forked from galaxyproject/training-material
-
Notifications
You must be signed in to change notification settings - Fork 0
/
Makefile
258 lines (217 loc) · 9.38 KB
/
Makefile
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
# Settings
UNAME := $(shell uname)
JEKYLL=jekyll
PORT?=4000
HOST?=0.0.0.0
FLAGS?=""
ENV?="development"
CHROME=google-chrome-stable
PDF_HOST?=127.0.0.1
SITE_URL=http://${PDF_HOST}:${PORT}/training-material
PDF_DIR=_pdf
REPO=$(shell echo "$${ORIGIN_REPO:-galaxyproject/training-material}")
BRANCH=$(shell echo "$${ORIGIN_BRANCH:-main}")
MINICONDA_URL=https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
SHELL=bash
RUBY_VERSION=2.4.4
CONDA_ENV=galaxy_training_material
ifeq ($(shell uname -s),Darwin)
CHROME=/Applications/Google\ Chrome.app/Contents/MacOS/Google\ Chrome
MINICONDA_URL=https://repo.anaconda.com/miniconda/Miniconda3-latest-MacOSX-x86_64.sh
endif
ifeq ($(UNAME),Darwin)
ENV_FILE=environment-osx.yml
else
ENV_FILE=environment.yml
endif
CONDA=$(shell which conda)
ifeq ($(CONDA),)
CONDA=${HOME}/miniconda3/bin/conda
endif
default: help
install-conda: ## install Miniconda
curl -L $(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 ${ENV_FILE}; \
else \
${CONDA} env create -f ${ENV_FILE}; \
fi
.PHONY: create-env
ACTIVATE_ENV = source $(shell dirname $(dir $(CONDA)))/bin/activate $(CONDA_ENV)
COND_ENV_DIR=$(shell dirname $(dir $(CONDA)))
install: clean create-env ## install dependencies
$(ACTIVATE_ENV) && \
gem update --no-document --system && \
ICONV_LIBS="-L${CONDA_PREFIX}/lib/ -liconv" gem install --no-document addressable:'2.5.2' jekyll jekyll-feed jekyll-redirect-from csl-styles awesome_bot html-proofer pkg-config kwalify bibtex-ruby citeproc-ruby fastimage && \
pushd ${COND_ENV_DIR}/envs/${CONDA_ENV}/share/rubygems/bin && \
ln -sf ../../../bin/ruby ruby
.PHONY: install
bundle-install: clean ## install gems if Ruby is already present (e.g. on gitpod.io)
bundle install
.PHONE: bundle-install
serve: api/swagger.json ## run a local server (You can specify PORT=, HOST=, and FLAGS= to set the port, host or to pass additional flags)
@echo "Tip: Want faster builds? Use 'serve-quick' in place of 'serve'."
@echo "Tip: to serve in incremental mode (faster rebuilds), use the command: make serve FLAGS=--incremental" && echo "" && \
$(ACTIVATE_ENV) && \
mv Gemfile Gemfile.backup || true && \
mv Gemfile.lock Gemfile.lock.backup || true && \
${JEKYLL} serve --trace --strict_front_matter -d _site/training-material -P ${PORT} -H ${HOST} ${FLAGS}
.PHONY: serve
serve-quick: api/swagger.json ## run a local server (faster, some plugins disabled for speed)
@echo "This will build the website with citations and other content disabled, and incremental on by default. To run the full preview (slower), use make serve" && echo "" && \
$(ACTIVATE_ENV) && \
mv Gemfile Gemfile.backup || true && \
mv Gemfile.lock Gemfile.lock.backup || true && \
${JEKYLL} serve --strict_front_matter -d _site/training-material --incremental --config _config.yml,_config-dev.yml -P ${PORT} -H ${HOST} ${FLAGS}
.PHONY: serve-quick
serve-gitpod: bundle-install ## run a server on a gitpod.io environment
bundle exec jekyll serve --config _config.yml --incremental
.PHONY: serve-gitpod
build-gitpod: bundle-install ## run a build on a gitpod.io environment
bundle exec jekyll build --config _config.yml
.PHONY: build-gitpod
build: clean api/swagger.json ## build files but do not run a server (You can specify FLAGS= to pass additional flags to Jekyll)
$(ACTIVATE_ENV) && \
mv Gemfile Gemfile.backup || true && \
mv Gemfile.lock Gemfile.lock.backup || true && \
JEKYLL_ENV=${ENV} ${JEKYLL} build --strict_front_matter -d _site/training-material ${FLAGS}
.PHONY: build
check-frontmatter: ## Validate the frontmatter
$(ACTIVATE_ENV) && \
bundle exec ruby bin/validate-frontmatter.rb
.PHONY: check-frontmatter
check-contributors: ## Validate the contributors.yaml file
$(ACTIVATE_ENV) && \
bundle exec ruby bin/validate-contributors.rb
.PHONY: check-contributors
_check-html: # Internal
$(ACTIVATE_ENV) && \
htmlproofer \
--assume-extension \
--http-status-ignore 405,503,999 \
--url-ignore "/.*localhost.*/","/.*vimeo\.com.*/","/.*gitter\.im.*/","/.*drmaa\.org.*/" \
--url-swap "github.com/galaxyproject/training-material/tree/main:github.com/${REPO}/tree/${BRANCH}" \
--file-ignore "/.*\/files\/.*/","/.*\/node_modules\/.*/","/\/tutorials\/.*\/docker\//" \
