Handling .Rmd files.

Author: gvwilson

.config.yml

@@ -4,7 +4,7 @@
 collections:
   en:
     output: true
-    permalink: /:collection/:title/
+    permalink: /:collection/:title.html
 
 # Specify the use of the "lesson" template for elements of the "en" collection.
 defaults:
@@ -42,5 +42,7 @@ exclude:
 - misc
 - node_modules
 - requirements.txt
+- site.mk
+- site.yml
 - src
 - tex

Makefile

@@ -7,6 +7,9 @@ endif
 # Pick up project-specific setting for STEM.
 include site.mk
 
+# Overall configuration file.
+CONFIG_YML=_config.yml
+
 # Tools.
 JEKYLL=jekyll
 PANDOC=pandoc
@@ -15,13 +18,15 @@ BIBTEX=bibtex
 PYTHON=python
 
 # Language-dependent settings.
-CONFIG_YML=_config.yml
 DIR_MD=_${lang}
+DIR_RMD=${lang}_rmd
+RMD_SRC=$(wildcard ${DIR_RMD}/*.Rmd)
+RMD_DST=$(patsubst ${DIR_RMD}/%.Rmd,${DIR_MD}/%.md,${RMD_SRC})
 PAGES_MD=$(wildcard ${DIR_MD}/*.md)
 BIB_MD=${DIR_MD}/bib.md
 TOC_JSON=_data/${lang}_toc.json
 DIR_HTML=_site/${lang}
-PAGES_HTML=${DIR_HTML}/index.html $(patsubst ${DIR_MD}/%.md,${DIR_HTML}/%/index.html,$(filter-out ${DIR_MD}/index.md,${PAGES_MD}))
+PAGES_HTML=$(patsubst ${DIR_MD}/%.md,${DIR_HTML}/%.html,${PAGES_MD})
 DIR_TEX=tex/${lang}
 BIB_TEX=${DIR_TEX}/book.bib
 ALL_TEX=${DIR_TEX}/all.tex
@@ -54,6 +59,9 @@ config : ${CONFIG_YML}
 ## toc            : regenerate the table of contents JSON file.
 toc : ${TOC_JSON}
 
+## rmarkdown      : rebuild Markdown source from R Markdown.
+rmarkdown : ${RMD_DST}
+
 # ----------------------------------------
 
 # Regenerate PDF once 'all.tex' has been created.
@@ -83,6 +91,10 @@ test-pandoc:
 	| ${PYTHON} bin/transform.py --pre ${lang} _includes \
 	| ${PANDOC} --wrap=preserve -f html -t latex -o -
 
+# Build Markdown from R Markdown.
+${DIR_MD}/%.md : ${DIR_RMD}/%.Rmd
+	@bin/build.R $< $@
+
 # Create all the HTML pages once the Markdown files are up to date.
 ${PAGES_HTML} : ${PAGES_MD} ${BIB_MD} ${CONFIG_YML} ${TOC_JSON}
 	${JEKYLL} build
@@ -188,14 +200,17 @@ clean :
 	@find . -name '*~' -delete
 	@find . -name __pycache__ -prune -exec rm -r "{}" \;
 	@find . -name '_minted-*' -prune -exec rm -r "{}" \;
-	@rm -r -f tex/*/all.tex tex/*/*.aux tex/*/*.bbl tex/*/*.blg tex/*/*.log tex/*/*.out tex/*/*.toc
+	@rm -f tex/*/all.tex tex/*/*.{aux,bbl,blg,lof,log,lot,out,toc}
 	@find . -name .DS_Store -prune -exec rm -r "{}" \;
+	@touch ${RMD_SRC} # to ensure rebuild the next time
 
 ## settings       : show macro values.
 settings :
 	@echo "CONFIG_YML=${CONFIG_YML}"
 	@echo "JEKYLL=${JEKYLL}"
 	@echo "DIR_MD=${DIR_MD}"
+	@echo "RMD_SRC=${RMD_SRC}"
+	@echo "RMD_DST=${RMD_DST}"
 	@echo "PAGES_MD=${PAGES_MD}"
 	@echo "BIB_MD=${BIB_MD}"
 	@echo "DIR_HTML=${DIR_HTML}"

