{simulist} full package review

.Rbuildignore

@@ -9,3 +9,6 @@
 ^.*\.Rproj$
 ^\.Rproj\.user$
 ^CITATION\.cff$
+^doc$
+^Meta$
+^tools$

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

@@ -22,6 +22,7 @@ on:
       - 'LICENSE'
       - '.Rbuildignore'
       - '.github/workflows/R-CMD-check.yaml'
+  merge_group:
   pull_request:
     paths:
       - 'data/**'
@@ -85,6 +86,7 @@ jobs:
         id: rcmdcheck
         with:
           upload-snapshots: true
+          error-on: '"note"'
 
       # fail-fast but only if rcmdcheck step fails
       - name: Manual fail-fast

.github/workflows/dependency-change.yaml

@@ -0,0 +1,75 @@
+# 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
+
+jobs:
+  dependency-changes:
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    permissions:
+      pull-requests:
+        write
+    steps:
+      - name: Setup R
+        uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - name: Install dependencies
+        uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          packages: any::pak, glue, gh
+
+      - name: Analyze dependency changes
+        shell: Rscript {0}
+        run: |
+          deps_base <- pak::pkg_deps("${{ 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$ref)
+
+          if (nrow(deps_added) + nrow(deps_removed) > 0) {
+
+            message("Dependencies have changed! Analyzing...")
+
+            msg <- glue::glue(
+              .sep = "\n",
+              "This pull request:",
+              "- Adds {nrow(deps_added)} new dependencies (direct and indirect)",
+              "- Adds {length(unique(deps_added$sysreqs))} new system dependencies",
+              "- Removes {nrow(deps_removed)} existing dependencies (direct and indirect)",
+              "- Removes {length(unique(deps_removed$sysreqs))} existing system dependencies",
+              "",
+              "(Note that results may be inacurrate if you branched from an outdated version of the target branch.)"
+            )
+
+            message("Posting results as a pull request comment.")
+
+            gh::gh(
+              "POST /repos/{repo}/issues/{issue_number}/comments",
+              repo = "${{ github.repository }}",
+              issue_number = "${{ github.event.number }}",
+              body = msg
+            )
+
+          }

.github/workflows/pkgdown.yaml

@@ -21,6 +21,7 @@ on:
       - 'DESCRIPTION'
       - '.Rbuildignore'
       - '.github/**'
+  merge_group:
   pull_request:
     paths:
       - 'README.Rmd'
@@ -70,7 +71,7 @@ jobs:
         shell: Rscript {0}
 
       - name: Deploy to GitHub pages 🚀
-        if: github.event_name != 'pull_request'
+        if: github.event_name != 'merge_group' && github.event_name != 'pull_request'
         uses: JamesIves/[email protected]
         with:
           # We clean on releases because we want to remove old vignettes,

.github/workflows/render_readme.yml

@@ -26,6 +26,10 @@ name: render-readme
 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'
@@ -85,4 +89,5 @@ jobs:
             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"

.github/workflows/test-coverage.yaml

@@ -16,6 +16,7 @@ on:
       - 'inst/**'
       - 'DESCRIPTION'
       - '.github/workflows/test-coverage.yaml'
+  merge_group:
   pull_request:
     paths:
       - 'R/**'

.github/workflows/update-citation-cff.yaml

@@ -1,13 +1,14 @@
 # Workflow derived from https://github.com/r-lib/actions/tree/master/examples
 # The action runs when:
-# - A new release is published
 # - The DESCRIPTION or inst/CITATION are modified
 # - Can be run manually
 # For customizing the triggers, visit https://docs.github.com/en/actions/learn-github-actions/events-that-trigger-workflows
 on:
-  release:
-    types: [published]
   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:
       - DESCRIPTION
       - inst/CITATION
@@ -52,4 +53,5 @@ jobs:
           git config --local user.name "GitHub Action"
           git add CITATION.cff
           git commit -m 'Update CITATION.cff' || echo "No changes to commit"
+          git pull --rebase origin ${{ github.ref.name }}
           git push origin || echo "No changes to commit"

.gitignore

@@ -50,3 +50,6 @@ rsconnect/
 
 # macOS hidden files
 .DS_Store
+inst/doc
+/doc/
+/Meta/

.lintr

@@ -1,16 +1,37 @@
-linters: linters_with_tags(
-    tags = NULL, # include all linters
+linters: all_linters(
+    packages = c("lintr", "etdev"),
     object_name_linter = NULL,
-    undesirable_function_linter = NULL,
     implicit_integer_linter = NULL,
     extraction_operator_linter = NULL,
     todo_comment_linter = NULL,
+    undesirable_function_linter(
+      modify_defaults(
+        default_undesirable_functions,
+        citEntry = "use the more modern bibentry() function",
+        library = NULL # too many false positive in too many files
+      )
+    ),
     function_argument_linter = NULL,
     indentation_linter = NULL, # unstable as of lintr 3.1.0
     # Use minimum R declared in DESCRIPTION or fall back to current R version.
     # Install etdev package from https://github.com/epiverse-trace/etdev
     backport_linter(if (length(x <- etdev::extract_min_r_version())) x else getRversion())
   )
 exclusions: list(
-    "tests/testthat.R" = list(unused_import_linter = Inf)
+    "tests/testthat.R" = list(
+      unused_import_linter = Inf
+    ),
+    "tests" = list(
+      undesirable_function_linter = Inf
+    ),
+    "data-raw" = list(
+      missing_package_linter = Inf,
+      namespace_linter = Inf
+    ),
+    # RcppExports.R is auto-generated and will not pass many linters. In
+    # particular, it can create very long lines.
+    "R/RcppExports.R",
+    # R/stanmodels.R is auto-generated and will not pass many linters. In
+    # particular, it uses `sapply()`.
+    "R/stanmodels.R"
   )