Update set up instructions

_episodes/setup.md

@@ -1,44 +1,135 @@
-# Setup
+# Computer Set Up
 
-````{admonition} Overview
-:class: overview
+Completing this tutorial requires installing software and setting up a Python environment.
+If you are doing any kind of code development and are on Windows, we recommend installing the Windows Subsytem for Linux.
 
-Questions:
-- How do I setup my computer for the lessons?
+```{admonition} Windows users take note
+:class: attention
 
-Objectives:
-- Install anaconda for creating virtual environments.
-- Install lesson requirements in a conda environment.
-- Obtain lesson example materials.
+If you are working on a Windows computer, 
+participation in this workshop will require you to install the Windows Subsystem for Linux (WSL).
+You should install WSL 2, you will need to have the Windows 10 or Windows 11 OS with the following version requirements:
+
+* For x64 systems: Version 1903 or higher, with Build 18362 or higher.
+* For ARM64 systems: Version 2004 or higher, with Build 19041 or higher.  
+
+If you haven't updated your computer in a while, 
+these updates could take a considerable amount of time. 
+Plan accordingly!
+
+If you are on Windows 11, you can also [set up WSL to be able to use graphical interfaces](https://docs.microsoft.com/en-us/windows/wsl/tutorials/gui-apps).
+
+As an alternative to WSL, or in addition to it, you can setup and use a Docker container to follow along with the workshop.
+```
+
+Please follow the instructions given here to make sure you have the necessary software installed. 
+We will be using Python and the conda package manager. 
+If you are on MacOS, Linux, or WSL and you already have Anaconda (or Miniconda) installed,
+skip to the environment creation portion of these set-up instructions. 
+If you do not have Anaconda or Miniconda installed please see the appropriate section below. 
+**Note** If you are on Windows Miniconda has to be installed on WSL (not Windows). 
+This might be a separate installation.
+
+```{admonition} Anaconda vs. Minconda
+:class: info
+
+Anaconda is a distribution of Python, the conda package manager, and several third-party libraries that are commonly used in data science.
+Miniconda contains only Python and the conda package manager. You will be able to install any package you would like later using Miniconda. 
+Miniconda will take up a lot less space on your computer.
+We will be learning to manage conda environments and install the packages we need, so we consider Miniconda to be the better option between the two.
+If you already have Anaconda installed, however, there is no need to install Miniconda.
+```
+
+`````{admonition} Ensure that your conda version is up-to-date
+:class: tip
+
+If you already have `conda` installed using Anaconda or Miniconda,
+you should make sure your `conda` version is up-to-date.  
+Ensuring you have an up-to-date version of `conda` will ensure that you are more easily able to install the packages we will be using in this workshop.
+
+
+````{tab-set-code}
+
+```{code-block} shell
+conda update -n base conda
+```
 ````
 
-## Installing Python through Anaconda
-[Python](https://python.org/) is a popular language for scientific computing, and great for general-purpose programming as well. Installing all of its scientific packages individually can be a bit difficult, however, so we recommend the all-in-one installer Anaconda.
+`````
+
+## Installing WSL (Windows users only)
+If your computer uses the Windows operating system, we require installing Windows Subsystem for Linux (WSL). 
+Follow the installation instructions at [this link](https://docs.microsoft.com/en-us/windows/wsl/install). 
+If you don’t have a preference for Linux distribution, we recommend installing Ubuntu 22.04. 
+
+Once WSL is installed, open your ‘Start’ menu and choose ‘Ubuntu’. 
+This will open a terminal window. 
+A terminal is an interface you can use to interact with your computer using text.
+The first time you open Ubuntu, you may see a message which says “Installing, this may take a few minutes…”. 
+After the installation is done, you will have to create a username and password. 
+After these are created, you should be able to use the terminal.
+
+The Windows Subsystem for Linux is like running another computer inside your computer. 
+It is a different operating system with different software installed than your Windows computer. 
+For the WSL, you have to install Miniconda from the terminal in your Linux operating system. 
+Note that if you are using the WSL, 
+your Linux OS is completely separated from your Windows operating system. 
+This means that software installed on one operating system is not available on the other. 
+If you are running the Windows 11 operating system, 
+you can [set up WSL to use graphical interfaces on your computer](https://docs.microsoft.com/en-us/windows/wsl/tutorials/gui-apps). 
+Otherwise, you will only be able to interact with WSL through the terminal (and the text editor VSCode, 
+see later in the set-up for information on how to use VS Code in WSL).
+
+## Miniconda Installation
+You can install Miniconda through a graphical interface or using your terminal. 
+Pick either "Graphical Installation" or "Text-based (terminal) Installation". 
+**If you are using WSL, it may be easiest to complete this using the terminal installation.**
+
+### Graphical Installation
+Obtain the latest version of Miniconda for your OS at this [link](https://docs.conda.io/en/latest/miniconda.html). 
+This will download an installer you can run to install Miniconda on your system. 
+Note that if you are using WSL, you will need the **Linux** installer, 
+and you will have to move this file to WSL before running. 
+
+### Text-based (terminal) Installation
+You can also use the terminal to download and install the Miniconda compilers using the terminal. 
+If you are using Linux or WSL, type the following into your terminal.
+
+````{tab-set-code}
 
