Merge pull request #1 from rstudio/master

Merge RStudio version into my fork.

.Rbuildignore

@@ -1,7 +1,13 @@
 ^.*\.Rproj$
 ^\.Rproj\.user$
-tools/
-README\.(md|html)
-CONTRIBUTING\.(md|html)
-PANDOC\.(md|html)
+^tools/
 ^\.travis\.yml$
+^tests/testthat/site/.*\.html
+^tests/testthat/site/rsconnect/
+^tests/testthat/site/_site/
+^tests/testthat/site/lib/
+^tests/testthat/site/.*_files/
+^\.github$
+^pkgdown$
+^doc$
+^Meta$

.gitattributes

@@ -0,0 +1 @@
+/inst/NEWS merge=union

.github/CONTRIBUTING.md

@@ -0,0 +1,9 @@
+We welcome contributions to the **rmarkdown** package. To submit a contribution:
+
+1.  [Fork](https://github.com/rstudio/rmarkdown/fork) the repository and make your changes.
+
+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>.
+
+3.  Submit a [pull request](https://help.github.com/articles/using-pull-requests).
+
+We'll try to be as responsive as possible in reviewing and accepting pull requests. Appreciate your contributions very much!

.github/ISSUE_TEMPLATE.md

@@ -0,0 +1,17 @@
+
+<!--
+Please keep the below portion in your issue. Your issue will be closed if any of the boxes is not checked (i.e., replace `[ ]` by `[x]`). In certain (rare) cases, you may be exempted if you give a brief explanation (e.g., you are only making a suggestion for improvement). Thanks!
+-->
+
+---
+
+By filing an issue to this repo, I promise that
+
+- [ ] I have fully read the issue guide at https://yihui.org/issue/.
+- [ ] I have provided the necessary information about my issue.
+    - If I'm asking a question, I have already asked it on Stack Overflow or RStudio Community, waited for at least 24 hours, and included a link to my question there.
+    - If I'm filing a bug report, I have included a minimal, self-contained, and reproducible example, and have also included `xfun::session_info('rmarkdown')`. I have upgraded all my packages to their latest versions (e.g., R, RStudio, and R packages), and also tried the development version: `remotes::install_github('rstudio/rmarkdown')`.
+    - If I have posted the same issue elsewhere, I have also mentioned it in this issue.
+- [ ] I have learned the Github Markdown syntax, and formatted my issue correctly.
+
+I understand that my issue may be closed if I don't fulfill my promises.

.gitignore

@@ -2,7 +2,6 @@
 .Rhistory
 .RData
 .DS_Store
-README.html
-CONTRIBUTING.html
-PANDOC.html
-
+inst/doc
+doc
+Meta

.travis.yml

@@ -1,38 +1,26 @@
-language: c
-
-before_install:
-  - curl -OL http://raw.github.com/craigcitro/r-travis/master/scripts/travis-tool.sh
-  - chmod 755 ./travis-tool.sh
-  - ./travis-tool.sh bootstrap
-install:
-  # Install binary pandoc from Rstudio
-  - mkdir -p $HOME/opt/pandoc
-  - curl -O https://s3.amazonaws.com/rstudio-buildtools/pandoc-1.12.3.zip
-  - unzip -j pandoc-1.12.3.zip pandoc-1.12.3/linux/debian/x86_64/pandoc
-      -d $HOME/opt/pandoc
-  - chmod +x $HOME/opt/pandoc/pandoc*
-  - rm pandoc-1.12.3.zip
-  - $HOME/opt/pandoc/pandoc --version
-
-  - ./travis-tool.sh r_binary_install knitr
-  - ./travis-tool.sh r_binary_install yaml
-  - ./travis-tool.sh install_deps
-
-script: ./travis-tool.sh run_tests
-
-on_failure:
-  - ./travis-tool.sh dump_logs
+dist: bionic
+language: r
+cache:
+  packages: yes
+pandoc_version: 2.3.1
+cran: https://cran.rstudio.com
 
 env:
-  - global:
-    - WARNINGS_ARE_ERRORS=1
-
-branches:
-  except:
-  - /-expt$/
-
-notifications:
-  email:
-    on_success: change
-    on_failure: change
+  global:
+    - _R_CHECK_TESTS_NLINES_=0
+  matrix:
+    - PANDOC_VERSION=default NETLIFY_SITE_ID=5d77c13c-e2ee-4a31-87ca-2fe657196160
+    - PANDOC_VERSION=latest PATH=$HOME/bin:$PATH
 
+before_install:
+  - "[[ ${PANDOC_VERSION} = latest ]] && ./tools/install-pandoc.sh || true"
+  - pandoc --version
+  - tlmgr install units
+
+after_success:
+  - "[[ ${TRAVIS_BRANCH}  = master  ]] || exit 0"
+  - "[[ ${PANDOC_VERSION} = default ]] || exit 0"
+  - "[[ -z ${NETLIFY_AUTH_TOKEN} ]] && exit 0"
+  - nvm install stable
+  - npm install netlify-cli -g
+  - Rscript -e 'pkgdown::build_site(".", document = FALSE, preview = FALSE)' && netlify deploy --prod --dir docs

