Template repository for Jupyter workshops on Surf Research Cloud

Introduction

This repository is a template for creating a Jupyter workshop set up on the Surf Research Cloud. The repository contains a folder structure to organize the workshop material, a GitHub Actions workflow to automatically compress the workshop material, and an ansible playbook to automatically transfer the workshop material to the digital workspaces on the Surf Research Cloud. An example workshop that uses this template can be found here.

Steps to create a workshop (<60 minutes)

1. Create a new repository using this template repository.
2. Add the workshop material to the workshop-material folder.
3. Update the environment.yml file with the required packages.
4. Optionally: Update the README.md file with the workshop information.
5. Create a 'component' and 'catalog item' in the Surf Research Cloud portal, Instructions below.

Deployment

• Participants of the workshop can be invited to SRAM via email to give them temporary access to the virtual environments.
• Creating a workspace takes less than 5 minutes per workspace + 15 minutes deployment time.

Repository materials

• The workshop material can be edited found in the workshop-material folder. It contains the jupyter notebooks as well as the data used for the workshop.
• The folder playbooks is exclusively dedicated for automated transfer of the course materials to the digital workspaces on SURF Research Cloud. It is automatically updated by the GitHub Actions workflow, so no need to make changes to this folder.
• The environment.yml file describes the packages that are required to run the notebooks. The file is used to create a python kernel on SURF Research Cloud that has all the packages installed. By default the kernel will be called workshop-kernel unless you choose a different name.
• The .github folder contains a GitHub Actions workflow that will automatically update the zipped workshop-material.zip whenever there are changes to the workshop-material folder.

python | .gitignore | CITATION.cff | environment.yml | LICENSE | README.md | +---.github | \---workflows | update-course-materials.yml | +---playbooks | | transfer_workshop_material.yml | | | \---roles | \---transfer_workshop_material | \---tasks | main.yml | \---workshop_material +---data | README.md | \---notebooks Intro_Jupyter.ipynb

Creating a component and catalog item in the Surf Research Cloud portal

First make sure that you have an SRAM collaboration for the workshop. For UU researchers, you can request a collaboration by contacting RDM support. Secondly, add yourself to the src_co_developer group in the SRAM collaboration.

Create a component

Follow the instructions here to create a component in the Surf Research Cloud portal. Use the url of your newly created repository as the source code repository. And for Path playbooks/transfer_workshop_material.yml as the playbook path.

Create a catalog item

Follow the instructions here to create a catalog item in the Surf Research Cloud portal. For the components selection, select:

• SRC-OS
• SRC-CO
• SRC-Nginx
• SRC-External plugin
• jupyter
• Custom Packages
• Shared Working Directory
• AND your newly created component

IMPORTANT: In Step 6 you need to Overwrite several parameter settings:
- For requirements_file_repo_url and requirements_file_path (both used by the Custom Packages component). Check the instructions for Custom Packages component here and use the url of your newly created repository for requirements_file_repo_url and environment.yml for requirements_file_path.
- For paths (used by Shared Working Directory) fill /scratch

After creating the catalog item, you can now select the catalog item when creating a workspace in the Surf Research Cloud portal. Be aware that in order to use the environment, the user would need to select the workshop-kernel from the kernel dropdown in the Jupyter notebook.

Contact

• Geo Data Team
  
• Research Engineering team