Data Carpentry with Python

Netherlands eScience Center

Online

Apr 19-22, 2021

9:00-13:00

Instructors: Dafne van Kuppevelt, Sven van der Burg

Helpers: Hanno Spreeuw, Johan Hidding, Lieke de Boer

General Information

Data Carpentry workshops teach the fundamental data skills needed to conduct research. The target audience are researchers who have little to no prior computational experience. .The workshops build on learners' existing knowledge to enable them to quickly apply skills learned to their own research. Participants will be encouraged to help one another and to apply what they have learned to their own research problems. The workshop starts with a lesson on organizing data effectively in spreadsheets, followed by a lesson on data cleaning with OpenRefine. The largest part of the workshop consists of a lesson in Python, focusing on data import, exploratory data analysis, and visualization.

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

Who: The course is aimed at graduate students and other researchers. 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 information you will need to connect to this meeting.

When: Apr 19-22, 2021. Add to your Google Calendar.

Requirements: Participants must have access to a computer 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 training@esciencecenter.nl for more information.

Roles: To learn more about the roles at the workshop (who will be doing what), refer to our Workshop FAQ.

Register: You can register via this link.


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

Day 1 . Apr 19th

09:00 Welcome and pre-workshop survey
09:15 Data Organization in Spreadsheets
10:45 Coffee break
11:00 Data Organization in Spreadsheets (continued)
12:00 Coffee break
12:15 OpenRefine for Data Cleaning
12:45 Wrap-up
13:00 END

Day 2. Apr 20th

09:00 Introduction to Python
10:15 Coffee break
10:30 Starting with Data
11:30 Coffee break
11:45 Indexing, Slicing and Subsetting DataFrames in Python
12:45 Wrap-up
13:00 END

Day 3. Apr 21st

09:00 Data types and formats
10:15 Coffee break
10:30 Combining DataFrames with Pandas
11:30 Coffee break
11:45 Data workflows and automation
12:45 Wrap-up
13:00 END

Day 4. Apr 22nd

09:00 Making plots with plotnine
10:15 Coffee break
10:30 Matplotlib and Pandas
11:30 Coffee break
11:45 Matplotlib and Pandas (continued)
12:30 Wrap-up and post-workshop Survey
13:00 END

Setup

To participate in a 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.

Install the videoconferencing client

If you haven't used Zoom before, go to the official website to download and install the Zoom client for your computer.

Set up your workspace

Like other Carpentries workshops, you will be learning by "coding along" with the Instructors. To do this, you will need to have both the window for the tool you will be learning about (a terminal, RStudio, your web browser, etc..) and the window for the Zoom video conference client open. In order to see both at once, we recommend using one of the following set up options:

This blog post includes detailed information on how to set up your screen to follow along during the workshop.

Data

There are two zip-files with data that you need to download for this workshop:

Clicking the download link will automatically download all of the files to your default download directory as a single compressed (.zip) file. To expand this file, double click the folder icon in your file navigator application (for Macs, this is the Finder application).

For a full description of the data used in this workshop see this page.

Spreadsheet program

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 Lab, a programming environment that runs in a web browser (Jupyter Lab 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).

  1. Open https://www.anaconda.com/products/individual#download-section with your web browser.
  2. 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)
  3. 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. Open https://www.anaconda.com/products/individual#download-section with your web browser.
  2. Download the Anaconda Installer with Python 3 for macOS (you can either use the Graphical or the Command Line Installer).
  3. Install Python 3 by running the Anaconda Installer using all of the defaults for installation.

Video Tutorial

  1. Open https://www.anaconda.com/products/individual#download-section with your web browser.
  2. 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.)
  3. Open a terminal window and navigate to the directory where the executable is downloaded (e.g., `cd ~/Downloads`).
  4. Type
    bash Anaconda3-
    and then press Tab to autocomplete the full file name. The name of file you just downloaded should appear.
  5. 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).
  6. Close the terminal window.