UCSD Carpentries Bootcamp: Python, Unix Shell, & Git

Software Carpentry aims to help researchers get their work done in less time and with less pain by teaching them basic research computing skills. This hands-on workshop will cover basic concepts and tools used with the Python programming language and version control with Git. Participants will be encouraged to help one another and to apply what they have learned to their own research problems.

For more information on what we teach and why, please see our paper "Best Practices for Scientific Computing".

Who: This workshop is open to UCSD students, staff, and faculty.

You don't need to have any previous knowledge of programming or the tools presented in the workshop to attend. A laptop is required for each session.

Where: Event Room (G1E), Geisel Library, 9500 Gilman Drive, La Jolla, CA.

Requirements: Participants must bring a laptop with a few specific software packages installed (listed below).

Contact: Please mail kkt008@ucsd.edu or rotsuji@ucsd.edu for more information.

Assessment: A Co-Curricular of Record activity recognition may be requested for the student who:

Attend and participate in all sessions
Pass the post-workshop quiz

For more information on the UC San Diego Co-Curricular of Record (CCR), please visit the UCSD Engaged Learning Tools Co-Curricular Record page.

Code of Conduct

Everyone who participates in Carpentries activities is required to conform to the Code of Conduct. This document also outlines how to report an incident if needed.

Surveys

Please be sure to complete these surveys before and after the workshop.

Pre-workshop Survey

Post-workshop Survey

Schedule

Date	Session	Topics
Oct 3rd	Introduction to Python - Session 1	Jupyter Notebook - Running/Wuitting, Variables and Assignment, Data Types/Type Conversions, Built-in Functions, and Help
Oct 4th	Introduction to Python - Session 2	Libraries, Writing Functions, Reading/Writing data in Dataframes, and Pandas Dataframes
Oct 5th	Introduction to Python - Session 3	Plotting, Lists, For Loops, Looping over Datasets, and Conditionals
Oct 6th	Unix Shell & Version Control w/ Git	Unix Shell: Introduction, Navigating the file system, & working with files & directories Git: Introduction, Creating a Repository, Tracking Changes, and Collaborating

Curriculum

For this workshop we will be referencing the Plotting and Programming in Python, The UNIX Shell, and Version Control with Git Carpentries curricula.

Data

We will be using the 5 year gapminder data, the shell-lesson data, and inflammation data. Please download the both data prior to start of first session.

Collaborative Notes

We will use HackMD collaborative notes for taking notes, and sharing URLs and bits of code. Please use the following link to access the collaborative notes: https://hackmd.io/@kkt008/BJSsOgrfj.

Setup

To participate in this workshop, you will need access to the software described below. In addition, you will need an up-to-date web browser.

Python

We will teach Python using the Jupyter Notebook, a programming environment that runs in a web browser (Jupyter Notebook will be installed by Anaconda). For this to work you will need a reasonably up-to-date browser. The current versions of the Chrome, Safari and Firefox browsers are all supported (some older browsers, including Internet Explorer version 9 and below, are not).

Open https://www.anaconda.com/products/individual#download-section with your web browser.
Download the Anaconda for Windows installer with Python 3. (If you are not sure which version to choose, you probably want the 64-bit Graphical Installer Anaconda3-...-Windows-x86_64.exe)
Install Python 3 by running the Anaconda Installer, using all of the defaults for installation except make sure to check Add Anaconda to my PATH environment variable.

Video Tutorial: SWC Install Python on Windows

Open https://www.anaconda.com/products/individual#download-section with your web browser.
Download the Anaconda Installer with Python 3 for macOS (you can either use the Graphical or the Command Line Installer).
Install Python 3 by running the Anaconda Installer using all of the defaults for installation.

