Merge pull request #67 from ehrlinger/pkgdown-site

Enhance testing strategy and add regression tests for ggRandomForests

Author: ehrlinger

.Rbuildignore

@@ -38,3 +38,9 @@ framed.sty
 ^pkgdown$
 ^LICENSE\.md$
 ^memory$
+^\.lintr$
+^CONTRIBUTING\.md$
+^code-review\.md$
+^release-checklist.*\.md$
+# FUSE filesystem temporaries (safe to ignore; R CMD build already skips dotfiles)
+^R/\.fuse_hidden

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

@@ -28,6 +28,10 @@ jobs:
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
       R_KEEP_PKG_SOURCE: yes
+      # Skip vdiffr visual-regression tests in CI until reference SVGs are
+      # committed. To regenerate: run testthat::snapshot_accept() locally,
+      # commit tests/testthat/_snaps/, then remove this line.
+      VDIFFR_RUN_TESTS: "false"
 
     steps:
       - uses: actions/checkout@v4
@@ -41,14 +45,18 @@ jobs:
           r-version: ${{ matrix.config.r }}
           http-user-agent: ${{ matrix.config.http-user-agent }}
           use-public-rspm: true
-          rtools-version: '42'
+          rtools-version: '44'
 
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
           extra-packages: any::rcmdcheck
+          cache-version: 2
           needs: check
 
       - uses: r-lib/actions/check-r-package@v2
         with:
           upload-snapshots: true
           build_args: 'c("--no-manual","--compact-vignettes=gs+qpdf")'
+          # Treat NOTEs as errors on CRAN-submission platforms (devel + release);
+          # warnings are always errors everywhere.
+          error_on: '"warning"'

.github/workflows/check-release.yaml

@@ -14,8 +14,9 @@ jobs:
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
       R_KEEP_PKG_SOURCE: yes
+      VDIFFR_RUN_TESTS: "false"
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-pandoc@v2
 
@@ -27,6 +28,7 @@ jobs:
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
           extra-packages: rcmdcheck
+          cache-version: 2
 
       - uses: r-lib/actions/setup-tinytex@v2
       - uses: r-lib/actions/check-r-package@v2

.github/workflows/check-standard.yaml

@@ -27,9 +27,10 @@ jobs:
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
       R_KEEP_PKG_SOURCE: yes
+      VDIFFR_RUN_TESTS: "false"
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-pandoc@v2
 
@@ -43,6 +44,7 @@ jobs:
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
           extra-packages: rcmdcheck
+          cache-version: 2
 
       - uses: r-lib/actions/setup-tinytex@v2
       - uses: r-lib/actions/check-r-package@v2

.github/workflows/lint.yaml

@@ -1,29 +1,39 @@
-# Workflow derived from https://github.com/r-lib/actions/tree/master/examples
+# 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]
   pull_request:
-    branches: [main]
 
-name: lint
+name: lint.yaml
+
+permissions: read-all
 
 jobs:
   lint:
     runs-on: ubuntu-latest
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+
     steps:
-      - uses: actions/checkout@v2
+      - 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: lintr
+          extra-packages: any::lintr, any::cyclocomp, any::pak
+          needs: lint
+          cache-version: 2
 
       - name: Lint
-        run: lintr::lint_package()
+        run: |
+          lints <- lintr::lint_package()
+          print(lints)
+          if (length(lints) > 0L) {
+            message(sprintf("lintr found %d issue(s).", length(lints)))
+            quit(status = 1L)
+          }
         shell: Rscript {0}

.github/workflows/test-coverage.yaml

@@ -14,6 +14,7 @@ jobs:
     runs-on: ubuntu-latest
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      VDIFFR_RUN_TESTS: "false"
 
     steps:
       - uses: actions/checkout@v4
@@ -26,6 +27,7 @@ jobs:
         with:
           extra-packages: any::covr, any::xml2
           needs: coverage
+          cache-version: 2
 
       - name: Test coverage
         run: |
@@ -38,15 +40,6 @@ jobs:
           covr::to_cobertura(cov)
         shell: Rscript {0}
 
-      - uses: codecov/codecov-action@v4
-        with:
-          token: ${{ secrets.CODECOV_TOKEN }}
-          # Fail if error if not on PR, or if on PR and token is given
-          fail_ci_if_error: ${{ github.event_name != 'pull_request' || secrets.CODECOV_TOKEN }}
-          file: ./cobertura.xml
-          plugin: noop
-          disable_search: true
-
       - name: Show testthat output
         if: always()
         run: |
@@ -60,8 +53,13 @@ jobs:
         with:
           name: coverage-test-failures
           path: ${{ runner.temp }}/package
-          
+
       - name: Upload coverage reports to Codecov
         uses: codecov/codecov-action@v5
         with:
           token: ${{ secrets.CODECOV_TOKEN }}
+          # Fail if error if not on PR, or if on PR and token is given
+          fail_ci_if_error: ${{ github.event_name != 'pull_request' || secrets.CODECOV_TOKEN != '' }}
+          files: ./cobertura.xml
+          plugins: noop
+          disable_search: true

.gitignore

@@ -40,9 +40,8 @@ tests/testthat/Rplots.pdf
 vignettes/ggrfRegression.html
 vignettes/ggrfRegression.R
 docs
-NAMESPACE
-man/
-*.Rd
+# FUSE filesystem temporaries (macOS / Linux FUSE driver artefacts)
+.fuse_hidden*
 
 vignettes/ggRandomForests_files
 vignettes/ggRandomForests.html

.lintr

@@ -0,0 +1,16 @@
+linters: linters_with_defaults(
+    line_length_linter(120),
+    object_name_linter(styles = c("snake_case", "dotted.case", "camelCase", "symbols")),
+    cyclocomp_linter(complexity_limit = 20),
+    T_and_F_symbol_linter = NULL,
+    return_linter = NULL,
+    indentation_linter = NULL,
+    object_length_linter = NULL,
+    object_usage_linter = NULL,
+    commented_code_linter = NULL
+  )
+exclusions: list(
+    "R/ggrandomforests.news.R",
+    "R/zzz.R"
+  )
+encoding: "UTF-8"