X-Git-Url: https://git.arvados.org/rnaseq-cwl-training.git/blobdiff_plain/4c788a5b2f0f1ed76c40c3e017cccbb0a85cdd08..HEAD:/Makefile

diff --git a/Makefile b/Makefile
index 7b1b1b9..09d2d34 100644
--- a/Makefile
+++ b/Makefile
@@ -3,31 +3,67 @@
 
 # Settings
 MAKEFILES=Makefile $(wildcard *.mk)
-JEKYLL=jekyll
+JEKYLL=bundle config --local set path .vendor/bundle && bundle install && bundle update && bundle exec jekyll
 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)
+PYTHON3_EXE := $(shell which python3 2>/dev/null)
+ifneq (, $(PYTHON3_EXE))
+  ifeq (,$(findstring Microsoft/WindowsApps/python3,$(subst \,/,$(PYTHON3_EXE))))
+    PYTHON := python3
+  endif
+endif
+
+ifeq (,$(PYTHON))
+  PYTHON_EXE := $(shell which python 2>/dev/null)
+  ifneq (, $(PYTHON_EXE))
+    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
+endif
+
+
 # Controls
 .PHONY : commands clean files
-all : commands
 
-## commands       : show all commands.
-commands :
-	@grep -h -E '^##' ${MAKEFILES} | sed -e 's/## //g'
+# Default target
+.DEFAULT_GOAL := commands
 
-## serve          : run a local server.
-serve : lesson-rmd
-	${JEKYLL} serve --config _config.yml,_config_dev.yml
+## I. Commands for both workshop and lesson websites
+## =================================================
 
-## site           : build files but do not run a server.
-site : lesson-rmd
-	${JEKYLL} build --config _config.yml,_config_dev.yml
+## * serve            : render website and 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 website but do not run a server
+site : lesson-md
+	${JEKYLL} build
 
-## clean          : clean up junk files.
+## * docker-serve     : use Docker to serve the site
+docker-serve :
+	docker pull carpentries/lesson-docker:latest
+	docker run --rm -it \
+		-v $${PWD}:/home/rstudio \
+		-p 4000:4000 \
+		-p 8787:8787 \
+		-e USERID=$$(id -u) \
+		-e GROUPID=$$(id -g) \
+		carpentries/lesson-docker:latest
+
+## * repo-check       : check repository settings
+repo-check :
+	@${PYTHON} bin/repo_check.py -s .
+
+## * clean            : clean up junk files
 clean :
 	@rm -rf ${DST}
 	@rm -rf .sass-cache
@@ -36,73 +72,92 @@ 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 :
+## * clean-rmd        : clean intermediate R files (that need to be committed to the repo)
+clean-rmd :
 	@rm -rf ${RMD_DST}
 	@rm -rf fig/rmd-*
 
-## ----------------------------------------
-## Commands specific to workshop websites.
+
+##
+## II. Commands specific to workshop websites
+## =================================================
 
 .PHONY : workshop-check
 
-## workshop-check : check workshop homepage.
+## * 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
+##
+## III. Commands specific to lesson websites
+## =================================================
+
+.PHONY : lesson-check lesson-md lesson-files lesson-fixme install-rmd-deps
 
 # RMarkdown files
-RMD_SRC = $(wildcard _episodes_rmd/??-*.Rmd)
+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.
 MARKDOWN_SRC = \
   index.md \
-  CONDUCT.md \
+  CODE_OF_CONDUCT.md \
   setup.md \
-  $(wildcard _episodes/*.md) \
+  $(sort $(wildcard _episodes/*.md)) \
   reference.md \
-  $(wildcard _extras/*.md) \
-  LICENSE.md
+  $(sort $(wildcard _extras/*.md)) \
+  LICENSE.md \
+  CONTRIBUTING.md
 
 # Generated lesson files in the order they appear in the navigation menu.
 HTML_DST = \
   ${DST}/index.html \
   ${DST}/conduct/index.html \
   ${DST}/setup/index.html \
-  $(patsubst _episodes/%.md,${DST}/%/index.html,$(wildcard _episodes/*.md)) \
-  ${DST}/reference/index.html \
-  $(patsubst _extras/%.md,${DST}/%/index.html,$(wildcard _extras/*.md)) \
+  $(patsubst _episodes/%.md,${DST}/%/index.html,$(sort $(wildcard _episodes/*.md))) \
+  ${DST}/reference.html \
+  $(patsubst _extras/%.md,${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 $(RMD_SRC)
+## * install-rmd-deps : Install R packages dependencies to build the RMarkdown lesson
+install-rmd-deps:
+	@${SHELL} bin/install_r_deps.sh
+
+## * lesson-md        : convert Rmarkdown files to markdown
+lesson-md : ${RMD_DST}
+
+_episodes/%.md: _episodes_rmd/%.Rmd install-rmd-deps
+	@mkdir -p _episodes
+	@bin/knit_lessons.sh $< $@
 
-## lesson-check   : validate lesson Markdown.
-lesson-check :
-	@bin/lesson_check.py -s . -p ${PARSER}
+## * lesson-check     : validate lesson Markdown
+lesson-check : lesson-fixme
+	@${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 :
+	@${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     : show expected names of generated files for debugging
 lesson-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 ${MARKDOWN_SRC} || true
+	@grep --fixed-strings --word-regexp --line-number --no-messages FIXME ${MARKDOWN_SRC} || true
 
-#-------------------------------------------------------------------------------
-# Include extra commands if available.
-#-------------------------------------------------------------------------------
+##
+## IV. Auxililary (plumbing) commands
+## =================================================
 
--include commands.mk
+## * commands         : show all commands.
+commands :
+	@sed -n -e '/^##/s|^##[[:space:]]*||p' $(MAKEFILE_LIST)