Makefile

PARSE_DATA := results/data-comparison.md
THE_DATA   := data/clean_data.csv \
              data/raw_data.csv \
              data/sclerotinia_16_loci.rda
ANALYSES   := results/table-1.md \
              results/MCG-virulence.md \
              results/locus-stats.md \
              results/MLG-distribution.md \
              results/mlg-mcg.md \
              results/RDA-analysis.md \
              results/pop-diff.md \
              results/tree.md \
              results/wmn-differentiation.md\
              results/by-year.md \
              results/compare-aldrich-wolfe.md
MANUSCRIPT := doc/manuscript/manuscript.pdf doc/manuscript/manuscript_shell.tex
COMPONENTS := doc/manuscript/abstract.md \
              doc/manuscript/ssc_bibliography.bib \
              doc/manuscript/wlpeerj.cls \
              doc/manuscript/apa.csl
DIRS       := results/figures/publication results/tables/

ifndef VERSION
VERSION := master
endif

# Testing whether or not we are in a docker container
ifeq ("$(wildcard /proc/1/cgroup)","")
	RCMD="devtools::install()"
else ifneq ("$(shell grep -cq docker /proc/1/cgroup)","0")
	RCMD="Sys.Date()"
else
	RCMD="devtools::install()"
endif


# TARGETS
# ---------------------------------------------------------
.PHONY: all
all: $(DIRS) README.md $(ANALYSES) $(MANUSCRIPT)
# In reality $(ANALYSES) -> shared_data -> $(PARSE_DATA) -> bootstrap

# Bootstrap the  data by installing the dependencies
# This is a specific target for the convenience of typing make bootstrap
.PHONY: bootstrap
bootstrap: $(DIRS) results/bootstrap.txt

# Create the shared data set
$(THE_DATA) : bootstrap $(PARSE_DATA)

# All the analyses (defined above) depend on the shared data set
$(ANALYSES): $(THE_DATA)

# RECIPES
# ---------------------------------------------------------
$(DIRS) :
	mkdir -p $@

results/bootstrap.txt: DESCRIPTION
	R --slave -e $(RCMD)
	date > results/bootstrap.txt

README.md : README.Rmd $(MANUSCRIPT)
	R --slave -e 'rmarkdown::render("$<")'

results/%.md : doc/RMD/%.Rmd
	R --slave -e "ezknitr::ezknit('$<', \
	              fig_dir = './figures/$*/', \
	              out_dir = '$(@D)', \
	              keep_html = FALSE \
	              )"

doc/manuscript/manuscript_shell.tex : doc/manuscript/manuscript.pdf
	./move-supplementary.sh

doc/manuscript/%.pdf : doc/manuscript/%.Rmd $(COMPONENTS) $(ANALYSES)
	R --slave -e "rmarkdown::render('$<')"

.PHONY : tidy

# Tidy is for when you need to simply clear the results, but don't need to rerun
# ALL of the analyses (the cache still exists)
tidy:
	$(RM) $(PARSE_DATA)
	$(RM) data/*.{csv,rda,rdb,rds} 
	$(RM) $(ANALYSES)
	$(RM) $(MANUSCRIPT)
	$(RM) README
	$(RM) -r $(DIRS)
	$(RM) -r results/
	$(RM) doc/RMD/*html
	$(RM) doc/manuscript/*{tex,pdf}

.PHONY : clean

# clean is for when you want to burn everything to the ground and run the
# analysis anew. Note: this will take a while.
clean: tidy
	$(RM) cache/*

.PHONY : diff

diff : doc/manuscript/diff.pdf

doc/manuscript/diff.pdf : doc/manuscript/manuscript.pdf
	bash -c "latexdiff <(git show $(VERSION):doc/manuscript/manuscript.tex) doc/manuscript/manuscript.tex > doc/manuscript/diff.tex"
	cd doc/manuscript; pdflatex diff.tex; rm diff.{tex,aux,log,out}

# Ignoring Derivatives ----------------------------------------------------
#
# This part is useful when testing several changes

.PHONY: ignore

ignore :
	git update-index --assume-unchanged \
	doc/manuscript/manuscript.tex \
	doc/manuscript/manuscript.pdf

.PHONY: unignore

unignore :
	git update-index --no-assume-unchanged \
	doc/manuscript/manuscript.tex \
	doc/manuscript/manuscript.pdf