TNEL Python Tutorial

These first three steps will be a great starting point for anyone trying to learn python with a slight focus on neuroscience.

This was created and is being updated by Mark Schatza schat107@umn.edu. Feel free to use/share this freely. Reach out if you have any questions!

Step 1

Setting up Python

Only for windows. Mac and Linux have python set up already. However I would still look into using anaconda as it is a very useful tool for dealing with packages.

Option 1) Install anaconda (has a bunch of very useful modules and programs built-in) (https://www.anaconda.com/distribution/)

Option 2) Install basic python (https://www.python.org/)

Learn basic python

This may take a bit depending on your experience programming. learnpython.org looks like a very good starting point. I would work through the "Learn the Basics" and "Data Science Tutorials" as a first step. Make sure you understand for loops, dictionaries, arithmetic, and if/else statements. If you want some more help there are lots of other options too. Youtube, w3schools (only up to file handling), etc. If you have no programming experience an hour a day for a week should get you more than ready for step 2.

There are also some phone apps that are really great if you're looking to learn while riding the bus!

Setting up GitHub

• Create a github account. (DON'T USE UMN EMAIL!)

• If on windows or mac, download git (https://git-scm.com/downloads).

Ensure Jupyter is installed

Open a jupyter notebook and make sure you can get to your documents folder (or wherever you will store your code).

If you can't open jupyter. Open a command line window and type "python pip install jupyter" and try again. If you're struggling I would advise to just install anaconda.

Download data from google drive

https://drive.google.com/drive/folders/1f4Ym9FUcWXKRRy745LZKMaqW3Pwtpzs2?usp=sharing

Contact me schat107@umn.edu if you are having trouble accessing.

Step 2

Setting up GitHub

• Open Git Bash (or terminal if Linux/Mac)

• Use commands "cd" (change directory) and "ls" (list) to change to where you want to save your files. i.e. "cd Documents". Look up a "bash command tutorial" for more information.

• Create a new folder for GitHub "mkdir GitHub" (make directory), and go into it "cd GitHub".

• Now back to your browser and go to our github repository (https://github.com/tne-lab/learning-python). Click fork in the upper right corner. Then click on your account. This will make a private version for yourself.

• Now go to your private repo (https://github.com/CHANGETOYOURUSERNAME/learning-python) and copy the link from the green clone button.

• Back to git bash and type "git clone https://github.com/CHANGETOYOURUSERNAME/learning-python". This creates a local copy for yourself.

Move data into working folder

Create a folder called data in learning-python folder. Copy folder Sample_Data (from google drive) into here.

Open Main in juypter (in cmd line type: "jupyter notebook". You should then see it open in your browser)

Start a juypter notebook and open up the main.ipynb file which is located in the folder that you cloned from github.

Step 3

Push your new changes to github so they will be backed up.

• Return to git bash and "cd" into your learning-python folder.

• Use the command "git add -A" to add all files to be staged to be commited.

• Use the command "git commit -m "My first commit"" to commit the changes. This means that these files are the most up to date changes.

• Use the command "git push" to push the files up your github repository so they will be saved both locally and in the cloud. Go to your github repo (https://github.com/CHANGETOYOURUSERNAME/learning-python) and make sure your new changes are there.