install gems locally

[rnaseq-cwl-training.git] / Makefile

diff --git a/Makefile b/Makefile
index 9d874013fa4c9696f89b90d6b67bf6c5a519e11e..124e397b49988c93baafbcd747d072b2681ce2f1 100644 (file)
--- a/Makefile
+++ b/Makefile
@@ -3,11 +3,36 @@
 
 # Settings
 MAKEFILES=Makefile $(wildcard *.mk)
-JEKYLL=jekyll
-JEKYLL_VERSION=3.7.3
+JEKYLL_VERSION=3.8.5
+JEKYLL_DOCKER=${JEKYLL} serve --host 0.0.0.0
+JEKYLL=bundle install --path .vendor/bundle && 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
 .NOTPARALLEL:
@@ -15,11 +40,11 @@ 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
+       docker run --rm -it -v ${PWD}:/srv/jekyll -p 4000:4000 jekyll/jekyll:${JEKYLL_VERSION} ${JEKYLL_DOCKER}
 
 ## serve            : run a local server.
 serve : lesson-md
@@ -43,7 +68,7 @@ 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-*
 
@@ -54,7 +79,7 @@ clear-rmd :
 
 ## workshop-check   : check workshop homepage.
 workshop-check :
-       @bin/workshop_check.py .
+       @${PYTHON} bin/workshop_check.py .
 
 ## ----------------------------------------
 ## Commands specific to lesson websites.
@@ -68,7 +93,7 @@ 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 \
   $(sort $(wildcard _episodes/*.md)) \
   reference.md \
@@ -88,21 +113,20 @@ HTML_DST = \
 ## lesson-md        : convert Rmarkdown files to markdown
 lesson-md : ${RMD_DST}
 
-# Use of .NOTPARALLEL makes rule execute only once
-${RMD_DST} : ${RMD_SRC}
-       @bin/knit_lessons.sh ${RMD_SRC}
+_episodes/%.md: _episodes_rmd/%.Rmd
+       @bin/knit_lessons.sh $< $@
 
 ## lesson-check     : validate lesson Markdown.
-lesson-check :
-       @bin/lesson_check.py -s . -p ${PARSER} -r _includes/links.md
+lesson-check : lesson-fixme
+       @${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 :