Makefile: Specify shell. Don't include commands.mk

[rnaseq-cwl-training.git] / Makefile

diff --git a/Makefile b/Makefile
index 7e46acbb7f53c7c65c261e44bd1a4934b460ba4b..14a53a24d23bdd0b9357937d7eed373da70599bf 100644 (file)
--- a/Makefile
+++ b/Makefile
@@ -1,12 +1,40 @@
+# Use /bin/bash instead of /bin/sh
+export SHELL = /bin/bash
+
 ## ========================================
 ## Commands for both workshop and lesson websites.
 
 # Settings
 MAKEFILES=Makefile $(wildcard *.mk)
-JEKYLL=jekyll
+JEKYLL_VERSION=3.8.5
+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:
@@ -14,7 +42,15 @@ 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 --volume ${PWD}:/srv/jekyll \
+           --volume=${PWD}/.docker-vendor/bundle:/usr/local/bundle \
+           -p 127.0.0.1:4000:4000 \
+           jekyll/jekyll:${JEKYLL_VERSION} \
+           bin/run-make-docker-serve.sh
 
 ## serve            : run a local server.
 serve : lesson-md
@@ -38,7 +74,7 @@ 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-*
 
@@ -49,7 +85,7 @@ clear-rmd :
 
 ## workshop-check   : check workshop homepage.
 workshop-check :
-       @bin/workshop_check.py .
+       @${PYTHON} bin/workshop_check.py .
 
 ## ----------------------------------------
 ## Commands specific to lesson websites.
@@ -63,7 +99,7 @@ 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 \
@@ -75,33 +111,28 @@ 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-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
-
-## lesson-figures   : re-generate inclusion displaying all figures.
-lesson-figures :
-       @bin/extract_figures.py -p ${PARSER} ${MARKDOWN_SRC} > _includes/all_figures.html
+       @${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 :
@@ -114,8 +145,3 @@ lesson-files :
 lesson-fixme :
        @fgrep -i -n FIXME ${MARKDOWN_SRC} || true
 
-#-------------------------------------------------------------------------------
-# Include extra commands if available.
-#-------------------------------------------------------------------------------
-
--include commands.mk