DESCRIPTION

@@ -1,26 +1,111 @@
 Package: rmarkdown
 Type: Package
 Title: Dynamic Documents for R
-Version: 0.2.64
-Date: 2014-05-31
-Author: RStudio Inc.
-Maintainer: JJ Allaire <jj@rstudio.com>
-Description: Convert R Markdown documents into a variety of formats
-    including HTML, MS Word, PDF, and Beamer.
+Version: 2.0.5
+Authors@R: c(
+  person("JJ", "Allaire", role = "aut", email = "jj@rstudio.com"),
+  person("Yihui", "Xie", role = c("aut", "cre"), email = "xie@yihui.name", comment = c(ORCID = "0000-0003-0645-5666")),
+  person("Jonathan", "McPherson", role = "aut", email = "jonathan@rstudio.com"),
+  person("Javier", "Luraschi", role = "aut", email = "javier@rstudio.com"),
+  person("Kevin", "Ushey", role = "aut", email = "kevin@rstudio.com"),
+  person("Aron", "Atkins", role = "aut", email = "aron@rstudio.com"),
+  person("Hadley", "Wickham", role = "aut", email = "hadley@rstudio.com"),
+  person("Joe", "Cheng", role = "aut", email = "joe@rstudio.com"),
+  person("Winston", "Chang", role = "aut", email = "winston@rstudio.com"),
+  person("Richard", "Iannone", role = "aut", email = "rich@rstudio.com", comment = c(ORCID = "0000-0003-3925-190X")),
+  #
+  # Contributors, ordered alphabetically by first name
+  person("Andrew", "Dunning", role = "ctb", comment = c(ORCID = "0000-0003-0464-5036")),
+  person("Atsushi", "Yasumoto", role = "ctb", comment = c(ORCID = "0000-0002-8335-495X")),
+  person("Barret", "Schloerke", role = "ctb"),
+  person("Christophe", "Dervieux", role = "ctb"),
+  person("Frederik", "Aust", role = "ctb", email = "frederik.aust@uni-koeln.de", comment = c(ORCID = "0000-0003-4900-788X")),
+  person("Jeff", "Allen", role = "ctb", email = "jeff@rstudio.com"),
+  person("JooYoung", "Seo", role="ctb", comment = c(ORCID = "0000-0002-4064-6012")),
+  person("Malcolm", "Barrett", role = "ctb"),
+  person("Rob", "Hyndman", role = "ctb", email = "Rob.Hyndman@monash.edu"),
+  person("Romain", "Lesur", role = "ctb"),
+  person("Roy", "Storey", role = "ctb"),
+  person("Ruben", "Arslan", role = "ctb", email = "ruben.arslan@uni-goettingen.de"),
+  person("Sergio", "Oller", role = "ctb"),
+  #
+  # Copyright holders
+  person(family = "RStudio, Inc.", 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/rmd/h/jquery-AUTHORS.txt"),
+  person(family = "jQuery UI contributors", role = c("ctb", "cph"),
+         comment = "jQuery UI library; authors listed in inst/rmd/h/jqueryui-AUTHORS.txt"),
+  person("Mark", "Otto", role = "ctb",
+         comment = "Bootstrap library"),
+  person("Jacob", "Thornton", role = "ctb",
+         comment = "Bootstrap library"),
+  person(family = "Bootstrap contributors", role = "ctb",
+         comment = "Bootstrap library"),
+  person(family = "Twitter, Inc", role = "cph",
+         comment = "Bootstrap library"),
+  person("Alexander", "Farkas", role = c("ctb", "cph"),
+         comment = "html5shiv library"),
+  person("Scott", "Jehl", role = c("ctb", "cph"),
+         comment = "Respond.js library"),
+  person("Ivan", "Sagalaev", role = c("ctb", "cph"),
+         comment = "highlight.js library"),
+  person("Greg", "Franko", role = c("ctb", "cph"),
+         comment = "tocify library"),
+  person("John", "MacFarlane", role = c("ctb", "cph"),
+         comment = "Pandoc templates"),
+  person(family = "Google, Inc.", role = c("ctb", "cph"),
+         comment = "ioslides library"),
+  person("Dave", "Raggett", role = "ctb",
+         comment = "slidy library"),
+  person(family = "W3C", role = "cph",
+         comment = "slidy library"),
+  person("Dave", "Gandy", role = c("ctb", "cph"),
+         comment = "Font-Awesome"),
+  person("Ben", "Sperry", role = "ctb",
+         comment = "Ionicons"),
+  person(family = "Drifty", role = "cph",
+         comment = "Ionicons"),
+  person("Aidan", "Lister", role = c("ctb", "cph"), 
+         comment = "jQuery StickyTabs"),
+  person("Benct Philip", "Jonsson", role = c("ctb", "cph"), 
+         comment = "pagebreak lua filter"),
+  person("Albert", "Krewinkel", role = c("ctb", "cph"), 
+         comment = "pagebreak lua filter")
+  )
+Maintainer: Yihui Xie <xie@yihui.name>
+Description: Convert R Markdown documents into a variety of formats.
 Depends:
     R (>= 3.0)
 Imports:
     tools,
     utils,
-    knitr (>= 1.6),
-    yaml (>= 2.1.5),
-    htmltools (>= 0.2.4),
-    caTools
+    knitr (>= 1.22),
+    yaml (>= 2.1.19),
+    htmltools (>= 0.3.5),
+    evaluate (>= 0.13),
+    base64enc,
+    jsonlite,
+    mime,
+    tinytex (>= 0.11),
+    xfun,
+    methods,
+    stringr (>= 1.2.0)
 Suggests:
-    shiny (>= 0.9.1.9009),
+    shiny (>= 0.11),
+    tufte,
     testthat,
-    digest
-SystemRequirements: pandoc (>= 1.12.3) - http://johnmacfarlane.net/pandoc
-URL: http://rmarkdown.rstudio.com
+    digest,
+    dygraphs,
+    tibble,
+    fs,
+    pkgdown,
+    callr (>= 2.0.0)
+SystemRequirements: pandoc (>= 1.12.3) - http://pandoc.org
+URL: https://github.com/rstudio/rmarkdown
+BugReports: https://github.com/rstudio/rmarkdown/issues
 License: GPL-3
-Roxygen: list(wrap = FALSE)
+RoxygenNote: 7.0.2
+Encoding: UTF-8
+VignetteBuilder: knitr

