Dev fix review items

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

@@ -1,13 +1,49 @@
 # Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
 # Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+#
+# Reproduce locally by running:
+# ```r
+# pak::pak(c("any::rcmdcheck", "."), dependencies = "Config/Needs/check")
+# rcmdcheck::rcmdcheck()
+# ```
 on:
   push:
     branches: [main, master]
+    paths:
+      - 'data/**'
+      - 'R/**'
+      - 'inst/**'
+      - 'man/**'
+      - 'src/**'
+      - 'tests/**'
+      - 'vignettes/**'
+      - 'DESCRIPTION'
+      - 'NAMESPACE'
+      - 'LICENSE'
+      - '.Rbuildignore'
+      - '.github/workflows/R-CMD-check.yaml'
+  merge_group:
   pull_request:
-    branches: [main, master]
+    paths:
+      - 'data/**'
+      - 'R/**'
+      - 'inst/**'
+      - 'man/**'
+      - 'src/**'
+      - 'tests/**'
+      - 'vignettes/**'
+      - 'DESCRIPTION'
+      - 'NAMESPACE'
+      - 'LICENSE'
+      - '.Rbuildignore'
+      - '.github/workflows/R-CMD-check.yaml'
 
 name: R-CMD-check
 
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
 jobs:
   R-CMD-check:
     runs-on: ${{ matrix.config.os }}
@@ -29,13 +65,7 @@ jobs:
       R_KEEP_PKG_SOURCE: yes
 
     steps:
-      - name: Remove Microsoft repository configuration
-        if: runner.os == 'ubuntu-latest'
-        run: |
-          sudo rm /etc/apt/sources.list.d/microsoft-prod.list
-          sudo apt-get update
-
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-pandoc@v2
 
@@ -51,5 +81,14 @@ jobs:
           needs: check
 
       - uses: r-lib/actions/check-r-package@v2
+        id: rcmdcheck
         with:
           upload-snapshots: true
+          error-on: '"note"'
+
+      # fail-fast but only if rcmdcheck step fails
+      - name: Manual fail-fast
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        if: always() && steps.rcmdcheck.outcome == 'failure'
+        run: gh run cancel ${{ github.run_id }}

.github/workflows/dependency-change.yaml

@@ -0,0 +1,82 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+on:
+  pull_request:
+    paths:
+      - 'DESCRIPTION'
+
+name: Analyze dependency changes
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+permissions:
+  pull-requests: write
+
+jobs:
+  dependency-changes:
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    steps:
+      - name: Setup R
+        uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - name: Install dependencies
+        uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          packages: any::pak, glue, gh
+
+      - name: Analyze dependency changes
+        shell: Rscript {0}
+        run: |
+          deps_base <- pak::pkg_deps("${{ github.repository }}@${{ github.base_ref }}", dependencies = TRUE) |>
+            subset(!directpkg) |>
+            subset(is.na(priority))
+          # We install from PR number rather than branch to deal with the case
+          # of PR coming from forks
+          deps_head <- pak::pkg_deps("${{ github.repository }}#${{ github.event.number }}", dependencies = TRUE) |>
+            subset(!directpkg) |>
+            subset(is.na(priority))
+
+          deps_added <- deps_head |>
+            subset(!ref %in% deps_base$ref)
+
+          deps_removed <- deps_base |>
+            subset(!ref %in% deps_head$ref)
+
+          if (nrow(deps_added) + nrow(deps_removed) > 0) {
+
+            message("Dependencies have changed! Analyzing...")
+
+            if (nrow(deps_added) > 0) {
+              nudge <- "Reach out on slack (`#code-review` or `#help` channels) to double check if there are base R alternatives to the new dependencies.\n"
+            } else {
+              nudge <- ""
+            }
+
+            msg <- glue::glue(
+              .sep = "\n",
+              "This pull request:",
+              "- Adds {nrow(deps_added)} new dependencies (direct and indirect)",
+              "- Adds {length(unique(deps_added$sysreqs))} new system dependencies",
+              "- Removes {nrow(deps_removed)} existing dependencies (direct and indirect)",
+              "- Removes {length(unique(deps_removed$sysreqs))} existing system dependencies",
+              "",
+              nudge,
+              "(Note that results may be inaccurate if you branched from an outdated version of the target branch.)"
+            )
+
+            message("Posting results as a pull request comment.")
+
+            gh::gh(
+              "POST /repos/{repo}/issues/{issue_number}/comments",
+              repo = "${{ github.repository }}",
+              issue_number = "${{ github.event.number }}",
+              body = msg
+            )
+
+          }

