Merged with latest release of official RMarkdown.

Merge remote-tracking branch 'rstudio_origin/master' into jg-devel

* rstudio_origin/master: (26 commits)
  Use data-external=1 to prevent encoding by Pandoc of img src
  add `subdirs` documentation for site generator (rstudio#2058)
  fix: corrected typo in `ghostscript` (rstudio#2059)
  Add CoC contact email
  quillt has moved to rstudio/quillt
  fix invalid HTML code in shiny_prerendered documents (rstudio#1942)
  Allow pkgdown PR preview (rstudio#2055)
  Adding pkgdown site built by GHA (rstudio#1955)
  Add shiny bslib dependency inside html_document_base pre-process (rstudio#2049)
  start the next version
  CRAN release v2.7
  place <div> in \code{}
  amend 62ae2ed and rstudio#1989: make sure output_format_filter is a function; testing NULL is not enough, e.g., the radix package still calls
  use CRAN releases of shiny and bslib
  tweak news
  Only keep the first url in citation  (rstudio#2041)
  Fix for knit_print.data.frame (rstudio#2050)
  set gfm_auto_identifiers to input format if toc is TRUE (rstudio#2040)
  Enable pkgdown/downlit cross-package links to rmarkdown (rstudio#1843)
  update CONTRIBUTING.md
  ...

# Conflicts:
#	DESCRIPTION

Author: jonathan-g

.Rbuildignore

@@ -12,3 +12,6 @@
 ^doc$
 ^Meta$
 ^codecov\.yml$
+^docs$
+^reference$
+^vignettes/articles$

