Add more GHA workflows: strict check, vignette warnings, spell check (#…

…829) * Add metadata GHA workflow * Apply automatic changes * update meta * Update metadata.yaml * Apply automatic changes * retrigger CI * Update metadata.yaml * Apply automatic changes * add schedules and error on changed lints * clean up lints in code for creating datasets * Update check-all-examples.yaml * Update check-all-examples.yaml * Create check-vignette-warnings.yaml * silence ggside warnings; update ggcoef snapshots * Apply automatic changes * needs devel easystats? * Apply automatic changes * revert snapshot changes * Apply automatic changes * fix vignette warning * Apply automatic changes * improve idiom for conditional evaluation * Apply automatic changes * remove missing values in ggsignif * Apply automatic changes * remove manova example * Apply automatic changes * use devel performance * Apply automatic changes * avoid unneeded computations * Apply automatic changes * add strict workflow * Apply automatic changes * remove metadata workflow [skip ci] * Update R-CMD-check-strict.yaml * bump purrr version * minor [skip ci] * add spell check workflow * minor [skip ci] * use svglite device closes #812 * dealing with more warnings * Apply automatic changes * Update DESCRIPTION * fix build issues * sigh; I give up * skip problematic chunk * Update faq.Rmd * Apply automatic changes * Update ggbetweenstats.Rmd * remove svglite for now Co-authored-by: IndrajeetPatil <[email protected]>
IndrajeetPatil · Jan 14, 2023 · ade608e · ade608e
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diff --git a/.github/experimental-workflows/metadata.yaml b/.github/experimental-workflows/metadata.yaml
@@ -0,0 +1,41 @@
+on:
+  pull_request:
+    branches: [main, master]
+
+name: metadata
+
+jobs:
+  metadata:
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    steps:
+      - uses: actions/checkout@v3
+        with:
+          fetch-depth: 0
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          pak-version: devel
+          extra-packages: |
+            local::.
+            cboettig/codemeta
+            ropensci/cffr
+
+      - name: Generate codemeta metadata
+        run: |
+          options(crayon.enabled = TRUE)
+          codemeta::write_codemeta()
+        shell: Rscript {0}
+
+      - name: Generate CFF metadata
+        run: |
+          options(crayon.enabled = TRUE)
+          cffr::cff_write()
+        shell: Rscript {0}
+
+      - uses: stefanzweifel/git-auto-commit-action@v4
diff --git a/.github/workflows/R-CMD-check-strict.yaml b/.github/workflows/R-CMD-check-strict.yaml
@@ -0,0 +1,60 @@
+# 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
+#
+# R CMD Check will fail on NOTE.
+on:
+  push:
+    branches: [main, master]
+  pull_request:
+    branches: [main, master]
+  schedule:
+    # * is a special character in YAML so you have to quote this string
+    # Trigger once a week at 00:00 on Sunday
+    - cron: "0 0 * * SUN"
+
+name: R-CMD-check-strict
+
+jobs:
+  R-CMD-check-strict:
+    runs-on: ${{ matrix.config.os }}
+    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
+
+    strategy:
+      fail-fast: false
+      matrix:
+        config:
+          # CRAN does not provide macOS binaries for R-devel, so some packages
+          # need to be built from source. To avoid that, use R-release.
+          - { os: macos-latest, r: "release" }
+          - { os: windows-latest, r: "devel" }
+          - { os: ubuntu-latest, r: "devel" }
+
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      R_KEEP_PKG_SOURCE: yes
+
+    steps:
+      - uses: actions/checkout@v3
+
+      - uses: r-lib/actions/setup-pandoc@v2
+        with:
+          pandoc-version: "2.19.2"
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          r-version: ${{ matrix.config.r }}
+          http-user-agent: "release"
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          pak-version: devel
+          needs: check
+          extra-packages: |
+            any::rcmdcheck
+
+      - uses: r-lib/actions/check-r-package@v2
+        with:
+          upload-snapshots: true
+          upload-results: true
+          error-on: '"note"'
diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml
@@ -1,6 +1,5 @@
 # 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:
   push:
     branches: [main, master]
@@ -19,16 +18,18 @@ jobs:
       fail-fast: false
       matrix:
         config:
+          # Checks are not run on R-devel because they are already run in
+          # `R-CMD-check-strict` workflow
+
           #- { os: macos-latest,   r: 'devel' }
-          - { os: macos-latest, r: "release" }
+          #- { os: macos-latest, r: "release" }
           - { os: macos-latest, r: "oldrel-1" }
 
