added TELEMAC support, docs and tests

ec-jrc · May 24, 2024 · d264508 · d264508
1 parent b9d977c
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diff --git a/README.md b/README.md
@@ -14,6 +14,7 @@ Thalassa is currently supporting visualization of the output of the following so
 
 - [Schism](https://github.com/schism-dev/schism)
 - [ADCIRC](https://adcirc.org/)
+- [openTELEMAC](https://www.opentelemac.org/)
 
 Adding support for new solvers is relatively straight-forward.
 
@@ -30,6 +31,11 @@ Adding support for new solvers is relatively straight-forward.
 ```
 pip install thalassa
 ```
+for Selafin files (openTELEMAC outputs):
+```
+pip install thalassa
+pip install xarray-selafin
+```
 
 ### Conda
 

diff --git a/docs/index.md b/docs/index.md
@@ -16,6 +16,7 @@ Thalassa is currently supporting visualization of the output of the following so
 
 - [Schism](https://github.com/schism-dev/schism)
 - [ADCIRC](https://adcirc.org/)
+- [TELEMAC](https://www.opentelemac.org)
 
 Adding support for new solvers is relatively straight-forward.
 

diff --git a/docs/installation.md b/docs/installation.md
@@ -12,6 +12,11 @@
 ```
 pip install thalassa
 ```
+for Selafin files (openTELEMAC outputs):
+```
+pip install thalassa
+pip install xarray-selafin
+```
 
 ### Conda
 

diff --git a/poetry.lock b/poetry.lock
diff --git a/pyproject.toml b/pyproject.toml
@@ -49,6 +49,7 @@ ipykernel = "*"
 ipython = "*"
 papermill = "*"
 pandas-stubs = "*"
+xarray-selafin = "*"
 
 [tool.poetry.group.docs.dependencies]
 mkdocs = "*"

