X-Git-Url: https://git.arvados.org/rnaseq-cwl-training.git/blobdiff_plain/19beaaf0c2de344412c9e0410a592013cd1369fe..524847ac58fb07f0e50a6610ab41b130138e2d2f:/Makefile

diff --git a/Makefile b/Makefile
index 7508034..d291abe 100644
--- a/Makefile
+++ b/Makefile
@@ -4,30 +4,36 @@
 # Settings
 MAKEFILES=Makefile $(wildcard *.mk)
 JEKYLL=jekyll
+JEKYLL_VERSION=3.8.5
 PARSER=bin/markdown_ast.rb
 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 : lesson-rmd
-	${JEKYLL} serve --config _config.yml,_config_dev.yml
+## docker-serve     : use docker to build the site
+docker-serve :
+	docker run --rm -it -v ${PWD}:/srv/jekyll -p 127.0.0.1:4000:4000 jekyll/jekyll:${JEKYLL_VERSION} make serve
 
-## site           : build files but do not run a server.
-site : lesson-rmd
-	${JEKYLL} build --config _config.yml,_config_dev.yml
+## serve            : run a local server.
+serve : lesson-md
+	${JEKYLL} serve
 
-## figures        : re-generate inclusion displaying all figures.
-figures :
-	@bin/extract_figures.py -s _episodes -p ${PARSER} > _includes/all_figures.html
+## site             : build files but do not run a server.
+site : lesson-md
+	${JEKYLL} build
 
-## clean          : clean up junk files.
+# repo-check        : check repository settings.
+repo-check :
+	@bin/repo_check.py -s .
+
+## clean            : clean up junk files.
 clean :
 	@rm -rf ${DST}
 	@rm -rf .sass-cache
@@ -35,67 +41,78 @@ clean :
 	@find . -name .DS_Store -exec rm {} \;
 	@find . -name '*~' -exec rm {} \;
 	@find . -name '*.pyc' -exec rm {} \;
+
+## clean-rmd        : clean intermediate R files (that need to be committed to the repo).
+clean-rmd :
 	@rm -rf ${RMD_DST}
-	@rm -rf fig/swc-rmd-*
+	@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-rmd 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 \
+  CODE_OF_CONDUCT.md \
   setup.md \
-  $(wildcard _episodes/*.md) \
+  $(sort $(wildcard _episodes/*.md)) \
   reference.md \
-  $(wildcard _extras/*.md) \
+  $(sort $(wildcard _extras/*.md)) \
   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 \
-  $(patsubst _episodes/%.md,${DST}/%/index.html,$(wildcard _episodes/*.md)) \
+  $(patsubst _episodes/%.md,${DST}/%/index.html,$(sort $(wildcard _episodes/*.md))) \
   ${DST}/reference/index.html \
-  $(patsubst _extras/%.md,${DST}/%/index.html,$(wildcard _extras/*.md)) \
+  $(patsubst _extras/%.md,${DST}/%/index.html,$(sort $(wildcard _extras/*.md))) \
   ${DST}/license/index.html
 
-## lesson-rmd:    : convert Rmarkdown files to markdown
-lesson-rmd: $(RMD_SRC)
-	@bin/knit_lessons.sh
+## lesson-md        : convert Rmarkdown files to markdown
+lesson-md : ${RMD_DST}
+
+_episodes/%.md: _episodes_rmd/%.Rmd
+	@bin/knit_lessons.sh $< $@
+
+## lesson-check     : validate lesson Markdown.
+lesson-check : lesson-fixme
+	@bin/lesson_check.py -s . -p ${PARSER} -r _includes/links.md
 
-## lesson-check   : validate lesson Markdown.
-lesson-check :
-	@bin/lesson_check.py -s . -p ${PARSER}
+## lesson-check-all : validate lesson Markdown, checking line lengths and trailing whitespace.
+lesson-check-all :
+	@bin/lesson_check.py -s . -p ${PARSER} -r _includes/links.md -l -w --permissive
 
+## unittest         : run unit tests on checking tools.
 unittest :
-	python bin/test_lesson_check.py
+	@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 'RMarkdown:' ${RMD_SRC}
-	@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.