CVS commit: pkgsrc/textproc/R-rmarkdown

["Makoto Fujiwara" <mef%netbsd.org@localhost>]

Module Name:    pkgsrc
Committed By:   mef
Date:           Sun Dec 18 04:44:47 UTC 2022

Modified Files:
        pkgsrc/textproc/R-rmarkdown: Makefile distinfo

Log Message:
(textproc/R-rmarkdown) Updated 2.10 to 2.19

rmarkdown 2.19
================================================================================
- No longer use `xfun::isFALSE()` internally.

rmarkdown 2.18
================================================================================
- `rmarkdown::render()` argument `output_file` is now used for all
  output formats, if there is only one name for multiple output
  formats (thanks, @MaelAstruc, #2421).

- Custom output formats can provide a custom function to convert
  Markdown input to the desired output format now. To do so, define
  the output format via `output_format(pandoc =
  pandoc_options(convert_fun = function(...) {}))`. The default
  converting function is `pandoc_convert()` in this package. See the
  help page `?pandoc_options` for more details.

rmarkdown 2.17
================================================================================
- `rmarkdown::render_site()` will now also look for `index.rmd` in
  addition to `index.Rmd` for custom site generator in YAML with
  `site:` (thanks, @kamalsacranie, #2409).

- Icons in tabset dropdown are now correctly shown, including when
  `self_contained: false` (thanks, @cpsievert, #1697).

rmarkdown 2.16
================================================================================
- Pandoc 2.19 has deprecated the argument `--self-contained`. If you
  have installed Pandoc 2.19+, **rmarkdown** will use
  `--embed-resources --standalone` as recommended by Pandoc for output
  formats that use the option `self_contained = TRUE` (#2382).

- `pandoc_version()` returns a version number of the form
  `X.Y.Z.YYYY.MM.DD` for the nightly build of Pandoc now, where
  `YYYY.MM.DD` is its build date. Previously it would return
  `X.Y.Z.9999` to indicate the nightly version.

rmarkdown 2.15
================================================================================
- Fix navbar issue with website when using Boostrap 5 with **bslib**
  (thanks, @guasi, #2379, @cpsievert, #2384).

- The `tufte_handout()` function inside **rmarkdown** is defunct
  now. Its codebase was moved to the **tufte** package in 2016, and
  this function was marked as deprecated in 2021. Please use
  `tufte::tufte_handout()` instead of
  `rmarkdown::tufte_handout()`. The latter will be removed eventually
  from this package.

- `github_document()` gains `math_method = "default"` and defaults to
  it. No special processing will be done to inline maths in `$` and
  block maths in `$$` as now [Github supports
  it](https://github.blog/changelog/2022-05-19-render-mathematical-expressions-in-markdown/)
  and will render using Mathjax (thanks, @kylebutts, #2361).

rmarkdown 2.14
================================================================================

- Improved highlighting theme `arrow` regarding accessibility.

- Fixed an issue with `site_generator()` detection of a site project
  (thanks, @bhattmaulik, #2344).

- Fixed an issue with Shiny prerendered documents and Pandoc not
  correctly rendering last Markdown paragraph in HTML (thanks,
  @gadenbuie, #2336).

- Fixed a bug that `site_generator()` fails to detect the root dir of
  the site and causes infinite recursion (thanks, @fisher-j, #2339).

- `html_vignette()` gains `code_folding` argument (thanks, @atusy, #2340).

- `html_document()` can opt-out `code_folding = "show"` or `"hide"`
  for individual code blocks by adding the `fold-none` class to the
  code blocks (thanks, @atusy, #2348).

- When using a development version of Pandoc, a `.9999` suffix is
  appended to version number so that `pandoc_available()` can
  correctly compared version with last release.

rmarkdown 2.13
================================================================================
- Fix an issue with older R version and vignette building (#2324).

- Fix an issue with older R version and `preserve_yaml = TRUE` in
  `md_document()` (#2325).

