[telemac] addressed reviews and added docs

.pre-commit-config.yaml

@@ -71,8 +71,6 @@ repos:
             "--without-hashes",
             "--only",
             "main",
-            "-E",
-            "selafin",
             "-f",
             "requirements.txt",
             "-o",
@@ -87,8 +85,6 @@ repos:
             "dev",
             "--with",
             "docs",
-            "-E",
-            "selafin",
             "-f",
             "requirements.txt",
             "-o",

README.md

@@ -33,7 +33,8 @@ pip install thalassa
 ```
 for Selafin files (openTELEMAC outputs):
 ```
-pip install thalassa[selafin]
+pip install thalassa
+pip install xarray-selafin
 ```
 
 ### Conda

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.
 

docs/installation.md

@@ -12,6 +12,11 @@
 ```
 pip install thalassa
 ```
+for Selafin files (openTELEMAC outputs):
+```
+pip install thalassa
+pip install xarray-selafin
+```
 
 ### Conda
 

pyproject.toml

@@ -38,7 +38,6 @@ pyproj = "*"
 scipy = "*"
 shapely = "*"
 xarray = {version = "*", extras = ["io", "accel"]}
-xarray-selafin = { version = "*", optional = true }
 
 [tool.poetry.group.dev.dependencies]
 covdefaults = "*"
@@ -50,9 +49,7 @@ ipykernel = "*"
 ipython = "*"
 papermill = "*"
 pandas-stubs = "*"
-
-[tool.poetry.extras]
-selafin = ["xarray-selafin"]
+xarray-selafin = "*"
 
 [tool.poetry.group.docs.dependencies]
 mkdocs = "*"

requirements/requirements-dev.txt

@@ -50,7 +50,7 @@ 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"
 ghp-import==2.1.0 ; python_version >= "3.9" and python_version < "4.0"
-griffe==0.45.1 ; python_version >= "3.9" and python_version < "4.0"
+griffe==0.45.2 ; python_version >= "3.9" and python_version < "4.0"
 h5netcdf==1.3.0 ; 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"
@@ -64,7 +64,7 @@ jedi==0.19.1 ; python_version >= "3.9" and python_version < "4.0"
 jinja2==3.1.4 ; python_version >= "3.9" and python_version < "4.0"
 jsonschema-specifications==2023.12.1 ; python_version >= "3.9" and python_version < "4.0"
 jsonschema==4.22.0 ; python_version >= "3.9" and python_version < "4.0"
-jupyter-client==8.6.1 ; python_version >= "3.9" and python_version < "4.0"
+jupyter-client==8.6.2 ; python_version >= "3.9" and python_version < "4.0"
 jupyter-core==5.7.2 ; 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"
@@ -82,9 +82,9 @@ mergedeep==1.3.4 ; python_version >= "3.9" and python_version < "4.0"
 mkdocs-autorefs==1.0.1 ; python_version >= "3.9" and python_version < "4.0"
 mkdocs-get-deps==0.2.0 ; python_version >= "3.9" and python_version < "4.0"
 mkdocs-material-extensions==1.3.1 ; python_version >= "3.9" and python_version < "4.0"
-mkdocs-material==9.5.23 ; python_version >= "3.9" and python_version < "4.0"
+mkdocs-material==9.5.24 ; python_version >= "3.9" and python_version < "4.0"
 mkdocs==1.6.0 ; python_version >= "3.9" and python_version < "4.0"
-mkdocstrings-python==1.10.2 ; python_version >= "3.9" and python_version < "4.0"
+mkdocstrings-python==1.10.3 ; python_version >= "3.9" and python_version < "4.0"
 mkdocstrings==0.25.1 ; python_version >= "3.9" and python_version < "4.0"
 msgpack==1.0.8 ; python_version >= "3.9" and python_version < "4.0"
 multidict==6.0.5 ; python_version == "3.12"
@@ -106,7 +106,7 @@ packaging==24.0 ; python_version >= "3.9" and python_version < "4.0"
 paginate==0.5.6 ; python_version >= "3.9" and python_version < "4.0"
 pandas-stubs==2.2.2.240514 ; python_version >= "3.9" and python_version < "4.0"
 pandas==2.2.2 ; python_version >= "3.9" and python_version < "4.0"
-panel==1.4.2 ; python_version >= "3.9" and python_version < "4.0"
+panel==1.4.3 ; python_version >= "3.9" and python_version < "4.0"
 papermill==2.6.0 ; python_version >= "3.9" and python_version < "4.0"
 param==2.1.0 ; python_version >= "3.9" and python_version < "4.0"
 parso==0.8.4 ; python_version >= "3.9" and python_version < "4.0"
@@ -142,9 +142,9 @@ pyyaml==6.0.1 ; python_version >= "3.9" and python_version < "4.0"
 pyzmq==26.0.3 ; python_version >= "3.9" and python_version < "4.0"
 referencing==0.35.1 ; python_version >= "3.9" and python_version < "4.0"
 regex==2024.5.15 ; python_version >= "3.9" and python_version < "4.0"
-requests==2.31.0 ; python_version >= "3.9" and python_version < "4.0"
+requests==2.32.2 ; python_version >= "3.9" and python_version < "4.0"
 rpds-py==0.18.1 ; python_version >= "3.9" and python_version < "4.0"
-scipy==1.13.0 ; 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"
@@ -159,15 +159,15 @@ tqdm==4.66.4 ; python_version >= "3.9" and python_version < "4.0"
 traitlets==5.14.3 ; python_version >= "3.9" and python_version < "4.0"
 types-decorator==5.1.8.20240310 ; python_version >= "3.9" and python_version < "4.0"
 types-pytz==2024.1.0.20240417 ; python_version >= "3.9" and python_version < "4.0"
-typing-extensions==4.11.0 ; 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"
-watchdog==4.0.0 ; python_version >= "3.9" and python_version < "4.0"
+watchdog==4.0.1 ; python_version >= "3.9" and python_version < "4.0"
 wcwidth==0.2.13 ; 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-selafin==0.1.5 ; python_version >= "3.9" and python_version < "4.0"
+xarray-selafin==0.1.6 ; 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"

requirements/requirements.txt

@@ -12,7 +12,7 @@ click-plugins==1.1.1 ; python_version >= "3.9" and python_version < "4.0"
 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" or sys_platform == "win32")
+colorama==0.4.6 ; python_version >= "3.9" and python_version < "4.0" and platform_system == "Windows"
 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"
@@ -22,7 +22,6 @@ dask[array,complete,dataframe,diagnostics,distributed]==2024.5.1 ; python_versio
 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"
-exceptiongroup==1.2.1 ; python_version >= "3.9" and python_version < "3.11"
 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"
@@ -37,7 +36,6 @@ 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"
-iniconfig==2.0.0 ; python_version >= "3.9" and python_version < "4.0"
 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"
@@ -62,12 +60,11 @@ 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==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==1.4.2 ; 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"
-pluggy==1.5.0 ; 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"
@@ -77,29 +74,26 @@ pydap==3.4.1 ; python_version < "3.10" and python_version >= "3.9"
 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"
-pytest==8.2.1 ; 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==3.0.2 ; 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==1.13.0 ; 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"
-tomli==2.0.1 ; python_version >= "3.9" and python_version < "3.11"
 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==4.66.4 ; python_version >= "3.9" and python_version < "4.0"
-typing-extensions==4.11.0 ; 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-selafin==0.1.5 ; 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"

thalassa/api.py

@@ -67,7 +67,7 @@ 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``.
 
     """