Commit fae85a08 authored by Greg Wilson's avatar Greg Wilson
Browse files

Improving support for R Markdown. 

1.  Adding `tools/chunk-options.R` with support for Pandoc-based conversion of R Markdown to plain Markdown.
2.  Modifying `Makefile` to handle any R Markdown files that are present.

Changes have been checked by @jdblischak in the `r-novice-inflammation` project.
parent a005071a

Makefile

+23 −16
Original line number Diff line number Diff line 
# Files.

MARKDOWN = $(wildcard *.md)

EXCLUDES = README.md LAYOUT.md FAQ.md DESIGN.md

SRC_PAGES = $(filter-out $(EXCLUDES), $(MARKDOWN))

DST_PAGES = $(patsubst %.md,%.html,$(SRC_PAGES))

# R Markdown files.

SRC_RMD = $(wildcard ??-*.Rmd)

DST_RMD = $(patsubst %.Rmd,%.md,$(SRC_RMD))



# Pandoc filters

FILTERS = $(wildcard tools/filters/*.py)

# All Markdown files (hand-written and generated).

SRC_MD = $(wildcard *.md) $(DST_RMD)

DST_HTML = $(patsubst %.md,%.html,$(SRC_MD))



# All outputs.

DST_ALL = $(DST_HTML)



# Inclusions.

INCLUDES = \
@@ -14,11 +16,14 @@ INCLUDES = \ 
	-Vfooter="$$(cat _includes/footer.html)" \

	-Vjavascript="$$(cat _includes/javascript.html)"



# Chunk options for knitr (used in R conversion).

R_CHUNK_OPTS = tools/chunk-options.R



# Default action is to show what commands are available.

all : commands



## preview  : Build website locally for checking.

preview : $(DST_PAGES)

preview : $(DST_ALL)



# Pattern for slides (different parameters and template).

motivation.html : motivation.md _layouts/slides.html
@@ -27,7 +32,7 @@ motivation.html : motivation.md _layouts/slides.html 
	-o $@ $<



# Pattern to build a generic page.

%.html : %.md _layouts/page.html $(FILTERS)

%.html : %.md _layouts/page.html

	pandoc -s -t html \

	--template=_layouts/page \

	--filter=tools/filters/blockquote2div.py \
@@ -35,23 +40,25 @@ motivation.html : motivation.md _layouts/slides.html 
	$(INCLUDES) \

	-o $@ $<



# Pattern to convert R Markdown to Markdown.

%.md: %.Rmd $(R_CHUNK_OPTS)

	Rscript -e "knitr::knit('$$(basename $<)', output = '$$(basename $@)')"



## unittest : Run unit test (for Python 2 and 3)

unittest: tools/check.py tools/validation_helpers.py tools/test_check.py

	cd tools/ && python2 test_check.py

	cd tools/ && python3 test_check.py



# Pattern to convert R Markdown to Markdown.

%.md: %.Rmd $(R_CHUNK_OPTS)

	Rscript -e "knitr::knit('$$(basename $<)', output = '$$(basename $@)')"



## commands : Display available commands.

commands : Makefile

	@sed -n 's/^##//p' $<



## settings : Show variables and settings.

settings :

	@echo 'SRC_PAGES:' $(SRC_PAGES)

	@echo 'DST_PAGES:' $(DST_PAGES)

	@echo 'SRC_RMD:' $(SRC_RMD)

	@echo 'DST_RMD:' $(DST_RMD)

	@echo 'SRC_MD:' $(SRC_MD)

	@echo 'DST_HTML:' $(DST_HTML)



## clean    : Clean up temporary and intermediate files.

clean :
@@ -59,4 +66,4 @@ clean : 


# very-clean : Remove generated HTML.

very-clean :

	@rm -f $(DST_PAGES)
 
	@rm -f $(DST_MD)

tools/chunk-options.R

0 → 100644
+26 −0
Original line number Diff line number Diff line 
# These settings control the behavior of all chunks in the novice R materials.

# For example, to generate the lessons with all the output hidden, simply change

# `results` from "markup" to "hide".

# For more information on available chunk options, see

# http://yihui.name/knitr/options#chunk_options



library("knitr")

opts_chunk$set(tidy = FALSE, results = "markup", comment = NA,

               fig.align = "center")



# The hooks below add html tags to the code chunks and their output so that they

# are properly formatted when the site is built with jekyll.

hook_in <- function(x, options) {

  stringr::str_c("\n\n~~~{.r}\n",

                 paste0(x, collapse="\n"),

                 "\n~~~\n\n")

}



hook_out <- function(x, options) {

  stringr::str_c("\n\n~~~{.output}\n",

                   paste0(x, collapse="\n"),

                 "\n~~~\n\n")

}



knit_hooks$set(source = hook_in, output = hook_out, warning = hook_out,

               error = hook_out, message = hook_out)
 
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