Merged with latest changes from RStudio.

Merge branch 'jg-tree-fix' into jg-devel * jg-tree-fix: Use latest Pandoc in GHA and update workflow (rstudio#2244) Add class to book cover to size using CSS fix the syntax highlighting of |> in LaTeX/PDF output: rstudio/bookdown#1157 (rstudio#2228) Add an option to opt-out the header-attrs HTML dependency in `html_document_base()` (rstudio#2227) Clean up NEWS.md. # Conflicts: # DESCRIPTION # NEWS.md
jonathan-g · Nov 29, 2021 · 1a2f70a · 1a2f70a
2 parents f0cdc81 + 10da592
commit 1a2f70a
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diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml
@@ -28,32 +28,33 @@ jobs:
       matrix:
         config:
           # testing R release with last shipped pandoc version in RStudio IDE and new pandoc
-          # TODO: issue on windows with pandoc 2.11.4 - change when fixed
-          - {os: windows-latest, pandoc: '2.7.3',  r: 'release'}
-          - {os: macOS-latest,   pandoc: '2.11.4',  r: 'release'}
-          - {os: ubuntu-18.04,   pandoc: '2.11.4',  r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/bionic/latest"}
-          - {os: ubuntu-18.04,   pandoc: 'devel',   r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/bionic/latest"}
+          - {os: windows-latest, pandoc: '2.16.1',  r: 'release'}
+          - {os: macOS-latest,   pandoc: '2.16.1',  r: 'release'}
+          - {os: ubuntu-18.04,   pandoc: '2.16.1',  r: 'release'}
+          - {os: ubuntu-18.04,   pandoc: 'devel',   r: 'release'}
           # testing older pandoc versions
-          - {os: ubuntu-18.04,   pandoc: '2.7.3',   r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/bionic/latest"}
-          - {os: ubuntu-18.04,   pandoc: '2.5',     r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/bionic/latest"}
-          - {os: ubuntu-18.04,   pandoc: '2.0.0.1', r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/bionic/latest"}
+          - {os: ubuntu-18.04,   pandoc: '2.14.2',  r: 'release'}
+          - {os: ubuntu-18.04,   pandoc: '2.11.4',  r: 'release'}
+          - {os: ubuntu-18.04,   pandoc: '2.7.3',   r: 'release'}
+          - {os: ubuntu-18.04,   pandoc: '2.5',     r: 'release'}
+          - {os: ubuntu-18.04,   pandoc: '2.0.0.1', r: 'release'}
           # testing other R versions
-          - {os: ubuntu-18.04,   pandoc: '2.11.4',  r: 'oldrel',  rspm: "https://packagemanager.rstudio.com/cran/__linux__/bionic/latest"}
-          - {os: ubuntu-18.04,   pandoc: '2.11.4',  r: 'devel',   rspm: "https://packagemanager.rstudio.com/cran/__linux__/bionic/latest", http-user-agent: "R/4.0.0 (ubuntu-18.04) R (4.0.0 x86_64-pc-linux-gnu x86_64 linux-gnu) on GitHub Actions" }
+          - {os: ubuntu-18.04,   pandoc: '2.11.4',  r: 'oldrel'}
+          - {os: ubuntu-18.04,   pandoc: '2.11.4',  r: 'devel', http-user-agent: 'release'}
 
     env:
       R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
-      RSPM: ${{ matrix.config.rspm }}
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      R_KEEP_PKG_SOURCE: yes
 
     steps:
       - uses: actions/checkout@v2
 
       - uses: r-lib/actions/setup-r@v1
-        id: install-r
         with:
           r-version: ${{ matrix.config.r }}
           http-user-agent: ${{ matrix.config.http-user-agent }}
+          use-public-rspm: true
 
       - name: change temp dir
         if: runner.os == 'Windows'
@@ -79,52 +80,18 @@ jobs:
           cat(readLines("~/.Rprofile"), sep = "\n")
         shell: Rscript {0}
 
