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Fix validation for syntax highlight
[rnaseq-cwl-training.git]
/
Makefile
diff --git
a/Makefile
b/Makefile
index 154203a48540e7740050ba58feae0f8983aea6d1..df31f00cfc7ad62b0afc849061a287392998f06c 100644
(file)
--- a/
Makefile
+++ b/
Makefile
@@
-9,25
+9,26
@@
DST=_site
# Controls
.PHONY : commands clean files
# Controls
.PHONY : commands clean files
+.NOTPARALLEL:
all : commands
all : commands
-## commands : show all commands.
+## commands
: show all commands.
commands :
@grep -h -E '^##' ${MAKEFILES} | sed -e 's/## //g'
commands :
@grep -h -E '^##' ${MAKEFILES} | sed -e 's/## //g'
-## serve : run a local server.
-serve :
- ${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 :
- ${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 figure
s.
-
figures
:
- @bin/
extract_figures.py -s _episodes -p ${PARSER} > _includes/all_figures.html
+#
repo-check : check repository setting
s.
+
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
clean :
@rm -rf ${DST}
@rm -rf .sass-cache
@@
-36,55
+37,78
@@
clean :
@find . -name '*~' -exec rm {} \;
@find . -name '*.pyc' -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/rmd-*
+
## ----------------------------------------
## Commands specific to workshop websites.
.PHONY : workshop-check
## ----------------------------------------
## 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.
workshop-check :
@bin/workshop_check.py .
## ----------------------------------------
## Commands specific to lesson websites.
-.PHONY : lesson-check lesson-files lesson-fixme lesson-single
+.PHONY : lesson-check lesson-md lesson-files lesson-fixme
+
+# RMarkdown files
+RMD_SRC = $(wildcard _episodes_rmd/??-*.Rmd)
+RMD_DST = $(patsubst _episodes_rmd/%.Rmd,_episodes/%.md,$(RMD_SRC))
# Lesson source files in the order they appear in the navigation menu.
# Lesson source files in the order they appear in the navigation menu.
-
SRC_FILES
= \
+
MARKDOWN_SRC
= \
index.md \
CONDUCT.md \
setup.md \
index.md \
CONDUCT.md \
setup.md \
- $(
wildcard _episodes/*.md
) \
+ $(
sort $(wildcard _episodes/*.md)
) \
reference.md \
reference.md \
- $(
wildcard _extras/*.md
) \
+ $(
sort $(wildcard _extras/*.md)
) \
LICENSE.md
# Generated lesson files in the order they appear in the navigation menu.
LICENSE.md
# Generated lesson files in the order they appear in the navigation menu.
-HTML_
FILES
= \
+HTML_
DST
= \
${DST}/index.html \
${DST}/conduct/index.html \
${DST}/setup/index.html \
${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 \
${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
${DST}/license/index.html
-## lesson-check : validate lesson Markdown.
+## 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 :
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
+## unittest : run unit tests on checking tools.
unittest :
python bin/test_lesson_check.py
unittest :
python 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 :
lesson-files :
- @echo 'source:' ${SRC_FILES}
- @echo 'generated:' ${HTML_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 :
lesson-fixme :
- @fgrep -i -n FIXME ${
SRC_FILES
} || true
+ @fgrep -i -n FIXME ${
MARKDOWN_SRC
} || true
#-------------------------------------------------------------------------------
# Include extra commands if available.
#-------------------------------------------------------------------------------
# Include extra commands if available.