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noatgnu merged 4 commits into from
Aug 14, 2025
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Option to remove Anaconda as part of setup #1105

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Option to remove Anaconda as part of setup
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noatgnu Aug 14, 2025
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40 changes: 5 additions & 35 deletions learners/setup.md
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## Install Python

In this lesson, we will be using Python 3 with some of its most popular scientific libraries.
Although one can install a plain-vanilla Python and all required libraries by hand,
we recommend installing [Anaconda][anaconda-website],
a Python distribution that comes with everything we need for the lesson.
Detailed installation instructions for various operating systems can be found
on The Carpentries [template website for workshops][anaconda-instructions]
and in [Anaconda documentation][anaconda-install].
One can install a plain-vanilla Python and all required libraries by hand.

## Obtain lesson materials

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## Option A: Jupyter Notebook

A Jupyter Notebook provides a browser-based interface for working with Python.
If you installed Anaconda, you can launch a notebook in two ways:

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## Anaconda Navigator

1. Launch Anaconda Navigator.
It might ask you if you'd like to send anonymized usage information to Anaconda developers:
![](fig/anaconda-navigator-first-launch.png){alt='Anaconda Navigator first launch'}
Make your choice and click "Ok, and don't show again" button.
2. Find the "Notebook" tab and click on the "Launch" button:
![](fig/anaconda-navigator-notebook-launch.png){alt='Anaconda Navigator Notebook launch'}
Anaconda will open a new browser window or tab with a Notebook Dashboard showing you the
contents of your Home (or User) folder.
3. Navigate to the `data` directory by clicking on the directory names leading to it:
`Desktop`, `swc-python`, then `data`:
![](fig/jupyter-notebook-data-directory.png){alt='Anaconda Navigator Notebook directory'}
4. Launch the notebook by clicking on the "New" button and then selecting "Python 3":
![](fig/jupyter-notebook-launch-notebook.png){alt='Anaconda Navigator Notebook directory'}

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You can launch a notebook from the command line:

## Command line (Terminal)

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cd ~/Desktop/swc-python/data
```

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cd /D %userprofile%\Desktop\swc-python\data
```

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2\. Start Jupyter server

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jupyter notebook
```

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python -m notebook
```

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3\. Launch the notebook by clicking on the "New" button on the right and selecting "Python 3"
from the drop-down menu:
![](fig/jupyter-notebook-launch-notebook2.png){alt='Anaconda Navigator Notebook directory'}

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  <!-- vertical spacer -->

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IPython is an alternative solution situated somewhere in between the plain-vanilla Python
interpreter and Jupyter Notebook. It provides an interactive command-line based interpreter with
various convenience features and commands. You should have IPython on your system if you installed
[Anaconda][anaconda-instructions].
various convenience features and commands. You can install IPython on your system
[system](https://ipython.org/install.html).

To start using IPython, execute:

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winpty python
```

[anaconda-website]: https://www.anaconda.com/
[anaconda-instructions]: https://carpentries.github.io/workshop-template/install_instructions/#python
[anaconda-install]: https://docs.anaconda.com/anaconda/install

[zipfile1]: data/python-novice-inflammation-data.zip
[zipfile2]: ../episodes/files/code/python-novice-inflammation-code.zip
[gitbash]: https://gitforwindows.org
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