Reorganization of Jupyter content (#638)

Author: brian-rose

appendix/glossary.md

@@ -6,12 +6,12 @@ description: Glossary of terms used in Pythia Foundations.
 :::{glossary}
 
 [Binder](https://jupyter.org/binder)
-: An open-source service that allows users to create sharable, interactive computing environments from {term}`Jupyter Notebooks` and other repositories. Binder can reproduce a computational environment directly from a {term}`GitHub` repository, providing a seamless way to share and interact with code and data.
+: An open-source service that allows users to create sharable, interactive computing environments from {term}`Jupyter Notebook`s and other repositories. Binder can reproduce a computational environment directly from a {term}`GitHub` repository, providing a seamless way to share and interact with code and data.
 
 : The public service to run Binder is on <https://mybinder.org>, which is running {term}`BinderHub`. The Binder links on most Project Pythia pages point to <https://binder.projectpythia.org>, which is a Pythia-specific implementation of {term}`BinderHub` running on the NSF-supported [Jetstream2](https://jetstream-cloud.org/) cloud computing service.
 
 BinderHub
-: The underlying technology and infrastructure that powers {term}`Binder`. BinderHub deploys and manages the interactive computing environments for {term}`Jupyter Notebooks`, ensuring that users can access and share reproducible computational work.
+: The underlying technology and infrastructure that powers {term}`Binder`. BinderHub deploys and manages the interactive computing environments for {term}`Jupyter Notebook`s, ensuring that users can access and share reproducible computational work.
 
 branch
 : A separate workspace to make and track changes without impacting other branches of the code {term}`repository`.
@@ -68,19 +68,19 @@ GitHub
 issue
 : A common feature of collaborative development platforms such as {term}`GitHub` used to track bugs, request features, and manage work related for a specific repository.
 
-Jupyter Notebooks
-: The Jupyter Notebook software is an open-source web application that allows you to create and share Jupyter Notebooks (`*.ipynb` files). Jupyter Notebooks contain executable code, LaTeX equations, visualizations (e.g., plots, pictures), and narrative text. The code does not have to just be Python, other languages such as Julia or R are supported as well. Jupyter Notebooks are celebrated for their interactive output that allows movement between code, code output, explanations, and more code - similar to how scientists think and solve problems. Jupyter Notebooks can be thought of as a living, runnable publication and make for a great presentation platform. See also {term}`Jupyter Kernels`, {term}`Jupyter Lab`, {term}`Jupyter Hub`, {term}`Binder`, and {term}`BinderHub`.
+Jupyter Notebook
+: Jupyter Notebooks (`*.ipynb` files) are computational narrative documents that can contain executable code, LaTeX equations, visualizations (e.g., plots, pictures), and richly formatted text. The code is not limited to just Python, other languages such as Julia or R are supported as well. Jupyter Notebooks are celebrated for their interactive output that allows movement between code, code output, explanations, and more code — similar to how scientists think and solve problems. Jupyter Notebooks can be thought of as a living, runnable publication and make for a great presentation platform. See also {term}`Jupyter Kernels`, {term}`JupyterLab`, {term}`JupyterHub`, {term}`Binder`, and {term}`BinderHub`.
 
 Jupyter Kernels
-: Software engines and their environments (e.g., conda environments) that execute the code contained in {term}`Jupyter Notebooks`.
+: Software engines and their environments (e.g., conda environments) that execute the code contained in a {term}`Jupyter Notebook`.
 
-Jupyter Lab
-: A popular web application on which users can create and write their {term}`Jupyter Notebooks`, as well as explore data, install software, etc. You can find more information on running Jupyter Lab [here](https://jupyter.org/install).
+JupyterLab
+: A popular web application on which users can create and execute {term}`Jupyter Notebook` files, as well as explore data, install software, etc. You can find more information on running JupyterLab [here](https://jupyter.org/install).
 
 : See @installing-python-in-jupyter for more.
 
-Jupyter Hub
-: A web-based platform that authenticates users and launches {term}`Jupyter Lab` applications for users on remote systems.
+JupyterHub
+: A web-based platform that authenticates users and launches {term}`JupyterLab` applications for users on remote systems.
 
 Linux
 : A free and open-souce operating system based on [Unix](wiki:Unix).
@@ -89,7 +89,7 @@ local
 : Refering to something, such as a {term}`Git` repository, on your computer rather than a remote server.
 
 Markdown
-: A simple, human-readable text language used extensively in {term}`Jupyter Notebooks`, on {term}`GitHub` and other code repositories, and elsewhere on the Internet (e.g., forums and blogs). Markdown lets us write readable plain text that can rendered as nicely styled text on web pages and other media, with headings, links, and other formatting.
+: A simple, human-readable text language used extensively in {term}`Jupyter Notebook`s, on {term}`GitHub` and other code repositories, and elsewhere on the Internet (e.g., forums and blogs). Markdown lets us write readable plain text that can rendered as nicely styled text on web pages and other media, with headings, links, and other formatting.
 
 merge
 : A specific type of commit that combines changes from two branches.

