LETKF for single cycle

[CEgerer93]

Description

Completes support of LETKF in geos_atmosphere for a single cycle.
Need to establish conventions for updated ensemble members before cycling in earnest.

Dependencies

No dependencies, though the following needs to be addressed for an error-free Cylc workflow described by suites/letkf/flow.cylc:

• EvaObservations

Impact

None.

[danholdaway]

Thanks so much for adding this @CEgerer93. You can evaluate the Coding Norm and Code Testing failures on Discover. To do that you would install as follows:

Swell Code Testing:

module use -a /discover/nobackup/drholdaw/opt/modulefiles/core/
module load miniconda/py39_23.3.1
pip install --prefix=/path/to/core/swell/version --no-cache-dir -r requirements-standalone.txt .
module load swell/version
swell_tests_code

Python Coding Norms

cd /path/to/srd/swell/version
python pycodestyle_run.py

The YAML test can't be run on Discover so you have to look at the logs here. It looks like it doesn't like Jinja2 templates in the YAML but what you have is legit. Maybe we should ask @mathomp4 if he knows how to skip a file in the YAML linting.

[CEgerer93]

Thank you @danholdaway for the reminder on how to locally check the swell/python norms; minor changes, as expected.

To be clear, swell_tests_code isn't supported in a standard swell build? There are quite a few additional modules (e.g., flake8, etc.) required when installing for the swell code testing.

[danholdaway]

@CEgerer93 that is correct. The problem is that we normally build swell with the spack-stack modules so swell is installed in a manner consistent with how things it will run (i.e. JEDI) are built. However I found that flake8, which the test needs, requires some versions of dependencies newer than what's in spack-stack. So until we can add more to the spack-stack modules we have two installs.

[danholdaway]

Thanks @mathomp4 that suggestion works and is better than what I was doing since it doesn't diverge from the community maintained action for YAML linting.

[danholdaway]

Thanks again for adding this great new feature. Just a few minor things to change please. Also, as I'm reviewing the code I realize that "letkf" might not actually be the correct nomenclature for the suite and tasks etc. Perhaps we should go with LocalEnsembleDa / local_ensemble_da ?

[CEgerer93]

Addressed/implemented comments on PR #256.

[danholdaway]

I sorted out the conflicts and have a few extra comments.

[CEgerer93]

Addressed suggestions - perhaps the most important being the relocation of obs localization block into run_jedi_local_ensemble_da_executable.py.

[danholdaway]

Thanks for working on this great new feature @CEgerer93.

[danholdaway]

Just running the tier 1 tests to make sure there is no impact elsewhere https://github.com/GEOS-ESM/swell/actions/runs/6562412615