Upkeep 2024 (#147)

* Re-document * `use_tidy_description()` * Eliminate `expect_snapshot0()`. No longer needed due to testthat changes * `use_roxygen_md()` * `use_tidy_github_actions()` * Increment version number to 0.3.8.9000 * Change maintainer to Hadley; update posit metadata * Use standard site template; update readme style
r-lib · Jul 1, 2024 · 0d23c9a · 0d23c9a
1 parent a329c11
commit 0d23c9a
Show file tree

Hide file tree

Showing 23 changed files with 261 additions and 148 deletions.
diff --git a/.Rbuildignore b/.Rbuildignore
@@ -10,3 +10,6 @@
 ^cran-comments\.md$
 ^scripts$
 ^\.github$
+^codecov\.yml$
+^_pkgdown\.yml$
+^pkgdown$
diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml
@@ -1,4 +1,4 @@
-# Workflow derived from https://github.com/r-lib/actions/tree/master/examples
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
 # Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
 #
 # NOTE: This workflow is overkill for most R packages and
@@ -12,6 +12,8 @@ on:
 
 name: R-CMD-check
 
+permissions: read-all
+
 jobs:
   R-CMD-check:
     runs-on: ${{ matrix.config.os }}
@@ -22,49 +24,40 @@ 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-18.04,   r: 'devel', http-user-agent: 'release'}
-          - {os: ubuntu-18.04,   r: 'release'}
-          - {os: ubuntu-18.04,   r: 'oldrel-1'}
-          - {os: ubuntu-18.04,   r: 'oldrel-2'}
-          - {os: ubuntu-18.04,   r: 'oldrel-3'}
-          - {os: ubuntu-18.04,   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 }}
       R_KEEP_PKG_SOURCE: yes
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
 
-      - uses: r-lib/actions/setup-pandoc@v1
+      - uses: r-lib/actions/setup-pandoc@v2
 
-      - uses: r-lib/actions/setup-r@v1
+      - uses: r-lib/actions/setup-r@v2
         with:
           r-version: ${{ matrix.config.r }}
           http-user-agent: ${{ matrix.config.http-user-agent }}
           use-public-rspm: true
 
-      - uses: r-lib/actions/setup-r-dependencies@v1
+      - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          extra-packages: rcmdcheck
-
-      - uses: r-lib/actions/check-r-package@v1
-
-      - name: Show testthat output
-        if: always()
-        run: find check -name 'testthat.Rout*' -exec cat '{}' \; || true
-        shell: bash
+          extra-packages: any::rcmdcheck
+          needs: check
 
-      - name: Upload check results
-        if: failure()
-        uses: actions/upload-artifact@main
+      - uses: r-lib/actions/check-r-package@v2
         with:
-          name: ${{ runner.os }}-r${{ matrix.config.r }}-results
-          path: check
+          upload-snapshots: true
+          build_args: 'c("--no-manual","--compact-vignettes=gs+qpdf")'
diff --git a/.github/workflows/pkgdown.yaml b/.github/workflows/pkgdown.yaml
@@ -1,33 +1,50 @@
-# Workflow derived from https://github.com/r-lib/actions/tree/master/examples
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
 # Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
 on:
   push:
     branches: [main, master]
-    tags: ['*']
+  pull_request:
+    branches: [main, master]
+  release:
+    types: [published]
+  workflow_dispatch:
 
 name: pkgdown
 
+permissions: read-all
+
 jobs:
   pkgdown:
     runs-on: ubuntu-latest
+    # Only restrict concurrency for non-PR jobs
+    concurrency:
+      group: pkgdown-${{ github.event_name != 'pull_request' || github.run_id }}
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    permissions:
+      contents: write
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
 
-      - uses: r-lib/actions/setup-pandoc@v1
+      - uses: r-lib/actions/setup-pandoc@v2
 
