Full package review for v0.3.0 release

.Rbuildignore

@@ -5,3 +5,10 @@
 ^_pkgdown\.yml$
 ^docs$
 ^pkgdown$
+^\.lintr$
+^.*\.Rproj$
+^\.Rproj\.user$
+^doc$
+^Meta$
+^CITATION\.cff$
+^tools$

.gitattributes

@@ -0,0 +1 @@
+*.bib -linguist-detectable

.github/settings.yml

@@ -0,0 +1,22 @@
+repository:
+  # https://probot.github.io/apps/settings/
+  allow_merge_commit: false
+  allow_rebase_merge: true
+  allow_squash_merge: true
+  default_branch: main
+  delete_branch_on_merge: true
+  # has_discussions: false
+  has_issues: true
+  # has_projects: false
+  # has_wiki: false
+  # private: false
+branches:
+  - name: main
+    # https://docs.github.com/en/rest/reference/repos#update-branch-protection
+    protection:
+      required_pull_request_reviews:
+        required_approving_review_count: 0 # (1-6; optionally 0)
+        dismiss_stale_reviews: true
+        require_code_owner_reviews: false
+      required_status_checks:
+        strict: true

.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 }}
@@ -29,7 +65,7 @@ jobs:
       R_KEEP_PKG_SOURCE: yes
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-pandoc@v2
 
@@ -45,5 +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

@@ -1,40 +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
 on:
+  workflow_dispatch:
   pull_request:
     branches: [main, master]
+    paths:
+      - '**.R'
+      - '**.Rmd'
+      - '**/.lintr'
+      - '**/.lintr.R'
 
 name: lint-changed-files
 
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
 jobs:
   lint-changed-files:
     runs-on: ubuntu-latest
     env:
       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::gh
             any::lintr
             any::purrr
+            any::cyclocomp
+            epiverse-trace/etdev
           needs: check
 
-      - name: Add lintr options
-        run: |
-          cat('\noptions(lintr.linter_file = ".lintr")\n', file = "~/.Rprofile", append = TRUE)
-        shell: Rscript {0}
-
       - name: Install package
         run: R CMD INSTALL .
 
       - name: Extract and lint files changed by this PR
         run: |
-          files <- gh::gh("GET https://api.github.com/repos/${{ github.repository }}/pulls/${{ github.event.pull_request.number }}/files")
+          files <- gh::gh("/repos/${{ github.repository }}/pulls/${{ github.event.pull_request.number }}/files")
           changed_files <- purrr::map_chr(files, "filename")
           all_files <- list.files(recursive = TRUE)
           exclusions_list <- as.list(setdiff(all_files, changed_files))