-          - { os: windows-latest, r: "devel" }
+          #- { os: windows-latest, r: "devel" }
           - { os: windows-latest, r: "release" }
-          # DLL 'purrr' not found: maybe not installed for this architecture?
-          #- { os: windows-latest, r: "oldrel-1" }
+          - { os: windows-latest, r: "oldrel-1" }
 
-          - { os: ubuntu-latest, r: "devel", http-user-agent: "release" }
+          #- { os: ubuntu-latest, r: "devel", http-user-agent: "release" }
           - { os: ubuntu-latest, r: "release" }
           - { os: ubuntu-latest, r: "oldrel-1" }
 
@@ -46,13 +47,14 @@ jobs:
       - uses: r-lib/actions/setup-r@v2
         with:
           r-version: ${{ matrix.config.r }}
-          http-user-agent: ${{ matrix.config.http-user-agent }}
+          http-user-agent: "release"
           use-public-rspm: true
 
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
           pak-version: devel
-          extra-packages: any::rcmdcheck
+          extra-packages: |
+            any::rcmdcheck
           needs: check
 
       - uses: r-lib/actions/check-r-package@v2

diff --git a/.github/workflows/check-all-examples.yaml b/.github/workflows/check-all-examples.yaml
@@ -12,6 +12,10 @@ on:
     branches: [main, master]
   pull_request:
     branches: [main, master]
+  schedule:
+    # * is a special character in YAML so you have to quote this string
+    # Trigger once a week at 00:00 on Sunday
+    - cron: "0 0 * * SUN"
 
 name: check-all-examples
 
@@ -26,6 +30,7 @@ jobs:
 
       - uses: r-lib/actions/setup-r@v2
         with:
+          r-version: "devel"
           use-public-rspm: true
 
       - uses: r-lib/actions/setup-r-dependencies@v2
@@ -38,5 +43,5 @@ jobs:
       - name: Run examples
         run: |
           options(crayon.enabled = TRUE, warn = 2L)
-          devtools::run_examples(fresh = TRUE, run_dontrun = TRUE, run_donttest = TRUE)
+          devtools::run_examples(run_dontrun = TRUE, run_donttest = TRUE, document = FALSE)
         shell: Rscript {0}
diff --git a/.github/workflows/check-link-rot.yaml b/.github/workflows/check-link-rot.yaml
@@ -3,6 +3,10 @@ on:
     branches: [main, master]
   pull_request:
     branches: [main, master]
+  schedule:
+    # * is a special character in YAML so you have to quote this string
+    # Trigger once a week at 00:00 on Sunday
+    - cron: "0 0 * * SUN"
 
 name: check-link-rot
 
@@ -38,6 +42,6 @@ jobs:
           rotten_links <- urlchecker::url_check(progress = FALSE)
           print(rotten_links)
           if (length(rotten_links$URL) > 0L) {
-            stop("Some URLs are outdated and need to be updated.", call. = FALSE)
+            cli::cli_abort("Some URLs are outdated and need to be updated.")
           }
         shell: Rscript {0}
diff --git a/.github/workflows/check-spelling.yaml b/.github/workflows/check-spelling.yaml
@@ -0,0 +1,52 @@
+on:
+  push:
+    branches: [main, master]
+  pull_request:
+    branches: [main, master]
+  schedule:
+    # * is a special character in YAML so you have to quote this string
+    # Trigger once a week at 00:00 on Sunday
+    - cron: "0 0 * * SUN"
+
+name: check-spelling
+
+jobs:
+  check-spelling:
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      R_KEEP_PKG_SOURCE: yes
+    steps:
+      - uses: actions/checkout@v3
+
+      - uses: r-lib/actions/setup-pandoc@v2
+        with:
+          pandoc-version: "2.19.2"
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          r-version: "devel"
+          http-user-agent: "release"
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          pak-version: devel
+          dependencies: '"hard"'
+          extra-packages: |
+            any::rcmdcheck
+            any::spelling
+
+      - name: Spell check
+        run: |
+          options(crayon.enabled = TRUE)
+          spelling_mistakes <- spelling::spell_check_package()
+          cli::cli_rule()
+          if (length(spelling_mistakes$word) > 0L) {
+            print(spelling_mistakes)
+            cli::cli_abort("Spelling errors found. Either correct them or update `inst/WORDLIST` file.")
+          } else {
+            cli::cli_alert_success("No spelling errors found.")
+          }
+          cli::cli_rule()
+        shell: Rscript {0}
diff --git a/.github/workflows/check-test-warnings.yaml b/.github/workflows/check-test-warnings.yaml
@@ -18,6 +18,7 @@ jobs:
 
