Software installation

This page contains instructions for installing the required software on your computer. Please make sure before the course that you have all the required software installed or in any other way access to it.

For example, the workshop could be done with a remote Jupyter server, as long as you can use the terminal from the Jupyter (you need to be able to access the command line for some lessons).

Generic list of tools required

Note: The actual installation instructions are below.

  • Python 3 (Anaconda is recommended, it will include everything)

    • including some major packages which you can find in the miniconda instructions below. Again, anaconda includes everything.

  • Text editor (several lessons, can also be done through Jupyterlab)

  • Command-line shell (several lessons, can also be done through Jupyterlab)

  • git (not needed, this lesson is usually done as a demo)

Python

We expect you to have a working Python installation with some common libraries. We recommend that you install the Anaconda python distribution. The Anaconda Navigator provides a convenient way to access the software.

Other options

We recommend Anaconda, Anaconda Navigator, and JupyterLab in these instructions because it is simple and can be used by everyone. We recommend that you eventually explore other options as well, but that can come later.

Any other Python distribution which you can install libraries into would work, but because there are so many different ways to do this, we don’t support them. You would need the extra libraries mentioned in the Miniconda instructions above.

JupyterLab

We do most of the lessons from JupyterLab (and JupyterLab provides most of the other tools we need). If you install the full Anaconda distribution, this will be available and can be started either through Anaconda Navigator or command line.

Verification of Python and JupyterLab

Watch the video

See this verification in video form - if you can do this, you are ready to go for day one. Your exact steps may be a bit different.

You should be able to start JupyterLab. You can do this from the Anaconda Navigator (recommended if you have it):

../_images/anaconda-navigator-jupyterlab.png

Starting JupyterLab from the Anaconda Navigator.

… or you can start JupyterLab from the command line:

$ jupyter-lab
(... Jupyter starts in a web browser)

Verify that you can start a Jupyter notebook. We will learn how to do this in day 1, but you can try running print("Hello, world!") if you want.

../_images/jupyterlab-notebook.png

Starting a Jupyter Notebook from JupyterLab.

Text editor

For one portion of the course, you will need a text editor. If you don’t know what to use, you can use the text editor that comes from JupyterLab and it will do everything you need - no extra installation needed.

Other editors

For other editors, see the CodeRefinery instructions. You don’t exactly need a terminal editor - the graphical ones, such as VSCode or whatever you use now, will work as well.

Command line

You need access to the command line for some lessons. JupyterLab includes it, so no extra installation is needed. If you want to test in advance:

  • You can start it from JupyterLab (recommended):

    ../_images/jupyterlab-terminal.png

    From the JupyterLab launcher, select “Terminal”.

Other ways to access the command line

  • From the Anaconda Navigator:

    ../_images/anaconda-prompt.png

    From the Anaconda Navigator, you can select “environments” on the left, then click on one, then the arrow, then “Open terminal”.

  • From your operating system’s terminal applications, if you activate Anaconda.

Verification of the command line

To verify command line usage, type the following commands (without the $), and you should see the corresponding output that lists the Python version:

$ python -V
Python 3.8.3

## Or python3...
$ python3 -V
Python 3.8.3

Any version of Python 3 through a recent Anaconda should work for the course.

Zoom

If this is an online workshop, it might use Zoom. You can see CodeRefinery instructions for it.

Need help?

If you have access, come to one of the installation help sessions. Or, ask your colleagues: these are standard tools and you can definitely find someone can help you get set up!

See also