Merged upstream/main into olivroy-patch-4

r-lib · Jul 25, 2024 · 887c5b7 · 887c5b7
2 parents 706fe71 + 1f73587
commit 887c5b7
Show file tree

Hide file tree

Showing 65 changed files with 730 additions and 498 deletions.
diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml
@@ -12,6 +12,8 @@ on:
 
 name: R-CMD-check
 
+permissions: read-all
+
 jobs:
   R-CMD-check:
     runs-on: ${{ matrix.config.os }}
@@ -25,17 +27,15 @@ jobs:
           - {os: macos-latest,   r: 'release'}
 
           - {os: windows-latest, r: 'release'}
-          # Use 3.6 to trigger usage of RTools35
-          - {os: windows-latest, r: '3.6'}
           # use 4.1 to check with rtools40's older compiler
           - {os: windows-latest, r: '4.1'}
 
-          - {os: ubuntu-latest,   r: 'devel', http-user-agent: 'release'}
-          - {os: ubuntu-latest,   r: 'release'}
-          - {os: ubuntu-latest,   r: 'oldrel-1'}
-          - {os: ubuntu-latest,   r: 'oldrel-2'}
-          - {os: ubuntu-latest,   r: 'oldrel-3'}
-          - {os: ubuntu-latest,   r: 'oldrel-4'}
+          - {os: ubuntu-latest,  r: 'devel', http-user-agent: 'release'}
+          - {os: ubuntu-latest,  r: 'release'}
+          - {os: ubuntu-latest,  r: 'oldrel-1'}
+          - {os: ubuntu-latest,  r: 'oldrel-2'}
+          - {os: ubuntu-latest,  r: 'oldrel-3'}
+          - {os: ubuntu-latest,  r: 'oldrel-4'}
 
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
@@ -54,7 +54,7 @@ jobs:
 
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          extra-packages: any::rcmdcheck, magick=?ignore-before-r=4.0.0
+          extra-packages: any::rcmdcheck
           needs: check
 
       - name: Configure Git User
@@ -64,8 +64,6 @@ jobs:
           git config --global user.email 41898282+github-actions[bot]@users.noreply.github.com
 
       - uses: r-lib/actions/check-r-package@v2
-        env:
-          _R_CALLS_INVALID_NUMERIC_VERSION_: true
-          _R_CHECK_FORCE_SUGGESTS_: false
         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
@@ -11,6 +11,8 @@ on:
 
 name: pkgdown
 
+permissions: read-all
+
 jobs:
   pkgdown:
     runs-on: ubuntu-latest

diff --git a/.github/workflows/pr-commands.yaml b/.github/workflows/pr-commands.yaml
@@ -6,6 +6,8 @@ on:
 
 name: Commands
 
+permissions: read-all
+
 jobs:
   document:
     if: ${{ github.event.issue.pull_request && (github.event.comment.author_association == 'MEMBER' || github.event.comment.author_association == 'OWNER') && startsWith(github.event.comment.body, '/document') }}

diff --git a/.github/workflows/test-coverage.yaml b/.github/workflows/test-coverage.yaml
@@ -8,6 +8,8 @@ on:
 
 name: test-coverage
 
+permissions: read-all
+
 jobs:
   test-coverage:
     runs-on: ubuntu-latest
@@ -23,7 +25,7 @@ jobs:
 
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          extra-packages: any::covr
+          extra-packages: any::covr, any::xml2
           needs: coverage
 
       - name: git config
@@ -33,18 +35,27 @@ jobs:
 
       - 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")
           )
+          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

diff --git a/DESCRIPTION b/DESCRIPTION
@@ -19,9 +19,9 @@ Description: Automate package and project setup tasks that are otherwise
 License: MIT + file LICENSE
 URL: https://usethis.r-lib.org, https://github.com/r-lib/usethis
 BugReports: https://github.com/r-lib/usethis/issues
-Depends: 
+Depends:
     R (>= 3.6)
-Imports: 
+Imports:
     cli (>= 3.0.1),
     clipr (>= 0.3.0),
     crayon,
@@ -43,7 +43,7 @@ Imports:
     whisker,
     withr (>= 2.3.0),
     yaml
-Suggests: 
+Suggests:
     covr,
     knitr,
     magick,

diff --git a/NAMESPACE b/NAMESPACE
@@ -11,9 +11,7 @@ export(browse_cran)
 export(browse_github)
 export(browse_github_actions)
 export(browse_github_issues)
-export(browse_github_pat)
 export(browse_github_pulls)
-export(browse_github_token)
 export(browse_package)
 export(browse_project)
 export(browse_travis)
@@ -45,7 +43,6 @@ export(git_protocol)
 export(git_remotes)
 export(git_sitrep)
 export(git_vaccinate)
-export(github_token)
 export(issue_close_community)
 export(issue_reprex_needed)
 export(local_project)
@@ -56,10 +53,8 @@ export(pr_init)
 export(pr_merge_main)
 export(pr_pause)
 export(pr_pull)
-export(pr_pull_upstream)
 export(pr_push)
 export(pr_resume)
-export(pr_sync)
 export(pr_view)
 export(proj_activate)
 export(proj_get)