ci: update GHA workflows

Author: maelle

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

@@ -4,9 +4,10 @@ on:
   push:
     branches: [main, master]
   pull_request:
-    branches: [main, master]
 
-name: R-CMD-check
+name: R-CMD-check.yaml
+
+permissions: read-all
 
 jobs:
   R-CMD-check:
@@ -29,7 +30,7 @@ jobs:
       R_KEEP_PKG_SOURCE: yes
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-pandoc@v2
 
@@ -47,3 +48,4 @@ jobs:
       - uses: r-lib/actions/check-r-package@v2
         with:
           upload-snapshots: true
+          build_args: 'c("--no-manual","--compact-vignettes=gs+qpdf")'

.github/workflows/test-coverage.yaml

@@ -4,9 +4,10 @@ on:
   push:
     branches: [main, master]
   pull_request:
-    branches: [main, master]
 
-name: test-coverage
+name: test-coverage.yaml
+
+permissions: read-all
 
 jobs:
   test-coverage:
@@ -15,36 +16,47 @@ 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(normalizePath(Sys.getenv("RUNNER_TEMP"), winslash = "/"), "package")
           )
+          print(cov)
+          covr::to_cobertura(cov)
         shell: Rscript {0}
 
+      - uses: codecov/codecov-action@v4
+        with:
+          # 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
+          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

@@ -17,6 +17,7 @@ knitr::opts_chunk$set(
 
 <!-- badges: start -->
 [![R-CMD-check](https://github.com/maelle/saperlipopette/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/maelle/saperlipopette/actions/workflows/R-CMD-check.yaml)
+[![Codecov test coverage](https://codecov.io/gh/maelle/saperlipopette/graph/badge.svg)](https://app.codecov.io/gh/maelle/saperlipopette)
 <!-- badges: end -->
 
 The goal of saperlipopette is to hold functions creating Git messes, that users 

README.md

@@ -6,6 +6,8 @@
 <!-- badges: start -->
 
 [![R-CMD-check](https://github.com/maelle/saperlipopette/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/maelle/saperlipopette/actions/workflows/R-CMD-check.yaml)
+[![Codecov test
+coverage](https://codecov.io/gh/maelle/saperlipopette/graph/badge.svg)](https://app.codecov.io/gh/maelle/saperlipopette)
 <!-- badges: end -->
 
 The goal of saperlipopette is to hold functions creating Git messes,
@@ -47,10 +49,10 @@ This is a basic example which shows you how to solve a common problem:
 library("saperlipopette")
 parent_path <- withr::local_tempdir()
 path <- exo_one_small_change(parent_path)
-#> ℹ Follow along in /tmp/RtmpsiMrDj/file3e4f6663be0d/one-small-change!
+#> ℹ Follow along in /tmp/RtmprB2S8E/file10b5d656dc3da/one-small-change!
 # what's in path
 fs::dir_tree(path)
-#> /tmp/RtmpsiMrDj/file3e4f6663be0d/one-small-change
+#> /tmp/RtmprB2S8E/file10b5d656dc3da/one-small-change
 #> ├── R
 #> └── bla
 # with Git in a command line: git log
@@ -102,7 +104,7 @@ building documentation.
 ``` r
 parent_path <- withr::local_tempdir()
 path <- exo_one_small_change(parent_path)
-#> ℹ Follow along in /tmp/RtmpsiMrDj/file3e4f474cb413/one-small-change!
+#> ℹ Follow along in /tmp/RtmprB2S8E/file10b5d3fcba991/one-small-change!
 gert::git_log(repo = path)
 #> # A tibble: 2 × 6
 #>   commit                          author time                files merge message
@@ -111,7 +113,7 @@ gert::git_log(repo = path)
 #> 2 e227ecc55e421f70b6e30602e6a2ee… Jane … 2023-12-15 16:25:00     2 FALSE "First…
 parent_path2 <- withr::local_tempdir()
 path2 <- exo_one_small_change(parent_path2)
-#> ℹ Follow along in /tmp/RtmpsiMrDj/file3e4f65cbaffc/one-small-change!
+#> ℹ Follow along in /tmp/RtmprB2S8E/file10b5d92f231a/one-small-change!
 gert::git_log(repo = path2)
 #> # A tibble: 2 × 6
 #>   commit                          author time                files merge message