add tools to deal with episodes written in Rmd

	@grep -h -E '^##' ${MAKEFILES} | sed -e 's/## //g'

## serve          : run a local server.

serve :

serve : lesson-rmd

	${JEKYLL} serve --config _config.yml,_config_dev.yml

## site           : build files but do not run a server.

site :

site : lesson-rmd

	${JEKYLL} build --config _config.yml,_config_dev.yml

## figures        : re-generate inclusion displaying all figures.

	@find . -name .DS_Store -exec rm {} \;

	@find . -name '*~' -exec rm {} \;

	@find . -name '*.pyc' -exec rm {} \;

	@rm -rf ${RMD_DST}

	@rm -rf fig/swc-rmd-*

## ----------------------------------------

## Commands specific to workshop websites.

## ----------------------------------------

## Commands specific to lesson websites.

.PHONY : lesson-check lesson-files lesson-fixme lesson-single

.PHONY : lesson-check lesson-rmd lesson-files lesson-fixme lesson-single

# RMarkdown files

RMD_SRC = $(wildcard _episodes_rmd/??-*.Rmd)

RMD_DST = $(patsubst _episodes_rmd/%.Rmd,_episodes/%.md,$(RMD_SRC))

# Lesson source files in the order they appear in the navigation menu.

SRC_FILES = \

  $(patsubst _extras/%.md,${DST}/%/index.html,$(wildcard _extras/*.md)) \

  ${DST}/license/index.html

## lesson-rmd:    : convert Rmarkdown files to markdown

lesson-rmd: $(RMD_SRC)

	@bin/knit_lessons.sh

## lesson-check   : validate lesson Markdown.

lesson-check :

	@bin/lesson_check.py -s . -p ${PARSER}

## lesson-files   : show expected names of generated files for debugging.

lesson-files :

	@echo 'RMarkdown:' ${RMD_SRC}

	@echo 'source:' ${SRC_FILES}

	@echo 'generated:' ${HTML_FILES}

# 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")

fix_fig_path <- function(pth) file.path("..", pth)

## We use the swc-rmd- prefix for the figures generated by the lssons

## so they can be easily identified and deleted by `make clean`.  The

## working directory when the lessons are generated is the root so the

## figures need to be saved in fig/, but when the site is generated,

## the episodes will be one level down. We fix the path using the

## `fig.process` option.

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

               fig.align = "center", fig.path = "fig/swc-rmd-",

               fig.process = fix_fig_path)

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

# are properly formatted when the site is built.

hook_in <- function(x, options) {

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

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

                 "\n~~~\n{: .source}\n\n")

}

hook_out <- function(x, options) {

  stringr::str_c("\n\n~~~\n",

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

                 "\n~~~\n{: .output}\n\n")

}

hook_error <- function(x, options) {

  stringr::str_c("\n\n~~~\n",

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

                 "\n~~~\n{: .error}\n\n")

}

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

               error = hook_error, message = hook_out)

if (require("knitr")) {

    if (packageVersion("knitr") < '1.9.19') {

        stop("knitr must be version 1.9.20 or higher")

    }

} else stop("knitr 1.9.20 or above is needed to build the lessons.")

if (!require("stringr"))

    stop("The package stringr is required for generating the lessons.")

src_rmd <- list.files(pattern = "??-*.Rmd$", path = "_episodes_rmd", full.names = TRUE)

dest_md <- file.path("_episodes", gsub("Rmd$", "md", basename(src_rmd)))

for (i in seq_along(src_rmd)) {

    knitr::knit(src_rmd[i], output = dest_md[i])

}

#!/usr/bin/env bash

if [ -d "_episodes_rmd" ] ; then

    Rscript -e "source('bin/generate_md_episodes.R')"

fi