diff --git a/requirements/requirements-dev.txt b/requirements/requirements-dev.txt
diff --git a/requirements/requirements.txt b/requirements/requirements.txt
@@ -2,9 +2,9 @@ asciitree==0.3.3 ; python_version >= "3.9" and python_version < "4.0"
 attrs==23.2.0 ; python_version >= "3.9" and python_version < "4.0"
 beautifulsoup4==4.12.3 ; python_version < "3.10" and python_version >= "3.9"
 bleach==6.1.0 ; python_version >= "3.9" and python_version < "4.0"
-bokeh==3.3.4 ; python_version >= "3.9" and python_version < "4.0"
-bottleneck==1.3.7 ; python_version >= "3.9" and python_version < "4.0"
-cartopy==0.22.0 ; python_version >= "3.9" and python_version < "4.0"
+bokeh==3.4.1 ; python_version >= "3.9" and python_version < "4.0"
+bottleneck==1.3.8 ; python_version >= "3.9" and python_version < "4.0"
+cartopy==0.23.0 ; python_version >= "3.9" and python_version < "4.0"
 certifi==2024.2.2 ; python_version >= "3.9" and python_version < "4.0"
 cftime==1.6.3 ; python_version >= "3.9" and python_version < "4.0"
 charset-normalizer==3.3.2 ; python_version >= "3.9" and python_version < "4.0"
@@ -13,90 +13,90 @@ click==8.1.7 ; python_version >= "3.9" and python_version < "4.0"
 cligj==0.7.2 ; python_version >= "3.9" and python_version < "4"
 cloudpickle==3.0.0 ; python_version >= "3.9" and python_version < "4.0"
 colorama==0.4.6 ; python_version >= "3.9" and python_version < "4.0" and platform_system == "Windows"
-colorcet==3.0.1 ; python_version >= "3.9" and python_version < "4.0"
-contourpy==1.2.0 ; python_version >= "3.9" and python_version < "4.0"
+colorcet==3.1.0 ; python_version >= "3.9" and python_version < "4.0"
+contourpy==1.2.1 ; python_version >= "3.9" and python_version < "4.0"
 cycler==0.12.1 ; python_version >= "3.9" and python_version < "4.0"
-dask==2024.1.1 ; python_version >= "3.9" and python_version < "4.0"
-dask[array,complete,dataframe,diagnostics,distributed]==2024.1.1 ; python_version >= "3.9" and python_version < "4.0"
-datashader==0.16.0 ; python_version >= "3.9" and python_version < "4.0"
-distributed==2024.1.1 ; python_version >= "3.9" and python_version < "4.0"
+dask-expr==1.1.1 ; python_version >= "3.9" and python_version < "4.0"
+dask==2024.5.1 ; python_version >= "3.9" and python_version < "4.0"
+dask[array,complete,dataframe,diagnostics,distributed]==2024.5.1 ; python_version >= "3.9" and python_version < "4.0"
+datashader==0.16.1 ; python_version >= "3.9" and python_version < "4.0"
+distributed==2024.5.1 ; python_version >= "3.9" and python_version < "4.0"
 docopt==0.6.2 ; python_version < "3.10" and python_version >= "3.9"
-fasteners==0.19 ; python_version >= "3.9" and python_version < "4.0"
-fiona==1.9.5 ; python_version >= "3.9" and python_version < "4.0"
-flox==0.9.0 ; python_version >= "3.9" and python_version < "4.0"
-fonttools==4.48.1 ; python_version >= "3.9" and python_version < "4.0"
-fsspec==2024.2.0 ; python_version >= "3.9" and python_version < "4.0"
-future==0.18.3 ; python_version >= "3.9" and python_version < "4.0"
-geopandas==0.14.3 ; python_version >= "3.9" and python_version < "4.0"
-geoviews==1.11.0 ; python_version >= "3.9" and python_version < "4.0"
+fasteners==0.19 ; python_version >= "3.9" and python_version < "4.0" and sys_platform != "emscripten"
+fiona==1.9.6 ; python_version >= "3.9" and python_version < "4.0"
+flox==0.9.7 ; python_version >= "3.9" and python_version < "4.0"
+fonttools==4.51.0 ; python_version >= "3.9" and python_version < "4.0"
+fsspec==2024.5.0 ; python_version >= "3.9" and python_version < "4.0"
+future==1.0.0 ; python_version >= "3.9" and python_version < "4.0"
+geopandas==0.14.4 ; python_version >= "3.9" and python_version < "4.0"
+geoviews==1.12.0 ; python_version >= "3.9" and python_version < "4.0"
 h5netcdf==1.3.0 ; python_version >= "3.9" and python_version < "4.0"
-h5py==3.10.0 ; python_version >= "3.9" and python_version < "4.0"
