UBC EOAS MOAD Group Documentation

This is documentation by and for members of the MOAD (Mesoscale Ocean and Atmospheric Dynamics) group in the EOAS (Earth, Ocean, and Atmospheric Sciences) department at UBC (University of British Columbia).

Contents:

• Getting Started
  • Get Your EOAS Email Address and User Id
  • Get Set Up on GitHub
  • Set Up Secure Remote Access
  • Set Up Git
  • Set Up bash
  • Install Pixi
  • Set Up Your Analysis Repository
• Secure Remote Access
  • Generate ssh Keys
  • Set Up ssh Configuration
  • Copy Your Public ssh Key to Remote Computers
  • Copy Your Public ssh Key to Remote Computers (Windows 10)
  • Copy Your Public ssh Key to GitHub
  • SSH Commands
  • X2Go Remote Desktop
• Version Control Repositories
  • General Guidelines
• Version Control with Git
  • Installing Git
  • Git Configuration
  • .gitignore Files
• bash Configuration
  • Edit or Create .bash_profile
  • Edit or Create .bashrc
• Pixi Package and Environment Manager
  • Why Pixi?
  • Installing Pixi
  • Basic Usage
  • Pixi Details
  • Migrating to Pixi-Powered SalishSeaCmd
  • Migrating Your Analysis Repository to Pixi
  • Importing a Conda Environment Into a Pixi Workspace
  • Adding a New Pixi Environment
• Analysis Repositories
  • Set Up Your Analysis Repository
• Python
• Jupyter
  • Running Jupyter Locally
  • Running Jupyter Remotely
• Jupyter Notebook READMEs on GitHub
• VS Code
  • Remote - SSH Extension Notes
  • Recommended Extensions
  • Fortran Language Server (fortls)
• Working on Digital Research Alliance of Canada Clusters
  • Create a Digital Research Alliance of Canada Account
  • Initial Setup on nibi.alliancecan.ca
• Globus File Transfer
  • Transferring Files
• XIOS-2
  • Getting XIOS-2
  • Building XIOS-2
  • XIOS-2 Configuration Files
  • Switching from XIOS-1 to XIOS-2
• Ariane
  • Getting Ariane
  • Qualitative Mode
  • Quantitative Mode
  • Using tracers in Ariane
  • Multi-day runs
  • Frequency Sensitivity Sample
• OceanParcels
• Documentation with Sphinx
  • Installing Sphinx
  • Building and Previewing Documentation
  • Link Checking the Documentation
  • Writing Style
  • Links and Cross-references
  • Forcing Line Breaks
• Python Packages Development and Maintenance
  • How to Structure Python Packages and Why
• Contributing to These Docs
  • Getting the Repo
  • Docs Build Environment
  • Building and Previewing the Documentation
  • Link Checking the Documentation
  • Version Control Repository
  • Issue Tracker
  • License
• UBC EOAS MOAD Group Documentation Contributors
• Archival Documentation
  • Conda Package and Environment Manager
  • Version Control with Mercurial

License

The UBC EAOS MOAD Group documentation by the EOAS MOAD group and The University of British Columbia is licensed under a Creative Commons Attribution 4.0 International License .