Update Makefile

[rnaseq-cwl-training.git] / Makefile

diff --git a/Makefile b/Makefile
index ca981d3ee95ffaf6d07603673c30db648cde4e0a..c8b31c5b4f505b0944940f6ca1ef19c82a6d74bf 100644 (file)
--- a/Makefile
+++ b/Makefile
@@ -9,6 +9,7 @@ DST=_site
 
 # Controls
 .PHONY : commands clean files
+.NOTPARALLEL:
 all : commands
 
 ## commands         : show all commands.
@@ -16,22 +17,17 @@ 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 : lesson-md
+       ${JEKYLL} serve
 
 ## site             : build files but do not run a server.
-site : lesson-rmd
-       ${JEKYLL} build --config _config.yml,_config_dev.yml
-
-## figures          : re-generate inclusion displaying all figures.
-figures :
-       @bin/extract_figures.py -s _episodes -p ${PARSER} > _includes/all_figures.html
+site : lesson-md
+       ${JEKYLL} build
 
 # repo-check        : check repository settings.
 repo-check :
        @bin/repo_check.py -s .
 
-
 ## clean            : clean up junk files.
 clean :
        @rm -rf ${DST}
@@ -58,7 +54,7 @@ workshop-check :
 ## ----------------------------------------
 ## 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)
@@ -69,9 +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.
@@ -79,26 +75,29 @@ 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 :
-       @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} -l -w
+       @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 :