Add salinity restoring file generation

[ezhilsabareesh8]

This script processes and smooths sea water salinity data from the initial conditions NetCDF files generated using https://github.com/COSIMA/initial_conditions_access-om2 . It applies a uniform smoothing filter to the surface layer (0m depth) of the salinity for each month and concatenates the smoothed data into a single output NetCDF file.

[anton-seaice]

Thanks @ezhilsabareesh8 - I will review soon.

I assume this uses the hh5 conda/analysis module ?

If you run black on the script and commit the change, then the formatting test should pass.

From the Readme:

Python scripts are formatted using the black formatter. This is enforced using a github action running on pull requests. You will need to have pre-commit and black installed in your python environment. It is included in the conda/analysis enviornments in hh5, otherwise it can be installed through pip or conda. Then run pre-commit install once to ensure your commits have black run on them before committing.

[ezhilsabareesh8]

Thanks @anton-seaice, I just reformatted it using black.

[anton-seaice]

Thanks @ezhilsabareesh8

If you keep the data as an xarray object, it will save having to recreate all the attributes and dimensions etc. See the suggestions

[anton-seaice]

If you use xarray suggestions above, the only extra attributes you need are these (i think):

    salt_var.standard_name = "sea_water_salinity"
    salt_var.long_name = "Smoothed sea water salinity at level 0m"
    salt_var.units = "1"

you should just be able to set those and then say

salt_smoothed_da.to_netcdf()

[anton-seaice]

Have a look now @ezhilsabareesh8 - this should work if we fix the time:units attribute in the source data

[anton-seaice]

This change will contribute to COSIMA/access-om3#207

[anton-seaice]

Lets park this until

• Fix coordinates initial_conditions_access-om2#6
• Update to WOA23 initial_conditions_access-om2#7
• numba not supported for numpy masked array initial_conditions_access-om2#3

are completed, and then we can finish this review.

[ezhilsabareesh8]

@anton-seaice I noticed that the time variable was changed to match the initial conditions, but the salinity restoring should actually begin at the middle of each month. In my original code, I had overwritten the time variable with:

times[:] = np.arange(0.5, 12.5, 1)  # Time values from 0.5 to 11.5
times.units = "months since 0001-01-01 00:00:00"

Could you please revert the changes made to the time variable in this commit 8b0c207?