- Long title in `ioslides_presentation` failed to work with Pandoc
  2.17.x (thanks, @Am386DX-40, #2327).

rmarkdown 2.12
================================================================================
- `html_document()` and `html_document_base()` gains the `math_method`
 argument to support [all the math rendering engines from
 Pandoc] (https://pandoc.org/MANUAL.html #math rendering-in-html):
 "mathjax", "katex", "mathml", "webtex", and "gladtex". For backward
 compatibility, the `mathjax` argument still works and will take
 precedence over `math_method`, but we recommend using the new
 `math_method` argument instead of the `mathjax` argument, and the
 latter could be deprecated in the future.

  You can specify a math engine via `math_method` as an engine name, e.g.,

  ```yaml
  output:
    html_document:
      math_method: katex
  ```

  or provide both a name and a URL (for `mathjax`, `katex` and `webtex`):

  ```yaml
  output:
    html_document:
      math_method:
        engine: mathjax
        url: https://cdn.jsdelivr.net/npm/mathjax@3/es5/tex-chtml-full.js
  ```

  For `math_method = "katex"`, KaTeX CDN will be inserted in version
  0.15.2 by default (from jsdelivr). A custom URL toward another CDN
  can be passed as `url`.

  For `math_method = "webtex"`, it will default to inset SVG using
  `https://latex.codecogs.com/svg.image?`. Use
  `https://latex.codecogs.com/png.image?` for PNG. See
  https://latex.codecogs.com for supported options (dpi, background,
  ...).

  Most HTML output format using `html_document()` or
  `html_document_base()` as based format should benefit from this new
  feature.  See `?rmarkdown::html_document()` for details (thanks,
  @atusy, #1940).

- `github_document()` also gains the `math_method` argument set to
  `"webtex"` by default so that LaTeX equations can be rendered in the
  Github Markdown document as images. Previously, LaTeX equations were
  not rendered. Set `math_method = NULL` to deactivate.

- Added support for [**katex**](https://docs.ropensci.org/katex/) R
  package as a math engine with `math_method = "r-katex"` in HTML
  documents. This method offers server-side rendering of all the
  equations, which means no JS processing is needed in the browser as
  with usual KaTeX or MathJaX methods. (thanks, @jeroen, #2304).

- `anchor_sections` can now be easily customized using `style` or
  `depth` element for `anchor_sections`. For example:

  ```yaml
  output:
    html_document:
      anchor_sections:
        style: symbol # use symbol style ("hash", "symbol", "icon")
        depth: 2 # max depth to apply anchor on (default to max which is 6)
  ```

  Customizing using a CSS rule is still possible. Detailed explanation
  and examples have been added to the help page `?html_document`.

- Improved the highlighting mechanism in formats that supports `highlight` argument:

  * It is now possible to pass a custom theme file `.theme` in
    `highlight` argument for customizing the [syntax highlighting
    style used by
    Pandoc](https://pandoc.org/MANUAL.html#syntax-highlighting).

  * In addition to Pandoc's own supported themes, two more themes are
    bundled in the package: `highlight: arrow` a theme [optimized for
    accessibility and color contrast](https://www.a11yproject.com/)
    (thanks to @apreshill), and `highlight: rstudio` to mimic the
    RStudio editor theme.

  * For HTML output only, added optional
    [downlit](https://downlit.r-lib.org/) support in `html_document()`
    for R syntax highlighting and autolinking. Use `highlight_downlit
    = TRUE` to activate it (same argument as in **distill**). This
    features require the **downlit** package.

- Templates for `html_document()` and `ioslides_presentation()` gained
  a new CSS rule to display single line `<summary>` content inline
  (rstudio/rstudio#10589).