-      - name: Install pak and query dependencies
-        run: |
-          install.packages("pak", repos = "https://r-lib.github.io/p/pak/dev/")
-          saveRDS(pak::pkg_deps("local::.", dependencies = TRUE), ".github/r-depends.rds")
-        shell: Rscript {0}
-
-      - name: Restore R package cache
-        uses: actions/cache@v2
+      - uses: r-lib/actions/setup-r-dependencies@v1
         with:
-          path: |
-            ${{ env.R_LIBS_USER }}/*
-            !${{ env.R_LIBS_USER }}/pak
-          key: ${{ matrix.config.os }}-${{ steps.install-r.outputs.installed-r-version }}-1-${{ hashFiles('.github/r-depends.rds') }}
-          restore-keys: ${{ matrix.config.os }}-${{ steps.install-r.outputs.installed-r-version }}-1-
-
-      - name: Install system dependencies
-        if: runner.os == 'Linux'
-        run: |
-          pak::local_system_requirements(execute = TRUE)
-          pak::pkg_system_requirements("rcmdcheck", execute = TRUE)
-        shell: Rscript {0}
+          extra-packages: rcmdcheck
 
-      - name: Install dependencies
+      - name: Pandoc and Tinytex info
         run: |
-          pak::local_install_dev_deps(upgrade = TRUE)
-          pak::pkg_install("rcmdcheck")
-        shell: Rscript {0}
-
-      - name: Session info
-        run: |
-          options(width = 100)
-          pkgs <- .packages(TRUE)
-          sessioninfo::session_info(pkgs, include_base = TRUE)
           rmarkdown::find_pandoc()
           tinytex::tlmgr("--version")
           tinytex::tl_pkgs()
         shell: Rscript {0}
 
-      - name: Check
-        env:
-          _R_CHECK_CRAN_INCOMING_: false
-          _R_CHECK_TESTS_NLINES_: 0
-        run: |
-          options(crayon.enabled = TRUE)
-          rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran"), error_on = "warning", check_dir = "check")
-        shell: Rscript {0}
+      - uses: r-lib/actions/check-r-package@v1
 
       - name: Show testthat output
         if: always()

diff --git a/.github/workflows/check-pandoc-daily.yaml b/.github/workflows/check-pandoc-daily.yaml
@@ -18,18 +18,19 @@ jobs:
         config:
           - {os: windows-latest}
           - {os: macOS-latest}
-          - {os: ubuntu-18.04, rspm: "https://packagemanager.rstudio.com/cran/__linux__/bionic/latest"}
+          - {os: ubuntu-18.04}
 
     env:
       R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
-      RSPM: ${{ matrix.config.rspm }}
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      R_KEEP_PKG_SOURCE: yes
 
     steps:
       - uses: actions/checkout@v2
 
       - uses: r-lib/actions/setup-r@v1
-        id: install-r
+        with:
+          use-public-rspm: true
 
       - name: change temp dir
         if: runner.os == 'Windows'
@@ -50,52 +51,18 @@ jobs:
           cat(readLines("~/.Rprofile"), sep = "\n")
         shell: Rscript {0}
 
-      - name: Install pak and query dependencies
-        run: |
-          install.packages("pak", repos = "https://r-lib.github.io/p/pak/dev/")
-          saveRDS(pak::pkg_deps("local::.", dependencies = TRUE), ".github/r-depends.rds")
-        shell: Rscript {0}
-
-      - name: Restore R package cache
-        uses: actions/cache@v2
+      - uses: r-lib/actions/setup-r-dependencies@v1
         with:
-          path: |
-            ${{ env.R_LIBS_USER }}/*
-            !${{ env.R_LIBS_USER }}/pak
-          key: ${{ matrix.config.os }}-${{ steps.install-r.outputs.installed-r-version }}-1-${{ hashFiles('.github/r-depends.rds') }}
-          restore-keys: ${{ matrix.config.os }}-${{ steps.install-r.outputs.installed-r-version }}-1-
-
-      - name: Install system dependencies
-        if: runner.os == 'Linux'
-        run: |
-          pak::local_system_requirements(execute = TRUE)
-          pak::pkg_system_requirements("rcmdcheck", execute = TRUE)
-        shell: Rscript {0}
+          extra-packages: rcmdcheck
 
