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Harmony NetCDF4 to Zarr converter

A Harmony service to convert NetCDF4 files to Zarr files. Takes conventional Harmony messages and translates their input granules to Zarr using xarray.

This library intentionally does very little checking of the input files and file extensions. It is designed to work on NetCDF granules. It ought to work with any other file type that can be opened with xarray.open_mfdataset using the h5netcdf driver. This includes some HDF5 EOSDIS datasets. Individual collections must be tested to ensure compatibility.

Development Setup

Harmony Instance

It is recommended that the NetCDF-to-Zarr service is tested and developed using a local Harmony instance. This can be established following the instructions in the Harmony repository.

Environment File

This service uses the harmony-service-lib-py, and requires that certain environment variables be set, as shown in the Harmony Service Lib README. For example, STAGING_BUCKET and STAGING_PATH are required, and EDL_USERNAME and EDL_PASSWORD are required for any data behind Earthdata Login. For automated testing (not integrated into Harmony in a dev environment or AWS deployment), use the example .env file in this repo:

$ cp example/dotenv .env

and update the .env with the correct values.

Python & Project Dependencies

In order to be able to run the automated tests, install Python (3.9), and create a Python virtual environment.

Activate the newly created environment and install the project dependencies:

$ python -m pip install --upgrade pip
$ make install

Running & Testing the Service

If using Minikube, be sure your environment is pointed to the Minikube Docker daemon:

$ eval $(minikube docker-env)

Build the Docker image:

$ make build-image

or build the image using a local copy of harmony-service-lib-py (useful for concurrent development):

$ make build-image LOCAL_SVCLIB_DIR=../harmony-service-lib-py

You can now run a workflow in your local Harmony stack and it will execute using this image.

Restart the services in your local Harmony instance (the script below is contained in the Harmony repository):

$ bin/restart-services

Run through these steps again (build image, restart services) in order to pick up any new changes.

If you'd rather not build the image locally, you can simply pull the latest image:

$ docker pull ghcr.io/nasa/harmony-netcdf-to-zarr

Automated Tests

Run tests with coverage reports:

$ make test

You may be concurrently developing on this service as well as the harmony-service-lib-py. If so, and you want to test changes to it along with this service, install the harmony-service-lib-py in 'development mode'. Install it using pip and the path to the local clone of the service library:

pip install -e ../harmony-service-lib-py

Now any changes made to that local repo will be visible in this project when you run tests, etc.

Contributions:

Developers working on the NetCDF-to-Zarr service will need to create a feature branch for their work. The code in the repository has a unittest suite, which should be updated when any code is added or updated within the repository.

When a feature branch is ready for review, a Pull Request (PR) should be opened against the main branch. This will automatically trigger a GitHub workflow that will run the unittest suite (see: .github/workflows/run_tests_on_pull_requests.yml).

When a PR is merged against the main branch, a different workflow will check if there are updates to the version.txt file. This file should contain a semantic version number (see: .github/workflows/publish_docker_image.yml).

If there are updates to version.txt, the GitHub workflow will:

  • Extract the semantic version number from that file.
  • Extract the latest release notes from CHANGELOG.md.
  • Run the unittest suite.
  • Tag the most recent commit on the main branch with the semantic version number.
  • Create a GitHub release using the release notes and semantic version number.
  • Publish the NetCDF-to-Zarr service Docker image to ghcr.io. It will be tagged with the semantic version number.

For this reason, when releasing, please be sure to update both:

  • version.txt
  • CHANGELOG.md