This repository (hereafter, "repo") is a collection of all documents and template files needed for the completion of a Ph.D. in physics at Drexel University. Attempts will be made to keep this repo comprehensive and up-to-date.

The LaTeX dissertation template file entitled example.tex contains a bare bones example of a dissertation. A PDF version of this example can be generated by running from the Templates directory:

$ pdflatex example.tex

The LaTeX class file, drexel-thesis.cls, required for styling and arrangement, has also been included here.

A PDF document entitled, thesismanual.pdf has also been included and contains all requirements for formatting and arrangement of a Drexel Dissertation, according to the Drexel University Office of Research and Graduate Studies. The dissertation templates, should in principle, always be up-to-date to reflect these formatting and arrangement requirements.

This repo serves as a central (public) location for hosting references and templates to aid in the formatting of a Drexel dissertation. All Drexel University graduate physics students are allowed and encouraged to use this repo. Additionally, completed thesis by former students can be hosted here. These accepted thesis are often considerably more complex than the bare template provided and may serve as a better starting point.

Below are a few rules to ensure that this resource remains useful for everyone:

• All users are granted full privileges to this repo; no exceptions.
• All users are very much encouraged (but not required) to upload their own personal dissertations as examples for less senior students.
• All users should refrain from deleting files, unless it has been determined (and ideally confirmed by a qualified person) that something is either out-of-date or incorrect.
• Users should not modify others uploaded thesis without explict permission.

• Coleman Krawczyk: Spectral Energy Distributions, Dust, and Black Hole Properties: A Statistical, Multi-Wavelength Quasar Analysis
• Edward Damon: Measurement of Paraphotons in the Double Chooz Experiment Using Articulated Arm Calibration Methods
• Travis Hoppe: On the Role of Entropy in the Protein Folding Process
• Trevor King: Open Source Single Molecule Force Spectroscopy

Git/Github has a bit of a steep learning curve. The first step is to create a complete copy of the DrexelPhysics/DissertationDocs repo to associate with your own Github account. If you do not already have a Github account, now would be a good time to create one. Creating a new (and personal) remote copy of this repo is called "forking", and only needs to be done once.

To fork the DrexelPhysics/DissertationDocs repo, simply navigate to the project repository on Github, and click on Fork, most likely located in the upper right corner of the page. Make sure to select your own account as the location.

After the repo has been forked, you now have two versions of DissertationDocs. The first is the public project (owner: DrexelPhysics), and the other is your own personal copy (UNAME/DissertationDocs); WARNING: this repo is likely still public. Avoid putting any sensitive information here.

It is now time to create a local copy of your own repo, DissertationDocs. In the command line, navigate to some location on your local machine, and create a directory called, drexelphysics. Within this directory, create another directory called, dissertationdocs. Now clone your remote repo into this repository:

$ git clone https://github.com/UNAME/DissertationDocs.git

where UNAME is your Github username. This also only needs to be done once. You are now free to create or modify files within this new local git directory.

The last thing one needs to do, is to tell git where "upstream" is located. Upstream should always point to the larger DrexelPhysics/DissertationDocs repo. This ensures that updating your personal remote and local repos will always pull from the correct location. In order to set upstream, do the following within your local git directory (inside of DissertationDocs):

$ git remote add upstream git@github.com:DrexelPhysics/DissertationDocs.git

If this has worked, a simple:

$ git remote -v

will show the following:

$ origin	https://github.com/UNAME/DissertationDocs.git (fetch)
$ origin	https://github.com/UNAME/DissertationDocs.git (push)
$ upstream	git@github.com:DrexelPhysics/DissertationDocs.git (fetch)
$ upstream	git@github.com:DrexelPhysics/DissertationDocs.git (push)

The process of setting your upstream only needs to be done once.

As an example of how to update local and remote repos, let's try adding a specific thesis folder which contains all relevant thesis files. In the command line, navigate to the git directory DissertationDocs. Within this repository, create a new directory FirstLast (where First is your first name, and Last is your last name).

$ mkdir FirstLast

First, let's add a readme file, which describes and lists all files (and perhaps non-standard LaTeX packages used) which will exist in this sub-directory. Now let's tell git to begin tracking this file.

$ cd FirstLast
$ touch README.md 
$ git add README.md 

Now git knows about this file, and all modifications to it will be tracked as well. The next step is to bring our own remote repo up to speed with our local repo containing new content.

$ git commit -am "Added README.rst."
$ git push

Once thesis files have been added to your local git repo (and these changes have been pushed to your remote repo), the last step will be to push them upstream. Pushing content upstream will be done through 'pull requests'. Navigate to the DrexelPhysics page, and click on 'Pull Request'. At the very top, click on 'New Pull Request'. Then select 'compare across forks', with the base fork as DrexelPhysics/DissertationDocs:master; the head fork should always be your version of this repo (the one that contains modified content: UNAME/DissertationDocs:first-last-thesis). Step-by-step instructions are included below:

A Note About Branches: You will notice that the above discussion of submitting a pull request does not have you using the 'master' branch of your DissertationDocs repo. This is intentional, and requires a word on branching. In general, pushing content upstream should be done by creating a branch off of your own master branch, separating out the development of a single feature from the rest of the current working project. One feature, one branch.

Let's create a new branch. For this example we're pushing thesis documents upstream.

Which branch are we currently on?

$ git branch
* master

Creating a new branch will effectively create a new copy of the entire local repository:

$ git branch first-last-thesis
$ git branch
first-last-thesis
* master
$ git checkout first-last-thesis
$ git branch
* first-last-thesis
master
$ git push --set-upstream origin first-last-thesis

Now let's make some changes. First let's create a new folder in the Examples directory.

$ cd DissertationDocs/Examples
$ mkdir FirstLast
$ cd FirstLast

Next, move all relevant files into this directory through the command line. Git doesn't know they exist yet, so we'll have to tell it to begin tracking them. We'll also

$ git add .
$ git commit -am "Adding First Last thesis files."
$ git push

The above commit/push commands are necessary because we are submitting a pull request to DrexelPhysics through our remote repo, which needs to be up to date. We are now good to follow the above instructions for submitting a pull request:

Navigate to the DrexelPhysics page, and click on 'Pull Request'. At the very top, click on 'New Pull Request'. Then select 'compare across forks', with the base fork as DrexelPhysics/DissertationDocs:master; the head fork should always be your version of this repo (the one that contains modified content: UNAME/DissertationDocs:first-last-thesis).

Next, click on 'Create pull request'. Once this has been done, navigate to the pull request you've just submitted, and if it tells you that it is ready to merge, do so. Now all users can pull down these changes from upstream.

A last word on cleaning up: The 'first-last-thesis' branch is no longer needed. First, checkout your master branch, and pull in changes from upstream:

$ git checkout master
$ git fetch upstream
$ git merge upstream/master
$ git push

Check to make sure that your changes are present before contining on to the next step.

Now, we can delete the feature branch:

$ git branch -d first-last-thesis

You now have successfully added all of your thesis documents to your local, remote, and upstream repositories.

Luckily, most things in git can be un-done. Even if you think you've done irreparable damage to your repo, chances are, you haven't. For questions, comments, and concerns, contact:

Austen Groener: austen.m.groener (at) drexel.edu/austen.groener (at) gmail.com