.github/CODE_OF_CONDUCT.md

@@ -0,0 +1,125 @@
+# Contributor Covenant Code of Conduct
+
+## Our Pledge
+
+We as members, contributors, and leaders pledge to make participation in our
+community a harassment-free experience for everyone, regardless of age, body
+size, visible or invisible disability, ethnicity, sex characteristics, gender
+identity and expression, level of experience, education, socio-economic status,
+nationality, personal appearance, race, religion, or sexual identity and
+orientation.
+
+We pledge to act and interact in ways that contribute to an open, welcoming,
+diverse, inclusive, and healthy community.
+
+## Our Standards
+
+Examples of behavior that contributes to a positive environment for our
+community include:
+
+* Demonstrating empathy and kindness toward other people
+* Being respectful of differing opinions, viewpoints, and experiences
+* Giving and gracefully accepting constructive feedback
+* Accepting responsibility and apologizing to those affected by our mistakes,
+and learning from the experience
+* Focusing on what is best not just for us as individuals, but for the overall
+community
+
+Examples of unacceptable behavior include:
+
+* The use of sexualized language or imagery, and sexual attention or
+advances of any kind
+* Trolling, insulting or derogatory comments, and personal or political attacks
+* Public or private harassment
+* Publishing others' private information, such as a physical or email
+address, without their explicit permission
+* Other conduct which could reasonably be considered inappropriate in a
+professional setting
+
+## Enforcement Responsibilities
+
+Community leaders are responsible for clarifying and enforcing our standards
+of acceptable behavior and will take appropriate and fair corrective action in
+response to any behavior that they deem inappropriate, threatening, offensive,
+or harmful.
+
+Community leaders have the right and responsibility to remove, edit, or reject
+comments, commits, code, wiki edits, issues, and other contributions that are
+not aligned to this Code of Conduct, and will communicate reasons for moderation
+decisions when appropriate.
+
+## Scope
+
+This Code of Conduct applies within all community spaces, and also applies
+when an individual is officially representing the community in public spaces.
+Examples of representing our community include using an official e-mail
+address, posting via an official social media account, or acting as an appointed
+representative at an online or offline event.
+
+## Enforcement
+
+Instances of abusive, harassing, or otherwise unacceptable behavior may be
+reported to the community leaders responsible for enforcement at codeofconduct@rstudio.com. All complaints will be reviewed and investigated promptly and fairly.
+
+All community leaders are obligated to respect the privacy and security of the
+reporter of any incident.
+
+## Enforcement Guidelines
+
+Community leaders will follow these Community Impact Guidelines in determining
+the consequences for any action they deem in violation of this Code of Conduct:
+
+### 1. Correction
+
+**Community Impact**: Use of inappropriate language or other behavior deemed
+unprofessional or unwelcome in the community.
+
+**Consequence**: A private, written warning from community leaders, providing
+clarity around the nature of the violation and an explanation of why the
+behavior was inappropriate. A public apology may be requested.
+
+### 2. Warning
+
+**Community Impact**: A violation through a single incident or series of
+actions.
+
+**Consequence**: A warning with consequences for continued behavior. No
+interaction with the people involved, including unsolicited interaction with
+those enforcing the Code of Conduct, for a specified period of time. This
+includes avoiding interactions in community spaces as well as external channels
+like social media. Violating these terms may lead to a temporary or permanent
+ban.
+
+### 3. Temporary Ban
+
+**Community Impact**: A serious violation of community standards, including
+sustained inappropriate behavior.
+
+**Consequence**: A temporary ban from any sort of interaction or public
+communication with the community for a specified period of time. No public or
+private interaction with the people involved, including unsolicited interaction
+with those enforcing the Code of Conduct, is allowed during this period.
+Violating these terms may lead to a permanent ban.
+
+### 4. Permanent Ban
+
+**Community Impact**: Demonstrating a pattern of violation of community
+standards, including sustained inappropriate behavior, harassment of an
+individual, or aggression toward or disparagement of classes of individuals.
+
+**Consequence**: A permanent ban from any sort of public interaction within the
+community.
+
+## Attribution
+
+This Code of Conduct is adapted from the [Contributor Covenant][homepage],
+version 2.0,
+available at <https://www.contributor-covenant.org/version/2/0/code_of_conduct.html>.
+
+Community Impact Guidelines were inspired by [Mozilla's code of conduct
+enforcement ladder](https://github.com/mozilla/diversity).
+
+[homepage]: https://www.contributor-covenant.org
+
+For answers to common questions about this code of conduct, see the FAQ at
+<https://www.contributor-covenant.org/faq>. Translations are available at <https://www.contributor-covenant.org/translations>.

.github/CONTRIBUTING.md

@@ -1,9 +1,20 @@
-We welcome contributions to the **rmarkdown** package. To submit a contribution:
+# Contributing to R Markdown
 
-1.  [Fork](https://github.com/rstudio/rmarkdown/fork) the repository and make your changes.
+We welcome contributions to the **rmarkdown** package. 
 
-2.  Ensure that you have signed the [individual](https://rstudioblog.files.wordpress.com/2017/05/rstudio_individual_contributor_agreement.pdf) or [corporate](https://rstudioblog.files.wordpress.com/2017/05/rstudio_corporate_contributor_agreement.pdf) contributor agreement as appropriate. You can send the signed copy to <jj@rstudio.com>.
+You can contribute in many ways: 
 
-3.  Submit a [pull request](https://help.github.com/articles/using-pull-requests).
+* By opening issues to five feedback and share ideas.
+* By fixing typos in documentations
+* By submitting Pull Request (PR) to fix some opened issues
+* By submitting Pull Request (PR) to suggest some new features. (It is considered good practice to open issues before to discuss ideas)
+
+## To submit a contribution using a Pull Request:
+
+1.  [Fork](https://github.com/rstudio/rmarkdown/fork) the repository and make your changes in a new branch specific to the PR.
+
+2.  For significant changes (e.g not required for fixing typos), ensure that you have signed the [individual](https://rstudioblog.files.wordpress.com/2017/05/rstudio_individual_contributor_agreement.pdf) or [corporate](https://rstudioblog.files.wordpress.com/2017/05/rstudio_corporate_contributor_agreement.pdf) contributor agreement as appropriate. You can send the signed copy to <jj@rstudio.com>. 
+
+3.  Submit the [pull request](https://help.github.com/articles/using-pull-requests). It is ok to submit as draft in your are still working on it but would like some feedback from us. It always good to share in the open that you are working on it.
 