Video Tutorial: SWC Install Python on Mac

Open https://www.anaconda.com/products/individual#download-section with your web browser.
Download the Anaconda Installer with Python 3 for Linux.
(The installation requires using the shell. If you aren't comfortable doing the installation yourself stop here and request help at the workshop.)
Open a terminal window and navigate to the directory where the executable is downloaded (e.g., `cd ~/Downloads`).
Type
```
bash Anaconda3-
```
and then press Tab to autocomplete the full file name. The name of file you just downloaded should appear.
Press Enter (or Return depending on your keyboard). You will follow the text-only prompts. To move through the text, press Spacebar. Type yes and press enter to approve the license. Press Enter (or Return) to approve the default location for the files. Type yes and press Enter (or Return) to prepend Anaconda to your PATH (this makes the Anaconda distribution the default Python).
Close the terminal window.

The Bash Shell

Bash is a commonly-used shell that gives you the power to do tasks more quickly.

Download the Git for Windows installer.
Run the installer and follow the steps below:
1. Click on "Next" four times (two times if you've previously installed Git). You don't need to change anything in the Information, location, components, and start menu screens.
2. From the dropdown menu select "Use the nano editor by default" and click on "Next".
3. Ensure that "Git from the command line and also from 3rd-party software" is selected and click on "Next". (If you don't do this Git Bash will not work properly, requiring you to remove the Git Bash installation, re-run the installer and to select the "Git from the command line and also from 3rd-party software" option.)
4. Ensure that "Use the native Windows Secure Channel library" is selected and click on "Next".
5. Ensure that "Checkout Windows-style, commit Unix-style line endings" is selected and click on "Next".
6. Ensure that "Use Windows' default console window" is selected and click on "Next".
7. Ensure that "Default (fast-forward or merge) is selected and click "Next"
8. Ensure that "Enable file system caching" and "Enable Git Credential Manager" are selected and click on "Next".
9. Click on "Install".
10. Click on "Finish" or "Next".
If your "HOME" environment variable is not set (or you don't know what this is):
1. Open command prompt (Open Start Menu then type cmd and press Enter)
2. Type the following line into the command prompt window exactly as shown:
  setx HOME "%USERPROFILE%"
3. Press Enter, you should see SUCCESS: Specified value was saved.
4. Quit command prompt by typing exit then pressing Enter

This will provide you with both Git and Bash in the Git Bash program.

Video Tutorial: Windows Installation

The default shell in some versions of macOS is Bash, and Bash is available in all versions, so no need to install anything. You access Bash from the Terminal (found in /Applications/Utilities). See the Git installation video tutorial for an example on how to open the Terminal. You may want to keep Terminal in your dock for this workshop.

To see if your default shell is Bash type echo $SHELL in Terminal and press the Return key. If the message printed does not end with '/bash' then your default is something else and you can run Bash by typing bash

If you want to change your default shell, see this Apple Support article and follow the instructions on "How to change your default shell".

Video Tutorial MacOS Installation

The default shell is usually Bash and there is usually no need to install anything.

To see if your default shell is Bash type echo $SHELL in a terminal and press the Enter key. If the message printed does not end with '/bash' then your default is something else and you can run Bash by typing bash.

Git

Git is a version control system that lets you track who made changes to what when and has options for easily updating a shared or public version of your code on github.com. You will need a supported web browser.

You will need an account at github.com for parts of the Git lesson. Basic GitHub accounts are free. We encourage you to create a GitHub account if you don't have one already. Please consider what personal information you'd like to reveal. For example, you may want to review these instructions for keeping your email address private provided at GitHub.

Git should be installed on your computer as part of your Bash install (see the Shell installation instructions).

For macOS, install Git for Mac by downloading and running the most recent "mavericks" installer from this list. Because this installer is not signed by the developer, you may have to right click (control click) on the .pkg file, click Open, and click Open on the pop up window. After installing Git, there will not be anything in your /Applications folder, as Git is a command line program. For older versions of OS X (10.5-10.8) use the most recent available installer labelled "snow-leopard" available here.

Video Tutorial: SWC Install Shell, Git, and Nano on Mac

If Git is not already available on your machine you can try to install it via your distro's package manager. For Debian/Ubuntu run sudo apt-get install git and for Fedora run sudo dnf install git.