Skip to content

Update setup.md #2

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Open
murphyqm wants to merge 1 commit into
base: main
Choose a base branch
from
Open

Update setup.md #2

Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
146 changes: 4 additions & 142 deletions learners/setup.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -68,145 +68,7 @@ machine. Here are some instructions for you to follow *after* this course, to se
up Python on your machine.

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].

### Launch Python interface

To start working with Python, we need to launch a program that will interpret and execute our
Python commands. Below we list several options. If you don't have a preference, proceed with the
top option in the list that is available on your machine. Otherwise, you may use any interface
you like.

### 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:

::::::::::::::::: spoiler

### 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'}

:::::::::::::::::::::::::


::::::::::::::::: spoiler

### Command line (Terminal)

1\. Navigate to the `data` directory:

::::::::::::::::: spoiler

### Unix shell

If you're using a Unix shell application, such as Terminal app in macOS, Console or Terminal
in Linux, or [Git Bash][gitbash] on Windows, execute the following command:

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

:::::::::::::::::::::::::

::::::::::::::::: spoiler

### Command Prompt (Windows)

On Windows, you can use its native Command Prompt program. The easiest way to start it up is
pressing <kbd>Windows Logo Key</kbd>\+<kbd>R</kbd>, entering `cmd`, and hitting
<kbd>Return</kbd>. In the Command Prompt, use the following command to navigate to
the `data` folder:

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

:::::::::::::::::::::::::

2\. Start Jupyter server

::::::::::::::::: spoiler

### Unix shell

```bash
jupyter notebook
```

:::::::::::::::::::::::::


::::::::::::::::: spoiler

### Command Prompt (Windows)

```source
python -m notebook
```

:::::::::::::::::::::::::

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'}

:::::::::::::::::::::::::

  <!-- vertical spacer -->

### Option B: IPython interpreter

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].

To start using IPython, execute:

```source
ipython
```

  <!-- vertical spacer -->

### Option C: plain-vanilla Python interpreter

To launch a plain-vanilla Python interpreter, execute:

```source
python
```

If you are using [Git Bash on Windows][gitbash], you have to call Python *via* `winpty`:

```source
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



we recommend installing [Miniforge](https://conda-forge.org/download/), an open-source
installer. You can see a [quick start guide](https://kirenz.github.io/codelabs/codelabs/miniforge-setup/#0)
for using `conda` to run Python scripts. You can see the [Python docs](https://www.python.org/about/gettingstarted/)
here for more information.