NAMESPACE

@@ -1,37 +1,106 @@
-# Generated by roxygen2 (4.0.1): do not edit by hand
+# Generated by roxygen2: do not edit by hand
 
+S3method(knit_print,grouped_df)
+S3method(knit_print,rowwise_df)
+S3method(knit_print,tbl_sql)
+S3method(prepare_evaluate_output,default)
+S3method(prepare_evaluate_output,htmlwidget)
+S3method(prepare_evaluate_output,knit_asis)
+S3method(prepare_evaluate_output,list)
+export(all_output_formats)
 export(beamer_presentation)
+export(clean_site)
+export(context_document)
 export(default_output_format)
+export(default_site_generator)
 export(draft)
+export(find_external_resources)
+export(from_rmarkdown)
+export(github_document)
+export(html_dependency_bootstrap)
+export(html_dependency_font_awesome)
+export(html_dependency_highlightjs)
+export(html_dependency_ionicons)
+export(html_dependency_jquery)
+export(html_dependency_jqueryui)
+export(html_dependency_pagedtable)
+export(html_dependency_tocify)
 export(html_document)
 export(html_document_base)
 export(html_fragment)
+export(html_notebook)
+export(html_notebook_metadata)
+export(html_notebook_output_code)
+export(html_notebook_output_html)
+export(html_notebook_output_img)
+export(html_notebook_output_png)
+export(html_vignette)
 export(includes)
+export(includes_to_pandoc_args)
 export(ioslides_presentation)
+export(knit_params_ask)
 export(knitr_options)
 export(knitr_options_html)
 export(knitr_options_pdf)
+export(latex_dependency)
+export(latex_dependency_tikz)
+export(latex_document)
+export(latex_fragment)
 export(md_document)
 export(metadata)
+export(navbar_html)
+export(navbar_links_html)
+export(odt_document)
 export(output_format)
+export(output_metadata)
+export(paged_table)
 export(pandoc_available)
+export(pandoc_citeproc_convert)
 export(pandoc_convert)
+export(pandoc_exec)
 export(pandoc_highlight_args)
 export(pandoc_include_args)
+export(pandoc_latex_engine_args)
 export(pandoc_options)
 export(pandoc_path_arg)
 export(pandoc_self_contained_html)
 export(pandoc_template)
 export(pandoc_toc_args)
 export(pandoc_variable_arg)
+export(pandoc_version)
+export(parse_html_notebook)
 export(pdf_document)
+export(powerpoint_presentation)
+export(relative_to)
 export(render)
 export(render_delayed)
+export(render_site)
 export(render_supporting_files)
-export(revealjs_presentation)
+export(resolve_output_format)
 export(rmarkdown_format)
+export(rtf_document)
 export(run)
+export(shiny_prerendered_chunk)
+export(shiny_prerendered_clean)
+export(shiny_prerendered_server_start_code)
+export(site_config)
+export(site_generator)
+export(site_resources)
 export(slidy_presentation)
 export(tufte_handout)
 export(word_document)
-import(htmltools)
+export(yaml_front_matter)
+import(methods)
+import(stats)
+import(utils)
+importFrom(evaluate,evaluate)
+importFrom(htmltools,HTML)
+importFrom(htmltools,copyDependencyToDir)
+importFrom(htmltools,extractPreserveChunks)
+importFrom(htmltools,htmlDependency)
+importFrom(htmltools,makeDependencyRelative)
+importFrom(htmltools,renderDependencies)
+importFrom(htmltools,restorePreserveChunks)
+importFrom(htmltools,tagList)
+importFrom(htmltools,tags)
+importFrom(knitr,knit_print)