_includes/toc-bib.html

@@ -4,6 +4,6 @@
 
 <p>
   {% if page.slug == "bib" %}<strong>{% endif %}
-    <a href="{{'/'|append: include.language|append: '/bib/'|relative_url}}" class="toc">Bibliography</a>
+    <a href="{{'/'|append: include.language|append: '/bib.html'|relative_url}}" class="toc">Bibliography</a>
   {% if page.slug == "bib" %}</strong>{% endif %}
 </p>

_includes/toc-section.html

@@ -16,7 +16,7 @@
       {% comment %}If there's a match, add a link to the generated ToC.{% endcomment %}
       {%- if lesson == chap.slug -%}
         <li>{% if page.slug == chap.slug %}<strong>{% endif %}
-          <a href="{{'/'|append: include.language|append: '/'|append: chap.slug|append: '/'|relative_url}}" class="toc">
+          <a href="{{'/'|append: include.language|append: '/'|append: chap.slug|append: '.html'|relative_url}}" class="toc">
             {% if chap.undone %}<em>{% endif %}{{chap.title}}{% if chap.undone %} &#9734;</em>{% endif %}
           </a>
           {% if page.slug == chap.slug %}</strong>{% endif %}

bin/build.R

@@ -0,0 +1,16 @@
+#!/usr/bin/env Rscript
+
+library(stringr)
+library(purrr)
+library(knitr)
+
+USAGE = "Knit an RMarkdown files to create a Markdown file.
+
+Usage: build.R source dest"
+
+args <- commandArgs(trailingOnly = TRUE)
+if (((length(args) == 1) && (args[1] %in% c("-h", "--help"))) || (length(args) != 2)) {
+  message(USAGE)
+  quit(status = 0)
+}
+knit(args[1], output = args[2])

bin/get_body.py

@@ -35,7 +35,7 @@ def get_all(source_dir):
 def make_filenames(source_dir, slugs):
     '''Turn slugs into filenames.'''
 
-    return [os.path.join(source_dir, s, 'index.html') for s in slugs]
+    return [os.path.join(source_dir, '{}.html'.format(s)) for s in slugs]
 
 
 #-------------------------------------------------------------------------------

bin/transform.py

@@ -9,7 +9,8 @@
 import re
 from util import CHARACTERS, usage, get_crossref, get_toc
 
-PATH_TO_ROOT = '../../' # from TeX directory to root of project
+PATH_TO_ROOT = '../..' # from TeX directory to root of project
+PATH_FOR_RMD = '../'   # extra prefix for files generated from .Rmd
 
 #-------------------------------------------------------------------------------
 
@@ -313,6 +314,22 @@ class Figure(BaseRegexp):
 \end{{figure}}'''.replace('PATH_TO_ROOT', PATH_TO_ROOT)
 
 
+class FigureRmd(BaseRegexp):
+    '''
+    <p><img src="../figures/filename" alt="some text" /></p> # generated by knitr
+    =>
+    LaTeX: \begin{figure}\label{f:LABEL}\centering\includegraphics{PATH}\caption{TEXT}\end{figure}
+    '''
+    MATCH_HTML = r'<p><img\s+src="([^"]+)"\s+alt="(.+?)"\s+/></p>'
+    WRITE_TEMP = r'==figurermd=={0}=={1}=='
+    MATCH_TEMP = r'==figurermd==(.+)==(.+)=='
+    WRITE_LATEX = r'''\begin{{figure}}
+\centering
+\includegraphics{{PATH_FOR_RMD/{0}}}
+\caption{{{1}}}
+\end{{figure}}'''.replace('PATH_FOR_RMD', PATH_FOR_RMD)
+
+
 class FigureRef(BaseRegexp):
     '''
     References to figures.
@@ -438,6 +455,7 @@ class Newline(BaseStringMatch):
     GlossaryEntry,
     CrossRef,
     Figure,
+    FigureRmd,
     FigureRef,
     Table,
     TableRef,