Merge pull request #21 from oceanhackweek/copilot/update-book-content-for-jupyterhub

Restructure book for JupyterHub documentation

Author: eeholmes

book/CoC.md

@@ -1,33 +1,20 @@
 # Book settings
 # Learn more at https://jupyterbook.org/customize/config.html
 
-title: Fish-PACE Hackweek 2025
-author: content EE Holmes, template UW/eScience Institute
+title: NMFS Openscapes JupyterHub Guide
+author: NMFS Openscapes
 logo: logo.png
 only_build_toc_files: false
 
 parse:
   # https://jupyterbook.org/content/content-blocks.html?highlight=myst%20substitution#define-substitutions-for-your-whole-book
   # https://jupyterbook.org/content/content-blocks.html#using-substitutions-in-links
   myst_substitutions:
-    hackweek: "Fish-PACE Hackweek"
-    dates: "Oct 20 to 24, 2025"
-    github_org_url: "https://github.com/fish-pace"
-    book_repo: "hackweek-2025"
-    website_url: "https://fish-pace.github.io/hackweek-2025/"
     jupyterhub_url: "https://nmfs-openscapes.2i2c.cloud"
-    slack_workspace_url: "https://fish-pace.slack.com/"
-    contact_email: "eeholmes@uw.edu"
-    anon_reporting_url: ""
-    project_spreadsheet_url: "https://fish-pace.github.io/hackweek-2025/projects/list_of_projects.md"
-    l0: "<span style='color:#bbb'>{fas}`eye`</span>"
-    l1: "{fas}`eye;sd-text-primary`"
-    d0: "<span style='color:#bbb'>{fas}`download`</span>"
-    d1: "{fas}`download;sd-text-primary`"
-    v0: "<span style='color:#bbb'>{fab}`youtube`</span>"
-    v1: "{fab}`youtube;sd-text-primary`"
-    c0: "<span style='color:#bbb'>{fab}`google`</span>"
-    c1: "{fab}`google;sd-text-primary`"
+    contact_email: "nmfs.openscapes@noaa.gov"
+    github_org_url: "https://github.com/oceanhackweek"
+    book_repo: "oceanforge"
+    website_url: "https://oceanhackweek.github.io/oceanforge/"
   myst_enable_extensions:
     # Defaults
     - dollarmath
@@ -40,7 +27,7 @@ parse:
     https: null
     http: null
     mailto: null
-    nb: /hackweek-2025/_sources/presentations/notebooks/{{path}}
+    nb: /oceanforge/_sources/topics-skills/notebooks/{{path}}
 
 # See https://jupyterbook.org/content/execute.html
 execute:
@@ -59,9 +46,9 @@ latex:
 
 # Information about where the book exists on the web
 repository:
-  url: "https://github.com/fish-pace/hackweek-2025" # Online location of your book
-  path_to_book: book  # Optional path to your book, relative to the repository root
-  branch: main  # Which branch of the repository should be used when creating links (optional)
+  url: "https://github.com/oceanhackweek/oceanforge"
+  path_to_book: book
+  branch: main
 