 We'll try to be as responsive as possible in reviewing and accepting pull requests. Appreciate your contributions very much!

.github/workflows/R-CMD-check.yaml

@@ -5,10 +5,16 @@ on:
     branches:
       - main
       - master
+    paths-ignore:
+      - 'pkgdown/**'
+      - '.github/workflows/pkgdown.yaml'
   pull_request:
     branches:
       - main
       - master
+    paths-ignore:
+      - 'pkgdown/**'
+      - '.github/workflows/pkgdown.yaml'
 
 name: R-CMD-check
 
@@ -24,7 +30,7 @@ jobs:
           - {os: windows-latest, pandoc: '2.7.3',   r: 'release'}
           - {os: macOS-latest,   pandoc: '2.7.3',   r: 'release'}
           - {os: ubuntu-18.04,   pandoc: '2.7.3',   r: 'oldrel',  rspm: "https://packagemanager.rstudio.com/cran/__linux__/bionic/latest"}
-          - {os: ubuntu-18.04,   pandoc: '2.7.3',   r: 'devel',   rspm: "https://packagemanager.rstudio.com/cran/__linux__/bionic/latest"}
+          - {os: ubuntu-18.04,   pandoc: '2.7.3',   r: 'devel',   rspm: "https://packagemanager.rstudio.com/cran/__linux__/bionic/latest", http-user-agent: "R/4.0.0 (ubuntu-16.04) R (4.0.0 x86_64-pc-linux-gnu x86_64 linux-gnu) on GitHub Actions" }
           - {os: ubuntu-18.04,   pandoc: '2.7.3',   r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/bionic/latest"}
           - {os: ubuntu-18.04,   pandoc: '2.11.3.1',  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"}
@@ -38,8 +44,15 @@ jobs:
       - uses: actions/checkout@v2
 
       - uses: r-lib/actions/setup-r@v1
+        id: install-r
         with:
           r-version: ${{ matrix.config.r }}
+          http-user-agent: ${{ matrix.config.http-user-agent }}
+
+      - name: change temp dir
+        if: runner.os == 'Windows'
+        run: echo "TMPDIR=${{ runner.temp }}" >> $GITHUB_ENV
+        shell: bash
 
       - uses: r-lib/actions/setup-pandoc@v1
         if: matrix.config.pandoc != 'devel'
@@ -49,51 +62,44 @@ jobs:
       - uses: cderv/actions/setup-pandoc-nightly@nightly-pandoc
         if: matrix.config.pandoc == 'devel'
 
-      # TODO: Use next tag once this commit is in a release
-      - uses: r-lib/actions/setup-tinytex@5f1c134
+      - uses: r-lib/actions/setup-tinytex@v1
         env:
           # install full prebuilt version
-          TINYTEX_INSTALLER: TinyTeX-1
+          TINYTEX_INSTALLER: TinyTeX
 
       - name: Add some R options for later steps
         run: |
           cat("\noptions(tinytex.verbose = TRUE)\n", file = "~/.Rprofile", append = TRUE)
           cat(readLines("~/.Rprofile"), sep = "\n")
         shell: Rscript {0}
 
-      - name: Query dependencies
+      - name: Install pak and query dependencies
         run: |
-          install.packages('remotes')
-          saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
-          writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version")
+          install.packages("pak", repos = "https://r-lib.github.io/p/pak/dev/")
+          saveRDS(pak::pkg_deps_tree("local::.", dependencies = TRUE), ".github/r-depends.rds")
         shell: Rscript {0}
 
