setup.md: reorganize and update (#778)

+ Add "Overview" section
+ Reorder items in the "Launch Python Interpreter" section
+ Move instructions from "Navigate to the data folder" to the previous section

setup.md

@@ -5,97 +5,140 @@ permalink: /setup/index.html
 root: ..
 ---
 
-### Install Python
+## Overview
 
-In this lesson we will be using Python 3 with some of its scientific libraries.
-Although one can install a "plain vanilla" Python 3 and all required libraries "by hand",
-we recommend installing [Anaconda][workshop-template-python-instructions], a Python distribution
-that comes with everything we need for the lesson.
+This lesson is designed to be run on a personal computer.
+All of the software and data used in this lesson are freely available online,
+and instructions on how to obtain them are provided below.
 
-&nbsp; <!-- vertical spacer -->
+## 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].
 
-### Obtain lesson materials
+## Obtain lesson materials
 
 1. Download [python-novice-inflammation-data.zip][zipfile1]
         and [python-novice-inflammation-code.zip][zipfile2].
 2. Create a folder called `swc-python` on your Desktop.
-3. Move downloaded files into this newly created folder.
+3. Move downloaded files to `swc-python`.
 4. Unzip the files.
 
-You should now see two new folders called `data` and `code` in your `swc-python` directory on your
+You should see two folders called `data` and `code` in the `swc-python` directory on your
 Desktop.
 
-&nbsp; <!-- vertical spacer -->
-
-### Navigate to the `data` folder
+## Launch Python interface
 
-If you're using a Unix shell application, such as Terminal app in macOS, Console or Terminal in
-Linux, or [Git Bash](https://gitforwindows.org/) on Windows, execute the following command:
-
-~~~
-$ cd ~/Desktop/swc-python/data
-~~~
-{: .source}
-
-On Windows, you can use its native Command Prompt program.  The easiest way to start it up is by
-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:
-~~~
-$ cd /D %userprofile%\Desktop\swc-python\data
-~~~
-{: .source}
+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:
+
+> ## Anaconda Navigator
+>
+> 1. Launch Anaconda Navigator.
+> It might ask you if you'd like to send anonymized usage information to Anaconda developers:
+> ![Anaconda Navigator first launch](../fig/anaconda-navigator-first-launch.png)
+> Make your choice and click "Ok, and don't show again" button.
+> 2. Find the "Notebook" tab and click on the "Launch" button:
+> ![Anaconda Navigator Notebook launch](../fig/anaconda-navigator-notebook-launch.png)
+> 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`:
+> ![Anaconda Navigator Notebook directory](../fig/jupyter-notebook-data-directory.png)
+> 4. Launch the notebook by clicking on the "New" button and then selecting "Python 3":
+> ![Anaconda Navigator Notebook directory](../fig/jupyter-notebook-launch-notebook.png)
+{: .solution}
+
+> ## Command line (Terminal)
+>
+> 1\. Navigate to the `data` directoty:
+>
+> > ## 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:
+> > ~~~
+> > cd ~/Desktop/swc-python/data
+> > ~~~
+> > {: .language-bash}
+> {: .solution}
+>
+> > ## 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:
+> > ~~~
+> > cd /D %userprofile%\Desktop\swc-python\data
+> > ~~~
+> > {: .source}
+> {: .solution}
+>
+> 2\. Start Jupyter server
+>
+> > ## Unix shell
+> > ~~~
+> > jupyter notebook
+> > ~~~
+> > {: .language-bash}
+> {: .solution}
+>
+> > ## Command Prompt (Windows)
+> > ~~~
+> > python -m notebook
+> > ~~~
+> > {: .source}
+> {: .solution}
+>
+> 3\. Launch the notebook by clicking on the "New" button on the right and selecting "Python 3"
+> from the drop-down menu:
+> ![Anaconda Navigator Notebook directory](../fig/jupyter-notebook-launch-notebook2.png)
+{: .solution}
 
 &nbsp; <!-- vertical spacer -->
 
-### Option 1: Launch "plain vanilla" Python interpreter
+## Option B: IPython interpreter
 
-To start working with Python, we need to launch a program that will interpret and execute our Python
-commands. To launch a "plain vanilla" Python interpreter, execute:
-~~~
-$ python
-~~~
-{: .source}
+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].
 
-If you are using Git Bash on Windows, you have to call Python _via_ `winpty`:
+To start using IPython, execute:
 ~~~
-$ winpty python
+ipython
 ~~~
 {: .source}
 
 &nbsp; <!-- vertical spacer -->
 
-### Option 2: Start Jupyter Notebook
-
-Jupyter Notebook provides a browser-based interface for working with Python. If you would like to
-use a notebook during the lesson, make sure to install [Anaconda](http://carpentries.github.io/workshop-template/#python)
-distribution.
+## Option C: plain-vanilla Python interpreter
 
-To start a Jupyter server, execute:
+To launch a plain-vanilla Python interpreter, execute:
 ~~~
-$ jupyter notebook
+python
 ~~~
 {: .source}
 
-Then create a new notebook by clicking "New" button on the right and selecting "Python 3" from the
-drop-down menu:
-
-![](../fig/new-notebook.png)
-
-&nbsp; <!-- vertical spacer -->
-
-### Option 3: Start 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](http://carpentries.github.io/workshop-template/#python) distribution.
-
-To start using IPython, execute:
+If you are using [Git Bash on Windows][gitbash], you have to call Python _via_ `winpty`:
 ~~~
-$ ipython
+winpty python
 ~~~
 {: .source}
 
+[anaconda-install]: https://docs.anaconda.com/anaconda/install
+[anaconda-instructions]: https://carpentries.github.io/workshop-template/#python
+[anaconda-website]: https://www.anaconda.com/
+[gitbash]: https://gitforwindows.org
 [zipfile1]: {{ page.root }}/data/python-novice-inflammation-data.zip
 [zipfile2]: {{ page.root }}/code/python-novice-inflammation-code.zip
-[workshop-template-python-instructions]: https://carpentries.github.io/workshop-template/#python