 # Bibliography
 bibtex_bibfiles:

book/_config.yml

@@ -3,40 +3,35 @@
 root: intro
 format: jb-book
 parts:
-- caption: Details
+- caption: JupyterHub Skills
   chapters:
-    - file: logistics
-    - title: Schedule
-      url: https://fish-pace.github.io/hackweek-2025/index.html?jump_to=schedule
-    - title: Team
-      url: https://fish-pace.github.io/hackweek-2025/index.html?jump_to=team
-    - title: JupyterHub
-      url:  https://nmfs-openscapes.2i2c.cloud
-    - file: CoC
-- caption: Preparation
-  chapters:
-    - file: preliminary/index
-    - file: preliminary/checklist
-    - file: preliminary/git
-    - file: reference/intro_to_python
-- caption: Presentations
-  chapters:
-    - file: presentations/lectures
-    - file: presentations/tutorials
-    - file: presentations/extras
-- caption: Projects
-  chapters:
-    - file: projects/index
-    - file: projects/list_of_projects
-- caption: Reference
-  chapters:
-    - file: preliminary/learning
-    - url: https://ocean-satellite-tools.github.io/hyper-fish-book/
-      title: Hyperspectral products for fisheries
-    - url: https://pace.oceansciences.org/applications.htm
-      title: PACE Applications
-    - url: https://pace.oceansciences.org/data_table.htm
-      title: Data availability
-    - file: reference/glossary
-    - file: reference/questions
+    - file: topics-skills/index
+    - file: content/jhub
+      title: About the Hub
+    - file: content/setup
+      title: Quick Start
+    - file: topics-skills/01-intro-to-jupyterhub
+      title: Intro to JupyterHubs
+    - file: topics-skills/02-intro-to-lab
+      title: JupyterLab
+    - file: topics-skills/02-git
+      title: Intro to Git
+    - file: topics-skills/02-git-authentication
+      title: Git Authentication
+    - file: topics-skills/02-git-jupyter
+      title: Git in JupyterLab
+    - file: topics-skills/02-rstudio
+      title: RStudio
+    - file: topics-skills/02-git-rstudio
+      title: Git in RStudio
+    - file: topics-skills/02-git-terminal
+      title: Git in the terminal
+    - file: topics-skills/04-other-images
+      title: Other images
+    - file: topics-skills/03-earthdata
+      title: Earthdata login
+    - file: topics-skills/03-ScratchBucket
+      title: S3 Scratch Bucket
+    - file: topics-skills/03-AWS_S3_bucket
+      title: AWS S3 Bucket
 

book/_toc.yml

@@ -0,0 +1,33 @@
+# About the Hub
+
+## NMFS Openscapes JupyterHub
+
+The NMFS Openscapes JupyterHub is a cloud-based computing environment that provides access to Python, R, RStudio, and other tools for data analysis and visualization. The hub is hosted on Amazon Web Services (AWS) and is available to NOAA staff and collaborators.
+
+## Features
+
+- **Multiple Environments**: Choose from Python, R, or geospatial images with pre-installed packages
+- **RStudio Integration**: Full RStudio IDE available in your browser
+- **JupyterLab**: Modern interface for Jupyter notebooks and code editing
+- **Persistent Storage**: Your files and work are saved between sessions
+- **Shared Resources**: Access shared datasets and collaborate with colleagues
+- **Git Integration**: Built-in Git support for version control
+
+## Access
+
+The JupyterHub is available at: <https://nmfs-openscapes.2i2c.cloud/>
+
+You'll need a GitHub account to log in. Contact the NMFS Openscapes team if you need access.
+
+## Support
+
+For questions and support:
+
+- **Discussions**: <https://github.com/nmfs-opensci/NOAAHackDays/discussions>
+- **Issues**: <https://github.com/nmfs-opensci/NOAAHackDays/issues>
+- **NMFS Python User Group**: Great resource for Python questions
+- **NMFS R User Group**: <https://nmfs-opensci.github.io/NMFS-R-UG/>
+
+## Acknowledgements
+
+The NMFS Openscapes JupyterHub is supported by NOAA Fisheries and built on infrastructure from 2i2c.org. The hub setup and documentation has benefited from the work of the University of Washington eScience Institute, CryoCloud, and Openscapes communities.

