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Merge pull request #67 from gvwilson/clean-rmd
[rnaseq-cwl-training.git]
/
Makefile
diff --git
a/Makefile
b/Makefile
index 154203a48540e7740050ba58feae0f8983aea6d1..7b1b1b9710278773c04ac93197913fa6c22698c7 100644
(file)
--- a/
Makefile
+++ b/
Makefile
@@
-16,11
+16,11
@@
commands :
@grep -h -E '^##' ${MAKEFILES} | sed -e 's/## //g'
## serve : run a local server.
@grep -h -E '^##' ${MAKEFILES} | sed -e 's/## //g'
## serve : run a local server.
-serve :
+serve :
lesson-rmd
${JEKYLL} serve --config _config.yml,_config_dev.yml
## site : build files but do not run a server.
${JEKYLL} serve --config _config.yml,_config_dev.yml
## site : build files but do not run a server.
-site :
+site :
lesson-rmd
${JEKYLL} build --config _config.yml,_config_dev.yml
## figures : re-generate inclusion displaying all figures.
${JEKYLL} build --config _config.yml,_config_dev.yml
## figures : re-generate inclusion displaying all figures.
@@
-36,6
+36,11
@@
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.
## ----------------------------------------
## Commands specific to workshop websites.
@@
-48,10
+53,14
@@
workshop-check :
## ----------------------------------------
## Commands specific to lesson websites.
## ----------------------------------------
## Commands specific to lesson websites.
-.PHONY : lesson-check lesson-files lesson-fixme lesson-single
+.PHONY : lesson-check lesson-rmd 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 \
@@
-61,7
+70,7
@@
SRC_FILES = \
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 \
@@
-70,6
+79,10
@@
HTML_FILES = \
$(patsubst _extras/%.md,${DST}/%/index.html,$(wildcard _extras/*.md)) \
${DST}/license/index.html
$(patsubst _extras/%.md,${DST}/%/index.html,$(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-check : validate lesson Markdown.
lesson-check :
@bin/lesson_check.py -s . -p ${PARSER}
## lesson-check : validate lesson Markdown.
lesson-check :
@bin/lesson_check.py -s . -p ${PARSER}
@@
-79,12
+92,14
@@
unittest :
## lesson-files : show expected names of generated files for debugging.
lesson-files :
## lesson-files : show expected names of generated files for debugging.
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 :
## lesson-fixme : show FIXME markers embedded in source files.
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.