Update GitHub Actions workflows

ArchaeoStat · Dec 17, 2024 · 07c6511 · 07c6511
1 parent 01d13c4
commit 07c6511
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Showing 5 changed files with 44 additions and 26 deletions.
diff --git a/.github/workflows/R-CMD-check.yaml b/.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")'
diff --git a/.github/workflows/pkgdown.yaml b/.github/workflows/pkgdown.yaml
@@ -4,12 +4,13 @@ on:
   push:
     branches: [main, master]
   pull_request:
-    branches: [main, master]
   release:
     types: [published]
   workflow_dispatch:
 
-name: pkgdown
+name: pkgdown.yaml
+
+permissions: read-all
 
 jobs:
   pkgdown:
@@ -22,7 +23,7 @@ jobs:
     permissions:
       contents: write
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-pandoc@v2
 
@@ -41,7 +42,7 @@ 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@v4.5.0
         with:
           clean: false
           branch: gh-pages

diff --git a/.github/workflows/test-coverage.yaml b/.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 +16,46 @@ 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 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: ${{ runner.temp }}/package
diff --git a/README.Rmd b/README.Rmd
@@ -17,11 +17,10 @@ knitr::opts_chunk$set(
 # ArchaeoCal
 
 <!-- badges: start -->
-[![R-CMD-check](https://github.com/ArchaeoStat/ArchaeoCal/workflows/R-CMD-check/badge.svg)](https://github.com/ArchaeoStat/ArchaeoCal/actions)
-[![codecov](https://codecov.io/gh/ArchaeoStat/ArchaeoCal/branch/main/graph/badge.svg?token=fXOWoBzKIw)](https://codecov.io/gh/ArchaeoStat/ArchaeoCal)
+[![R-CMD-check](https://github.com/ArchaeoStat/ArchaeoCal/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/ArchaeoStat/ArchaeoCal/actions/workflows/R-CMD-check.yaml)
+[![codecov](https://codecov.io/gh/ArchaeoStat/ArchaeoCal/branch/main/graph/badge.svg?token=fXOWoBzKIw)](https://app.codecov.io/gh/ArchaeoStat/ArchaeoCal)
 
 [![r-universe](https://archaeostat.r-universe.dev/badges/ArchaeoCal)](https://archaeostat.r-universe.dev){.pkgdown-devel}
-
 [![Project Status: WIP – Initial development is in progress, but there has not yet been a stable, usable release suitable for the public.](https://www.repostatus.org/badges/latest/wip.svg)](https://www.repostatus.org/#wip)
 <!-- badges: end -->
 
@@ -32,7 +31,10 @@ knitr::opts_chunk$set(
 You can install the latest version of **ArchaeoCal** from [our repository](https://ArchaeoStat.r-universe.dev) with:
 
 ```{r universe-installation, eval=FALSE}
-install.packages("ArchaeoCal", repos = "https://archaeostat.r-universe.dev")
+options(repos = c(CRAN = "https://cloud.r-project.org",
+                  tesselle = "https://archaeostat.r-universe.dev"))
+
+install.packages("ArchaeoCal")
 ```
 
 And the development version from [GitHub](https://github.com/) with:

diff --git a/README.md b/README.md
@@ -5,15 +5,14 @@
 
 <!-- badges: start -->
 
-[![R-CMD-check](https://github.com/ArchaeoStat/ArchaeoCal/workflows/R-CMD-check/badge.svg)](https://github.com/ArchaeoStat/ArchaeoCal/actions)
-[![codecov](https://codecov.io/gh/ArchaeoStat/ArchaeoCal/branch/main/graph/badge.svg?token=fXOWoBzKIw)](https://codecov.io/gh/ArchaeoStat/ArchaeoCal)
+[![R-CMD-check](https://github.com/ArchaeoStat/ArchaeoCal/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/ArchaeoStat/ArchaeoCal/actions/workflows/R-CMD-check.yaml)
+[![codecov](https://codecov.io/gh/ArchaeoStat/ArchaeoCal/branch/main/graph/badge.svg?token=fXOWoBzKIw)](https://app.codecov.io/gh/ArchaeoStat/ArchaeoCal)
 
 <a href="https://archaeostat.r-universe.dev" class="pkgdown-devel"><img
 src="https://archaeostat.r-universe.dev/badges/ArchaeoCal"
-alt="r-universe" /></a>
-
-[![Project Status: WIP – Initial development is in progress, but there
-has not yet been a stable, usable release suitable for the
+alt="r-universe" /></a> [![Project Status: WIP – Initial development is
+in progress, but there has not yet been a stable, usable release
+suitable for the
 public.](https://www.repostatus.org/badges/latest/wip.svg)](https://www.repostatus.org/#wip)
 <!-- badges: end -->
 
@@ -25,7 +24,10 @@ You can install the latest version of **ArchaeoCal** from [our
 repository](https://ArchaeoStat.r-universe.dev) with:
 
 ``` r
-install.packages("ArchaeoCal", repos = "https://archaeostat.r-universe.dev")
+options(repos = c(CRAN = "https://cloud.r-project.org",
+                  tesselle = "https://archaeostat.r-universe.dev"))
+
+install.packages("ArchaeoCal")
 ```
 
 And the development version from [GitHub](https://github.com/) with: