`FieldSet.from_netcdf` when the NetCDF files have `depth` dimension

[albertotb]

Parcels version

3.1.2

Description

I'm trying to update from OceanParcels v2.3.0 to v3.1.2. I was following the example to create a FieldSet from netCDF files: https://docs.oceanparcels.org/en/latest/examples/parcels_tutorial.html#Reading-in-data-from-arbritrary-NetCDF-files

However, my files do have a depth dimension:

Otherwise, they have a similar structure to the example ones:

However, when trying to create a FieldSet I'm getting this error:

fieldset = parcels.FieldSet.from_netcdf(
    {
        "U": ["./test/data/uv/2020-03-20.nc", "./test/data/uv/2020-03-21.nc"],
        "V": ["./test/data/uv/2020-03-20.nc", "./test/data/uv/2020-03-21.nc"],
    },
    variables={"U": "uo", "V": "vo"},
    dimensions={
        "time": "time",
        "depth": "depth",
        "lat": "latitude",
        "lon": "longitude",
    },
)

AssertionError: Field uo expecting a data shape of [tdim=2, zdim=26, ydim=241, xdim=241] but got shape (1, 26, 241, 241). Flag transpose=True could help to reorder the data.

I tried the suggestion of using transpose=True, but no luck. For some reason, it seems to expect 2 values in the time dimension, but each NetCDF file only has one, you need to combine them both. I went ahead and removed the depth dimension from the files:

And that seems to work:

fieldset = parcels.FieldSet.from_netcdf(
    {
        "U": [
            "./test/data/uv/2020-03-20_nodepth.nc",
            "./test/data/uv/2020-03-21_nodepth.nc",
        ],
        "V": [
            "./test/data/uv/2020-03-20_nodepth.nc",
            "./test/data/uv/2020-03-21_nodepth.nc",
        ],
    },
    variables={"U": "uo", "V": "vo"},
    dimensions={
        "time": "time",
        "lat": "latitude",
        "lon": "longitude",
    },
)

I'm not sure if this is a bug, but this same code used to work in OceanParcels v2.3.0 with both depth and time dimension.

Code sample

I know that to run the example you need the data files. If required, I can try and upload them somewhere, because they are too big to be attached directly in Github.

fieldset = parcels.FieldSet.from_netcdf(
    {
        "U": ["./test/data/uv/2020-03-20.nc", "./test/data/uv/2020-03-21.nc"],
        "V": ["./test/data/uv/2020-03-20.nc", "./test/data/uv/2020-03-21.nc"],
    },
    variables={"U": "uo", "V": "vo"},
    dimensions={
        "time": "time",
        "depth": "depth",
        "lat": "latitude",
        "lon": "longitude",
    },
)

AssertionError: Field uo expecting a data shape of [tdim=2, zdim=26, ydim=241, xdim=241] but got shape (1, 26, 241, 241). Flag transpose=True could help to reorder the data.