DAS-2252 Initial Repository Import

[flamingbear]

Description

This is the first import of the software to be used in the SMAP-L2-Gridding-Service.

This PR contains the software and tests to allow a user to create gridded NetCDF4-CF output data from SMAP Enhanced L2 Radiometer Half-Orbit 9 km EASE-Grid Soil Moisture data (SPL2SMP_E).

The Acceptance Criteria for this ticket are:

• Software is available in a public repository on GitHub (should be under NASA organization, but could be personal repo if the NAMS request is held up.)
• All code is properly formatted and named according to black and pep8.
• pre-commit hooks are set up and run automatically on the repository as well as for developers locally.
• Bonus points for mypy checking

To satisfy those critera:

• pre-commit has been enabled locally with the standard DAS .pre-commit-config.yaml file to enable black formatting and sort imports.
• pre-commit.ci has been enabled on this GitHub repository (see the checks run on this PR).
• Mypy checking has been enabled as a first reuable action in the run_tests_on_pull_requests.yml action.
• You can look at the forked actions that have run https://github.com/flamingbear/harmony-SMAP-L2-gridding-service/pull/2/checks
• Code has been placed in the proper locations according to the DAS Harmony Services General Repository Structure wiki page.
• DAS Harmony Services General Repository Structure wiki page has been updated for smap_l2_gridder

What is not complete:

• Wrapping with harmony service built with Docker (DAS-2254)
• Building Docker Images and Testing with GitHub actions (DAS-2267)
• Connecting Service to Harmony with UMM-S and harmony PRs (DAS-2255)

Jira Issue ID

DAS-2252

Local Test Steps

• Complete a full review of the codebase.

• Download a SPL2SMP_E granule (two ways):

  • Download the .h5 file directly from Earthdata Search to be used as your input file.
  • Use Earthdata Search customization and reformat to NetCDF4-CF without any other transformations to get your processed_granule.nc file

• Create an isolated python 3.12 environment installing packages from the pip_requirements.txt and pip_dev_requirements.txt file.

• run the tests:
  ❯ PYTHONPATH=. pytest .
  not sure why I needed to set my PYTHONPATH...

• You can check the test coverage:
  ❯ PYTHONPATH=. pytest --cov=smap_l2_gridder --cov-report=term-missing --cov-report=html
  you have to install pytest-coverage and __main__.py is not tested.

• regrid your granule. From the root directory run:
  python -m smap_l2_gridder --input [path/to/input-file.h5] --output [path/to/output_granule.nc]

• Validate your output against the processed_granule.nc from EDS. (Look on the DAS-2252 ticket for notebook that you can use.)

  • You should be able to open both the processed_granule.nc and your output_granule.nc files with panoply.
  • Run the notebook and verify all of the data is the same with the exception of the incorrect coordinate variables in the EDS generated file.

PR Acceptance Checklist

• Jira ticket acceptance criteria met.
• CHANGELOG.md updated to include high level summary of PR changes.
• [N/A] docker/service_version.txt updated if publishing a release.
• Tests added/updated and passing.
• Documentation updated (if needed).

[lyonthefrog]

I reviewed the code to the best of my understanding. Most of my feedback are questions for my own benefit, with the real requested changes being typos and a potential mistake in grid.get_metadata_children().

Also, would we like to add a check for unused variables? I think we could just add --unused-variable to the ruff args list in .pre-commit-config.yaml.

Other than that, I appreciate how clean this code is and I hope to get to know it better in the future!

[lyonthefrog]

I ran the pytests, set up the local development environment to run the SMAP L2 Gridder locally, and ran notebook attached to the ticket using two different granules, SMAP_L2_SM_P_E_52352_D_20241119T043136_R19240_001.h5 and SMAP_L2_SM_P_E_52397_D_20241122T062227_R19240_001.h5.

All tests passed. Hurray!

[flamingbear]

@owenlittlejohns I'm merging this and will address anything in follow on PRs if you find problems.