-Regardless of how you choose to install it, *please make sure you install Python version 3.x (e.g., 3.4 is fine, 2.7 is not)*.  Also, please set up your python environment at least a day in advance of the workshop. If you encounter problems with the installation procedure, the instructors will be available 30 minutes before the workshop begins to help you.
+```{code-block} shell
+curl -O https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
+bash Miniconda3-latest-Linux-x86_64.sh
+```
+````
 
-## Windows - [Video Tutorial](https://www.youtube.com/watch?v=xxQ0mzZ8UvA)
+If you are using a Mac, you should pick the appropriate link for your architecture from the Miniconda installer page.
 
-1. Open the [Anaconda Windows download page](https://www.anaconda.com/download/#windows).
-2. Download the installer.  **Be sure you get the Python 3 version.**
-3. Double-click the installer icon and follow the setup instructions on screen.  You can use MOST of the default options.  The only exception is to check the **Make Anaconda the default Python** option.
+M1: https://repo.anaconda.com/miniconda/Miniconda3-latest-MacOSX-arm64.sh  
+x86: https://repo.anaconda.com/miniconda/Miniconda3-latest-MacOSX-x86_64.sh
 
-## Mac OS X - [Video Tutorial](https://www.youtube.com/watch?v=TcSAln46u9U)
+After installation, 
+close and reopen your terminal window. 
+If you do not see `(base)` before your username on the command line, type
 
-1. Open the [Anaconda MacOS download page](https://www.anaconda.com/download/#macos).
-2. Download the installer. **Be sure you get the Python 3 version.**
-3. Double click the installer icon and follow the setup instructions.  You can use all of the default options.
 
-## Obtain lesson materials
+````{tab-set-code}
+
+```{code-block} shell
+conda init
+```
+````
+
+## Make Lesson Environment
 We are utilizing two Molecular Dynamics packages to show examples of some of the design patterns.
-[MDanalysis] and [MDTraj] are both available through conda-forge.
+[MDanalysis](https://www.mdanalysis.org) and [MDTraj](http://mdtraj.org) are both available through conda-forge.
 
 To start, open an Anaconda prompt.
 Then enter 
 ````{tab-set-code} 
 
 ```{code-block} shell
-conda create --name design_patterns python=3.9
+conda create --name design_patterns "python=3.11"
 ```
 ````
 
@@ -49,7 +140,7 @@ We now need to activate our new environment.
 ````{tab-set-code} 
 
 ```{code-block} shell
-$ conda activate design_patterns
+conda activate design_patterns
 ```
 ````
 
@@ -58,25 +149,67 @@ Then we will install MDAnalysis and MDTraj.
 ````{tab-set-code} 
 
 ```{code-block} shell
-$ conda install -c conda-forge mdanalysis
+conda install -c conda-forge mdanalysis mdtraj numpy
 ```
 ````
 
+
+
+
+
+## Downloading Workshop Materials<a name="materials_download"></a>
+
+We have included a sample trajectory file to use with the example design patterns.
+The [provided trajectory](./data/protein.pdb) was extracted from the [MDAnalysisTests](https://pypi.org/project/MDAnalysisTests/)
+
+- {download}`Starting materials for lesson <../data/protein.pdb>`.
+
+
+## Text Editor
+Everyone should have a text editor they can use to edit code. 
+If you do not have a preference for text editors, we recommend [Visual Studio Code](https://code.visualstudio.com/). 
+If you are using WSL, see [these instructions](https://code.visualstudio.com/docs/remote/wsl) for installing Visual Studio Code for use with WSL.
+If you are using Mac, follow [these instructions](https://code.visualstudio.com/docs/setup/mac#:~:text=Launching%20from%20the%20command%20line,code'%20command%20in%20PATH%20command.) to set-up VS Code so that you can use it from the command line.
+
+```{admonition} Remote Development Extension (for WSL or ssh)
+:class: tip
+
+The [Remote Development Extension](https://marketplace.visualstudio.com/items?itemName=ms-vscode-remote.vscode-remote-extensionpack) will allow you to connect to remote machines (like an HPC system) and use VS Code as if it were running on your local machine.
+This can be **very** useful for computational scientists.
+
+Note that if you are using WSL, you will *have* to install this extension to use VS Code with WSL.
+This is in the [above linked instructions](https://code.visualstudio.com/docs/remote/wsl).
+```
+
+When using VSCode with the Python extension, you will want to have it use the correct Python version and installation for analyzing your code.
+You will want it to use the Python installation and packages that are installed in the `design_patterns` environment you created earlier.
+
+To set the Python interpreter for VSCode, first open a Python file using the editor.
+In order to change the Python interpreter, you will need to have a Python file open.
+Open a Python file called `test.py` by typing
+
 ````{tab-set-code} 
 
 ```{code-block} shell
-$ conda install -c conda-forge mdtraj
+code test.py
 ```
 ````
 
+Once you have an editor open, you can click the button on the bottom of VSCode, shown in the screenshot below as (1) (this could also say a Python version like "3.10"). 
+Alternatively, you can open the command palette (Ctrl+Shift+P on Windows/Linux, Cmd+Shift+P on Mac) and type "Python: Select Interpreter".
 
-We have included a sample trajectory file to use with the example design patterns.
-The [trajectory] was extracted from the [MDAnalysisTests]
+```{image} ../fig/vscode-button1.png
+:align: center
+```
+
+After you have clicked the button, you will see a list of Python interpreters that VSCode can use.
+You will want to choose the one that is in your `design_patterns` environment.
+
+```{image} ../fig/vscode-button2.png
+:align: center
+```
 
+You should do this for every Python file or project that you open in VSCode.
+Once you have correctly set your Python environment, VSCode can analyze your code as you write it.
+VSCode will be able to check that certain libraries are installed in your environment or that functions are being called correctly.
 
-{% include links.md %}
-[trajectory]: ./data/protein.pdb
-[MDAnalysisTests]: https://pypi.org/project/MDAnalysisTests/
-[MDAnalysis]: https://www.mdanalysis.org/
-[MDTraj]: http://mdtraj.org/1.9.0/
-[NumPy]: http://www.numpy.org/