NOAA Changing, Ecosystems, and Fisheries Initiative (CEFI) - Data Portal Team

Regional MOM6 preprocessing package

This is a developing regional mom6 module help both preprocessing the data and perform various statistical analysis shown in Ross et al., 2023. Many scripts are the modified version of the GFDL CEFI github repository.

Current stage of the module is for estabilishing the processing workflow in the CEFI data portal. Future availability of a more sophisticated python pakcage for various end-user purposes is in the roadmap of this project.

We welcome external contribution to the package. Please feel free to submit issue for any inputs and joining the development core team. Thank you!

Installing the package using Conda

We recommand using conda to mamage the virtual environment that one is going to install the package. Due to the esmpy and ESMF are complex, compiled librarie, pip will not be able to install the module. Therefore a installation of the xesmf package using conda with conda-forge channel is needed. Please following the steps to install the package correctly

1. Install the xesmf using conda install

   conda install -c conda-forge xesmf
   

2. Install the mom6 package using pip install

   pip install rmom6_preprocessing
   

Test installation of the package

import mom6

or

from mom6.mom6_module import mom6_regrid

Setting up the developement environment

1. Fork this repository using the button in the upper right of the GitHub page. This will create a copy of the repository in your own GitHub profile, giving you full control over it.

2. Clone the repository to your local machine from your forked version.

   git clone <fork-repo-url-under-your-github-account>
   

   This create a remote origin to your forked version (not the NOAA-CEFI-Portal version)

3. Create a conda/mamba env based on the environment.yml

   cd regional_mom6/
   conda env create -f environment.yml
   

4. Activate the conda env regional-mom6

   conda activate regional-mom6
   

5. pip install the package in develop mode

   pip install -e .
   

Syncing with the NOAA-CEFI-Portal version

1. Create a remote upstream to track the changes that is on NOAA-CEFI-Portal

   git remote add upstream git@github.com:NOAA-CEFI-Portal/regional_mom6.git   
   

2. Create a feature branch to make code changes

   git branch <feature-branch-name>
   git checkout <feature-branch-name>
   

   This prevents making direct changes to the main branch in your local repository.

3. Sync your local repository with the upstream changes regularly

   git fetch upstream
   git checkout main
   git merge upstream/main
   

   This updates your local main branch with the latest changes from the upstream repository.

4. Merge updated local main branch into your local <feature-branch-name> branch to keep it up to date.

   git checkout <feature-branch-name>
   git merge main
   

5. Push your changes to your forked version on GitHub

   git push origin <feature-branch-name>
   

   Make sure you have included the upstream/main changes before creating a pull request on NOAA-CEFI-Portal/regional_mom6