       - name: Cache R packages
         uses: actions/cache@v2
         with:
           path: ${{ env.R_LIBS_USER }}
-          key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }}
-          restore-keys: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-
+          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: |
-          while read -r cmd
-          do
-            eval sudo $cmd
-          done < <(Rscript -e 'writeLines(remotes::system_requirements("ubuntu", "18.04"))')
+        run: Rscript -e 'pak::local_system_requirements(execute = TRUE)'
 
       - name: Install dependencies
         run: |
-          remotes::install_deps(dependencies = TRUE)
-          remotes::install_cran("rcmdcheck")
-          remotes::install_cran("sessioninfo")
+          pak::local_install_dev_deps(upgrade = TRUE)
+          pak::pkg_install("rcmdcheck")
         shell: Rscript {0}
 
       - name: Session info
         run: |
           options(width = 100)
-          pkgs <- installed.packages()[, "Package"]
+          pkgs <- .packages(TRUE)
           sessioninfo::session_info(pkgs, include_base = TRUE)
           rmarkdown::find_pandoc()
           tinytex::tlmgr("--version")
@@ -104,7 +110,6 @@ jobs:
         env:
           _R_CHECK_CRAN_INCOMING_: false
           _R_CHECK_TESTS_NLINES_: 0
-          TMPDIR: ${{ runner.temp }}
         run: rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran"), error_on = "warning", check_dir = "check")
         shell: Rscript {0}
 
@@ -123,6 +128,6 @@ jobs:
       - name: Test coverage
         if: success() && runner.os == 'Linux' && matrix.config.r == 'release' && matrix.config.pandoc == '2.7.3'
         run: |
-          remotes::install_cran("covr")
+          pak::pkg_install('covr')
           covr::codecov()
         shell: Rscript {0}

.github/workflows/pkgdown.yaml

@@ -1,54 +1,77 @@
 on:
-  workflow_run:
-    workflows: ["R-CMD-check"]
-    branches: [main,master]
-    types: completed
+  push:
+    branches:
+     - main
+     - master
+  pull_request:
+    branches:
+     - main
+     - master
 
 name: pkgdown
 
 jobs:
   pkgdown:
-    runs-on: macOS-latest
+    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
 
       - uses: r-lib/actions/setup-pandoc@v1
 
-      - name: Query dependencies
+      - name: Install pak and query dependencies
         run: |
-          install.packages('remotes')
-          saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
-          writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version")
+          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
         with:
           path: ${{ env.R_LIBS_USER }}
-          key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }}
-          restore-keys: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-
+          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 dependencies
-        run: remotes::install_deps(dependencies = TRUE)
+      - 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}
 
       - name: Install package
         run: R CMD INSTALL .
 
       - name: Build pkgdown site
-        run: |
-          install.packages("pkgdown", type = "binary")
-          pkgdown::build_site(new_process = FALSE)
+        run: pkgdown::build_site(new_process = FALSE)
         shell: Rscript {0}
 
-      - name: Publish
-        run: |
-          npm install netlify-cli -g
-          netlify deploy --prod --dir docs
+      - name: Deploy to Netlify
+        id: netlify-deploy
+        uses: nwtgck/actions-netlify@v1.1
+        with:
+          publish-dir: 'reference'
+          production-branch: master
+          github-token: ${{ secrets.GITHUB_TOKEN }}
+          deploy-message:
+            'Deploy from GHA: ${{ github.event.head_commit.message }} (${{ github.sha }})'
+          enable-pull-request-comment: false
+          enable-commit-comment: false
+          enable-commit-status: true
+          alias: deploy-preview-${{ github.event.number }}
         env:
           NETLIFY_AUTH_TOKEN: ${{ secrets.NETLIFY_AUTH_TOKEN }}
           NETLIFY_SITE_ID: ${{ secrets.NETLIFY_SITE_ID }}

.gitignore

@@ -5,3 +5,4 @@
 inst/doc
 doc
 Meta
+docs