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Add several FIXMEs to the template episode
[rnaseq-cwl-training.git]
/
Makefile
diff --git
a/Makefile
b/Makefile
index 71166297823615ef511eda638c301c55cc02036a..74f655d6f8c79d9d3f847d2efb229a17d51a3a06 100644
(file)
--- a/
Makefile
+++ b/
Makefile
@@
-9,6
+9,7
@@
DST=_site
# Controls
.PHONY : commands clean files
# Controls
.PHONY : commands clean files
+.NOTPARALLEL:
all : commands
## commands : show all commands.
all : commands
## commands : show all commands.
@@
-16,16
+17,16
@@
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 : lesson-
r
md
- ${JEKYLL} serve
--config _config.yml,_config_dev.yml
+serve : lesson-md
+ ${JEKYLL} serve
## site : build files but do not run a server.
## site : build files but do not run a server.
-site : lesson-
r
md
- ${JEKYLL} build
--config _config.yml,_config_dev.yml
+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 : clean up junk files.
clean :
@@
-53,7
+54,7
@@
workshop-check :
## ----------------------------------------
## Commands specific to lesson websites.
## ----------------------------------------
## Commands specific to lesson websites.
-.PHONY : lesson-check lesson-
r
md lesson-files lesson-fixme
+.PHONY : lesson-check lesson-md lesson-files lesson-fixme
# RMarkdown files
RMD_SRC = $(wildcard _episodes_rmd/??-*.Rmd)
# RMarkdown files
RMD_SRC = $(wildcard _episodes_rmd/??-*.Rmd)
@@
-62,11
+63,11
@@
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 \
# Lesson source files in the order they appear in the navigation menu.
MARKDOWN_SRC = \
index.md \
- CONDUCT.md \
+ CO
DE_OF_CO
NDUCT.md \
setup.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.
@@
-74,26
+75,29
@@
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-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}
+lesson-check :
lesson-fixme
+ @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 :
## 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 :
## 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 :
## lesson-files : show expected names of generated files for debugging.
lesson-files :