nemo2cmor doesn't find bathymetry/subbasins in linked directories

[uwefladrich]

ece2cmor constructs the paths for the bathymetry and subbasins files (if not given as env vars) as follows:

expdir = os.path.abspath(os.path.join(os.path.realpath(path), "..", "..", ".."))
# [...]
bathy_file_ = os.environ.get("ECE2CMOR3_NEMO_BATHY_METER", os.path.join(expdir, "bathy_meter.nc"))
# [...]
basin_file_ = os.environ.get("ECE2CMOR3_NEMO_SUBBASINS", os.path.join(expdir, "subbasins.nc"))

The problem is that this does not necessarily works if symbolic links are involved. Consider the following structure:

> tree .
.
├── bar
└── foo
    ├── bar -> ../bar
    └── file
3 directories, 1 file

So ./foo/bar is a symbolic link to ./bar. Then we have

> ls foo/file 
foo/file

but

> ls foo/bar/../file
ls: cannot access 'foo/bar/../file': No such file or directory

I had a corresponding situation in our linked-up rundirs and cmorisation dropped some Ofx variables as a consequence.

It might be a better implementation to use the Python pathlib to construct the paths with something like this (not tested!):

from pathlib import Path
expdir = Path(path).parents[3]
bathy_file_ = expdir / 'bathy_meter.nc'
basin_file_ = expdir / 'subbasins.nc'