Makefile

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+AUX_DIR=.aux
+LATEX=$(basename $(shell grep -l '\\begin{document' *.tex))
+LETTER=letter
+COVER=cover
+HIGHLIGHTS=highlights
+HTML_OUT=$(LETTER).html
+
+.PHONY: all cover clean highlights latex letter zip
+
+all: $(COVER).pdf $(LETTER).pdf | zip
+
+$(AUX_DIR):
+	@mkdir -p $(AUX_DIR)
+
+$(LETTER).pdf: $(LETTER).md | $(AUX_DIR)
+	@pandoc -s -H style.html $(LETTER).md -o $(HTML_OUT)
+	@wkhtmltopdf $(HTML_OUT) $(LETTER).pdf
+	@echo Letter generated: $(LETTER)
+
+$(LATEX).pdf: *.tex | $(AUX_DIR)
+# An alternative to doing three passes is using latexmk
+	@pdflatex -interaction=batchmode -output-directory=$(AUX_DIR) $(LATEX) >/dev/null
+# openout_any=a -> write to a folder (AUX_DIR)
+# TEXMFOUTPUT -> find the aux files in that folder
+	@openout_any=a TEXMFOUTPUT="$(AUX_DIR)/" bibtex $(AUX_DIR)/$(LATEX) >/dev/null
+	@pdflatex -interaction=batchmode -output-directory=$(AUX_DIR) $(LATEX) >/dev/null
+	@pdflatex -interaction=batchmode -output-directory=$(AUX_DIR) $(LATEX)
+	@mv $(AUX_DIR)/$(LATEX).pdf .
+	@echo "Finished"
+
+$(HIGHLIGHTS).pdf: $(HIGHLIGHTS).md
+	pandoc $(HIGHLIGHTS).md -o (HIGHLIGHTS).pdf
+
+$(COVER).pdf: $(COVER).md
+	pandoc $(COVER).md -o $(COVER).pdf
+
+$(PAPER).zip: $(LATEX).pdf $(LETTER).pdf
+	@zip $(LATEX).zip *.tex  $(LETTER).pdf $(COVER).pdf $(HIGHLIGHTS).pdf $(LATEX).pdf
+	@for r in `sed -n 's/.*bibliography{\(.*\)}.*/\1/p' *.tex`; do \
+		zip $().zip  $$r.bib; \
+	done
+	@for i in `sed -n 's/.*includegraphics{\(.*\)}.*/\1/p' *.tex`; do \
+		zip $(LATEX).zip  figures/$$i.eps; \
+	done
+
+clean:
+	@-rm -rf $(AUX_DIR)
+	@-rm -f $(HTML_OUT)
+
+clean_all: clean
+	@rm -f $(LATEX).zip
+	@rm -f $(LATEX).pdf
+	@rm -f $(REVIEW).pdf
+	@rm -f $(COVER).pdf
+	@rm -f $(HIGHLIGHTS).pdf
+
+view: $(LATEX).pdf
+	xdg-open $(LATEX).pdf
+
+cover: $(COVER).pdf
+highlights: $(HIGHLIGHTS).pdf
+latex: $(LATEX).pdf
+letter: $(LETTER).pdf
+zip: $(PAPER).zip