       - uses: r-lib/actions/setup-r@v2
         with:
+          r-version: "devel"
           use-public-rspm: true
 
       - uses: r-lib/actions/setup-r-dependencies@v2

diff --git a/.github/workflows/check-vignette-warnings.yaml b/.github/workflows/check-vignette-warnings.yaml
@@ -0,0 +1,39 @@
+# Run vignettes with `options(warn = 2)` to fail on warnings
+on:
+  push:
+    branches: [main, master]
+  pull_request:
+    branches: [main, master]
+
+name: check-vignette-warnings
+
+jobs:
+  check-vignette-warnings:
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+
+    steps:
+      - uses: actions/checkout@v3
+
+      - uses: r-lib/actions/setup-pandoc@v2
+        with:
+          pandoc-version: "2.19.2"
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          r-version: "devel"
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          pak-version: devel
+          extra-packages: |
+            local::.
+
+      - name: Build vignettes
+        run: |
+          # options(crayon.enabled = TRUE, warn = 2L)
+          vignettes <- fs::dir_ls("vignettes/", glob = "*.Rmd", recurse = TRUE)
+          purrr::walk(vignettes, rmarkdown::render)
+        shell: Rscript {0}
diff --git a/.github/workflows/lint-changed-files.yaml b/.github/workflows/lint-changed-files.yaml
@@ -26,11 +26,6 @@ jobs:
             any::purrr
           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 .
 

diff --git a/.github/workflows/lint.yaml b/.github/workflows/lint.yaml
@@ -5,6 +5,10 @@ on:
     branches: [main, master]
   pull_request:
     branches: [main, master]
+  schedule:
+    # * is a special character in YAML so you have to quote this string
+    # Trigger once a week at 00:00 on Sunday
+    - cron: "0 0 * * SUN"
 
 name: lint
 

diff --git a/.github/workflows/styler.yaml b/.github/workflows/styler.yaml
@@ -64,7 +64,7 @@ jobs:
       - name: Style package
         run: |
           options(crayon.enabled = TRUE)
-          styler::style_pkg(filetype = c(".R", ".Rmd", ".Rmarkdown", ".Rnw"))
+          styler::style_pkg(filetype = c(".qmd", ".R", ".Rmd", ".Rmarkdown", ".Rnw"))
         shell: Rscript {0}
 
       - name: Document

diff --git a/.github/workflows/test-coverage-examples.yaml b/.github/workflows/test-coverage-examples.yaml
@@ -32,7 +32,7 @@ jobs:
           options(crayon.enabled = TRUE)
           library(covr)
           coverage <- covr::package_coverage(
-            type = "examples",
+            type = c("examples", "vignettes"),
             quiet = TRUE,
             commentDonttest = FALSE,
             commentDontrun = FALSE

diff --git a/.gitignore b/.gitignore
@@ -1,41 +1,51 @@
 Meta
 doc
+docs
+
 # Windows image file caches
 Thumbs.db
 ehthumbs.db
 
 # Folder config file
 Desktop.ini
+
 # Recycle Bin used on file shares
 $RECYCLE.BIN/
+
 # Windows Installer files
 *.cab
 *.msi
 *.msm
 *.msp
+
 # Windows shortcuts
 *.lnk
+
 # =========================
 # Operating System Files
 # OSX
 .AppleDouble
 .DS_Store
 .LSOverride
+
 # Thumbnails
 ._*
+
 # Files that might appear in the root of a volume
 .DocumentRevisions-V100
 .Spotlight-V100
 .TemporaryItems
 .Trashes
 .VolumeIcon.icns
 .fseventsd
+
 # Directories potentially created on remote AFP share
 .AppleDB
 .AppleDesktop
 .apdisk
 Network Trash Folder
 Temporary Items
+
 # R Studio files
 .RData
 .Rhistory