X-Git-Url: https://git.arvados.org/rnaseq-cwl-training.git/blobdiff_plain/c2f89a7a8d78a71070e91ac3a2b6e5a99095e8b3..d454d5916a5271ec645b219fbdf6e925db187b9f:/Makefile

diff --git a/Makefile b/Makefile
index 7116629..a4268d7 100644
--- a/Makefile
+++ b/Makefile
@@ -4,28 +4,50 @@
 # Settings
 MAKEFILES=Makefile $(wildcard *.mk)
 JEKYLL=jekyll
+JEKYLL_VERSION=3.8.5
 PARSER=bin/markdown_ast.rb
 DST=_site
 
+# Check Python 3 is installed and determine if it's called via python3 or python
+# (https://stackoverflow.com/a/4933395)
+ifneq (, $(shell which python3))
+  PYTHON := python3
+else ifneq (, $(shell which python))
+  PYTHON_VERSION_FULL := $(wordlist 2,4,$(subst ., ,$(shell python --version 2>&1)))
+  PYTHON_VERSION_MAJOR := $(word 1,${PYTHON_VERSION_FULL})
+  ifneq (3, ${PYTHON_VERSION_MAJOR})
+    $(error "Your system does not appear to have Python 3 installed.")
+  endif
+  PYTHON := python
+else
+    $(error "Your system does not appear to have any Python installed.")
+endif
+
+
 # Controls
 .PHONY : commands clean files
+.NOTPARALLEL:
 all : commands
 
 ## commands         : show all commands.
 commands :
-	@grep -h -E '^##' ${MAKEFILES} | sed -e 's/## //g'
+	@grep -h -E '^##' ${MAKEFILES} | sed -e "s/## //g"
+
+## 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
 
 ## serve            : run a local server.
-serve : lesson-rmd
-	${JEKYLL} serve --config _config.yml,_config_dev.yml
+serve : lesson-md
+	${JEKYLL} serve
 
 ## site             : build files but do not run a server.
-site : lesson-rmd
-	${JEKYLL} build --config _config.yml,_config_dev.yml
+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 :
@@ -37,7 +59,7 @@ clean :
 	@find . -name '*.pyc' -exec rm {} \;
 
 ## clean-rmd        : clean intermediate R files (that need to be committed to the repo).
-clear-rmd :
+clean-rmd :
 	@rm -rf ${RMD_DST}
 	@rm -rf fig/rmd-*
 
@@ -48,12 +70,12 @@ clear-rmd :
 
 ## workshop-check   : check workshop homepage.
 workshop-check :
-	@bin/workshop_check.py .
+	@${PYTHON} bin/workshop_check.py .
 
 ## ----------------------------------------
 ## Commands specific to lesson websites.
 
-.PHONY : lesson-check lesson-rmd lesson-files lesson-fixme
+.PHONY : lesson-check lesson-md lesson-files lesson-fixme
 
 # RMarkdown files
 RMD_SRC = $(wildcard _episodes_rmd/??-*.Rmd)
@@ -62,11 +84,11 @@ RMD_DST = $(patsubst _episodes_rmd/%.Rmd,_episodes/%.md,$(RMD_SRC))
 # Lesson source files in the order they appear in the navigation menu.
 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.
@@ -74,26 +96,28 @@ 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 $(RMD_SRC)
+## 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 :
-	@bin/lesson_check.py -s . -p ${PARSER}
+lesson-check : lesson-fixme
+	@${PYTHON} 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 ${PARSER} -l -w
+	@${PYTHON} 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
+	@${PYTHON} bin/test_lesson_check.py
 
 ## lesson-files     : show expected names of generated files for debugging.
 lesson-files :