-holoviews==1.18.1 ; python_version >= "3.9" and python_version < "4.0"
-idna==3.6 ; python_version >= "3.9" and python_version < "4.0"
-importlib-metadata==7.0.1 ; python_version >= "3.9" and python_version < "4.0"
-importlib-resources==6.1.1 ; python_version >= "3.9" and python_version < "3.10"
-jinja2==3.1.3 ; python_version >= "3.9" and python_version < "4.0"
+h5py==3.11.0 ; python_version >= "3.9" and python_version < "4.0"
+holoviews==1.18.3 ; python_version >= "3.9" and python_version < "4.0"
+idna==3.7 ; python_version >= "3.9" and python_version < "4.0"
+importlib-metadata==7.1.0 ; python_version >= "3.9" and python_version < "3.12"
+importlib-resources==6.4.0 ; python_version >= "3.9" and python_version < "3.10"
+jinja2==3.1.4 ; python_version >= "3.9" and python_version < "4.0"
 kiwisolver==1.4.5 ; python_version >= "3.9" and python_version < "4.0"
 linkify-it-py==2.0.3 ; python_version >= "3.9" and python_version < "4.0"
 llvmlite==0.42.0 ; python_version >= "3.9" and python_version < "4.0"
 locket==1.0.0 ; python_version >= "3.9" and python_version < "4.0"
 lz4==4.3.3 ; python_version >= "3.9" and python_version < "4.0"
 markdown-it-py==3.0.0 ; python_version >= "3.9" and python_version < "4.0"
-markdown==3.5.2 ; python_version >= "3.9" and python_version < "4.0"
+markdown==3.6 ; python_version >= "3.9" and python_version < "4.0"
 markupsafe==2.1.5 ; python_version >= "3.9" and python_version < "4.0"
-matplotlib==3.8.2 ; python_version >= "3.9" and python_version < "4.0"
-mdit-py-plugins==0.4.0 ; python_version >= "3.9" and python_version < "4.0"
+matplotlib==3.9.0 ; python_version >= "3.9" and python_version < "4.0"
+mdit-py-plugins==0.4.1 ; python_version >= "3.9" and python_version < "4.0"
 mdurl==0.1.2 ; python_version >= "3.9" and python_version < "4.0"
-msgpack==1.0.7 ; python_version >= "3.9" and python_version < "4.0"
+msgpack==1.0.8 ; python_version >= "3.9" and python_version < "4.0"
 multipledispatch==1.0.0 ; python_version >= "3.9" and python_version < "4.0"
 netcdf4==1.6.5 ; python_version >= "3.9" and python_version < "4.0"
-numba==0.59.0 ; python_version >= "3.9" and python_version < "4.0"
-numbagg==0.8.0 ; python_version >= "3.9" and python_version < "4.0"
+numba==0.59.1 ; python_version >= "3.9" and python_version < "4.0"
+numbagg==0.8.1 ; python_version >= "3.9" and python_version < "4.0"
 numcodecs==0.12.1 ; python_version >= "3.9" and python_version < "4.0"
-numpy-groupies==0.10.2 ; python_version >= "3.9" and python_version < "4.0"
+numpy-groupies==0.11.1 ; python_version >= "3.9" and python_version < "4.0"
 numpy-indexed==0.3.7 ; python_version >= "3.9" and python_version < "4.0"
 numpy==1.26.4 ; python_version >= "3.9" and python_version < "4.0"
 opt-einsum==3.3.0 ; python_version >= "3.9" and python_version < "4.0"
-packaging==23.2 ; python_version >= "3.9" and python_version < "4.0"
-pandas==2.2.0 ; python_version >= "3.9" and python_version < "4.0"
-panel==1.3.8 ; python_version >= "3.9" and python_version < "4.0"
-param==2.0.2 ; python_version >= "3.9" and python_version < "4.0"
-partd==1.4.1 ; python_version >= "3.9" and python_version < "4.0"
-pillow==10.2.0 ; python_version >= "3.9" and python_version < "4.0"
-platformdirs==4.2.0 ; python_version >= "3.9" and python_version < "4.0"
-pooch==1.8.0 ; python_version >= "3.9" and python_version < "4.0"
+packaging==24.0 ; python_version >= "3.9" and python_version < "4.0"
+pandas==2.2.2 ; python_version >= "3.9" and python_version < "4.0"
+panel==1.4.3 ; python_version >= "3.9" and python_version < "4.0"
+param==2.1.0 ; python_version >= "3.9" and python_version < "4.0"
+partd==1.4.2 ; python_version >= "3.9" and python_version < "4.0"
+pillow==10.3.0 ; python_version >= "3.9" and python_version < "4.0"
+platformdirs==4.2.2 ; python_version >= "3.9" and python_version < "4.0"
