Implement config, recipe loader & recipe runner.

[BSchilperoort]

This PR implements a simple config loader, recipe loader, a recipe runner, and a CLI to run the recipes.

To review this PR: follow the instructions in docs/using_zampy.md.

• Additionally, I have set up the config required for mkdocs. The docs can now be viewed with hatch run docs:serve
• We can split up the recipe steps in the future, if a user only wants to re-run a single step.

[SarahAlidoost]

@BSchilperoort great to see the documentation is set up 👍 , thank you. please see my comments. Two more major issues:

1. I was able to run the test_recipe and inspected the results using ncdump -h. It seems that the time and coordinates aren't correct. can you please check it? see:

ncdump -h output/test_recipe/era5_2020-2020.nc
netcdf era5_2020-2020 {
dimensions:
        time = 8040 ;
        latitude = 9 ;
        longitude = 7 ;
variables:
        float Wind_N(time, latitude, longitude) ;
                Wind_N:_FillValue = NaNf ;
                Wind_N:units = "meter_per_second" ;
                Wind_N:long_name = "10 metre V wind component" ;
                Wind_N:description = "" ;
        float Psurf(time, latitude, longitude) ;
                Psurf:_FillValue = NaNf ;
                Psurf:units = "pascal" ;
                Psurf:long_name = "Surface pressure" ;
                Psurf:standard_name = "surface_air_pressure" ;
                Psurf:description = "" ;
        double latitude(latitude) ;
                latitude:_FillValue = NaN ;
        double longitude(longitude) ;
                longitude:_FillValue = NaN ;
        int64 time(time) ;
                time:units = "hours since 2020-01-01 00:00:00" ;
                time:calendar = "proleptic_gregorian" ;

// global attributes:
                :Conventions = "ALMA" ;
                :history = "2023-08-08 06:11:32 GMT by grib_to_netcdf-2.25.1: /opt/ecmwf/mars-client/bin/grib_to_netcdf.bin -S param -o /cache/data4/adaptor.mars.internal-1691475090.8238995-25715-3-57d6b3c1-c339-4cf0-90bf-0630504e6dbf.nc /cache/tmp/57d6b3c1-c339-4cf0-90bf-0630504e6dbf-adaptor.mars.internal-1691475052.0872161-25715-5-tmp.grib" ;
}

ncdump -h output/test_recipe/eth_canopy_height_2020-2020.nc 
netcdf eth_canopy_height_2020-2020 {
dimensions:
        time = 1 ;
        latitude = 9 ;
        longitude = 7 ;
variables:
        float Hveg(time, latitude, longitude) ;
                Hveg:_FillValue = NaNf ;
                Hveg:AREA_OR_POINT = "Area" ;
                Hveg:units = "meter" ;
                Hveg:description = "" ;
        double latitude(latitude) ;
                latitude:_FillValue = NaN ;
        double longitude(longitude) ;
                longitude:_FillValue = NaN ;
        int64 time(time) ;
                time:units = "days since 2020-07-01 00:00:00" ;
                time:calendar = "proleptic_gregorian" ;

// global attributes:
                :Conventions = "ALMA" ;
}

2. I see that you set up the documentation using mkdoc. However, read the docs or GitHub actions aren't still set up. Shall we make an issue for those?

[BSchilperoort]

1. I was able to run the test_recipe and inspected the results using ncdump -h. It seems that the time and coordinates aren't correct. can you please check it? see:

Yeah we have to decide how to deal with the canopy height dataset, as technically it is only a snapshot and not a timeseries... I am not sure what is best. See #24

2. I see that you set up the documentation using mkdoc. However, read the docs or GitHub actions aren't still set up. Shall we make an issue for those?

I'll make an issue for that.

[SarahAlidoost]

@BSchilperoort nice work on adding tests and thank you for addressing the comments. A suggestion about eth_canopy_height in the recipe example in the documentation: it would be nicer to remove it from there and when issue #24 is fixed, we add it again.

[sonarqubecloud]

Kudos, SonarCloud Quality Gate passed!   

0 Bugs
0 Vulnerabilities
0 Security Hotspots
0 Code Smells

87.1% Coverage
0.0% Duplication

[geek-yang]

WoW! Very fast movement...😂 Thought I would take a look when all the tests were added. It is merged already. Nice work!