Merge branch 'main' into ALT15

README.md

@@ -1,4 +1,4 @@
 # CryoCloudWebsite
 CryoCloud JupyterBook
 
-We welcome contributions! Have a look at our [Code of Conduct](https://book.cryointhecloud.com/content/Code_of_Conduct.html) and [contributing guide](https://book.cryointhecloud.com/contributing/workflow.html).
+Thank you for checking out our content. We welcome contributions! Have a look at our [Code of Conduct](https://book.cryointhecloud.com/content/Code_of_Conduct.html) and [contributing guide](https://book.cryointhecloud.com/contributing/workflow.html).

book/_config.yml

@@ -1,9 +1,11 @@
 # Book settings
 # Learn more at https://jupyterbook.org/customize/config.html
 
-title: CryoCloud
-author: Mines Glaciology Laboratory, Colorado School of Mines
-logo: logo.png
+title :      CryoCloud
+author :     CryoCloud Team and Community, Colorado School of Mines
+logo :       logo.png
+copyright : "2022" # Goes in the footer
+
 only_build_toc_files: true
 
 parse:
@@ -30,11 +32,17 @@ parse:
     - colon_fence
     # Extras
     - html_image
+    - amsmath
+    - deflist
+    - html_admonition
+    - replacements
+    - smartquotes
+    - tasklist
 
 # Force re-execution of notebooks on each build.
 # See https://jupyterbook.org/content/execute.html
 execute:
-  execute_notebooks: 'off'
+  execute_notebooks: 'force'
 #  execute_notebooks: 'cache'
 #  exclude_patterns:
 #    - "**/dataintegration-1.ipynb"
@@ -52,6 +60,7 @@ latex:
 launch_buttons:
   notebook_interface: jupyterlab
   binderhub_url: "https://mybinder.org"
+  jupyterhub_url: "https://hub.cryointhecloud.com/"
 
 # Information about where the book exists on the web
 repository:

book/_toc.yml

@@ -34,11 +34,6 @@ parts:
             - file: how_tos/data_access/Instructions_for_configuring_AWS_S3_bucket
             - file: how_tos/data_access/CryoCloudScratchBucket
             - file: external/ICESat2_Earthaccess
-            - file: external/Earthdata_Cloud__Single_File__HTTPS_Access_COG_Example
-            - file: external/Earthdata_Cloud__Single_File_Direct_S3_Access_COG_Example
-            - file: external/Multi-File_Direct_S3_Access_COG_Example
-            - file: external/Earthdata_Cloud__Single_File__Direct_S3_Access_NetCDF4_Example
-            - file: external/Multi-File_Direct_S3_Access_NetCDF_Example
 - caption: Tutorials
   chapters:
     - file: tutorials/index
@@ -53,6 +48,7 @@ parts:
           - file: tutorials/NASA-Earthdata-Cloud-Access/2.earthdata_search
           - file: tutorials/NASA-Earthdata-Cloud-Access/3.earthaccess
           - file: tutorials/NASA-Earthdata-Cloud-Access/4.icepyx
+          - file: tutorials/NASA-Earthdata-Cloud-Access/4b.icepyx-ATL06
         - file: tutorials/SlideRule_applications/SlideRule_applications
         - file: tutorials/dask_for_geoscientists
         - file: tutorials/ARCOdata_writingZarrs
@@ -65,6 +61,7 @@ parts:
         - file: contributing/workflow
 - caption: Reference
   chapters:
+    - file: reference/projects_supported
     - file: reference/glossary
     - file: reference/IS2-resources
     - file: reference/open_science

book/content/Getting_Started.md

@@ -1,33 +1,34 @@
 # Getting started
 
-The majority of our users will join the CryoCloud through specific events, but we understand
-extenuating circumstances will prevent some members of the ICESat-2 community from being present. If you 
-are part of the ICESat-2 community and want to join the CryoCloud, please follow these instructions which 
-will guide you through taking the two onboarding surveys and gaining access to the CryoCloud. 
+The majority of our users will join CryoCloud through specific events, but we understand
+extenuating circumstances will prevent some members of our scientific communities from being present. If you 
+are part of the ICESat-2, cryosphere, or associated Earth science communities and want to join CryoCloud, please follow these instructions which 
+will guide you through taking the two onboarding surveys and gaining access to CryoCloud. 
 
 1. Fill out this short [Getting Started Survey](https://forms.gle/d8oP1gp9YikS2ixM8) to give us the 
 required credentials and information to get you on the hub.
 
 
-2. Once we have your survey, within the next day or two we will invite you to the CryoCloud GitHub organization and CryoCloudUsers team (you will receive an email when we do this from GitHub at the email you have linked to your GitHub profile). Please accept this invitation within 7 days or it will disappear and we will have to resend it. Your membership on that GitHub team provides you with access to the CryoCloud.
+2. Once we have your survey, within the next day or two we will invite you to the CryoCloud GitHub organization and CryoCloudUsers team (you will receive an email when we do this from GitHub **at the email you have linked to your GitHub profile**). Please accept this invitation within 7 days or it will disappear and we will need to resend it. Your membership on that GitHub team provides you with access to the CryoCloud hub.
 
 
 4. Open up the [CryoCloud JupyterHub](https://hub.cryointhecloud.com) to make sure it works for you. 
-You will need your Github username and password to sign on.
+You will need your Github username and password to sign on. A 404 error message means you are not yet part of the GitHub org
+and need to accept the invitation from GitHub first.
 
