Makefile

# Settings
JEKYLL=jekyll
PORT?=4000
HOST?=localhost
FLAGS?=""
CHROME=google-chrome-stable
TUTORIALS=$(shell find _site/training-material -name 'tutorial.html' | sed 's/_site\/training-material\///')
SLIDES=$(shell find _site/training-material -name 'slides.html' | sed 's/_site\/training-material\///')
SLIDES+=$(shell find _site/training-material/*/*/slides/* | sed 's/_site\/training-material\///')
SITE_URL=http://${HOST}:${PORT}/training-material
PDF_DIR=_pdf
REPO=$(shell echo "$${ORIGIN_REPO:-galaxyproject/training-material}")
BRANCH=$(shell echo "$${ORIGIN_BRANCH:-master}")
MINICONDA_URL=https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh
SHELL=bash
RUBY_VERSION=2.4.4
CONDA_ENV=galaxy_training_material

ifeq ($(shell uname -s),Darwin)
	CHROME=/Applications/Google\ Chrome.app/Contents/MacOS/Google\ Chrome
	MINICONDA_URL=https://repo.continuum.io/miniconda/Miniconda3-latest-MacOSX-x86_64.sh
endif

CONDA=$(shell which conda)
ifeq ($(CONDA),)
	CONDA=${HOME}/miniconda3/bin/conda
endif

default: help

install-conda: ## install Miniconda
	curl $(MINICONDA_URL) -o miniconda.sh
	bash miniconda.sh -b
.PHONY: install-conda

create-env: ## create conda environment
	if ${CONDA} env list | grep '^${CONDA_ENV}'; then \
	    ${CONDA} env update -f environment.yml; \
	else \
	    ${CONDA} env create -f environment.yml; \
	fi
.PHONY: create-env

ACTIVATE_ENV = source $(shell dirname $(dir $(CONDA)))/bin/activate $(CONDA_ENV)

install: clean ## install dependencies
	$(ACTIVATE_ENV) && \
		npm install decktape && \
		gem update --system && \
		gem install nokogiri:'1.10.0' -- --use-system-libraries --with-xml=$(CONDA_PREFIX)/lib && \
		gem install addressable:'2.5.2' jekyll jekyll-feed jekyll-environment-variables jekyll-github-metadata jekyll-scholar csl-styles awesome_bot html-proofer pkg-config
.PHONY: install

serve: ## run a local server (You can specify PORT=, HOST=, and FLAGS= to set the port, host or to pass additional flags)
	$(ACTIVATE_ENV) && \
		${JEKYLL} serve --strict_front_matter -d _site/training-material -P ${PORT} -H ${HOST} ${FLAGS}
.PHONY: serve

detached-serve: ## run a local server in detached mode (You can specify PORT=, HOST=, and FLAGS= to set the port, host or to pass additional flags to Jekyll)
	$(ACTIVATE_ENV) && \
		${JEKYLL} serve --strict_front_matter --detach -d _site/training-material -P ${PORT} -H ${HOST} ${FLAGS}
.PHONY: detached-serve

build: clean ## build files but do not run a server (You can specify FLAGS= to pass additional flags to Jekyll)
	$(ACTIVATE_ENV) && \
		${JEKYLL} build --strict_front_matter -d _site/training-material ${FLAGS}
.PHONY: build

check-frontmatter: build ## Validate the frontmatter
	$(ACTIVATE_ENV) && \
		find topics/ -name tutorial.md -or -name slides.html -or -name metadata.yaml | \
	    xargs -n1 ruby bin/validate-frontmatter.rb
.PHONY: check-frontmatter

check-html: build ## validate HTML
	$(ACTIVATE_ENV) && \
	  	htmlproofer \
	      	--assume-extension \
	      	--http-status-ignore 405,503,999 \
	      	--url-ignore "/.*localhost.*/","/.*vimeo\.com.*/","/.*gitter\.im.*/","/.*drmaa\.org.*/" \
	      	--url-swap "github.com/galaxyproject/training-material/tree/master:github.com/${REPO}/tree/${BRANCH}" \
	      	--file-ignore "/.*\/files\/.*/","/.*\/node_modules\/.*/" \
	      	--allow-hash-href \
	      	./_site
.PHONY: check-html

check-workflows: build ## validate Workflows
	$(ACTIVATE_ENV) && \
		bash bin/validate-json.sh
.PHONY: check-workflows

