Code: Thesis:

This is the PhD Thesis of Stuart Mumford.

To build this thesis you should be able to run:

git clone [email protected]:Cadair/Thesis.git
cd Thesis
git annex get
conda env create -f conda_requirements.yml
source activate thesis
python run.py thesis

This assumes a few things:

1. You have pythontex, pdfLaTeX and bibtex.
2. You have conda installed.
3. You have an ssh key configured for GitLab
4. You have git-annex installed.

If you need more information continue reading!

This is based on the thesis template here. To run this you need Python 2.7 with PythonTex, PDFLaTeX and BibTeX. The Python dependencies needed are given in conda_requirements.txt.

You can build the thesis from inside a conda environment as long as you have TexLive and pythontex installed in your system path. You can create a conda environment with the following command:

conda env create -f conda_requirements.yml

activate the new environment with:

source activate thesis

The data needed to run the Python code in this thesis is managed using git-annex. Firstly, therefore, you will need to install git-annex.

Once you have installed git-annex you will need to have the GitLab Repository as a remote, as this hosts the git-annex data. If you have already cloned from GitHub you will need to run:

git remote add gitlab [email protected]:Cadair/Thesis.git

NOTE: You must have an ssh key configured on GitLab for git-annex to work. If you have cloned directly from the GitLab repository you can skip this step.

once you have this remote run:

git fetch --all
git annex get

to download the data.

Once the data has been obtained and the environment built, you can build the pdf with the following command:

python run.py thesis

This will produce a file: thesis/smumford_thesis.pdf.

The LaTeX here I used is copyright Krishna Kumar and licensed under the terms of the MIT licence. All LaTeX code (not embedded Python) is licenced under the MIT license. All Python code contained in this repository is copyright Stuart Mumford and is made availble under the MIT or 2-clause BSD license.

The actual content of the document is made availble under the terms of the CC-BY 4.0 license. The contents of Chapter 4 form part of Mumford et. al (2015) and is subject to the license of that journal. Permission for the material to be included and distributed as part of this thesis has been obtained, but derivative works are a murky area.