book/content/jhub.md

@@ -0,0 +1,71 @@
+# Quick Start
+
+Welcome! This guide will help you get started with the NMFS Openscapes JupyterHub.
+
+## Prerequisites
+
+Before you begin, make sure you have:
+
+1. **GitHub Account**: You'll need a GitHub account to log in. Create one at <https://github.com/signup> if you don't have one.
+2. **Web Browser**: We recommend using Chrome, Firefox, or Safari. Make sure your browser is up to date.
+
+## Getting Started
+
+### Step 1: Log In
+
+1. Go to <https://nmfs-openscapes.2i2c.cloud/>
+2. Click **"Login to continue"**
+3. Log in with your GitHub account if prompted
+4. Authorize the JupyterHub application to access your GitHub account
+
+### Step 2: Select Your Environment
+
+After logging in, you'll be asked to choose:
+
+1. **Image Type**: Select the environment that matches your needs
+   - **Openscapes Python** (default): Python with geospatial packages
+   - **Openscapes R**: R and RStudio with common packages
+   - **Geospatial**: Python and R with geospatial libraries
+
+2. **Server Size**: Choose based on your computational needs
+   - **Small** (2 GB RAM): Sufficient for most tutorials and light analysis
+   - **Medium** (8 GB RAM): For larger datasets
+   - **Large** (16 GB RAM): For intensive computations (use sparingly)
+
+3. Click **Start** and wait for your server to start (may take 1-2 minutes)
+
+### Step 3: Explore the Interface
+
+Once your server starts, you'll see the JupyterLab interface with a Launcher showing:
+
+- **Notebook**: Create a new Jupyter notebook (Python, R, etc.)
+- **Console**: Interactive Python or R console
+- **Terminal**: Command-line access
+- **RStudio**: Full RStudio IDE (opens in a new tab)
+- **Other**: Text files, markdown files, and more
+
+## Next Steps
+
+Now that you're up and running:
+
+1. **Learn JupyterLab basics**: See [Intro to JupyterLab](../topics-skills/02-intro-to-lab.md)
+2. **Learn RStudio basics**: See [RStudio](../topics-skills/02-rstudio.md)
+3. **Set up Git**: See [Git in JupyterLab](../topics-skills/02-git-jupyter.md)
+4. **Explore tutorials**: Browse the skills sections in the navigation
+
+## Important Notes
+
+- **Saving Work**: Your files are automatically saved in your home directory and persist between sessions
+- **Logging Out**: Always log out when done (File → Log Out) to free up resources
+- **Automatic Timeout**: Your session will automatically shut down after 90 minutes of inactivity
+- **Lost Session**: If your server crashes, go to File → Hub Control Panel → Stop My Server, then restart
+
+## Getting Help
+
+If you run into issues:
+
+- Check the [FAQ](../topics-skills/01-intro-to-jupyterhub.md)
+- Post in [Discussions](https://github.com/nmfs-opensci/NOAAHackDays/discussions)
+- Report bugs in [Issues](https://github.com/nmfs-opensci/NOAAHackDays/issues)
+
+Happy computing!

book/content/setup.md

@@ -1,16 +1,32 @@
-# Welcome to {{hackweek}}!
+# Welcome to the NMFS Openscapes JupyterHub!
 
 ![banner](img/banner.png)
 
+## About This Guide
 
-📖 On this JupyterBook website you'll find [lectures](presentations/lectures) and [tutorials](presentations/tutorials). Lectures provide science background for how hyperspectral ocean color can be used in ocean ecosystem and fisheries contexts. Tutorials can include slides and Jupyter Notebooks, designed to be run interactively, but also rendered on this website for convenience.
+This guide provides comprehensive documentation and tutorials for using the NMFS Openscapes JupyterHub - a cloud-based computing environment for data analysis and collaboration.
 
-👩‍💻 During a Hackweek teams work collaboratively on different projects. Read more about the projects and results on our [projects page](projects/list_of_projects)
+## What You'll Find Here
 
+📚 **Getting Started**: Quick start guides to help you log in and begin using the hub
 
-```{admonition} Quick links for the event
+💻 **JupyterLab & RStudio**: Tutorials on using the JupyterLab interface and RStudio IDE
+
+🔧 **Git & Version Control**: Learn how to use Git for version control in JupyterLab, RStudio, and the terminal
+
+☁️ **Cloud Resources**: Access AWS S3 buckets, Earthdata, and other cloud resources
+
+🎯 **Skills Development**: Step-by-step tutorials to build your data science skills
+
+## Quick Access
+
+```{admonition} JupyterHub Access
 :class: seealso
-* JupyterHub: {{ jupyterhub_url }}
-* Slack Workspace: {{ slack_workspace_url }}
-* Projects Spreadsheet: {{ '[Hackweek Projects]({url})'.format(url=project_spreadsheet_url) }}
+* **JupyterHub**: <https://nmfs-openscapes.2i2c.cloud/>
+* **Support**: [GitHub Discussions](https://github.com/nmfs-opensci/NOAAHackDays/discussions)
+* **Report Issues**: [GitHub Issues](https://github.com/nmfs-opensci/NOAAHackDays/issues)
 ```
+
+## Get Started
+
+New to the JupyterHub? Start with our [Quick Start Guide](content/setup.md) to learn how to log in and set up your environment.