+pooch==1.8.1 ; python_version >= "3.9" and python_version < "4.0"
 psutil==5.9.8 ; python_version >= "3.9" and python_version < "4.0"
 pyarrow-hotfix==0.6 ; python_version >= "3.9" and python_version < "4.0"
-pyarrow==15.0.0 ; python_version >= "3.9" and python_version < "4.0"
+pyarrow==16.1.0 ; python_version >= "3.9" and python_version < "4.0"
 pyct==0.5.0 ; python_version >= "3.9" and python_version < "4.0"
 pydap==3.4.1 ; python_version < "3.10" and python_version >= "3.9"
-pyparsing==3.1.1 ; python_version >= "3.9" and python_version < "4.0"
+pyparsing==3.1.2 ; python_version >= "3.9" and python_version < "4.0"
 pyproj==3.6.1 ; python_version >= "3.9" and python_version < "4.0"
 pyshp==2.3.1 ; python_version >= "3.9" and python_version < "4.0"
-python-dateutil==2.8.2 ; python_version >= "3.9" and python_version < "4.0"
+python-dateutil==2.9.0.post0 ; python_version >= "3.9" and python_version < "4.0"
 pytz==2024.1 ; python_version >= "3.9" and python_version < "4.0"
-pyviz-comms==3.0.1 ; python_version >= "3.9" and python_version < "4.0"
+pyviz-comms==3.0.2 ; python_version >= "3.9" and python_version < "4.0"
 pyyaml==6.0.1 ; python_version >= "3.9" and python_version < "4.0"
-requests==2.31.0 ; python_version >= "3.9" and python_version < "4.0"
-scipy==1.12.0 ; python_version >= "3.9" and python_version < "4.0"
-setuptools==69.0.3 ; python_version >= "3.9" and python_version < "4.0"
-shapely==2.0.2 ; python_version >= "3.9" and python_version < "4.0"
+requests==2.32.2 ; python_version >= "3.9" and python_version < "4.0"
+scipy==1.13.1 ; python_version >= "3.9" and python_version < "4.0"
+shapely==2.0.4 ; python_version >= "3.9" and python_version < "4.0"
 six==1.16.0 ; python_version >= "3.9" and python_version < "4.0"
 sortedcontainers==2.4.0 ; python_version >= "3.9" and python_version < "4.0"
 soupsieve==2.5 ; python_version < "3.10" and python_version >= "3.9"
 tblib==3.0.0 ; python_version >= "3.9" and python_version < "4.0"
 toolz==0.12.1 ; python_version >= "3.9" and python_version < "4.0"
 tornado==6.4 ; python_version >= "3.9" and python_version < "4.0"
-tqdm==4.66.1 ; python_version >= "3.9" and python_version < "4.0"
-typing-extensions==4.9.0 ; python_version >= "3.9" and python_version < "4.0"
-tzdata==2023.4 ; python_version >= "3.9" and python_version < "4.0"
-uc-micro-py==1.0.2 ; python_version >= "3.9" and python_version < "4.0"
-urllib3==2.2.0 ; python_version >= "3.9" and python_version < "4.0"
+tqdm==4.66.4 ; python_version >= "3.9" and python_version < "4.0"
+typing-extensions==4.12.0 ; python_version >= "3.9" and python_version < "4.0"
+tzdata==2024.1 ; python_version >= "3.9" and python_version < "4.0"
+uc-micro-py==1.0.3 ; python_version >= "3.9" and python_version < "4.0"
+urllib3==2.2.1 ; python_version >= "3.9" and python_version < "4.0"
 webencodings==0.5.1 ; python_version >= "3.9" and python_version < "4.0"
 webob==1.8.7 ; python_version >= "3.9" and python_version < "3.10"
-xarray==2024.1.1 ; python_version >= "3.9" and python_version < "4.0"
-xarray[accel,io]==2024.1.1 ; python_version >= "3.9" and python_version < "4.0"
-xyzservices==2023.10.1 ; python_version >= "3.9" and python_version < "4.0"
-zarr==2.16.1 ; python_version >= "3.9" and python_version < "4.0"
+xarray==2024.5.0 ; python_version >= "3.9" and python_version < "4.0"
+xarray[accel,io]==2024.5.0 ; python_version >= "3.9" and python_version < "4.0"
+xyzservices==2024.4.0 ; python_version >= "3.9" and python_version < "4.0"
+zarr==2.18.1 ; python_version >= "3.9" and python_version < "4.0"
 zict==3.0.0 ; python_version >= "3.9" and python_version < "4.0"
-zipp==3.17.0 ; python_version >= "3.9" and python_version < "4.0"
+zipp==3.18.2 ; python_version >= "3.9" and python_version < "3.12"
diff --git a/tests/api_test.py b/tests/api_test.py
@@ -9,11 +9,17 @@
 from thalassa import normalization
 