appendix/template.ipynb

@@ -126,7 +126,7 @@
    "metadata": {},
    "source": [
     "### A content subsection\n",
-    "Divide and conquer your objectives with Markdown subsections, which will populate the helpful navbar in Jupyter Lab and here on the Jupyter Book!"
+    "Divide and conquer your objectives with Markdown subsections, which will populate the helpful navbar in JupyterLab and here on the Jupyter Book!"
    ]
   },
   {

foundations/conda.md

@@ -19,7 +19,9 @@ Here we will cover:
 | --------------------------------------------------------------------------------------------------------- | ---------- | ----- |
 | [Installing and Running Python](how-to-run-python.md)                                                     | Helpful    |       |
 
-- **Time to learn**: 20 minutes
+:::{tip icon=false} ⏱️ Time to learn
+20 minutes
+:::
 
 ---
 

foundations/getting-started-jupyter.ipynb

@@ -0,0 +1,15 @@
+# Getting Started with Jupyter
+
+```{image} https://jupyter.org/assets/homepage/main-logo.svg
+:width: 200px
+```
+
+Project Jupyter [@https://doi.org/10.1109/MCSE.2021.3059263] is a project and community whose goal is to
+
+> develop open-source software, open-standards, and services for interactive computing across dozens of programming languages.
+>
+> -- [Wikipedia: Project Jupyter](wiki:Project_Jupyter)
+
+Jupyter lets us create expressive, interactive computational narratives, and execute them on a wide variety of computing platforms from a local laptop to a remote supercomputer.
+
+In this section, we will first go over the key [components of the Jupyter ecosystem](jupyter-components.md) and discuss local vs. remote execution. Next we will give an [overview of JupyterLab](jupyterlab.ipynb), which is our recommended software environment for scientific analysis and visualization. Then we take a deeper dive into creating and running [Jupyter notebooks](jupyterlab-notebooks.ipynb) with Python code in JupyterLab. Finally we give some references for working with [Markdown](markdown.md) to create expressive formatted text in notebooks.

foundations/getting-started-jupyter.md

@@ -54,7 +54,7 @@ That's the first thing to understand. GitHub is a web-based platform for hosting
 
 #### A little history and nomenclature
 
-Git has been around [since the mid-2000s](https://en.wikipedia.org/wiki/Git). It was originally written by Linus Torvalds specifically for use in development of the Linux kernel. Git is [FOSS](https://foundations.projectpythia.org/foundations/github/what-is-github#free-and-open-source-software-foss) and comes pre-installed on many Linux and macOS systems.
+Git has been around [since the mid-2000s](https://en.wikipedia.org/wiki/Git). It was originally written by Linus Torvalds specifically for use in development of the Linux kernel. Git is [FOSS](what-is-github#free-and-open-source-software-foss) and comes pre-installed on many Linux and macOS systems.
 
 :::{note}
 Don't have git on your system already? Check out these [installation guides from the Carpentries](https://swcarpentry.github.io/git-novice/#installing-git).

foundations/github/basic-git.md

@@ -33,7 +33,7 @@ Now that you have become more familiar with how to use Git and GitHub, you might
 
 ## Suggest a change
 
-One simple way to contribute is to fix a typo or suggest a change to one of the tutorials. For example, in the [Computations and Masks with Xarray tutorial](https://foundations.projectpythia.org/core/xarray/computation-masking), let's suggest a clarification that the sea surface temperature is called `tos` in the dataset we are using.
+One simple way to contribute is to fix a typo or suggest a change to one of the tutorials. For example, in the [Computations and Masks with Xarray tutorial](../../core/xarray/computation-masking), let's suggest a clarification that the sea surface temperature is called `tos` in the dataset we are using.
 
 ```{image} ../../images/GitHubContrXarray.png
 :alt: Computations and Masks with Xarray
@@ -84,7 +84,7 @@ Now, going to our remote repo on GitHub, forked from `pythia-foundations`, we se
 :alt: GitHub Forked Repo
 ```
 
-Project Pythia has an automated reviewer system: when a PR is created, two members of the organization will be randomly chosen to review it. If your PR is not immediately ready to be approved and merged, open it as a draft to delay the review process. As shown in this [Git Branches section](https://foundations.projectpythia.org/foundations/github/git-branches#merging-branches), the "Draft pull request" button is found using the arrow on the "Create pull request" button.
+Project Pythia has an automated reviewer system: when a PR is created, two members of the organization will be randomly chosen to review it. If your PR is not immediately ready to be approved and merged, open it as a draft to delay the review process. As shown in this [Git branches section](git-branches.md#merging-branches), the "Draft pull request" button is found using the arrow on the "Create pull request" button.
 
 Let's add the `content` tag and open this one as a draft for now:
 

foundations/github/contribute-to-pythia.md

@@ -58,7 +58,7 @@ As you can see by the recent timestamps, these repositories are actively changin
 :class: tip
 Notice that each of the three *repositories* each exist as part of their own *organization*. In other words, the NumPy repository exists within the NumPy organization; the Xarray repo exists within the PyData org, and so forth.
 
-When you [create your own GitHub account](https://foundations.projectpythia.org/foundations/github/what-is-github), your user ID functions as the *organization*. Any repositories you create (and therefore, *own*) will exist within that org.
+When you [create your own GitHub account](what-is-github.md), your user ID functions as the *organization*. Any repositories you create (and therefore, *own*) will exist within that org.
 ```
 
 Another example is this project's [Pythia Foundations repository](https://github.com/ProjectPythia/pythia-foundations), on which this tutorial is stored. It is owned by the [Project Pythia organization](https://github.com/ProjectPythia). This organization also owns several other repositories that store the files needed to generate <https://projectpythia.org/>, among other things.