Merge pull request #264 from r-lib/upkeep-2024-07

Upkeep 2024-07
r-lib · Jul 30, 2024 · 5bbba33 · 5bbba33
2 parents b016a9c + 047cf00
commit 5bbba33
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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 }}
@@ -22,19 +24,18 @@ jobs:
       fail-fast: false
       matrix:
         config:
-          - {os: macOS-latest,   r: 'release'}
+          - {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'}
 
-          # Use older ubuntu to maximise backward compatibility
-          - {os: ubuntu-20.04,   r: 'devel', http-user-agent: 'release'}
-          - {os: ubuntu-20.04,   r: 'release'}
-          - {os: ubuntu-20.04,   r: 'oldrel-1'}
-          - {os: ubuntu-20.04,   r: 'oldrel-2'}
-          - {os: ubuntu-20.04,   r: 'oldrel-3'}
-          - {os: ubuntu-20.04,   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 }}
@@ -62,3 +63,4 @@ 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
@@ -11,6 +11,8 @@ on:
 
 name: pkgdown
 
+permissions: read-all
+
 jobs:
   pkgdown:
     runs-on: ubuntu-latest
@@ -19,6 +21,8 @@ jobs:
       group: pkgdown-${{ github.event_name != 'pull_request' || github.run_id }}
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    permissions:
+      contents: write
     steps:
       - uses: actions/checkout@v4
 
@@ -39,7 +43,7 @@ jobs:
 
       - name: Deploy to GitHub pages 🚀
         if: github.event_name != 'pull_request'
-        uses: JamesIves/github-pages-deploy-action@4.1.4
+        uses: JamesIves/github-pages-deploy-action@v4.5.0
         with:
           clean: false
           branch: gh-pages

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
@@ -23,9 +25,37 @@ jobs:
 
       - 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(quiet = FALSE)
+        run: |
+          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
+        shell: bash
+
+      - name: Upload test results
+        if: failure()
+        uses: actions/upload-artifact@v4
+        with:
+          name: coverage-test-failures
+          path: ${{ runner.temp }}/package
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,67 +1,45 @@
 Package: withr
 Title: Run Code 'With' Temporarily Modified Global State
 Version: 3.0.0.9000
-Authors@R: 
-    c(person(given = "Jim",
-             family = "Hester",
-             role = "aut"),
-      person(given = "Lionel",
-             family = "Henry",
-             role = c("aut", "cre"),
-             email = "[email protected]"),
-      person(given = "Kirill",
-             family = "Müller",
-             role = "aut",
-             email = "[email protected]"),
-      person(given = "Kevin",
-             family = "Ushey",
-             role = "aut",
-             email = "[email protected]"),
-      person(given = "Hadley",
-             family = "Wickham",
-             role = "aut",
-             email = "[email protected]"),
-      person(given = "Winston",
-             family = "Chang",
-             role = "aut"),
-      person(given = "Jennifer",
-             family = "Bryan",
-             role = "ctb"),
-      person(given = "Richard",
-             family = "Cotton",
-             role = "ctb"),
-      person(given = "Posit Software, PBC",
-             role = c("cph", "fnd")))
-Description: A set of functions to run code 'with' safely and
-    temporarily modified global state. Many of these functions were
-    originally a part of the 'devtools' package, this provides a simple
-    package with limited dependencies to provide access to these
-    functions.
+Authors@R: c(
+    person("Jim", "Hester", role = "aut"),
+    person("Lionel", "Henry", , "[email protected]", role = c("aut", "cre")),
+    person("Kirill", "Müller", , "[email protected]", role = "aut"),
+    person("Kevin", "Ushey", , "[email protected]", role = "aut"),
+    person("Hadley", "Wickham", , "[email protected]", role = "aut"),
+    person("Winston", "Chang", role = "aut"),
+    person("Jennifer", "Bryan", role = "ctb"),
+    person("Richard", "Cotton", role = "ctb"),
+    person("Posit Software, PBC", role = c("cph", "fnd"))
+  )
+Description: A set of functions to run code 'with' safely and temporarily
+    modified global state. Many of these functions were originally a part
+    of the 'devtools' package, this provides a simple package with limited
+    dependencies to provide access to these functions.
 License: MIT + file LICENSE
-URL: https://withr.r-lib.org,
-    https://github.com/r-lib/withr#readme
+URL: https://withr.r-lib.org, https://github.com/r-lib/withr#readme
 BugReports: https://github.com/r-lib/withr/issues
 Depends:
     R (>= 3.5.0)
 Imports:
     graphics,
-    grDevices,
+    grDevices
 Suggests:
     callr,
-    covr,
     DBI,
     knitr,
-    lattice,
     methods,
     rlang,
     rmarkdown (>= 2.12),
     RSQLite,
     testthat (>= 3.0.0)
 VignetteBuilder: 
     knitr
+Config/Needs/website: tidyverse/tidytemplate
+Config/testthat/edition: 3
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.3.0.9000
+RoxygenNote: 7.3.2
 Collate: 
     'aaa.R'
     'collate.R'
@@ -93,5 +71,3 @@ Collate:
     'torture.R'
     'utils.R'
     'with.R'
-Config/testthat/edition: 3
-Config/Needs/website: tidyverse/tidytemplate
diff --git a/R/torture.R b/R/torture.R
@@ -4,6 +4,7 @@
 #'
 #' @template with
 #' @param new `[integer]`\cr run GC every 'step' allocations.
+#' @param wait integer; number of allocations to wait before starting GC torture.
 #' @inheritParams base::gctorture
 #' @inheritParams local_
 with_gctorture2 <- with_(gctorture2)

diff --git a/R/with.R b/R/with.R
@@ -59,3 +59,6 @@
 #' }
 #' Sys.getenv("WITHR")
 "_PACKAGE"
+
+# Enable pkgload to hotpatch `::` in detached namespaces
+on_load(`::` <- base::`::`)
diff --git a/man/devices.Rd b/man/devices.Rd
diff --git a/man/with_gctorture2.Rd b/man/with_gctorture2.Rd
diff --git a/man/with_tempfile.Rd b/man/with_tempfile.Rd
diff --git a/tests/testthat/_snaps/defer.md b/tests/testthat/_snaps/defer.md
@@ -35,15 +35,15 @@
     Output
       
       
-      ```r
+      ``` r
       withr::deferred_run()
       ```
       
       ```
       ## No deferred expressions to run
       ```
       
-      ```r
+      ``` r
       defer(writeLines('1'))
       writeLines('2')
       ```
@@ -52,19 +52,19 @@
       ## 2
       ```
       
-      ```r
+      ``` r
       defer(writeLines('3'))
       ```
       
-      ```r
+      ``` r
       writeLines('4')
       ```
       
       ```
       ## 4
       ```
       
-      ```r
+      ``` r
       withr::deferred_run()
       ```
       

diff --git a/tests/testthat/helper.R b/tests/testthat/helper.R
@@ -1,7 +1,3 @@
-set_state_inspector(function() {
-  dir(".")
-})
-
 expect_no_output <- function(...) {
   testthat::expect_output(..., regexp = NA)
 }