-      - uses: r-lib/actions/setup-r@v1
+      - uses: r-lib/actions/setup-r@v2
         with:
           use-public-rspm: true
 
-      - uses: r-lib/actions/setup-r-dependencies@v1
+      - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          extra-packages: pkgdown
+          extra-packages: any::pkgdown, local::.
           needs: website
 
-      - name: Deploy package
-        run: |
-          git config --local user.name "$GITHUB_ACTOR"
-          git config --local user.email "[email protected]"
-          Rscript -e 'pkgdown::deploy_to_branch(new_process = FALSE)'
+      - 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/[email protected]
+        with:
+          clean: false
+          branch: gh-pages
+          folder: docs
diff --git a/.github/workflows/pr-commands.yaml b/.github/workflows/pr-commands.yaml
@@ -1,35 +1,39 @@
-# Workflow derived from https://github.com/r-lib/actions/tree/master/examples
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
 # Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
 on:
   issue_comment:
     types: [created]
 
 name: Commands
 
+permissions: read-all
+
 jobs:
   document:
-    if: startsWith(github.event.comment.body, '/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') }}
     name: document
     runs-on: ubuntu-latest
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
 
-      - uses: r-lib/actions/pr-fetch@v1
+      - uses: r-lib/actions/pr-fetch@v2
         with:
           repo-token: ${{ secrets.GITHUB_TOKEN }}
 
-      - uses: r-lib/actions/setup-r@v1
+      - uses: r-lib/actions/setup-r@v2
         with:
           use-public-rspm: true
 
-      - uses: r-lib/actions/setup-r-dependencies@v1
+      - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          extra-packages: roxygen2
+          extra-packages: any::roxygen2
+          needs: pr-document
 
       - name: Document
-        run: Rscript -e 'roxygen2::roxygenise()'
+        run: roxygen2::roxygenise()
+        shell: Rscript {0}
 
       - name: commit
         run: |
@@ -38,30 +42,32 @@ jobs:
           git add man/\* NAMESPACE
           git commit -m 'Document'
 
-      - uses: r-lib/actions/pr-push@v1
+      - uses: r-lib/actions/pr-push@v2
         with:
           repo-token: ${{ secrets.GITHUB_TOKEN }}
 
   style:
-    if: startsWith(github.event.comment.body, '/style')
+    if: ${{ github.event.issue.pull_request && (github.event.comment.author_association == 'MEMBER' || github.event.comment.author_association == 'OWNER') && startsWith(github.event.comment.body, '/style') }}
     name: style
     runs-on: ubuntu-latest
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
 
-      - uses: r-lib/actions/pr-fetch@v1
+      - uses: r-lib/actions/pr-fetch@v2
         with:
           repo-token: ${{ secrets.GITHUB_TOKEN }}
 
-      - uses: r-lib/actions/setup-r@v1
+      - uses: r-lib/actions/setup-r@v2
 
       - name: Install dependencies
-        run: Rscript -e 'install.packages("styler")'
+        run: install.packages("styler")
+        shell: Rscript {0}
 
       - name: Style
-        run: Rscript -e 'styler::style_pkg()'
+        run: styler::style_pkg()
+        shell: Rscript {0}
 
       - name: commit
         run: |
@@ -70,6 +76,6 @@ jobs:
           git add \*.R
           git commit -m 'Style'
 
