chore: update workflows & rerender README.Rmd

Author: jemus42

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

@@ -6,7 +6,9 @@ on:
   pull_request:
     branches: [main, master]
 
-name: R-CMD-check
+name: R-CMD-check.yaml
+
+permissions: read-all
 
 jobs:
   R-CMD-check:
@@ -29,7 +31,7 @@ jobs:
       R_KEEP_PKG_SOURCE: yes
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-pandoc@v2
 
@@ -47,3 +49,4 @@ jobs:
       - uses: r-lib/actions/check-r-package@v2
         with:
           upload-snapshots: true
+          build_args: 'c("--no-manual","--compact-vignettes=gs+qpdf")'

.github/workflows/pkgdown.yaml

@@ -9,7 +9,9 @@ on:
     types: [published]
   workflow_dispatch:
 
-name: pkgdown
+name: pkgdown.yaml
+
+permissions: read-all
 
 jobs:
   pkgdown:
@@ -22,7 +24,7 @@ jobs:
     permissions:
       contents: write
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-pandoc@v2
 
@@ -32,19 +34,16 @@ jobs:
 
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          cache-version: 2
           extra-packages: any::pkgdown, local::.
-          needs: |
-            website
-            coverage
+          needs: website
 
       - name: Build site
         run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)
         shell: Rscript {0}
 
       - 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@v4.5.0
         with:
           clean: false
           branch: gh-pages

.github/workflows/test-coverage.yaml

@@ -6,7 +6,9 @@ on:
   pull_request:
     branches: [main, master]
 
-name: test-coverage
+name: test-coverage.yaml
+
+permissions: read-all
 
 jobs:
   test-coverage:
@@ -15,36 +17,45 @@ jobs:
       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::covr
+          extra-packages: any::covr, any::xml2
           needs: coverage
 
       - name: Test coverage
         run: |
-          covr::codecov(
+          cov <- covr::package_coverage(
             quiet = FALSE,
             clean = FALSE,
-            install_path = file.path(Sys.getenv("RUNNER_TEMP"), "package")
+            install_path = file.path(normalizePath(Sys.getenv("RUNNER_TEMP"), winslash = "/"), "package")
           )
+          covr::to_cobertura(cov)
         shell: Rscript {0}
 
+      - uses: codecov/codecov-action@v4
+        with:
+          fail_ci_if_error: ${{ github.event_name != 'pull_request' && true || false }}
+          file: ./cobertura.xml
+          plugin: noop
+          disable_search: true
+          token: ${{ secrets.CODECOV_TOKEN }}
+
       - name: Show testthat output
         if: always()
         run: |
           ## --------------------------------------------------------------------
-          find ${{ runner.temp }}/package -name 'testthat.Rout*' -exec cat '{}' \; || true
+          find '${{ runner.temp }}/package' -name 'testthat.Rout*' -exec cat '{}' \; || true
         shell: bash
 
       - name: Upload test results
         if: failure()
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
           name: coverage-test-failures
           path: ${{ runner.temp }}/package

README.Rmd

@@ -21,7 +21,7 @@ set.seed(1)
 
 <!-- badges: start -->
 [![R-CMD-check](https://github.com/PlantedML/randomPlantedForest/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/PlantedML/randomPlantedForest/actions/workflows/R-CMD-check.yaml)
-[![Codecov test coverage](https://codecov.io/gh/PlantedML/randomPlantedForest/branch/master/graph/badge.svg)](https://app.codecov.io/gh/PlantedML/randomPlantedForest?branch=master)
+[![Codecov test coverage](https://codecov.io/gh/PlantedML/randomPlantedForest/graph/badge.svg)](https://app.codecov.io/gh/PlantedML/randomPlantedForest)
 [![randomPlantedForest status badge](https://plantedml.r-universe.dev/badges/randomPlantedForest)](https://plantedml.r-universe.dev/randomPlantedForest)
 <!-- badges: end -->
 

README.md

@@ -7,7 +7,7 @@
 
 [![R-CMD-check](https://github.com/PlantedML/randomPlantedForest/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/PlantedML/randomPlantedForest/actions/workflows/R-CMD-check.yaml)
 [![Codecov test
-coverage](https://codecov.io/gh/PlantedML/randomPlantedForest/branch/master/graph/badge.svg)](https://app.codecov.io/gh/PlantedML/randomPlantedForest?branch=master)
+coverage](https://codecov.io/gh/PlantedML/randomPlantedForest/graph/badge.svg)](https://app.codecov.io/gh/PlantedML/randomPlantedForest)
 [![randomPlantedForest status
 badge](https://plantedml.r-universe.dev/badges/randomPlantedForest)](https://plantedml.r-universe.dev/randomPlantedForest)
 <!-- badges: end -->
@@ -66,12 +66,12 @@ predict(rpfit, new_data = mtcars) |>
   cbind(mpg = mtcars$mpg) |>
   head()
 #>      .pred  mpg
-#> 1 20.81459 21.0
-#> 2 20.72354 21.0
-#> 3 26.04526 22.8
-#> 4 21.26845 21.4
-#> 5 18.45921 18.7
-#> 6 19.54406 18.1
+#> 1 20.96451 21.0
+#> 2 21.06539 21.0
+#> 3 23.24140 22.8
+#> 4 21.17155 21.4
+#> 5 18.22740 18.7
+#> 6 18.76736 18.1
 ```
 
 Prediction components can be accessed via `predict_components`,
@@ -86,14 +86,14 @@ components <- predict_components(rpfit, new_data = mtcars)
 str(components)
 #> List of 3
 #>  $ m        :Classes 'data.table' and 'data.frame':  32 obs. of  6 variables:
-#>   ..$ cyl   : num [1:32] 0.445 0.445 0.863 0.445 -1.274 ...
-#>   ..$ wt    : num [1:32] -0.0615 -0.1421 2.3182 -0.0155 -0.3116 ...
-#>   ..$ hp    : num [1:32] 0.162 0.162 2.021 0.162 -0.941 ...
-#>   ..$ cyl:wt: num [1:32] 0.00389 0.00389 0.69586 0.17156 0.4615 ...
-#>   ..$ cyl:hp: num [1:32] 0.1453 0.1453 -0.0511 0.1453 0.1179 ...
-#>   ..$ hp:wt : num [1:32] -0.1264 -0.1367 -0.0487 0.1138 0.1596 ...
+#>   ..$ cyl   : num [1:32] 0.224 0.224 0.873 0.224 -0.803 ...
+#>   ..$ wt    : num [1:32] 0.177 -0.102 1.229 -0.154 -0.863 ...
+#>   ..$ hp    : num [1:32] 1.253 1.253 1.559 1.253 -0.586 ...
+#>   ..$ cyl:wt: num [1:32] -0.0516 0.0326 -0.0978 0.0279 0.1207 ...
+#>   ..$ cyl:hp: num [1:32] -0.0549 -0.0549 0.1872 -0.0549 0.3816 ...
+#>   ..$ hp:wt : num [1:32] -0.5891 -0.2933 -0.5148 -0.1305 -0.0282 ...
 #>   ..- attr(*, ".internal.selfref")=<externalptr> 
-#>  $ intercept: num 20.2
+#>  $ intercept: num 20
 #>  $ x        :Classes 'data.table' and 'data.frame':  32 obs. of  3 variables:
 #>   ..$ cyl: Factor w/ 3 levels "4","6","8": 2 2 1 2 3 2 3 1 1 2 ...
 #>   ..$ wt : num [1:32] 2.62 2.88 2.32 3.21 3.44 ...