Initial commit

.gitignore

@@ -0,0 +1,4 @@
+.sconsign.dblite
+_build
+*.pyc
+_ignore

SConstruct

@@ -0,0 +1,29 @@
+import glob
+import os
+
+VariantDir('_build', src_dir='.')
+
+env = Environment(ENV=os.environ)
+inkscape = Builder(action = 'inkscape --without-gui --export-pdf=$TARGET $SOURCE')
+env['BUILDERS']['Inkscape'] = inkscape
+env['BUILDERS']['Latexdiff'] = Builder(action = 'latexdiff $SOURCES > $TARGET')
+env['BUILDERS']['Copier'] = Builder(action = Copy('$TARGET', '$SOURCE'))
+
+figure_pdfs = [env.Inkscape(target="figures/" + os.path.basename(svg).replace('.svg','.pdf'), source=svg)
+               for svg in glob.glob('prep-figures/*.svg')]
+
+pdfs = [env.Copier(target = '_build/' + os.path.basename(pdf), source = pdf)
+        for pdf in glob.glob('figures/*.pdf')]
+
+Depends(Flatten([pdfs]), Flatten([figure_pdfs]))
+
+main=env.PDF(target='_build/main.pdf',source='main.tex')
+
+Depends(Flatten([main]),
+        Flatten([pdfs, figure_pdfs, 'main.bib']))
+
+cont_build = env.Command('.continuous', ['main.bib', 'main.tex'],
+    'while :; do inotifywait -e modify $SOURCES; scons -Q; done')
+Alias('continuous', cont_build)
+
+Default(main)

main.bib

@@ -0,0 +1,15 @@
+
+@ARTICLE{Felsenstein1981-zs,
+title = "Evolutionary trees from {DNA} sequences: a maximum likelihood approach",
+author = "Felsenstein, J",
+journal = "J. Mol. Evol.",
+publisher = "Springer",
+volume =  17,
+number =  6,
+pages = "368--376",
+year =  1981,
+url = "http://www.ncbi.nlm.nih.gov/pubmed/7288891",
+issn = "0022-2844",
+pmid = "7288891"
+}
+

main.tex

@@ -0,0 +1,36 @@
+\documentclass{article}
+
+\usepackage{graphicx}
+\usepackage[hidelinks]{hyperref}
+
+
+\hyphenation{Ge-nome Ge-nomes hyper-mut-ation through-put}
+
+\title{Template}
+\author{You}
+
+\begin{document}
+\maketitle
+
+\begin{abstract}
+Abstract here.
+\end{abstract}
+
+
+\section{Introduction}
+\cite{Felsenstein1981-zs}
+
+% \begin{figure}[h]
+% \centering
+% \includegraphics[width=0.35\textwidth]{figures/subsplit.pdf}
+% \caption{\
+% A subsplit structure.
+% }
+% \label{fig:subsplit}
+% \end{figure}
+
+
+\bibliographystyle{plain}
+\bibliography{main}
+
+\end{document}