WHOI Python Workshop Series

Woods Hole Oceanographic Institution

Online

See schedule below for workshop dates and times

Instructors: Harriet Alexander, Stewart Jamieson

Helpers: Stace Beaulieu, Levi Cai, Arianna Krinos

General Information

Software Carpentry aims to help researchers get their work done in less time and with less pain by teaching them basic research computing skills. Python is one of the best first programming languages to learn because new practitioners can quickly learn the skills necessary to perform highly useful tasks such as data processing, analysis, and plotting. For this reason among others, Python is one of the most highly recommended first languages for data scientists.

Bash and Git are two other essential components of most data scientist toolkits. Bash is a general purpose tool that makes it easy to manipulate the files on your computer by enabling you to reorganize, split, or combine files, or run the same operation on many files. Git is the most popular version-control software and the saviour of many theses and research projects. It enables you to save snapshots of a project at different points in time, backup the project on a cloud service like GitHub in case of a computer failure, and even collaborate on the project with other researchers.

The instructors seek to provide all participants with a fun and accessible learning environment. Participants will be encouraged to help one another and to apply what they have learned to their own research problems. These workshops are sponsored by a WHOI Academic Programs Doherty Award.

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

Who: The course is aimed at undergraduate and graduate students. You don't need to have any previous knowledge of the tools that will be presented at the workshop.

Where: This training will take place online. The instructors will provide you with the infromation you will need to connect to this meeting.

When: See schedule below for workshop dates and times. Add to your Google Calendar.

Requirements: Participants must bring a laptop with a Mac, Linux, or Windows operating system (not a tablet, Chromebook, etc.) that they have administrative privileges on. They should have a few specific software packages installed (listed below).

Accessibility: We are dedicated to providing a positive and accessible learning environment for all. Please notify the instructors in advance of the workshop if you require any accommodations or if there is anything we can do to make this workshop more accessible to you.

Contact: Please email halexander@whoi.edu or sjamieson@whoi.edu for more information.


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.


Collaborative Notes

We will use this collaborative document for chatting, taking notes, and sharing URLs and bits of code.


Surveys

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

Pre-workshop Survey

Post-workshop Survey


Schedule

June 16 12:00 - 15:00 EDT

Before Pre-workshop survey
Before Install the bash shell
12:00 Introducing the Unix Shell
13:25 Short break
13:35 Automating Tasks with the Unix Shell
15:00 END

June 18 12:00 - 15:00 EDT

Before Install Git
12:00 Version Control with Git
13:25 Short break
13:35 Using Git in Teams
15:00 END

June 19 13:00 - 16:00 EDT

Before Install Python (Anaconda)
13:00 Python Fundamentals
14:25 Short break
14:35 Python Loops and Conditionals
16:00 END

June 22 13:00 - 16:00 EDT

13:00 Writing Functions in Python
14:25 Short break
14:35 Writing Safe and Correct Code
16:00 END

June 25 13:00 - 16:00 EDT

13:00 Using Tabular Data in Python
14:25 Short break
14:35 Visualizing Data in Python
16:00 END
After Post-workshop survey

Syllabus

The Unix Shell

  • Files and Directories
  • History and Tab Completion
  • Pipes and Redirection
  • Looping Over Files
  • Creating and Running Shell Scripts
  • Finding Things
  • Reference...

Programming in Python

  • Using Libraries
  • Working with Arrays
  • Loops and Conditionals
  • Creating and Using Functions
  • Defensive Programming
  • Reading and Plotting Data
  • Reference...

Version Control with Git

  • Creating a Repository
  • Recording Changes to Files: add, commit, ...
  • Viewing Changes: status, diff, ...
  • Ignoring Files
  • Working on the Web: clone, pull, push, ...
  • Resolving Conflicts
  • Open Licenses
  • Where to Host Work, and Why
  • Reference...

Setup

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

We maintain a list of common issues that occur during installation as a reference for instructors that may be useful on the Configuration Problems and Solutions wiki page.

The Bash Shell

Bash is a commonly-used shell that gives you the power to do simple tasks more quickly. In addition to installing Bash (see OS-specific instructions below), please download data-shell.zip to your desktop and unzip/extract it. You should then have a folder called "data-shell" on your desktop.

Video Tutorial
  1. Download the Git for Windows installer.
  2. 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 "Enable file system caching" and "Enable Git Credential Manager" are selected and click on "Next".
    8. Click on "Install".
    9. Click on "Finish".
  3. 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.

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 enter/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".

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/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.

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 (described above).

Video Tutorial

For OS X 10.9 and higher, 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.

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.

Python

Python is a popular language for research computing, and great for general-purpose programming as well. Installing all of its research packages individually can be a bit difficult, so we recommend Anaconda, an all-in-one installer.

Regardless of how you choose to install it, please make sure you install Python version 3.x (e.g., 3.6 is fine).

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).

Video Tutorial
  1. Download the Anaconda for Windows installer with Python 3 -- you probably want this one, the 64-bit graphical installer. Otherwise, open https://www.anaconda.com/distribution/#download-section with your web browser to find the correct download, making sure to choose the Python 3.7 version.
  2. 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
  1. Download the Anaconda Installer with Python 3 for macOS -- you probably want this one, the 64-bit graphical installer. Otherwise, open https://www.anaconda.com/distribution/#download-section with your web browser to find the correct download, making sure to choose the Python 3.7 version.
  2. Install Python 3 by running the Anaconda Installer using all of the defaults for installation.
  1. Download the Anaconda Installer with Python 3 for Linux -- you probably want this one, the 64-bit installer. Otherwise, open https://www.anaconda.com/distribution/#download-section with your web browser to find the correct download, making sure to choose the Python 3.7 version.
    (The installation requires using the Bash shell. If you aren't comfortable doing the installation yourself stop here and request help at the workshop.)
  2. Open a terminal window and navigate to the directory where the executable is downloaded (e.g., `cd ~/Downloads`).
  3. Type
    bash Anaconda3-
    and then press Tab to autocomplete the full file name. The name of file you just downloaded should appear.
  4. Press Enter. 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 to approve the default location for the files. Type yes and press Enter to prepend Anaconda to your PATH (this makes the Anaconda distribution the default Python).
  5. Close the terminal window.