WIP: episode about environment management

episodes/99-env.md

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+---
+title: Managing your Project Environment
+---
+
+:::::::::::::::::::::::::::::: questions
+
+FIXME
+
+::::::::::::::::::::::::::::::::::::::::
+
+::::::::::::::::::::::::::::: objectives
+
+* Identify some advantages of creating an environment for their scripts to run in.
+* Create a new environment.
+* Install Python libraries into an environment.
+* Activate and deactivate an environment.
+
+::::::::::::::::::::::::::::::::::::::::
+
+:::::::::::::::::::::::::::::::::::::::: challenge
+
+### Benefits of an Isolated Environment
+Consider the following scenarios.
+In which circumstances would it be appropriate to create a new environment to work in?
+In which would it be better to continue working in the existing environment?
+
+1. You have completed an analysis of the current inflammation data and receive a new dataset that you want to process and analyse in the same way.
+1. You want to expand your analysis to compare these two datasets in a different way that requires a new library to be installed.
+1. You need to begin a new project, which you expect to use the same libraries you already have installed in your first project environment.
+1. You need to begin a new project, which will use a completely different set of libraries to those you are currently working with.
+
+::::::::::::::::::::: solution
+
+#### Solution
+
+1. Use the same environment. This is exactly the kind of reproducible analysis that an encapsulated environment is perfect for.
+1. As this new analysis is an extension of the same project, you should use the same environment and install the new dependency there.
+1. Even though you expect to use the same libraries as you currently have installed in the existing environment, it is good practice to create a new environment anyway.
+   As a project develops we often find that we need to install a new dependency and when this happens, the environment you need for the new project will diverge from what is needed in the previous one.
+1. Create a new environment and install the dependencies there.
+
+::::::::::::::::::::::::::::::
+
+::::::::::::::::::::::::::::::::::::::::::::::::::
+
+:::::::::::::::::::::::::::::::::::::::: challenge
+
+### Creating and Managing Environments
+You want to begin a new project to keep track of the side effects from Dr. Maverick's new medication.
+
+1. Create an environment for this project, called `side-effects`. 
+1. Activate the new environment.
+1. Install the following dependencies for the project:
+    * `numpy`
+    * `matplotlib`
+    * `skimage`, a popular library for image processing
+1. Deactivate the environment.
+1. Finally, activate the `carpentries` environment for the workshop again.
+
+::::::::::::::::::::: solution
+
+1. `conda create --name=side-effects`
+1. `conda activate side-effects`
+1. `conda install numpy matplotlib skimage`
+1. `conda deactivate side-effects`
+1. `conda activate carpentries`
+
+::::::::::::::::::::::::::::::
+
+
+
+::::::::::::::::::::::::::::::::::::::::::::::::::
+
+
+:::::::::::::::::::::::::::::: keypoints
+
+FIXME
+
+::::::::::::::::::::::::::::::::::::::::