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setup.md

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@@ -68,145 +68,7 @@ machine. Here are some instructions for you to follow *after* this course, to se
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up Python on your machine.
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Although one can install a plain-vanilla Python and all required libraries by hand,
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we recommend installing [Anaconda][anaconda-website],
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a Python distribution that comes with everything we need for the lesson.
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Detailed installation instructions for various operating systems can be found
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on The Carpentries [template website for workshops][anaconda-instructions]
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and in [Anaconda documentation][anaconda-install].
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### Launch Python interface
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To start working with Python, we need to launch a program that will interpret and execute our
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Python commands. Below we list several options. If you don't have a preference, proceed with the
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top option in the list that is available on your machine. Otherwise, you may use any interface
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you like.
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### Option A: Jupyter Notebook
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A Jupyter Notebook provides a browser-based interface for working with Python.
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If you installed Anaconda, you can launch a notebook in two ways:
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::::::::::::::::: spoiler
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### Anaconda Navigator
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1. Launch Anaconda Navigator.
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It might ask you if you'd like to send anonymized usage information to Anaconda developers:
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![](fig/anaconda-navigator-first-launch.png){alt='Anaconda Navigator first launch'}
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Make your choice and click "Ok, and don't show again" button.
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2. Find the "Notebook" tab and click on the "Launch" button:
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![](fig/anaconda-navigator-notebook-launch.png){alt='Anaconda Navigator Notebook launch'}
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Anaconda will open a new browser window or tab with a Notebook Dashboard showing you the
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contents of your Home (or User) folder.
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3. Navigate to the `data` directory by clicking on the directory names leading to it:
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`Desktop`, `swc-python`, then `data`:
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![](fig/jupyter-notebook-data-directory.png){alt='Anaconda Navigator Notebook directory'}
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4. Launch the notebook by clicking on the "New" button and then selecting "Python 3":
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![](fig/jupyter-notebook-launch-notebook.png){alt='Anaconda Navigator Notebook directory'}
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:::::::::::::::::::::::::
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::::::::::::::::: spoiler
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### Command line (Terminal)
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1\. Navigate to the `data` directory:
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::::::::::::::::: spoiler
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### Unix shell
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If you're using a Unix shell application, such as Terminal app in macOS, Console or Terminal
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in Linux, or [Git Bash][gitbash] on Windows, execute the following command:
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```bash
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cd ~/Desktop/swc-python/data
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```
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:::::::::::::::::::::::::
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::::::::::::::::: spoiler
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### Command Prompt (Windows)
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On Windows, you can use its native Command Prompt program. The easiest way to start it up is
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pressing <kbd>Windows Logo Key</kbd>\+<kbd>R</kbd>, entering `cmd`, and hitting
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<kbd>Return</kbd>. In the Command Prompt, use the following command to navigate to
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the `data` folder:
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```source
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cd /D %userprofile%\Desktop\swc-python\data
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```
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:::::::::::::::::::::::::
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2\. Start Jupyter server
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::::::::::::::::: spoiler
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### Unix shell
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```bash
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jupyter notebook
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```
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:::::::::::::::::::::::::
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::::::::::::::::: spoiler
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### Command Prompt (Windows)
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```source
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python -m notebook
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```
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:::::::::::::::::::::::::
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3\. Launch the notebook by clicking on the "New" button on the right and selecting "Python 3"
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from the drop-down menu:
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![](fig/jupyter-notebook-launch-notebook2.png){alt='Anaconda Navigator Notebook directory'}
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:::::::::::::::::::::::::
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  <!-- vertical spacer -->
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### Option B: IPython interpreter
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IPython is an alternative solution situated somewhere in between the plain-vanilla Python
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interpreter and Jupyter Notebook. It provides an interactive command-line based interpreter with
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various convenience features and commands. You should have IPython on your system if you installed
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[Anaconda][anaconda-instructions].
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To start using IPython, execute:
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```source
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ipython
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```
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  <!-- vertical spacer -->
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### Option C: plain-vanilla Python interpreter
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To launch a plain-vanilla Python interpreter, execute:
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```source
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python
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```
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If you are using [Git Bash on Windows][gitbash], you have to call Python *via* `winpty`:
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```source
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winpty python
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```
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[anaconda-website]: https://www.anaconda.com/
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[anaconda-instructions]: https://carpentries.github.io/workshop-template/install_instructions/#python
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[anaconda-install]: https://docs.anaconda.com/anaconda/install
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[zipfile1]: data/python-novice-inflammation-data.zip
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[zipfile2]: ../episodes/files/code/python-novice-inflammation-code.zip
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[gitbash]: https://gitforwindows.org
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we recommend installing [Miniforge](https://conda-forge.org/download/), an open-source
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installer. You can see a [quick start guide](https://kirenz.github.io/codelabs/codelabs/miniforge-setup/#0)
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for using `conda` to run Python scripts. You can see the [Python docs](https://www.python.org/about/gettingstarted/)
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here for more information.

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