- `md_document()` gained a new `standalone` argument, which is `FALSE`
  by default unless `toc = TRUE`. This allows to output authors, date
  and other metadata per the Pandoc's template. Due to limitation in
  how Pandoc is handling metadata blocks in its extensions
  `yaml_metadata_block`, `preserve_yaml = TRUE` now deactivate any
  extension to let **rmarkdown** directly handle the keeping of YAML
  block - this means it does not set `standalone = TRUE` by
  default. Meanwhile, `github_document()` gained the `preserve_yaml`
  argument (thanks, @florisvdh, #2297).

- Added `available_templates()` to list all the templates from a
  specific package that can be used with `rmarkdown::draft()`.

- Following support in Pandoc 2.15, `powerpoint_presentation()` gained
  a `incremental` argument as other slide formats. As a reminder,
  setting `incremental = TRUE` will make lists to display
  incrementally. See more in [Pandoc's
  MANUAL](https://pandoc.org/MANUAL.html#incremental-lists).

- Added support for Pandoc's `dir` variable in HTML templates. This is
  the second [Language
  Variables](https://pandoc.org/MANUAL.html#language-variables) after
  `lang`.

- 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).

- Rendering using `runtime: shiny_prerendered` or `runtime: shinyrmd`
  now natively supports custom templates. Previously since 2.8,
  developers had to add a special comment, `<!-- HEAD_CONTENT -->`,
  conditionally to `shiny-prerendered` variable. (See also NEWS from
  2.8 for the previous behavior). The new behavior inserts required
  special comment `<!-- HEAD_CONTENT -->` as a last element of
  `$header-includes$`. If templates rely on the old behavior and
  require some contents between `$header-includes$` and `<!--
  HEAD_CONTENT -->`, consider including them with `$header-includes$`
  (thanks, @atusy, @gadenbuie #2249).

- A shiny prerendered document with only a empty server context does
  not error anymore. Document will be rendered with a empty server
  function and `server.R` file will be ignored. To use `server.R`, no
  server context should be present in the Rmd document (thanks,
  @jcheng5, #2305).

- Fixed a regression with rendering `shiny_prerendered` document
  (thanks, @aronatkins, @gadenbuie, #2218).

- Fixed an issue in `beamer_presentation()` where `header-includes`
  would be overwritten by `includes = list(in_header =)` (thanks,
  @samcarter, #2294). Same fix as for `pdf_document()` (#1359).

- Fixed broken links to section headers when `number_sections = TRUE`
  is specified in `md_document` and `github_document` (thanks, @atusy,
  #2093).

- `draft()` now works with `devtools::load_all()` and **testthat**
  when used in other packages.

- Lua Filters: Added two more functions in `shared.lua` for other package to use:

  * Added `type()` function backward compatible following Pandoc 2.17 changes.
  * Added `print_debug()` for easier logging during debug.

- Add opt-in `tabset` option to the `html_vignette`. In contrast to
  the similar feature from `html_document`, this feature supports
  navigation from ToC and URL. Any custom formats can introduce this
  feature by using an exported function `html_dependency_tabset()`
  (thanks, @atusy, #2313).

rmarkdown 2.11
================================================================================
- Relative paths in parent directories in the `css` argument of
  `html_document()` were incorrectly normalized to absolute paths by
  #2095 in v2.8. Now relative paths in parent directories will no
  longer be converted to absolute paths (thanks, @daijiang,
  yihui/xaringan#331).

- It is possible to specify the version of jQuery via a global option
  now, e.g., `options(rmarkdown.jquery.version = 2)` (note that the
  default major version is `3`). This is mainly for advanced users and
  developers to test different versions of jQuery.

- `pandoc_citeproc_convert()` now handles correctly bib file
  containing specific UTF-8 characters on non default UTF-8 systems
  like Windows (thanks, @mitchelloharawild, #2195).

- Shiny prerendered documents are now pre-rendered in a child
  environment to avoid allowing the results of static code chunks to
  exist in the Shiny app environment (@gadenbuie, #2203).

- The previously unexported function `convert_ipynb()` is exported now
  (thanks, @acircleda).


