Update Makefile

[rnaseq-cwl-training.git] / Makefile

diff --git a/Makefile b/Makefile
index c8011ddeedbbc546607b7b8413bcfcd2ffdcf78d..c8b31c5b4f505b0944940f6ca1ef19c82a6d74bf 100644 (file)
--- a/Makefile
+++ b/Makefile
@@ -9,25 +9,26 @@ DST=_site
 
 # Controls
 .PHONY : commands clean files
+.NOTPARALLEL:
 all : commands
 
-## commands       : show all commands.
+## commands         : show all commands.
 commands :
        @grep -h -E '^##' ${MAKEFILES} | sed -e 's/## //g'
 
-## serve          : run a local server.
-serve : lesson-rmd
-       ${JEKYLL} serve --config _config.yml,_config_dev.yml
+## serve            : run a local server.
+serve : lesson-md
+       ${JEKYLL} serve
 
-## site           : build files but do not run a server.
-site : lesson-rmd
-       ${JEKYLL} build --config _config.yml,_config_dev.yml
+## site             : build files but do not run a server.
+site : lesson-md
+       ${JEKYLL} build
 
-## figures        : re-generate inclusion displaying all figures.
-figures :
-       @bin/extract_figures.py -s _episodes -p ${PARSER} > _includes/all_figures.html
+# repo-check        : check repository settings.
+repo-check :
+       @bin/repo_check.py -s .
 
-## clean          : clean up junk files.
+## clean            : clean up junk files.
 clean :
        @rm -rf ${DST}
        @rm -rf .sass-cache
@@ -35,22 +36,25 @@ clean :
        @find . -name .DS_Store -exec rm {} \;
        @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 :
        @rm -rf ${RMD_DST}
-       @rm -rf fig/swc-rmd-*
+       @rm -rf fig/rmd-*
 
 ## ----------------------------------------
 ## Commands specific to workshop websites.
 
 .PHONY : workshop-check
 
-## workshop-check : check workshop homepage.
+## workshop-check   : check workshop homepage.
 workshop-check :
        @bin/workshop_check.py .
 
 ## ----------------------------------------
 ## Commands specific to lesson websites.
 
-.PHONY : lesson-check lesson-rmd lesson-files lesson-fixme
+.PHONY : lesson-check lesson-md lesson-files lesson-fixme
 
 # RMarkdown files
 RMD_SRC = $(wildcard _episodes_rmd/??-*.Rmd)
@@ -61,9 +65,9 @@ MARKDOWN_SRC = \
   index.md \
   CONDUCT.md \
   setup.md \
-  $(wildcard _episodes/*.md) \
+  $(sort $(wildcard _episodes/*.md)) \
   reference.md \
-  $(wildcard _extras/*.md) \
+  $(sort $(wildcard _extras/*.md)) \
   LICENSE.md
 
 # Generated lesson files in the order they appear in the navigation menu.
@@ -71,30 +75,38 @@ 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-rmd:    : convert Rmarkdown files to markdown
-lesson-rmd: $(RMD_SRC)
-       @bin/knit_lessons.sh $(RMD_SRC)
+## 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}
 
-## lesson-check   : validate lesson Markdown.
+## lesson-check     : validate lesson Markdown.
 lesson-check :
-       @bin/lesson_check.py -s . -p ${PARSER}
+       @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} -r _includes/links.md -l -w --permissive
 
+## unittest         : run unit tests on checking tools.
 unittest :
-       python bin/test_lesson_check.py
+       @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