From 504335dfcafda2607653ba619520838a83d5a260 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?J=2E=20Fernando=20S=C3=A1nchez?= <balkian@gmail.com>
Date: Thu, 26 Mar 2015 03:15:37 +0100
Subject: [PATCH 1/5]

---
 Makefile | 64 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 64 insertions(+)
 create mode 100644 Makefile

diff --git a/Makefile b/Makefile
new file mode 100644
index 0000000..7be5991
--- /dev/null
+++ b/Makefile
@@ -0,0 +1,64 @@
+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
\ No newline at end of file

From 720a2d1efd5360739a709a28d866ffbfe8483115 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?J=2E=20Fernando=20S=C3=A1nchez?= <balkian@gmail.com>
Date: Wed, 25 Mar 2015 19:25:34 -0700
Subject: [PATCH 2/5]

---
 Makefile | 12 ++++++++++--
 1 file changed, 10 insertions(+), 2 deletions(-)

diff --git a/Makefile b/Makefile
index 7be5991..bbd4969 100644
--- a/Makefile
+++ b/Makefile
@@ -1,13 +1,21 @@
-AUX_DIR=.aux
+# Some automation to submit to a journal (e.g. Elsevier).
+# It detects the main latex file and eps files used.
+# Author: @balkian
+# TODO: Only import the tex files used in the main file, and their images.
+
 LATEX=$(basename $(shell grep -l '\\begin{document' *.tex))
 LETTER=letter
 COVER=cover
 HIGHLIGHTS=highlights
+
 HTML_OUT=$(LETTER).html
+AUX_DIR=.aux
 
 .PHONY: all cover clean highlights latex letter zip
 
-all: $(COVER).pdf $(LETTER).pdf | zip
+default: latex
+
+all: $(LATEX).pdf $(LETTER).pdf $(COVER).pdf $(HIGHLIGHTS).pdf | zip
 
 $(AUX_DIR):
 	@mkdir -p $(AUX_DIR)

From c04a4b302faa558cdc713151c12df08a3983d541 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?J=2E=20Fernando=20S=C3=A1nchez?= <balkian@gmail.com>
Date: Thu, 26 Mar 2015 08:14:23 -0700
Subject: [PATCH 3/5]

---
 Makefile | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/Makefile b/Makefile
index bbd4969..7441add 100644
--- a/Makefile
+++ b/Makefile
@@ -45,7 +45,7 @@ $(COVER).pdf: $(COVER).md
 $(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  $$r.bib; \
+		zip $(LATEX).zip  $$r.bib; \
 	done
 	@for i in `sed -n 's/.*includegraphics{\(.*\)}.*/\1/p' *.tex`; do \
 		zip $(LATEX).zip  figures/$$i.eps; \
@@ -69,4 +69,4 @@ cover: $(COVER).pdf
 highlights: $(HIGHLIGHTS).pdf
 latex: $(LATEX).pdf
 letter: $(LETTER).pdf
-zip: $(PAPER).zip
\ No newline at end of file
+zip: $(LATEX).zip
\ No newline at end of file

From c47b562b397026bc95d6da6ed7ff5ed5b88bae15 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?J=2E=20Fernando=20S=C3=A1nchez?= <balkian@gmail.com>
Date: Thu, 26 Mar 2015 08:18:25 -0700
Subject: [PATCH 4/5]

---
 Makefile | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/Makefile b/Makefile
index 7441add..f7c7e73 100644
--- a/Makefile
+++ b/Makefile
@@ -47,7 +47,7 @@ $(PAPER).zip: $(LATEX).pdf $(LETTER).pdf
 	@for r in `sed -n 's/.*bibliography{\(.*\)}.*/\1/p' *.tex`; do \
 		zip $(LATEX).zip  $$r.bib; \
 	done
-	@for i in `sed -n 's/.*includegraphics{\(.*\)}.*/\1/p' *.tex`; do \
+	@for i in `sed -n 's/.*includegraphics\[.*\]{\(.*\)}.*/\1/p' *.tex`; do \
 		zip $(LATEX).zip  figures/$$i.eps; \
 	done
 
@@ -69,4 +69,4 @@ cover: $(COVER).pdf
 highlights: $(HIGHLIGHTS).pdf
 latex: $(LATEX).pdf
 letter: $(LETTER).pdf
-zip: $(LATEX).zip
\ No newline at end of file
+zip: $(LATEX).zip

From 9491756c9549d502a43e828cf402ee23ece444b2 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?J=2E=20Fernando=20S=C3=A1nchez?= <balkian@gmail.com>
Date: Thu, 26 Mar 2015 08:25:38 -0700
Subject: [PATCH 5/5]

---
 Makefile | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/Makefile b/Makefile
index f7c7e73..5301b09 100644
--- a/Makefile
+++ b/Makefile
@@ -3,13 +3,12 @@
 # Author: @balkian
 # TODO: Only import the tex files used in the main file, and their images.
 
+AUX_DIR=.aux
 LATEX=$(basename $(shell grep -l '\\begin{document' *.tex))
 LETTER=letter
 COVER=cover
 HIGHLIGHTS=highlights
-
 HTML_OUT=$(LETTER).html
-AUX_DIR=.aux
 
 .PHONY: all cover clean highlights latex letter zip
 
@@ -42,14 +41,15 @@ $(HIGHLIGHTS).pdf: $(HIGHLIGHTS).md
 $(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 $(LATEX).pdf
+$(LATEX).zip: $(LATEX).pdf $(LETTER).pdf $(HIGHLIGHTS).pdf $(COVER).pdf
+	@zip $(LATEX).zip *.tex  $(LETTER).pdf $(COVER).pdf $(HIGHLIGHTS).pdf
 	@for r in `sed -n 's/.*bibliography{\(.*\)}.*/\1/p' *.tex`; do \
 		zip $(LATEX).zip  $$r.bib; \
 	done
 	@for i in `sed -n 's/.*includegraphics\[.*\]{\(.*\)}.*/\1/p' *.tex`; do \
 		zip $(LATEX).zip  figures/$$i.eps; \
 	done
+	zip Makefile
 
 clean:
 	@-rm -rf $(AUX_DIR)
@@ -69,4 +69,4 @@ cover: $(COVER).pdf
 highlights: $(HIGHLIGHTS).pdf
 latex: $(LATEX).pdf
 letter: $(LETTER).pdf
-zip: $(LATEX).zip
+zip: $(LATEX).zip
\ No newline at end of file