X-Git-Url: https://git.arvados.org/rnaseq-cwl-training.git/blobdiff_plain/9c447b8e6ca87637b4ada4a6361c56d06cd8f0f8..0c9c1533a0956617f7c14b8adced2057d70169bc:/Makefile

diff --git a/Makefile b/Makefile
index b645947..ddc68bd 100644
--- a/Makefile
+++ b/Makefile
@@ -4,6 +4,7 @@
 # Settings
 MAKEFILES=Makefile $(wildcard *.mk)
 JEKYLL=jekyll
+PARSER=bin/markdown_ast.rb
 DST=_site
 
 # Controls
@@ -15,16 +16,16 @@ commands :
 	@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.
 figures :
-	@bin/extract_figures.py -s _episodes -p bin/markdown-ast.rb > _includes/all_figures.html
+	@bin/extract_figures.py -s _episodes -p ${PARSER} > _includes/all_figures.html
 
 ## clean          : clean up junk files.
 clean :
@@ -34,6 +35,8 @@ clean :
 	@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.
@@ -47,7 +50,11 @@ workshop-check :
 ## ----------------------------------------
 ## Commands specific to lesson websites.
 
-.PHONY : lesson-check lesson-files lesson-fixme lesson-single
+.PHONY : lesson-check lesson-rmd lesson-files lesson-fixme
+
+# 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 = \
@@ -69,15 +76,20 @@ HTML_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 bin/markdown-ast.rb
+	@bin/lesson_check.py -s . -p ${PARSER}
 
 unittest :
 	python bin/test_lesson_check.py
 
 ## lesson-files   : show expected names of generated files for debugging.
 lesson-files :
+	@echo 'RMarkdown:' ${RMD_SRC}
 	@echo 'source:' ${SRC_FILES}
 	@echo 'generated:' ${HTML_FILES}