To generate a diff of this commit:
cvs rdiff -u -r1.5 -r1.6 pkgsrc/textproc/R-rmarkdown/Makefile
cvs rdiff -u -r1.6 -r1.7 pkgsrc/textproc/R-rmarkdown/distinfo

Please note that diffs are not public domain; they are subject to the
copyright notices on the relevant files.

Modified files:

Index: pkgsrc/textproc/R-rmarkdown/Makefile
diff -u pkgsrc/textproc/R-rmarkdown/Makefile:1.5 pkgsrc/textproc/R-rmarkdown/Makefile:1.6
--- pkgsrc/textproc/R-rmarkdown/Makefile:1.5    Sun Sep  5 01:50:39 2021
+++ pkgsrc/textproc/R-rmarkdown/Makefile        Sun Dec 18 04:44:47 2022
@@ -1,7 +1,7 @@
-# $NetBSD: Makefile,v 1.5 2021/09/05 01:50:39 mef Exp $
+# $NetBSD: Makefile,v 1.6 2022/12/18 04:44:47 mef Exp $
 
 R_PKGNAME=     rmarkdown
-R_PKGVER=      2.10
+R_PKGVER=      2.19
 CATEGORIES=    textproc
 
 MAINTAINER=    pkgsrc-users%NetBSD.org@localhost
@@ -19,13 +19,17 @@ DEPENDS+=   R-stringr>=1.2.0:../../textpro
 DEPENDS+=      R-yaml>=2.1.19:../../textproc/R-yaml
 DEPENDS+=      R-tinytex-[0-9]*:../../print/R-tinytex
 DEPENDS+=      R-withr>=2.4.2:../../devel/R-withr
+DEPENDS+=      R-jquerylib-[0-9]*:../../www/R-jquerylib
+DEPENDS+=      R-bslib>=0.2.5.1:../../www/R-bslib
+
+# Packages suggested but not available:
+#  'dygraphs', 'rsconnect', 'katex', 'tufte'
 
-# Packages suggested but not available: 'tufte', 'dygraphs', 'rsconnect'
-#
 TEST_DEPENDS+= R-base64enc-[0-9]*:../../converters/R-base64enc
 TEST_DEPENDS+= R-fs-[0-9]*:../../devel/R-fs
 TEST_DEPENDS+= R-shiny-[0-9]*:../../www/R-shiny
 TEST_DEPENDS+= R-testthat-[0-9]*:../../devel/R-testthat
+TEST_DEPENDS+= R-downlit-[0-9]*:../../www/R-downlit
 
 USE_LANGUAGES= # none
 

Index: pkgsrc/textproc/R-rmarkdown/distinfo
diff -u pkgsrc/textproc/R-rmarkdown/distinfo:1.6 pkgsrc/textproc/R-rmarkdown/distinfo:1.7
--- pkgsrc/textproc/R-rmarkdown/distinfo:1.6    Tue Oct 26 11:21:32 2021
+++ pkgsrc/textproc/R-rmarkdown/distinfo        Sun Dec 18 04:44:47 2022
@@ -1,5 +1,5 @@
-$NetBSD: distinfo,v 1.6 2021/10/26 11:21:32 nia Exp $
+$NetBSD: distinfo,v 1.7 2022/12/18 04:44:47 mef Exp $
 
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-SHA512 (R/rmarkdown_2.10.tar.gz) = 800f3b132097236d60a703c0d89da11aeae872a17f10475b502b5b936059b268c013b07e0c0e9cdf4ee8cd47fc82b0b5bc901db36962d9084d1819748675b059
-Size (R/rmarkdown_2.10.tar.gz) = 3248794 bytes
+BLAKE2s (R/rmarkdown_2.19.tar.gz) = f2daa66f9ccef373318dd1c990ab28e994ea255623a44177cbb9cd2985f44dd6
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+Size (R/rmarkdown_2.19.tar.gz) = 3243575 bytes