Software Setup

In short, you’ll need:

  • Exercise files (Download)

  • Python and Jupyter (Recommended: Anaconda)

  • Tabula and WebPlotDigitizer (Free software)

If you have any issues with these steps: Please ask a TA! We will gladly help you set up your environment.

Exercises Files

We will work through a number of programming exercises in this workshop. We have consolidated the exercise notebooks and installation files in a single zip; download the following and unzip.

Save this to a stable location on your computer; for instance, your Documents folder.

Python and Jupyter Installation

We recommend Anaconda python, which will provide almost everything you need. Make sure to install python version >= 3.0.

Windows Installation

If you are on Windows, you may need to install Visual C++ Build Tools. You will need to download the file under Tools for Visual Studio 2019 > Build Tools for Visual Studio 2019: This Stack Overflow post gives more details; note that Microsoft continually “updates” these links. If the build tools link above does not work for you, try Googling "microsoft visual c++ build tools": This is (honestly!) the best way to find a working link.

Make sure to select the build tools

When installing Visual C++, you may see the following interface. If yes, do not click launch; instead, first click Modify.

Click Modify

Within this menu, make sure the C++ build tools are selected, as pictured below.

Select C++

Once you’ve selected these tools, you can click Install.

Tutorial: Using a Terminal

Many software tools are most easily accessed through a programmatic interface called a terminal. This section is a brief tutorial on using a terminal. We will make minimal use of the terminal in this workshop, but it will be absolutely essential for setting up your computer for the workshop. Please ask a TA if you have any issues using a terminal.

Opening a terminal

  • Mac: terminal.app is your terminal – you can find this through Spotlight search (Command + Spacebar).

  • Windows: After you have installed Anaconda python, you will have access to Anaconda prompt – use this as your terminal for the workshop.

  • Linux: If you’re on Linux, you probably already use a terminal regularly. On Ubuntu the shortcut to open a terminal is Ctrl + Alt + T.

After opening your terminal, you should see a window that looks something like the following.

terminal example

To use the terminal, you manually type commands, then press Enter to execute.

Changing directory

When looking for files (Mac: Finder, Windows: Explorer, Linux: e.g. Nautilus), we use a program to look at directories. Your terminal does something similar – at any point it is located in a particular directory. The following screenshot illustrates changing directories (cd) to my Downloads folder, then listing (ls) the contents of said directory. This is where I placed the exercises.zip archive for the workshop. (Note: On Windows, you must use the command dir, rather than ls.)

terminal change directories

I unzip the archive exercises.zip from within terminal with the command unzip exercises.zip -d exercises, which results in the following:

terminal unzip

Note: On Windows, instead of unzip, you will need to run tar -xf exercises.zip.

I can then cd into the unzipped folder and install the required Python packages with pip install -r requirements.txt. However, I can only do this after I’ve installed Anaconda!

Python Module Installation

Once you have installed python, you will need to install a handful of python modules to complete all the workshop exercises. Anaconda provides a package installer called pip; from the command line, you can simply execute the following commands.

In your terminal, change directory to where you unzipped the exercises, and execute the command:

pip install -r requirements.txt

This will install the requirements for the workshop.

terminal pip

Opening Jupyter Notebooks

Jupyter notebooks are a particular way of working with Python code. They are designated with the file extension .ipynb. Unfortunately, you cannot simply double-click on a Jupyter notebook to open it. Instead, you must launch the Jupyter client from your terminal. Navigate to the directory where you want Jupyter to launch (for the workshop, this is where you unzipped the contents of exercises.zip), and execute the command jupyter notebook.

terminal launch jupyter

This will open a webpage in your browser with a file explorer-like view; you can then click on the notebooks in that directory to open them. Go ahead and open check_install.ipynb, which you will run at the end of installation to check if everything is set up correctly.

Tabula

Tabula is a free program for liberating data from PDF’s. Please follow the previous link and install Tabula before the workshop.

WebPlotDigitizer

WebPlotDigitizer is a free program for extracting data from images. Please follow the previous link and install WebPlotDigitizer before the workshop.

Final Check

To check that you’ve successfully set up your computer for the workshop, please run the following jupyter notebook.

Test your installation

Download and run check_install.ipynb. This is also included in the exercises.zip file above.

Navigate to the folder where you downloaded check_install.ipynb, execute the command jupyter notebook, open check_install.ipynb, and click on Cells > Run All. If you can successfully run the notebook (without errors), then you are ready for the workshop!