Update journal paper

Makefile

@@ -0,0 +1,56 @@
+.PHONY: all paper help html publish watch clean cp-figs
+
+SHELL := /bin/bash
+PAPERDIR=paper
+MATLABDIR=matlab
+TIKZDIR=tikz
+
+PAPERNAME=paper
+
+all: paper html publish
+
+paper: cp-figs tangle tex pdf clean
+
+help:
+	@echo "Usage: make <command>"
+	@echo "  all     - Cp-figs tex pdf html publish"
+	@echo "  paper   - Compile the org file to a pdf"
+	@echo "  html    - Export all the org files to html"
+	@echo "  publish - Commit everything and push to repository"
+	@echo "  tex     - Export to paper in org format to tex"
+	@echo "  tangle  - Tangle everything that is in the org paper and tikz file"
+	@echo "  pdf     - Compile the tex file to pdf"
+	@echo "  watch   - Watch the tex file for changes and compile"
+	@echo "  clean   - Clean the paper directory"
+	@echo "  cp-figs - Copy all the necessary figures from tikz and matlab folder to paper folder"
+
+html:
+	for f in *.org;              do emacsclient -e "(progn (find-file \"$$f\") (org-html-export-to-html))"; done
+	for f in $(TIKZDIR)/*.org;    do emacsclient -e "(progn (find-file \"$$f\") (org-html-export-to-html))"; done
+	for f in $(MATLABDIR)/*.org; do emacsclient -e "(progn (find-file \"$$f\") (org-html-export-to-html))"; done
+
+publish:
+	git add . && git commit -m "Update - $$(date +%F)" && git push origin master
+
+tex: $(PAPERDIR)/$(PAPERNAME).org
+	emacsclient -e '(progn (find-file "$(PAPERDIR)/$(PAPERNAME).org") (org-latex-export-to-latex))'
+
+tangle: $(PAPERDIR)/$(PAPERNAME).org
+	emacsclient -e '(progn (find-file "$(PAPERDIR)/$(PAPERNAME).org") (org-babel-tangle))'
+	emacsclient -e '(progn (find-file "$(TIKZDIR)/index.org") (org-babel-tangle))'
+
+pdf: $(PAPERDIR)/$(PAPERNAME).tex
+	latexmk -cd -quiet -bibtex $(PREVIEW_CONTINUOUSLY) -f -pdf -pdflatex="xelatex -synctex=1 -interaction nonstopmode" -use-make $(PAPERDIR)/$(PAPERNAME).tex
+
+# Set the PREVIEW_CONTINUOUSLY variable to -pvc to switch latexmk into the preview continuously mode
+watch: PREVIEW_CONTINUOUSLY=-pvc
+watch: pdf
+
+watch-org: $(PAPERDIR)/$(PAPERNAME).org
+	echo $(PAPERDIR)/$(PAPERNAME).org | entr -s 'make tangle tex pdf'
+
+clean:
+	latexmk -cd -c -bibtex $(PAPERDIR)/$(PAPERNAME).tex
+
+cp-figs:
+	bash scripts/cp-figs.sh