.github/workflows/lint-changed-files.yaml

@@ -22,7 +22,7 @@ jobs:
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-r@v2
         with:
@@ -34,6 +34,7 @@ jobs:
             any::gh
             any::lintr
             any::purrr
+            any::cyclocomp
             epiverse-trace/etdev
           needs: check
 

.github/workflows/pkgdown.yaml

@@ -45,15 +45,16 @@ concurrency:
   group: ${{ github.workflow }}-${{ github.ref }}
   cancel-in-progress: true
 
+permissions:
+  contents: write
+
 jobs:
   pkgdown:
     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/setup-pandoc@v2
 
@@ -72,7 +73,7 @@ jobs:
 
       - name: Deploy to GitHub pages 🚀
         if: github.event_name != 'merge_group' && github.event_name != 'pull_request'
-        uses: JamesIves/github-pages-deploy-action@4.1.4
+        uses: JamesIves/github-pages-deploy-action@v4.6.1
         with:
           # We clean on releases because we want to remove old vignettes,
           # figures, etc. that have been deleted from the `main` branch.

.github/workflows/render_readme.yml

@@ -0,0 +1,96 @@
+# Reproduce locally by running:
+# ```r
+# pak::pak(c("any::rmarkdown", "any::usethis", "."))
+# writeLines(
+#   knitr::knit_expand(
+#     "README.Rmd",
+#     packagename = read.dcf("DESCRIPTION", "Package"),
+#     gh_repo = usethis:::github_remote_list()$repo_spec
+#   ),
+#   "README_expanded.Rmd"
+# )
+# rmarkdown::render(
+#   "README_expanded.Rmd",
+#   output_file = "README.md",
+#   output_dir = "."
+# )
+# unlink("README_expanded.Rmd")
+# ```
+name: render-readme
+
+# Controls when the action will run. Triggers include:
+#
+# - button trigger from github action page
+# - on changes to readme.Rmd
+
+on:
+  workflow_dispatch:
+  push:
+    branches:
+      # This may seem like a no-op but it prevents triggering on tags
+      # We use '**' rather '*' to accomodate names like 'dev/branch-1'
+      - '**'
+    paths:
+      - 'README.Rmd'
+      - '.github/workflows/render_readme.yml'
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+permissions:
+  contents: write
+
+# A workflow run is made up of one or more jobs that can run sequentially or in parallel
+jobs:
+  render-readme:
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    steps:
+      - name: Checkout repos
+        uses: actions/checkout@v4
+
+      - name: Setup R
+        uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - name: Setup pandoc
+        uses: r-lib/actions/setup-pandoc@v2
+
+      - name: Install dependencies
+        uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::rmarkdown, local::.
+
+      - name: Compile the readme
+        run: |
+          writeLines(
+            knitr::knit_expand(
+              "README.Rmd",
+              packagename = read.dcf("DESCRIPTION", "Package"),
+              gh_repo = Sys.getenv("GITHUB_REPOSITORY")
+            ),
+            "README_expanded.Rmd"
+          )
+          rmarkdown::render(
+            "README_expanded.Rmd",
+            output_file = "README.md",
+            output_dir = "."
+          )
+        shell: Rscript {0}
+
+      - name: Commit files
+        run: |
+          git config --local user.email "[email protected]"
+          git config --local user.name "GitHub Action"
+          git add README.md
+          # Also add README figures if they exist
+          if [ -d man/figures ]
+          then
+            git add man/figures/
+          fi
+          git diff-index --quiet HEAD || git commit -m "Automatic readme update"
+          git pull --rebase origin ${{ github.ref.name }}
+          git push origin || echo "No changes to push"