Feature/data tree cleanup

[sliu008]

Github Issue: #295

Description

• Rewrite l2ss-py to use xarray DataTree instead of flattening the arrays

Overview of work done

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Overview of verification done

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Overview of integration done

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PR checklist:

• Linted
• Updated unit tests
• Updated changelog
• Integration testing

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[sliu008]

Pending Implementations

• SNDR Time Variable Removal: Not yet implemented.
  https://github.com/podaac/l2ss-py/blob/develop/podaac/subsetter/subset.py#L1249
• Changing Variable Dimensions in DataTree Datasets: Not yet implemented.
  https://github.com/podaac/l2ss-py/blob/develop/podaac/subsetter/subset.py#L1249

Recent Changes & Issues

• File Handling: No longer using netCDF4 to open files for preprocessing.
• DataTree Compatibility: DataTree cannot use netCDF4 store to open netCDF4 objects after preprocessing.

DataTree Coordinate Handling

• Issue: When subsetting a DataTree, child nodes inherit a copy of the coordinates from the parent. When subsetting and creating a new data tree the coords are also in the new tree although might not have been in the original dataset.
• Solution: Implemented a function to remove coordinates from child nodes.
• Impact: Unclear if retaining or removing these coordinates matters, but currently removing them.

Memory Optimization in Harmony

• Previously, variables were loaded and then written to a NetCDF file to optimize memory usage in Harmony.
• Open Question: Can we achieve the same memory efficiency with DataTree, or will it require handling each group and variable separately?