--allow-hash-href \
./_site
.PHONY: _check-html
check-html: build ## validate HTML
$(MAKE) _check-html
.PHONY: check-html
_check-html-internal: # Internal
$(ACTIVATE_ENV) && \
htmlproofer \
--assume-extension \
--http-status-ignore 405,503,999 \
--url-ignore "/.*localhost.*/","/.*vimeo\.com.*/","/.*gitter\.im.*/","/.*drmaa\.org.*/","/.*slides.html#/","/#embedded_jbrowse/","/.*videos.*.mp4.png/" \
--url-swap "github.com/galaxyproject/training-material/tree/main:github.com/${REPO}/tree/${BRANCH}" \
--file-ignore "/.*\/files\/.*/","/.*\/node_modules\/.*/","/\/tutorials\/.*\/docker\//" \
--disable-external \
--allow-hash-href \
./_site
.PHONY: _check-html-internal
check-html-internal: build ## validate HTML (internal links only)
$(MAKE) _check-html-internal
.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-diffs: ## lint diffs in tutorials
find ./topics/admin/ -name '*.md' -type f -print0 | xargs -n 1 -0 python3 bin/lint-diffs.py
.PHONY: check-diffs
check-yaml: ## lint yaml files
find . -name '*.yaml' | grep -v .github | xargs -L 1 -I '{}' sh -c "yamllint -c .yamllint {}"
.PHONY: check-yaml
check-framework:
$(ACTIVATE_ENV) && \
ruby _plugins/jekyll-notranslate.rb
.PHONY: check-framework
check-broken-boxes: build ## List tutorials containing broken boxes
./bin/check-broken-boxes
.PHONY: check-broken-boxes
check: check-html-internal check-html check-broken-boxes check-slides ## run checks which require compiled HTML
.PHONY: check
lint: check-frontmatter check-contributors ## run linting checks which do not require a built site
.PHONY: lint
check-links-gh-pages: ## validate HTML on gh-pages branch (for daily cron job)
$(ACTIVATE_ENV) && \
htmlproofer \
--assume-extension \
--http-status-ignore 405,503,999 \
--url-ignore "/.*localhost.*/","/.*vimeo\.com.*/","/.*gitter\.im.*/","/.*drmaa\.org.*/" \
--file-ignore "/.*\/files\/.*/","/\/tutorials\/.*\/docker\//" \
--allow-hash-href \
. && \
find . -path "**/slides*.html" \
| xargs -L 1 -I '{}' sh -c "awesome_bot \
--allow 405 \
--allow-redirect \
--white-list localhost,127.0.0.1,fqdn,vimeo.com,drmaa.com \
--allow-ssl \
--allow-dupe \
--skip-save-results \
-f {}"
.PHONY: check-links-gh-pages
TUTORIAL_PDFS=$(shell find _site/training-material -name 'tutorial.html' | sed 's/html$$/pdf/g')
SLIDE_PDFS=$(shell find _site/training-material -name 'slides.html' | sed 's/html$$/pdf/g')
SLIDE_PDFS+=$(shell find _site/training-material/*/*/slides/* | sed 's/html$$/pdf/g')
pdf: $(SLIDE_PDFS) $(TUTORIAL_PDFS) ## generate the PDF of the tutorials and slides
.PHONY: pdf
_site/%/tutorial.pdf: _site/%/tutorial.html
if ! grep 'http-equiv="refresh"' $< --quiet; then \
$(ACTIVATE_ENV) && \
sed "s|/training-material/|$(shell pwd)/_site/training-material/|g" $< | \
sed "s|<head>|<head><base href=\"file://$(shell pwd)/$(<:_site/training/material%=%)\">|" | \
wkhtmltopdf \
--enable-javascript --javascript-delay 1000 \
- $@; \
fi
_site/%/slides.pdf: _site/%/slides.html
$(ACTIVATE_ENV) && \
$(shell npm bin)/http-server _site -p 9876 & \
docker run --rm --network host -v $(shell pwd):/slides astefanutti/decktape automatic -s 1920x1080 http://127.0.0.1:9876/$(<:_site/%=%) /slides/$@
_site/%/slides_ES.pdf: _site/%/slides_ES.html
$(ACTIVATE_ENV) && \
$(shell npm bin)/http-server _site -p 9876 & \
docker run --rm --network host -v $(shell pwd):/slides astefanutti/decktape automatic -s 1920x1080 http://127.0.0.1:9876/$(<:_site/%=%) /slides/$@
_site/%/slides_CAT_ES.pdf: _site/%/slides_CAT_ES.html
$(ACTIVATE_ENV) && \
$(shell npm bin)/http-server _site -p 9876 & \
docker run --rm --network host -v $(shell pwd):/slides astefanutti/decktape automatic -s 1920x1080 http://127.0.0.1:9876/$(<:_site/%=%) /slides/$@
video: ## Build all videos
bash bin/ari-make.sh
annotate: ## annotate the tutorials with usable Galaxy instances
${ACTIVATE_ENV} && \
wget https://github.com/hexylena/toolshed-version-database/raw/main/guid-rev.json -O metadata/toolshed-revisions.json && \
python bin/supported-fetch.py
.PHONY: annotate
rebuild-search-index: ## Rebuild search index
node bin/lunr-index.js > search.json
api/swagger.json: metadata/swagger.yaml
$(ACTIVATE_ENV) && \
cat metadata/swagger.yaml | python bin/yaml2json.py > api/swagger.json
clean: ## clean up junk files
@rm -rf _site
@rm -rf .sass-cache
@rm -rf .bundle
@rm -rf vendor
@rm -rf node_modules
@rm -rf .jekyll-metadata
@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