Albert Einstein Science Park, Potsdam, Germany

Feb 22-23, 2018

09:00 am - 18:00 pm

Instructors: Frank Hellmann (PIK), Sebastian Heimann (GFZ), Robert Gieseke (PIK), Joachim Krois (Charité), Stefan Lüdtke (GFZ), Peter Evans (GFZ), Knut Günther (GFZ), Martin Hammitzsch (GFZ), Marvin Reich (GFZ), Benoit Bovy (GFZ), Marius Isken (GFZ)

Helpers: Berry Boessenkool (UP), Michel Wortmann (PIK), Daniel Beiter (GFZ), Daniel Kreyling (AWI), Katrin Leinweber (TIB), ...

Python Novice workshop

An Introduction to Scientific Computing and Reproducible Research

General Information

This workshop is a Python-Novice-Workshop with a focus on scientific computing and reproducible research. Everyone with basic knowledge of Python or a similar scripting language, such as R or Matlab, among others, is invited to join and getting in touch with tools and structures to write scientific code with a high-quality, that is reproducible and follows a well-documented standard. If you know what a variable and a loop are, you are fine. If you wonder whether this workshop is appropriate for you, don't hesitate to get in touch.

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, including program design, version control, data management, and task automation. 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: The course aims at scientists and researchers who are interested in extending their skills in scientific programming and techniques on "how to write good scientific code" as well as with the broader context. Basic knowledge of Python or a similar scripting language is required. If you know what a loop and a variable are, you are fine. If in doubt, get in touch. We start the workshop with an introduction to Python to get everyone on board.

Where: PIK (Potsdam Institute for Climate Impact Research), Lecture Hall in house A56, Albert-Einstein Wissenschaftspark, Telegrafenberg, 14473 Potsdam. Get directions with OpenStreetMap or Google Maps.

When: Feb 22-23, 2018. Add to your Google Calendar.

Application: Register online for the workshop by February 02, 2018. There are limited places available. The application form is found here.

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). They are also required to abide by Software Carpentry's Code of Conduct.

Accessibility: We are committed to making this workshop accessible to everybody. Please contact the organisers if you have any requirements and/or need assistance to access the workshop rooms.

Contact: Please email for more information.

Organization: We're happy to announce that these workshops are jointly organised by Potsdam Institute for Climate Impact Research (PIK), GFZ German Research Centre for Geosciences, University of Potsdam (UP), Charité – Universitätsmedizin Berlin, and others.

Workshop materials: You may access the lessons and other workshop materials via our online repository 4learners.



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

Pre-workshop Survey

Post-workshop Survey

Day 1 - 2018/02/22

09:00 Arrival & coffee
09:30 Welcome & introduction
09:45 Lightning talks by participants
10:30 Software set-up
11:00 Coffee
11:30 The Unix Shell
13:00 Lunch
14:00 Version Control with Git
15:30 Coffee
16:00 Introduction to Python
18:00 End Day 1

Day 2 - 2018/02/23

09:00 Arrival & coffee
09:30 Functions and Code Structures
11:00 Coffee
11:30 Defensive Programming
13:00 Lunch
14:00 Exploratory Data Analysis I: Time Series and plotting
15:30 Coffee
16:00 (optional) Exploratory Data Analysis II: Higher Dimensional (Spatial) Data
17:30 Wrap-up

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


The Unix Shell

  • Files and directories
  • History and tab completion
  • Pipes and redirection
  • Looping over files
  • Creating and running shell scripts
  • Finding things

Version Control with Git

  • Creating a repository
  • Recording changes to files: add, commit, ...
  • Viewing changes: status, diff, ...
  • Ignoring files

Programming with Python

  • Introduction to Python, Anaconda and Jupyter Notebooks
  • Writing functions and documentation
  • Writing modules and using version control
  • Magic functions %matplotlib inline, %timeit, %debug and %save
  • Writing simple assertions
  • Debugging, traceback and errors
  • Using numpy, pandas and xarray for scientific data analysis


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.


There will be an eduroam wlan during the workshop. We will provide WiFi guest tickets as a backup as well.

The Bash Shell

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


Video Tutorial
  1. Download the Git for Windows installer.
  2. Run the installer and follow the steps bellow:
    1. Click on "Next".
    2. Click on "Next".
    3. Keep "Use Git from the Windows Command Prompt" selected and click on "Next". If you forgot to do this programs that you need for the workshop will not work properly. If this happens rerun the installer and select the appropriate option.
    4. Click on "Next".
    5. Keep "Checkout Windows-style, commit Unix-style line endings" selected and click on "Next".
    6. Keep "Use Windows' default console window" selected and click on "Next".
    7. Click on "Install".
    8. 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.

Mac OS X

The default shell in all versions of Mac OS X is Bash, 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.


The default shell is usually Bash, but if your machine is set up differently you can run it by opening a terminal and typing bash. There is no need to install anything.


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 You will need a supported web browser (current versions of Chrome, Firefox or Safari, or Internet Explorer version 9 or above).

You will need an account at 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).

Mac OS X

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. 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.

Text Editor

When you're writing code, it's nice to have a text editor that is optimized for writing code, with features like automatic color-coding of key words. The default text editor on Mac OS X and Linux is usually set to Vim, which is not famous for being intuitive. if you accidentally find yourself stuck in it, try typing the escape key, followed by :q! (colon, lower-case 'q', exclamation mark), then hitting Return to return to the shell.


Video Tutorial

nano is a basic editor and the default that instructors use in the workshop. To install it, download the Software Carpentry Windows installer and double click on the file to run it. This installer requires an active internet connection.

Others editors that you can use are Notepad++ or Sublime Text. Be aware that you must add its installation directory to your system path. Please ask your instructor to help you do this.

Mac OS X

nano is a basic editor and the default that instructors use in the workshop. See the Git installation video tutorial for an example on how to open nano. It should be pre-installed.

Others editors that you can use are Text Wrangler or Sublime Text.


nano is a basic editor and the default that instructors use in the workshop. It should be pre-installed.

Others editors that you can use are Gedit, Kate or Sublime Text.


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. 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. Open with your web browser.
  2. Download the Python 3 installer for Windows.
  3. Install Python 3 using all of the defaults for installation except make sure to check Make Anaconda the default Python.

Mac OS X

Video Tutorial
  1. Open with your web browser.
  2. Download the Python 3 installer for OS X.
  3. Install Python 3 using all of the defaults for installation.


  1. Open with your web browser.
  2. Download the Python 3 installer 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.
  4. Type
    bash Anaconda3-
    and then press tab. The name of the file you just downloaded should appear. If it does not, navigate to the folder where you downloaded the file, for example with:
    cd Downloads
    Then, try again.
  5. Press enter. You will follow the text-only prompts. To move through the text, press the space key. 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).
  6. Close the terminal window.