-      - name: Install dependencies
+      - name: Pandoc and Tinytex info
         run: |
-          pak::local_install_dev_deps(upgrade = TRUE)
-          pak::pkg_install("rcmdcheck")
-        shell: Rscript {0}
-
-      - name: Session info
-        run: |
-          options(width = 100)
-          pkgs <- .packages(TRUE)
-          sessioninfo::session_info(pkgs, include_base = TRUE)
           rmarkdown::find_pandoc()
           tinytex::tlmgr("--version")
           tinytex::tl_pkgs()
         shell: Rscript {0}
 
-      - name: Check
-        env:
-          _R_CHECK_CRAN_INCOMING_: false
-          _R_CHECK_TESTS_NLINES_: 0
-        run: |
-          options(crayon.enabled = TRUE)
-          rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran"), error_on = "warning", check_dir = "check")
-        shell: Rscript {0}
+      - uses: r-lib/actions/check-r-package@v1
 
       - name: Show testthat output
         if: always()

diff --git a/.github/workflows/pkgdown.yaml b/.github/workflows/pkgdown.yaml
@@ -15,42 +15,22 @@ jobs:
     if: ${{ github.event_name == 'push' || startsWith(github.head_ref, 'pkgdown/') }}
     runs-on: ubuntu-18.04
     env:
-      RSPM: https://packagemanager.rstudio.com/cran/__linux__/bionic/latest
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
     steps:
       - uses: actions/checkout@v2
 
       - uses: r-lib/actions/setup-r@v1
-        id: install-r
+        with:
+          use-public-rspm: true
 
       - uses: r-lib/actions/setup-pandoc@v1
 
-      - name: Install pak and query dependencies
-        run: |
-          install.packages("pak", repos = "https://r-lib.github.io/p/pak/dev/")
-          saveRDS(pak::pkg_deps("local::.", dependencies = TRUE), ".github/r-depends.rds")
-        shell: Rscript {0}
-
-      - name: Cache R packages
-        uses: actions/cache@v2
+      - uses: r-lib/actions/setup-r-dependencies@v1
         with:
-          path: ${{ env.R_LIBS_USER }}
-          key: ${{ runner.os }}-${{ steps.install-r.outputs.installed-r-version }}-1-${{ hashFiles('.github/r-depends.rds') }}
-          restore-keys: ${{ runner.os }}-${{ steps.install-r.outputs.installed-r-version }}-1-
-
-      - name: Install system dependencies
-        if: runner.os == 'Linux'
-        run: |
-          pak::local_system_requirements(execute = TRUE)
-          pak::pkg_system_requirements("pkgdown", execute = TRUE)
-        shell: Rscript {0}
-
-      - name: Install package and dependencies
-        run: |
-          pak::local_install_dev_deps(upgrade = TRUE)
-          pak::pkg_install("r-lib/pkgdown")
-          pak::pkg_install("rstudio/quillt")
-        shell: Rscript {0}
+          extra-packages: |
+            r-lib/pkgdown
+            rstudio/quillt
+          needs: website
 
       - name: Install package
         run: R CMD INSTALL .

diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: rmarkdown
 Type: Package
 Title: Dynamic Documents for R
-Version: 2.11.2.9000
+Version: 2.11.3.9000
 Authors@R: c(
   person("JJ", "Allaire", role = "aut", email = "[email protected]"),
   person("Yihui", "Xie", role = c("aut", "cre"), email = "[email protected]", comment = c(ORCID = "0000-0003-0645-5666")),

diff --git a/NEWS.md b/NEWS.md
@@ -7,6 +7,9 @@ rmarkdown 2.12
   <dir>". This makes it possible to have a directory structure for HTML output
   where there is a shared master library with css, javascript, etc. and separate 
   child directories with RMarkdown files. #146 and #1859.
+
+- Added a global option `rmarkdown.html_dependency.header_attr` (`TRUE` by default). It can be set to `FALSE` to opt-out the HTML dependency `html_dependency_header_attrs()` in documents based on `html_document_base()` (thanks, @salim-b rstudio/bookdown#865, @maelle r-lib/downlit#1538).
+
 - `draft()` now works with `devtools::load_all()` and **testthat** when used in other packages. 
 
