Review {cfr} v0.1.0 for CRAN release

.Rbuildignore

@@ -15,3 +15,4 @@
 ^revdep$
 ^CRAN-SUBMISSION$
 ^_pkgdown\.yml$
+^CITATION\.cff$

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

@@ -1,14 +1,48 @@
 # 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'
   pull_request:
-    branches:
-      - "*"
+    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 }}
@@ -19,7 +53,7 @@ jobs:
       fail-fast: false
       matrix:
         config:
-          - {os: macos-latest,   r: 'release'}
+          - {os: macOS-latest,   r: 'release'}
           - {os: windows-latest, r: 'release'}
           - {os: ubuntu-latest,   r: 'devel', http-user-agent: 'release'}
           - {os: ubuntu-latest,   r: 'release'}
@@ -28,6 +62,8 @@ jobs:
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
       R_KEEP_PKG_SOURCE: yes
+      # Exists since R 4.3.0 but `false` by default
+      _R_CHECK_LENGTH_COLON_: true
 
     steps:
       - uses: actions/checkout@v3
@@ -46,5 +82,13 @@ jobs:
           needs: check
 
       - uses: r-lib/actions/check-r-package@v2
+        id: rcmdcheck
         with:
           upload-snapshots: true
+
+      # 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/pkgdown.yaml

@@ -1,22 +1,52 @@
 # 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::pkgdown", "."), dependencies = "Config/Needs/website")
+# pkgdown::build_site()
+# ```
 on:
   push:
     branches: [main, master]
+    paths:
+      - 'README.Rmd'
+      - 'README.md'
+      - 'index.Rmd'
+      - 'index.md'
+      - 'man/**'
+      - 'vignettes/**'
+      - '_pkgdown.yml'
+      - 'pkgdown/**'
+      - 'DESCRIPTION'
+      - '.Rbuildignore'
+      - '.github/**'
   pull_request:
-    branches: [main, master]
+    paths:
+      - 'README.Rmd'
+      - 'README.md'
+      - 'index.Rmd'
+      - 'index.md'
+      - 'man/**'
+      - 'vignettes/**'
+      - '_pkgdown.yml'
+      - 'pkgdown/**'
+      - 'DESCRIPTION'
+      - '.Rbuildignore'
+      - '.github/**'
   release:
     types: [published]
   workflow_dispatch:
 
 name: pkgdown
 
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
 jobs:
   pkgdown:
     runs-on: ubuntu-latest
-    # Only restrict concurrency for non-PR jobs
-    concurrency:
-      group: pkgdown-${{ github.event_name != 'pull_request' || github.run_id }}
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
     permissions:
@@ -41,8 +71,13 @@ 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@4.1.4
         with:
-          clean: false
+          # We clean on releases because we want to remove old vignettes,
+          # figures, etc. that have been deleted from the `main` branch.
+          # But we clean ONLY on releases because we want to be able to keep
+          # both the 'stable' and 'dev' websites.
+          # Also discussed in https://github.com/r-lib/actions/issues/484
+          clean: ${{ github.event_name == 'release' }}
           branch: gh-pages
           folder: docs

.github/workflows/render_readme.yml

@@ -1,8 +1,7 @@
-# Name of the workflow
 name: render-readme
 
 # Controls when the action will run. Triggers include:
-# 
+#
 # - button trigger from github action page
 # - on changes to readme.Rmd
 
@@ -34,12 +33,12 @@ jobs:
 
       - 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(
@@ -56,7 +55,7 @@ jobs:
             output_dir = "."
           )
         shell: Rscript {0}
-        
+
       - name: Commit files
         run: |
           git config --local user.email "action@github.com"

.github/workflows/test-coverage.yaml

@@ -3,9 +3,25 @@
 on:
   push:
     branches: [main, master]
+    paths:
+      - 'R/**'
+      - 'src/**'
+      - 'tests/**'
+      - 'inst/**'
+      - 'DESCRIPTION'
+      - '.github/workflows/test-coverage.yaml'
   pull_request:
-    branches:
-      - "*"
+    paths:
+      - 'R/**'
+      - 'src/**'
+      - 'tests/**'
+      - 'inst/**'
+      - 'DESCRIPTION'
+      - '.github/workflows/test-coverage.yaml'
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
 
 name: test-coverage
 
@@ -28,24 +44,5 @@ jobs:
           needs: coverage
 
       - name: Test coverage
-        run: |
-          covr::codecov(
-            quiet = FALSE,
-            clean = FALSE,
-            install_path = file.path(Sys.getenv("RUNNER_TEMP"), "package")
-          )
+        run: covr::codecov(quiet = FALSE)
         shell: Rscript {0}
-
-      - name: Show testthat output
-        if: always()
-        run: |
-          ## --------------------------------------------------------------------
-          find ${{ runner.temp }}/package -name 'testthat.Rout*' -exec cat '{}' \; || true
-        shell: bash
-
-      - name: Upload test results
-        if: failure()
-        uses: actions/upload-artifact@v3
-        with:
-          name: coverage-test-failures
-          path: ${{ runner.temp }}/package

.gitignore

@@ -1,11 +1,55 @@
-.Rproj.user
+# History files
 .Rhistory
+.Rapp.history
+
+# Session Data files
 .RData
+.RDataTmp
+
+# User-specific files
 .Ruserdata
+
+# Example code in package build process
+*-Ex.R
+
+# Output files from R CMD build
+/*.tar.gz
+
+# Output files from R CMD check
+/*.Rcheck/
+
+# RStudio files
+.Rproj.user/
+
+# produced vignettes
+vignettes/*.html
+vignettes/*.pdf
+
+# OAuth2 token, see https://github.com/hadley/httr/releases/tag/v0.3
+.httr-oauth
+
+# knitr and R markdown default cache directories
+*_cache/
+/cache/
+
+# Temporary files created by R markdown
+*.utf8.md
+*.knit.md
+
+# R Environment Variables
+.Renviron
+
+# pkgdown site
+docs/
+
+# translation temp files
+po/*~
+
+# RStudio Connect folder
+rsconnect/
+
+# macOS hidden files
 .DS_Store
-docs
-inst/doc
-/doc/
-/Meta/
+
+# ignore development file
 scratch.R
-pkgdown/favicon/

.lintr

@@ -7,6 +7,14 @@ linters: linters_with_tags(
     todo_comment_linter = NULL,
     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
+    # 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),
+    "data-raw" = list(
+      missing_package_linter = Inf,
+      namespace_linter = Inf
+    )
+  )