BUG: need to upgrade I/O for hydraulic mesh

[leobpujol]

Calling smash.io.read_mesh or smash.io.read_model causes errors linked to the hydraulic mesh.

• Reading a mesh generated without the "hy1d_options" argument in smash.factory.generate_mesh leads to errors
• The dictionary that contains hydraulic mesh parameters seems to be saved as a string in the hdf5 file

NB; this is linked to dev branches enh-add-hy1d-modules and hy1d_amine_devs

[leobpujol]

Details :

---

Error 1: branch enh-add-hy1d-modules

Generating a mesh without a hy1d_options argument, then saving and reading it :

mesh = smash.factory.generate_mesh(
    rr_options={
        "flwdir_path": str(flwdir_smash),
        #"bbox": bbox, # works also with "bbox": [-np.inf, np.inf, -np.inf, np.inf]
        "x":list(gauge_attributes.x),
        "y":list(gauge_attributes.y),
        "area":list(gauge_attributes.area * 1e6),
        "code":gauge_attributes.code.values,
    },
    #hy1d_options={
    #    "river_line_path": str(river_line),
        #"bbox": bbox, # works also with "bbox": [-np.inf, np.inf, -np.inf, np.inf]
    #}
)

smash.io.save_setup(setup, "setup.yaml")
smash.io.save_mesh(mesh, "mesh.hdf5")

model = smash.Model(setup, mesh)

smash.io.save_model(model, "model.hdf5")

setup = smash.io.read_setup("setup.yaml")
mesh = smash.io.read_mesh("mesh.hdf5")

model = smash.io.read_model("model.hdf5")

This error is obtained, where the i/o routine tries to read parameters that were not created thus not saved :

Traceback (most recent call last):
File "/home/leo/RUNS/SMASH/MARONI/CALIBRATION/run_direct.py", line 107, in
model = smash.io.read_model("model.hdf5")
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/leo/miniconda3/envs/dassflow-1d/lib/python3.11/site-packages/smash/io/model.py", line 151, in read_model
model.mesh = MeshDT(
^^^^^^^
TypeError: MeshDT.init() missing 7 required positional arguments: 'ncs', 'nlevels', 'nlat', 'nup', 'nseg', 'nds_seg', and 'nus_seg'

NB: rebuilding "model" from read "setup" and "mesh" causes no errors, i.e.
model = smash.Model(setup, mesh)

---

Erreur 2: branche hy1d_amine_devs

Same script, this time with a "hy1d_options" argument, reading the model leads to :

mesh = smash.factory.generate_mesh(
    rr_options={
        "flwdir_path": str(flwdir_smash),
        #"bbox": bbox, # works also with "bbox": [-np.inf, np.inf, -np.inf, np.inf]
        "x":list(gauge_attributes.x),
        "y":list(gauge_attributes.y),
        "area":list(gauge_attributes.area * 1e6),
        "code":gauge_attributes.code.values,
    },
    hy1d_options={
       "river_line_path": str(river_line),
        "bbox": bbox, # works also with "bbox": [-np.inf, np.inf, -np.inf, np.inf]
    }
)
...
smash.io.save_setup(setup, "setup.yaml")
smash.io.save_mesh(mesh, "mesh.hdf5")

model = smash.Model(setup, mesh)

setup = smash.io.read_setup("setup.yaml")
mesh = smash.io.read_mesh("mesh.hdf5")

model = smash.Model(setup, mesh)

Following error obtained after executing the last line :

File "/home/leo/RUNS/SMASH/MARONI/CALIBRATION/run_direct.py", line 108, in
model = smash.Model(setup, mesh)
^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/leo/miniconda3/envs/dassflow-1d/lib/python3.11/site-packages/smash/core/model/model.py", line 448, in init
[mesh["cross_sections"][i]["nlevels"] for i in range(mesh["ncs"])],
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/leo/miniconda3/envs/dassflow-1d/lib/python3.11/site-packages/smash/core/model/model.py", line 448, in
[mesh["cross_sections"][i]["nlevels"] for i in range(mesh["ncs"])],
~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^
TypeError: string indices must be integers, not 'str'