIME_CONTRIBUTOR'
+    
+    runs-on: ubuntu-latest
+    permissions:
+      contents: read
+      pull-requests: read
+      issues: read
+      id-token: write
+    
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v4
+        with:
+          fetch-depth: 1
+
+      - name: Run Claude Code Review
+        id: claude-review
+        uses: anthropics/claude-code-action@beta
+        with:
+          anthropic_api_key: ${{ secrets.ANTHROPIC_API_KEY }}
+
+          # Optional: Specify model (defaults to Claude Sonnet 4, uncomment for Claude Opus 4.1)
+          # model: "claude-opus-4-1-20250805"
+
+          # Direct prompt for automated review (no @claude mention needed)
+          direct_prompt: |
+            Please review this pull request and MINIMAL provide feedback on
+            potential bugs or issues. Never praise or flatter. Be concise. 
+            Use simple, clear language. If you don't have anything significant
+            to add, just reply LGTM.
+
+          # Optional: Use sticky comments to make Claude reuse the same comment on subsequent pushes to the same PR
+          # use_sticky_comment: true
+          
+          # Optional: Add specific tools for running tests or linting
+          # allowed_tools: "Bash(npm run test),Bash(npm run lint),Bash(npm run typecheck)"
+          
+          # Optional: Skip review for certain conditions
+          # if: |
+          #   !contains(github.event.pull_request.title, '[skip-review]') &&
+          #   !contains(github.event.pull_request.title, '[WIP]')

.github/workflows/claude.yml

@@ -0,0 +1,75 @@
+name: Claude Code
+
+on:
+  issue_comment:
+    types: [created]
+  pull_request_review_comment:
+    types: [created]
+  issues:
+    types: [opened, assigned]
+  pull_request_review:
+    types: [submitted]
+
+jobs:
+  claude:
+    if: |
+      (github.event_name == 'issue_comment' && contains(github.event.comment.body, '@claude')) ||
+      (github.event_name == 'pull_request_review_comment' && contains(github.event.comment.body, '@claude')) ||
+      (github.event_name == 'pull_request_review' && contains(github.event.review.body, '@claude')) ||
+      (github.event_name == 'issues' && (contains(github.event.issue.body, '@claude') || contains(github.event.issue.title, '@claude')))
+    runs-on: ubuntu-latest
+    permissions:
+      contents: read
+      pull-requests: read
+      issues: read
+      id-token: write
+      actions: read # Required for Claude to read CI results on PRs
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v4
+        with:
+          fetch-depth: 1
+
+      - name: Install air
+        uses: posit-dev/setup-air@v1
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::rcmdcheck,roxygen2
+          needs: check
+
+      - name: Run Claude Code
+        id: claude
+        uses: anthropics/claude-code-action@beta
+        with:
+          anthropic_api_key: ${{ secrets.ANTHROPIC_API_KEY }}
+
+          # This is an optional setting that allows Claude to read CI results on PRs
+          additional_permissions: |
+            actions: read
+          
+          # Optional: Specify model (defaults to Claude Sonnet 4, uncomment for Claude Opus 4.1)
+          # model: "claude-opus-4-1-20250805"
+          
+          # Optional: Customize the trigger phrase (default: @claude)
+          # trigger_phrase: "/claude"
+          
+          # Optional: Trigger when specific user is assigned to an issue
+          # assignee_trigger: "claude-bot"
+          
+          # Optional: Allow Claude to run specific commands
+          allowed_tools: "Bash(R:*);Bash(air format:*)"
+          
+          # Optional: Add custom instructions for Claude to customize its behavior for your project
+          # custom_instructions: |
+          #   Follow our coding standards
+          #   Ensure all new code has tests
+          #   Use TypeScript for new files
+          
+          # Optional: Custom environment variables for Claude
+          # claude_env: |
+          #   NODE_ENV: test

.github/workflows/pkgdown.yaml

@@ -4,12 +4,13 @@ on:
   push:
     branches: [main, master]
   pull_request:
-    branches: [main, master]
   release:
     types: [published]
   workflow_dispatch:
 
-name: pkgdown
+name: pkgdown.yaml
+
+permissions: read-all
 
 jobs:
   pkgdown:
@@ -19,8 +20,10 @@ jobs:
       group: pkgdown-${{ github.event_name != 'pull_request' || github.run_id }}
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    permissions:
+      contents: write
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-pandoc@v2
 
@@ -39,7 +42,7 @@ jobs:
 
       - name: Deploy to GitHub pages 🚀
         if: github.event_name != 'pull_request'
-        uses: JamesIves/github-pages-deploy-action@v4.4.1
+        uses: JamesIves/github-pages-deploy-action@v4.5.0
         with:
           clean: false
           branch: gh-pages

.github/workflows/pr-commands.yaml

@@ -4,7 +4,9 @@ on:
   issue_comment:
     types: [created]
 
-name: Commands
+name: pr-commands.yaml
+
+permissions: read-all
 
 jobs:
   document:
@@ -13,8 +15,10 @@ jobs:
     runs-on: ubuntu-latest
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    permissions:
+      contents: write
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/pr-fetch@v2
         with:
@@ -50,8 +54,10 @@ jobs:
     runs-on: ubuntu-latest
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    permissions:
+      contents: write
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/pr-fetch@v2
         with:

.github/workflows/test-coverage.yaml

@@ -4,9 +4,10 @@ on:
   push:
     branches: [main, master]
   pull_request:
-    branches: [main, master]
 
-name: test-coverage
+name: test-coverage.yaml
+
+permissions: read-all
 
 jobs:
   test-coverage:
@@ -15,36 +16,47 @@ jobs:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-r@v2
         with:
           use-public-rspm: true
 
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          extra-packages: any::covr
+          extra-packages: any::covr, any::xml2
           needs: coverage
 
       - name: Test coverage
         run: |
-          covr::codecov(
+          cov <- covr::package_coverage(
             quiet = FALSE,
             clean = FALSE,
-            install_path = file.path(Sys.getenv("RUNNER_TEMP"), "package")
+            install_path = file.path(normalizePath(Sys.getenv("RUNNER_TEMP"), winslash = "/"), "package")
           )
+          print(cov)
+          covr::to_cobertura(cov)
         shell: Rscript {0}
 
+      - uses: codecov/codecov-action@v5
+        with:
+          # Fail if error if not on PR, or if on PR and token is given
+          fail_ci_if_error: ${{ github.event_name != 'pull_request' || secrets.CODECOV_TOKEN }}
+          files: ./cobertura.xml
+          plugins: noop
+          disable_search: true
+          token: ${{ secrets.CODECOV_TOKEN }}
+
       - name: Show testthat output
         if: always()
         run: |
           ## --------------------------------------------------------------------
-          find ${{ runner.temp }}/package -name 'testthat.Rout*' -exec cat '{}' \; || true
+          find '${{ runner.temp }}/package' -name 'testthat.Rout*' -exec cat '{}' \; || true
         shell: bash
 
       - name: Upload test results
         if: failure()
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
           name: coverage-test-failures
           path: ${{ runner.temp }}/package

.vscode/extensions.json

@@ -0,0 +1,5 @@
+{
+    "recommendations": [
+        "Posit.air-vscode"
+    ]
+}