From 4e5488f741ede83a80ea9333b285108856df0005 Mon Sep 17 00:00:00 2001
From: Jarrod Millman <jarrod.millman@gmail.com>
Date: Thu, 8 Oct 2015 09:01:53 -0700
Subject: [PATCH] Add project skeleton

---
 .gitignore        | 60 +++++++++++++++++++++++++++++++++++++++++++++++
 code/.gitignore   |  0
 data/.gitignore   |  0
 paper/.gitignore  |  0
 paper/Makefile    | 11 +++++++++
 paper/project.bib | 10 ++++++++
 paper/report.tex  | 47 +++++++++++++++++++++++++++++++++++++
 slides/.gitignore |  0
 8 files changed, 128 insertions(+)
 create mode 100644 .gitignore
 create mode 100644 code/.gitignore
 create mode 100644 data/.gitignore
 create mode 100644 paper/.gitignore
 create mode 100644 paper/Makefile
 create mode 100644 paper/project.bib
 create mode 100644 paper/report.tex
 create mode 100644 slides/.gitignore

diff --git a/.gitignore b/.gitignore
new file mode 100644
index 0000000..c546c9c
--- /dev/null
+++ b/.gitignore
@@ -0,0 +1,60 @@
+.DS_Store
+
+
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+env/
+bin/
+build/
+develop-eggs/
+dist/
+eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+*.egg-info/
+.installed.cfg
+*.egg
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.coverage
+.cache
+nosetests.xml
+coverage.xml
+
+# Translations
+*.mo
+
+# Mr Developer
+.mr.developer.cfg
+.project
+.pydevproject
+
+# Rope
+.ropeproject
+
+# Django stuff:
+*.log
+*.pot
+
+# Sphinx documentation
+doc/build/
+doc/source/_static/test.png
+
+\#*
+*~
diff --git a/code/.gitignore b/code/.gitignore
new file mode 100644
index 0000000..e69de29
diff --git a/data/.gitignore b/data/.gitignore
new file mode 100644
index 0000000..e69de29
diff --git a/paper/.gitignore b/paper/.gitignore
new file mode 100644
index 0000000..e69de29
diff --git a/paper/Makefile b/paper/Makefile
new file mode 100644
index 0000000..232a5dd
--- /dev/null
+++ b/paper/Makefile
@@ -0,0 +1,11 @@
+TITLE="report"
+
+all:
+	pdflatex $(TITLE).tex
+	bibtex $(TITLE)
+	pdflatex $(TITLE).tex
+	pdflatex $(TITLE).tex
+
+
+clean:
+	rm -f *.{aux,log,bbl,lof,lot,blg,out}
diff --git a/paper/project.bib b/paper/project.bib
new file mode 100644
index 0000000..f817c59
--- /dev/null
+++ b/paper/project.bib
@@ -0,0 +1,10 @@
+@article{lindquist2008statistical,
+  title={The statistical analysis of fMRI data},
+  author={Lindquist, Martin A and others},
+  journal={Statistical Science},
+  volume={23},
+  number={4},
+  pages={439--464},
+  year={2008},
+  publisher={Institute of Mathematical Statistics}
+}
diff --git a/paper/report.tex b/paper/report.tex
new file mode 100644
index 0000000..170ad51
--- /dev/null
+++ b/paper/report.tex
@@ -0,0 +1,47 @@
+\documentclass[11pt]{article}
+
+\usepackage[margin=0.75in]{geometry}
+
+\title{The title of your project proposal}
+\author{
+  LastName1, FirstName1\\
+  \texttt{github1}
+  \and
+  LastName2, FirstName2\\
+  \texttt{github2}
+  \and
+  LastName3, FirstName3\\
+  \texttt{github3}
+  \and
+  LastName4, FirstName4\\
+  \texttt{github4}
+}
+
+\bibliographystyle{siam}
+
+\begin{document}
+\maketitle
+
+\abstract{You should have a short abstract.}
+
+\section{Introduction}
+
+Identify a published fMRI paper and the accompanying data
+\cite{lindquist2008statistical}.  You should explain the basic idea of the
+paper in a paragraph.  You should also perform basic sanity check on the data
+(e.g., can you downloaded, can you load the files, confirm that you have the
+correct number of subjects).
+
+Briefly explain what reproducibility means and in what sense you will
+try to reproduce this study.
+
+\section{Data}
+
+\section{Methods}
+\section{Results}
+\section{Discussion}
+
+
+\bibliography{project}
+
+\end{document}
diff --git a/slides/.gitignore b/slides/.gitignore
new file mode 100644
index 0000000..e69de29