 
-5. Watch the [CryoCloud training recording](https://youtu.be/bBNPuVEG4lE) to learn your way around the CryoCloud.
+6. Watch the [CryoCloud training recording](https://youtu.be/bBNPuVEG4lE) to learn your way around CryoCloud.
 
 
-6. Fill out the [CryoCloud Onboarding Survey](https://forms.gle/8Mr9Ykc8M7jY9fCd7). This 
+7. Fill out the [CryoCloud Onboarding Survey](https://forms.gle/8Mr9Ykc8M7jY9fCd7). This 
 Onboarding Survey will be one of the most important outcomes of the CryoCloud program to help 
 us ensure we are building infrastructure and community 
 practices that best meet your needs. We will gather a subset of the survey information at 6-month intervals to gauge the change that CryoCloud has produced. This survey will take ~5-10 min. Thank you for your time in filling out this survey!
 
 
-7. Add yourself to our [Slack channel](https://join.slack.com/t/cryospherecloud/shared_invite/zt-1isgbeuhh-q~cYYKtn_6i3PR1alGca_g) 
+8. Add yourself to our [Slack channel](https://join.slack.com/t/cryospherecloud/shared_invite/zt-1isgbeuhh-q~cYYKtn_6i3PR1alGca_g) 
 to join the community, get updates, and ask any questions.
 
 
-8. We welcome feedback on the onboarding training in a [short anonymous feedback form](https://forms.gle/2C7mHpwnwzWa8USk9), 
+9. We welcome feedback on the onboarding training in a [short anonymous feedback form](https://forms.gle/2C7mHpwnwzWa8USk9), 
 which will help us to improve the training system for the next group of CryoCloud users. 


book/content/citing_cryocloud.md

@@ -2,7 +2,10 @@
 # Citing CryoCloud
 
 To track the impact that CryoCloud has on publications and research output, 
-we ask that any projects and publications that the CryoCloud supports use 
-our doi: [10.5281/zenodo.7576601](https://doi.org/10.5281/zenodo.7576601).
+we ask that any projects and publications that the CryoCloud supports, do one of two things: 
 
-Snow, Tasha, Millstein, Joanna, Scheick, Jessica, Sauthoff, Wilson, Leong, Wei Ji, Colliander, James, Pérez, Fernando, James Munroe, Felikson, Denis, Sutterley, Tyler, & Siegfried, Matthew. (2023). CryoCloud JupyterBook (2023.01.26). Zenodo. https://doi.org/10.5281/zenodo.7576602.
+1. In the acknowledgements section, include CryoCloud and our NASA funding sources that make it possible for us to use CryoCloud (NASA grants 80NSSC22K1877, 80NSSC23K0002)
+
+2. Cite us in your methods as you mention running your code using a JupyterHub:
+
+Snow, Tasha, Millstein, Joanna, Scheick, Jessica, Sauthoff, Wilson, Leong, Wei Ji, Colliander, James, Pérez, Fernando, James Munroe, Felikson, Denis, Sutterley, Tyler, & Siegfried, Matthew. (2023). CryoCloud JupyterBook (2023.01.26). Zenodo. https://doi.org/10.5281/zenodo.7576601.

book/content/hub_best_practices.md

@@ -4,6 +4,10 @@ Who and how you can access the CryoCloud - Setup instructions in the [Getting St
 
 ***
 
+Close out your browser tab every time that you log out. This keeps each log in clean and can prevent weird artifacts from popping up on your next log in.
+
+***
+
 To save money for us, when you finish on the Hub
 * Go to `File` > `Hub Control Panel` > push `Stop Server`
 * Once that button disappears, your server has stopped
@@ -21,6 +25,10 @@ Keep personal storage to <10 Gb unless you talk to us about it
 
 ***
 
+The `shared` drive is a folder everyone can read files from and only admins can write to. `shared-public` everyone can read and write to. When deleting files, please be careful to leave other users' files intact in those directories. This means that while it is easy to share data, especially `shared-public` carries an inherent risk of losing the data if someone else accidentally deletes it. We do not recommend this folder for long term storage unless the files are copies or easily recreated. This storage space is best suited for sharing files and then deleting those files as soon as your team is done using them. 
+
+***
+
 Pip installs on your hub last only for that session
 * If multiple people use a missing package, let us know and we will add it to everyone's environment
 * Guidance for adding packages in [Contributing/Workflows](../contributing/workflow.md)
@@ -46,4 +54,4 @@ If you want to use a tag from Docker Hub
 
 ***
 
-Get better oriented with open science practices and broaden the impact of your work through the [NASA Open Science 101 curriculum](https://nasa.github.io/Transform-to-Open-Science/take-os101/). This curriculum comes with a NASA certificate and takes users through the ethos of open science, open tools and resources, open data, open code, and open results. With some background knowledge in open science, you may be able to take the fast track through the certificate without needing to go through all of the modules.
+Get better oriented with open science practices and broaden the impact of your work through the [NASA Open Science 101 curriculum](https://nasa.github.io/Transform-to-Open-Science/take-os101/). This curriculum comes with a NASA certificate and takes users through the ethos of open science, open tools and resources, open data, open code, and open results. It has really practical content. With some background knowledge in open science, you may be able to take the fast track through the certificate without needing to go through all of the modules.