X-Git-Url: https://git.arvados.org/rnaseq-cwl-training.git/blobdiff_plain/600e4a3f3cc4532b83601fc8fbf022dbed419af8..220eedc6ff3dedb08901e65e88c0d190e8f86f20:/Makefile

diff --git a/Makefile b/Makefile
index 154203a..b5dfe2f 100644
--- a/Makefile
+++ b/Makefile
@@ -9,25 +9,26 @@ DST=_site
 
 # Controls
 .PHONY : commands clean files
+.NOTPARALLEL:
 all : commands
 
-## commands       : show all commands.
+## commands         : show all commands.
 commands :
 	@grep -h -E '^##' ${MAKEFILES} | sed -e 's/## //g'
 
-## serve          : run a local server.
-serve :
-	${JEKYLL} serve --config _config.yml,_config_dev.yml
+## serve            : run a local server.
+serve : lesson-md
+	${JEKYLL} serve
 
-## site           : build files but do not run a server.
-site :
-	${JEKYLL} build --config _config.yml,_config_dev.yml
+## site             : build files but do not run a server.
+site : lesson-md
+	${JEKYLL} build
 
-## figures        : re-generate inclusion displaying all figures.
-figures :
-	@bin/extract_figures.py -s _episodes -p ${PARSER} > _includes/all_figures.html
+# repo-check        : check repository settings.
+repo-check :
+	@bin/repo_check.py -s .
 
-## clean          : clean up junk files.
+## clean            : clean up junk files.
 clean :
 	@rm -rf ${DST}
 	@rm -rf .sass-cache
@@ -36,22 +37,31 @@ clean :
 	@find . -name '*~' -exec rm {} \;
 	@find . -name '*.pyc' -exec rm {} \;
 
+## clean-rmd        : clean intermediate R files (that need to be committed to the repo).
+clear-rmd :
+	@rm -rf ${RMD_DST}
+	@rm -rf fig/rmd-*
+
 ## ----------------------------------------
 ## Commands specific to workshop websites.
 
 .PHONY : workshop-check
 
-## workshop-check : check workshop homepage.
+## workshop-check   : check workshop homepage.
 workshop-check :
 	@bin/workshop_check.py .
 
 ## ----------------------------------------
 ## Commands specific to lesson websites.
 
-.PHONY : lesson-check lesson-files lesson-fixme lesson-single
+.PHONY : lesson-check lesson-md 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 = \
+MARKDOWN_SRC = \
   index.md \
   CONDUCT.md \
   setup.md \
@@ -61,7 +71,7 @@ SRC_FILES = \
   LICENSE.md
 
 # Generated lesson files in the order they appear in the navigation menu.
-HTML_FILES = \
+HTML_DST = \
   ${DST}/index.html \
   ${DST}/conduct/index.html \
   ${DST}/setup/index.html \
@@ -70,21 +80,39 @@ HTML_FILES = \
   $(patsubst _extras/%.md,${DST}/%/index.html,$(wildcard _extras/*.md)) \
   ${DST}/license/index.html
 
-## lesson-check   : validate lesson Markdown.
+## lesson-md        : convert Rmarkdown files to markdown
+lesson-md : ${RMD_DST}
+
+# Use of .NOTPARALLEL makes rule execute only once
+${RMD_DST} : ${RMD_SRC}
+	@bin/knit_lessons.sh ${RMD_SRC}
+
+## lesson-check     : validate lesson Markdown.
 lesson-check :
-	@bin/lesson_check.py -s . -p ${PARSER}
+	@bin/lesson_check.py -s . -p ${PARSER} -r _includes/links.md
+
+## lesson-check-all : validate lesson Markdown, checking line lengths and trailing whitespace.
+lesson-check-all :
+	@bin/lesson_check.py -s . -p ${PARSER} -l -w
+
+## lesson-figures   : re-generate inclusion displaying all figures.
+lesson-figures :
+	@bin/extract_figures.py -p ${PARSER} ${MARKDOWN_SRC} > _includes/all_figures.html
 
+## unittest         : run unit tests on checking tools.
 unittest :
 	python bin/test_lesson_check.py
 
-## lesson-files   : show expected names of generated files for debugging.
+## lesson-files     : show expected names of generated files for debugging.
 lesson-files :
-	@echo 'source:' ${SRC_FILES}
-	@echo 'generated:' ${HTML_FILES}
+	@echo 'RMD_SRC:' ${RMD_SRC}
+	@echo 'RMD_DST:' ${RMD_DST}
+	@echo 'MARKDOWN_SRC:' ${MARKDOWN_SRC}
+	@echo 'HTML_DST:' ${HTML_DST}
 
-## lesson-fixme   : show FIXME markers embedded in source files.
+## lesson-fixme     : show FIXME markers embedded in source files.
 lesson-fixme :
-	@fgrep -i -n FIXME ${SRC_FILES} || true
+	@fgrep -i -n FIXME ${MARKDOWN_SRC} || true
 
 #-------------------------------------------------------------------------------
 # Include extra commands if available.