Salish Sea MEOPAR Tools Documentation

This is the documentation for the Salish Sea MEOPAR project tools collection. The docs describe a collection of tools for working with the Salish Sea MEOPAR NEMO model, its results, and associated data. There is a companion collection of project documentation.

The tools repo contains several Python packages:

• SalishSeaToolsPackage - a collection of Python modules that facilitate code reuse across the Salish Sea MEOPAR project

• SOGTools - Python functions for working with the output of the SOG 1-D model

• Marlin - the Salish Sea NEMO svn-hg Maintenance Tool

Also documented here are:

• Notes are how the Python packages in the repo are developed and maintained

• How we create netCDF4 files and the metadata conventions that we use in them

• How to build and use the REBUILD_NEMO that we use to combine per-processor results files from NEMO-3.4 runs

• Some of the Jupyter Notebooks and Python scripts that we use to prepare bathymetry and initial conditions & forcing files for NEMO runs

There is also some Legacy Documentation from our early days of learning to configure and run NEMO.

Contents:

• SalishSeaTools Package
  • SalishSeaTools Package Installation and Use
  • SalishSeaTools API
  • SalishSeaTools Package Development
• SOGTools Package
• Salish Sea NEMO Command Processor
• SalishSeaNowcast Package
• netCDF4 Files Creation and Conventions
  • Creating netCDF4 Files
  • netCDF4 File Conventions
  • Applying netCDF4 Variable-Level Compression
• Building ERDDAP Datasets
  • Surface Field Datasets
  • Model Grid Geo-location and Bathymetry Datasets
  • EC HDRPS Atmospheric Forcing Datasets
• Visualisation of NEMO/GEM/Observations using XArray
  • Loading NEMO results, GEM forcing files, and drifter observations
  • Visualisation
  • Animation
• Bathymetry Notebooks and Tools
  • Full Salish Sea Domain Bathymetry
  • Initial Sub-domain Test Bathymetry
  • Bathymetric Attributed Grid (BAG) Datasets
• Initial Conditions and Forcing Notebooks and Tools
• Live Ocean Boundary Conditions Tools
  • Overview
  • Dependencies
  • Bash Scripts
  • Storage of Files
• Marlin – Salish Sea NEMO svn-hg Maintenance Tool
  • Installation
  • Marlin Commands
• Python Packages Development and Maintenance
  • Guidelines and Best Practices for Writing Library Code
  • Mercurial Named Branches
  • Importing Files from Another Mercurial Repo
• NEMOGCM Tools
  • REBUILD_NEMO
• Legacy Documentation
  • Run_Files Directory
  • NOCSCOMBINE

Licenses

Unless otherwise specified, the Salish Sea MEOPAR tools and documentation are copyright 2013-2021 by the Salish Sea MEOPAR Project Contributors and The University of British Columbia.

They are licensed under the Apache License, Version 2.0. http://www.apache.org/licenses/LICENSE-2.0 Please see the LICENSE file for details of the license.

The salishsea_tools.namelist and salishsea_tools.tests.test_namelist modules are based on https://gist.github.com/krischer/4943658. They are copyright 2013 by Lion Krischer <krischer@geophysik.uni-muenchen.de> and are licensed under the GNU Lesser General Public License, Version 3 (http://www.gnu.org/copyleft/lesser.html).