-      - uses: r-lib/actions/pr-push@v1
+      - uses: r-lib/actions/pr-push@v2
         with:
           repo-token: ${{ secrets.GITHUB_TOKEN }}
diff --git a/.github/workflows/test-coverage.yaml b/.github/workflows/test-coverage.yaml
@@ -0,0 +1,61 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+on:
+  push:
+    branches: [main, master]
+  pull_request:
+    branches: [main, master]
+
+name: test-coverage
+
+permissions: read-all
+
+jobs:
+  test-coverage:
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+
+    steps:
+      - 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, any::xml2
+          needs: coverage
+
+      - name: Test coverage
+        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/.gitignore b/.gitignore
@@ -6,3 +6,4 @@
 inst/doc
 src/*.o
 src/*.so
+docs
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,18 +1,28 @@
 Package: profvis
 Title: Interactive Visualizations for Profiling R Code
-Version: 0.3.8
+Version: 0.3.8.9000
 Authors@R: c(
-    person("Winston", "Chang", email = "[email protected]", role = c("aut", "cre")),
-    person("Javier", "Luraschi", email = "[email protected]", role = "aut"),
+    person("Hadley", "Wickham", , "[email protected]", role = c("aut", "cre")),
+    person("Winston", "Chang", role = "aut"),
+    person("Javier", "Luraschi", role = "aut"),
     person("Timothy", "Mastny", role = "aut"),
-    person(family = "RStudio", role = "cph"),
-    person(family = "jQuery Foundation", role = "cph", comment = "jQuery library"),
-    person(family = "jQuery contributors", role = c("ctb", "cph"), comment = "jQuery library; authors listed in inst/www/shared/jquery-AUTHORS.txt"),
-    person("Mike", "Bostock", role = c("ctb", "cph"), comment = "D3 library"),
-    person(family = "D3 contributors", role = "ctb", comment = "D3 library"),
-    person("Ivan", "Sagalaev", role = c("ctb", "cph"), comment = "highlight.js library")
-    )
+    person("Posit Software, PBC", role = c("cph", "fnd")),
+    person(, "jQuery Foundation", role = "cph",
+           comment = "jQuery library"),
+    person(, "jQuery contributors", role = c("ctb", "cph"),
+           comment = "jQuery library; authors listed in inst/www/shared/jquery-AUTHORS.txt"),
+    person("Mike", "Bostock", role = c("ctb", "cph"),
+           comment = "D3 library"),
+    person(, "D3 contributors", role = "ctb",
+           comment = "D3 library"),
+    person("Ivan", "Sagalaev", role = c("ctb", "cph"),
+           comment = "highlight.js library")
+  )
 Description: Interactive visualizations for profiling R code.
+License: GPL-3 | file LICENSE
+URL: https://rstudio.github.io/profvis/,
+    https://github.com/rstudio/profvis
+BugReports: https://github.com/rstudio/profvis/issues
 Depends:
     R (>= 3.0)
 Imports:
@@ -21,17 +31,16 @@ Imports:
     rlang (>= 0.4.9),
     stringr,
     vctrs
-License: GPL-3 | file LICENSE
 Suggests:
-    knitr,
+    devtools,
     ggplot2,
+    htmltools,
+    knitr,
     rmarkdown,
-    testthat (>= 3.0.0),
-    devtools,
     shiny,
-    htmltools
-RoxygenNote: 7.2.3
-URL: https://rstudio.github.io/profvis/, https://github.com/rstudio/profvis
-BugReports: https://github.com/rstudio/profvis/issues
-Encoding: UTF-8
+    testthat (>= 3.0.0)
+Config/Needs/website: tidyverse/tidytemplate
 Config/testthat/edition: 3
+Encoding: UTF-8
+Roxygen: list(markdown = TRUE)
+RoxygenNote: 7.3.1
diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,5 @@
+# profvis (development version)
+
 profvis 0.3.8
 =============================
 

diff --git a/R/parse.R b/R/parse.R
@@ -1,9 +1,9 @@
 #' Parse Rprof output file for use with profvis
 #'
-#' @param path Path to the \code{\link{Rprof}} output file.
+#' @param path Path to the [Rprof()] output file.
 #' @param expr_source If any source refs in the profiling output have an empty
 #'   filename, that means they refer to code executed at the R console. This
-#'   code can be captured and passed (as a string) as the \code{expr_source}
+#'   code can be captured and passed (as a string) as the `expr_source`
 #'   argument.
 #' @import stringr
 #' @export