check-html-internal: build ## validate HTML (internal links only)
	$(ACTIVATE_ENV) && \
		htmlproofer \
	      	--assume-extension \
	      	--http-status-ignore 405,503,999 \
	      	--url-ignore "/.*localhost.*/","/.*vimeo\.com.*/","/.*gitter\.im.*/","/.*drmaa\.org.*/" \
	      	--url-swap "github.com/galaxyproject/training-material/tree/master:github.com/${REPO}/tree/${BRANCH}" \
	      	--file-ignore "/.*\/files\/.*/","/.*\/node_modules\/.*/" \
	      	--disable-external \
	      	--allow-hash-href \
	      	./_site
.PHONY: check-html-internal

check-slides: build  ## check the markdown-formatted links in slides
	$(ACTIVATE_ENV) && \
		find _site -path "**/slides*.html" \
	      	| xargs -L 1 -I '{}' sh -c "awesome_bot \
				--allow 405 \
				--allow-redirect \
				--white-list localhost,127.0.0.1,fqdn,vimeo.com,drmaa.com \
				--allow-ssl \
				--allow-dupe \
				--skip-save-results \
				-f {}"
.PHONY: check-slides

check-yaml: ## lint yaml files
	$(ACTIVATE_ENV) && \
		find . -name "*.yaml" | xargs -L 1 -I '{}' sh -c "yamllint {}" \
		find topics -name '*.yml' | xargs -L 1 -I '{}' sh -c "yamllint {}"
.PHONY: check-yaml

check: check-yaml check-frontmatter check-html-internal check-html check-slides check-workflows ## run all checks
.PHONY: check

check-links-gh-pages:  ## validate HTML on gh-pages branch (for daily cron job)
	$(ACTIVATE_ENV) && \
	  	htmlproofer \
			--assume-extension \
			--http-status-ignore 405,503,999 \
			--url-ignore "/.*localhost.*/","/.*vimeo\.com.*/","/.*gitter\.im.*/","/.*drmaa\.org.*/" \
			--file-ignore "/.*\/files\/.*/" \
			--allow-hash-href \
			. && \
		find . -path "**/slides*.html" \
			| xargs -L 1 -I '{}' sh -c "awesome_bot \
				--allow 405 \
				--allow-redirect \
				--white-list localhost,127.0.0.1,fqdn,vimeo.com,drmaa.com \
				--allow-ssl \
				--allow-dupe \
				--skip-save-results \
				-f {}"
.PHONY: check-links-gh-pages


pdf: detached-serve ## generate the PDF of the tutorials and slides
	mkdir -p _pdf
	@for t in $(TUTORIALS); do \
		name="$(PDF_DIR)/$$(echo $$t | tr '/' '-' | sed -e 's/html/pdf/' -e 's/topics-//' -e 's/tutorials-//')"; \
		${CHROME} \
            --headless \
            --disable-gpu \
            --print-to-pdf="$$name" \
            "$(SITE_URL)/$$t?with-answers" \
            2> /dev/null ; \
	done
	@for s in $(SLIDES); do \
		name="$(PDF_DIR)/$$(echo $$s | tr '/' '-' | sed -e 's/html/pdf/' -e 's/topics-//' -e 's/tutorials-//')"; \
		$(ACTIVATE_ENV) ; \
		echo $$name; \
		echo "$(SITE_URL)/$$s"; \
		echo `which npm`; \
		`npm bin`/decktape \
			automatic \
			"$(SITE_URL)/$$s" \
			"$$name" ; \
	done
	pkill -f jekyll
.PHONY: pdf

annotate: ## annotate the tutorials with usable Galaxy instances and generate badges
	python bin/add_galaxy_instance_annotations.py
	python bin/add_galaxy_instance_badges.py
.PHONY: annotate

clean: ## clean up junk files
	@rm -rf _site
	@rm -rf .sass-cache
	@rm -rf .bundle
	@rm -rf vendor
	@rm -rf node_modules
	@find . -name .DS_Store -exec rm {} \;
	@find . -name '*~' -exec rm {} \;
.PHONY: clean

help:
	@grep -E '^[a-zA-Z_-]+:.*?## .*$$' $(MAKEFILE_LIST) | sort | awk 'BEGIN {FS = ":.*?## "}; {printf "\033[36m%-30s\033[0m %s\n", $$1, $$2}'
.PHONY: help