 rmarkdown 2.11

diff --git a/R/html_dependencies.R b/R/html_dependencies.R
@@ -552,12 +552,14 @@ html_dependency_rsiframe <- function() {
 # Pandoc 2.9 adds attributes on both headers and their parent divs. We remove
 # the ones on headers since they are unnecessary (#1723).
 html_dependency_header_attrs <- function() {
-  if (pandoc_available('2.9')) list(
-    htmlDependency(
-      "header-attrs",
-      version = packageVersion("rmarkdown"),
-      src = pkg_file("rmd/h/pandoc"),
-      script = "header-attrs.js"
+  if (getOption('rmarkdown.html_dependency.header_attr', TRUE) && pandoc_available('2.9')) {
+    list(
+      htmlDependency(
+        "header-attrs",
+        version = packageVersion("rmarkdown"),
+        src = pkg_file("rmd/h/pandoc"),
+        script = "header-attrs.js"
+      )
     )
-  )
+  }
 }
diff --git a/R/pdf_document.R b/R/pdf_document.R
@@ -188,6 +188,17 @@ pdf_document <- function(toc = FALSE,
                       output_dir)
   }
 
+  post_processor <- function(metadata, input_file, output_file, clean, verbose) {
+    # TODO: remove this temporary fix after the syntax highlighting problem is
+    # fixed in Pandoc https://github.com/rstudio/bookdown/issues/1157
+    x <- read_utf8(output_file)
+    s <- '\\SpecialCharTok{|}\\ErrorTok{\\textgreater{}}'
+    if (length(grep(s, x, fixed = TRUE)) == 0) return(output_file)
+    x <- gsub(s, '\\SpecialCharTok{|\\textgreater{}}', x, fixed = TRUE)
+    write_utf8(x, output_file)
+    output_file
+  }
+
   intermediates_generator <- function(...) {
     general_intermediates_generator(saved_files_dir, ...)
   }
@@ -207,6 +218,7 @@ pdf_document <- function(toc = FALSE,
     keep_md = keep_md,
     df_print = df_print,
     pre_processor = pre_processor,
+    post_processor = post_processor,
     intermediates_generator = intermediates_generator
   )
 }

diff --git a/README.md b/README.md
@@ -21,9 +21,8 @@ R Markdown documents can be rendered to many output formats including HTML docum
 
 ## Books
 
-
-<a href="https://bookdown.org/yihui/rmarkdown/"><img src="https://bookdown.org/yihui/rmarkdown/images/cover.png" alt="R Markdown: The Definitive Guide" height="400"></a>
-<a href="https://bookdown.org/yihui/rmarkdown-cookbook/"><img src="https://bookdown.org/yihui/rmarkdown-cookbook/images/cover.png" alt="R Markdown Cookbook" height="400"></a>
+<a href="https://bookdown.org/yihui/rmarkdown/"><img class="book" src="https://bookdown.org/yihui/rmarkdown/images/cover.png" alt="R Markdown: The Definitive Guide" height="400"></a>
+<a href="https://bookdown.org/yihui/rmarkdown-cookbook/"><img class="book" src="https://bookdown.org/yihui/rmarkdown-cookbook/images/cover.png" alt="R Markdown Cookbook" height="400"></a>
 
 See more about them in [Get Started](https://pkgs.rstudio.com/rmarkdown/articles/rmarkdown.html).
 

diff --git a/tests/testthat/test-html_dependencies.R b/tests/testthat/test-html_dependencies.R
@@ -196,3 +196,8 @@ test_that("html_dependencies_fonts loads the correct fonts dep", {
   expect_identical(html_dependencies_fonts(FALSE, TRUE), list(io))
   expect_identical(html_dependencies_fonts(TRUE, TRUE), list(fa, io))
 })
+
+test_that("header-attr can be opt-out", {
+  withr::local_options(list(rmarkdown.html_dependency.header_attr = FALSE))
+  expect_null(html_dependency_header_attrs())
+})