Organization of Mercurial Repositories

General

  • The central location for all repos is the SalishSea-MEOPAR team account on Bitbucket
  • People are free to push changes to code and docs that they own, but they should fork repos and create pull requests to provide changes to stuff owned by others so that changes are reviewed
  • All repos have issue trackers enabled on Bitbucket
  • Bitbucket wikis are disabled on all repos to force documentation into repo docs directories
  • Docs use Sphinx
  • Docs from public repos will be rendered as HTML on readthedocs.org. readthedocs also provides PDF rendering.
  • There is no provision for rendering docs from private repos.

Repositories

docs

private-docs

  • private to SalishSea-MEOPAR team members
  • meeting notes, plans, work-in-progress reports and papers, presentations, etc.
  • anything that might go in docs repo but are not ready for release, or which cannot be released for some reason
  • ideally at least some of this repo will eventually be moved to the public docs repo

tools

private-tools

  • private to SalishSea-MEOPAR team members
  • scripts and docs that might go in tools repo but are not ready for release, or which cannot be released for some reason
  • ideally this repo will eventually empty out as its contents are moved to the public tools repo
  • Bitbucket: https://bitbucket.org/salishsea/private-tools/

SalishSeaCmd

NEMO-Cmd

SalishSeaNowcast

  • public
  • Apache v2.0 license, copyright project contributors and UBC
  • The SalishSeaNowcast package is a collection of Python modules associated with running the Salish Sea NEMO model in a daily nowcast/forecast mode. The runs use as-recent-as-available (typically previous day) forcing data for the western boundary sea surface height and the Fraser River flow, and atmospheric forcing from the four-times-daily produced forecast results from the Environment Canada High Resolution Deterministic Prediction System (HRDPS) operational GEM 2.5km resolution model.
  • documentation is rendered at https://salishsea-nowcast.readthedocs.io/en/latest/
  • Bitbucket: https://bitbucket.org/salishsea/salishseanowcast/

analysis

  • Read-only legacy repo
  • public
  • Apache v2.0 license, copyright project contributors and UBC
  • analyses of the results of the Salish Sea MEOPAR NEMO model; most of the files are Jupyter Notebooks
  • Bitbucket: https://bitbucket.org/salishsea/analysis/

Note

This was the project’s original analysis repo. It got so big that it was in danger of hitting the Bitbucket 2Gb limit at which changesets would no longer be accepted. In April 2016 it was split into a collection of personal analysis repos for each team member, as well as some other application-specific analysis repos. They are all public with the same license and copyright a the original analysis repo. They can be found in the SalishSea-MEOPAR Analysis project collection of repos on Bitbucket.

NEMO-3.6-code

XIOS-2 (XML I/O Server)

XIOS-ARCH

grid

  • public

  • Apache v2.0 license, copyright project contributors and UBC

  • Coordinates, bathymetry, mesh mask, land processor elimination, and atmospheric forcing weights files for the Salish Sea NEMO model. Also included is the file that imposed the “no snow” atmospheric forcing condition. Files for AGRIF sub-grids are in appropriately names sub-directories of the subgrids/ directory.

    Many of these files originated in the (private) NEMO-forcing repository. The commit message history of files from that repository is included in their initial commit messages.

  • Bitbucket: https://bitbucket.org/salishsea/grid

rivers-climatology

  • public

  • Apache v2.0 license, copyright project contributors and UBC

  • Rivers runoff climatology files for the Salish Sea NEMO model. Included are discharge, temperature, nutrients & biological tracers, and depths over which river quantities are introduced into model grid. Files for AGRIF sub-grids are in appropriately names sub-directories of the subgrids/ directory.

    Many of these files originated in the (private) NEMO-forcing repository. The commit message history of files from that repository is included in their initial commit messages.

  • Bitbucket: https://bitbucket.org/salishsea/rivers-climatology

tides

  • public

  • Apache v2.0 license, copyright project contributors and UBC

  • Tide boundary condition files for the Salish Sea NEMO model.

    Many of these files originated in the (private) NEMO-forcing repository. The commit message history of files from that repository is included in their initial commit messages.

  • Bitbucket: https://bitbucket.org/salishsea/tides

tracers

  • public

  • Apache v2.0 license, copyright project contributors and UBC

  • Tracer boundary condition climatology files and domain initialization files for the Salish Sea NEMO model. Included are temperature, salinity, nutrients, and biological tracers.

    Many of these files originated in the (private) NEMO-forcing repository. The commit message history of files from that repository is included in their initial commit messages.

  • Bitbucket: https://bitbucket.org/salishsea/tracers

NEMO-forcing

Note

This was the project’s original repo of initial conditions, forcing, etc. files. It got so big that it was in danger of hitting the Bitbucket 2Gb limit at which changesets would no longer be accepted. It also contained multiple copies large binary files which are no longer used. Together, these factors make this repo very time consuming to clone and update. In August 2017 the repo was split into 4 smaller repos:

They are all public, licensed under Apache v2.0 license, and copyright by the project contributors and UBC. They can be found in the SalishSea-MEOPAR NEMO Model Runs collection of repos on Bitbucket.

SS-run-sets

salishsea-site

results

  • public
  • all rights reserved, copyright project contributors and UBC
  • a collection of model results and analysis produced by the Salish Sea MEOPAR project
  • Bitbucket: https://bitbucket.org/salishsea/results/

Storm-Surge

  • public
  • Apache v2.0 license, copyright project contributors and UBC, except the manuscript files which are copyright Taylor and Francis
  • Salish Sea MEOPAR storm surge paper
  • Soontiens, N., Allen, S., Latornell, D., Le Souef, K., Machuca, I., Paquin, J.-P., Lu, Y., Thompson, K., Korabel, V. (2016). Storm surges in the Strait of Georgia simulated with a regional model. Atmosphere-Ocean, volume 54, issue 1. https://dx.doi.org/10.1080/07055900.2015.1108899
  • Bitbucket: https://bitbucket.org/salishsea/storm-surge/

Barotropic-Tides

internal-tides

mixing-paper

plume-paper

XIOS (XML I/O Server)

Note

This is the XIOS-1.0 code. It is archival. The Salish Sea model now uses XIOS-2 (XML I/O Server), and that is the recommended code for any new projects.

NEMO-code

Note

This is the NEMO-3.4 code. It is archival. The Salish Sea model is now based on NEMO-3.6-code, and that is the recommended code for any new projects.

SoG-obs

  • private
  • a collection of observations made in the Salish Sea
  • This repo is a vestige of an experiment that didn’t work out because storing large binary files under Mercurial version control is not a good idea.
  • Bitbucket: https://bitbucket.org/salishsea/sog-obs/

NEMO_EastCoast

  • public
  • a collection of files for pre-processing, running, and post-processing of numerical simulations with NEMO for MEOPAR project with primary focus on the Scotia Shelf deployment of the model
  • Bitbucket: https://bitbucket.org/salishsea/nemo_eastcoast/

NEMO-3.1

CONCEPTS-110