 ADCIRC_NC = DATA_DIR / "fort.63.nc"
-
-
-def test_main_api():
-    variable = "zeta"
-    ds = api.open_dataset(ADCIRC_NC)
+SELAFIN = DATA_DIR / "iceland.slf"
+
+@pytest.mark.parametrize(
+    "file,variable",
+    [
+        pytest.param(ADCIRC_NC, "zeta"),
+        pytest.param(SELAFIN, "S"),
+    ],
+)
+def test_main_api(file, variable):
+    ds = api.open_dataset(file)
     assert normalization.is_generic(ds)
 
     # Create objects
@@ -34,9 +40,15 @@ def test_main_api():
     hv.render(pointer_ts, backend="bokeh")
 
 
-@pytest.mark.parametrize("variable", [None, "zeta"])
-def test_create_trimesh(variable):
-    ds = api.open_dataset(ADCIRC_NC)
+@pytest.mark.parametrize(
+    "file,variable",
+    [
+        pytest.param(ADCIRC_NC, "zeta"),
+        pytest.param(SELAFIN, "S"),
+    ],
+)
+def test_create_trimesh(file, variable):
+    ds = api.open_dataset(file)
     trimesh = api.create_trimesh(ds, variable=variable)
     assert isinstance(trimesh, gv.TriMesh)
 

diff --git a/tests/data/iceland.slf b/tests/data/iceland.slf
diff --git a/tests/normalization_test.py b/tests/normalization_test.py
@@ -12,6 +12,7 @@
     "ds,expected_fmt",
     [
         pytest.param(api.open_dataset(DATA_DIR / "fort.63.nc", normalize=False), THALASSA_FORMATS.ADCIRC, id="ADCIRC"),
+        pytest.param(api.open_dataset(DATA_DIR / "iceland.slf", normalize=False), THALASSA_FORMATS.TELEMAC, id="TELEMAC"),
         pytest.param(xr.Dataset(), THALASSA_FORMATS.UNKNOWN, id="Unknown"),
     ],
 )
@@ -24,6 +25,7 @@ def test_infer_format(ds, expected_fmt):
     "path,expected",
     [
         pytest.param(DATA_DIR / "fort.63.nc", True, id="ADCIRC"),
+        pytest.param(DATA_DIR / "iceland.slf", True, id="TELEMAC"),
         pytest.param(__file__, False, id="Unknown"),
     ],
 )

diff --git a/thalassa/api.py b/thalassa/api.py
@@ -67,14 +67,14 @@ def open_dataset(
     Parameters:
         path: The path to the dataset file (netCDF, zarr, grib)
         normalize: Boolean flag indicating whether the dataset should be converted/normalized to the "Thalassa schema".
-            Normalization is currently only supported for ``SCHISM`` and ``ADCIRC`` netcdf files.
+            Normalization is currently only supported for ``SCHISM``, ``TELEMAC``,  and ``ADCIRC`` netcdf files.
         kwargs: The ``kwargs`` are being passed through to ``xarray.open_dataset``.
 
     """
     import xarray as xr
 
     default_kwargs: dict[str, T.Any] = dict(
-        mask_and_scale=True,
+        # mask_and_scale=True,
         cache=False,
         drop_variables=ADCIRC_VARIABLES_TO_BE_DROPPED,
     )