From c44a011d299966b92ac3efe27cee9e1ab7fdb915 Mon Sep 17 00:00:00 2001 From: tomsail Date: Sun, 19 May 2024 13:37:51 +0200 Subject: [PATCH] added TELEMAC support and tests --- poetry.lock | 2769 +++++++++++++++-------------- pyproject.toml | 1 + requirements/requirements-dev.txt | 193 +- requirements/requirements.txt | 118 +- tests/api_test.py | 14 +- tests/normalization_test.py | 2 + thalassa/api.py | 2 +- thalassa/normalization.py | 96 +- 8 files changed, 1654 insertions(+), 1541 deletions(-) diff --git a/poetry.lock b/poetry.lock index df8ae78..bb91e3b 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,88 +1,88 @@ -# This file is automatically @generated by Poetry 1.7.1 and should not be changed by hand. +# This file is automatically @generated by Poetry 1.8.2 and should not be changed by hand. 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"4.0" beautifulsoup4==4.12.3 ; python_version < "3.10" and python_version >= "3.9" -black==24.1.1 ; python_version >= "3.9" and python_version < "4.0" +black==24.4.2 ; python_version >= "3.9" and python_version < "4.0" 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" cffi==1.16.0 ; python_version >= "3.9" and python_version < "4.0" and implementation_name == "pypy" cftime==1.6.3 ; python_version >= "3.9" and python_version < "4.0" @@ -20,155 +21,157 @@ click==8.1.7 ; python_version >= 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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" -debugpy==1.8.0 ; 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" +debugpy==1.8.1 ; python_version >= "3.9" and python_version < "4.0" decorator==5.1.1 ; python_version >= "3.9" and python_version < "4.0" -distributed==2024.1.1 ; 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" entrypoints==0.4 ; python_version >= "3.9" and python_version < "4.0" -exceptiongroup==1.2.0 ; python_version >= "3.9" and python_version < "3.11" +exceptiongroup==1.2.1 ; python_version >= "3.9" and python_version < "3.11" executing==2.0.1 ; python_version >= "3.9" and python_version < "4.0" -fasteners==0.19 ; 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" fastjsonschema==2.19.1 ; 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" +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" frozenlist==1.4.1 ; python_version == "3.12" -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" +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" ghp-import==2.1.0 ; python_version >= "3.9" and python_version < "4.0" -griffe==0.40.0 ; python_version >= "3.9" and python_version < "4.0" +griffe==0.45.1 ; 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" +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" iniconfig==2.0.0 ; python_version >= "3.9" and python_version < "4.0" -ipykernel==6.29.1 ; python_version >= "3.9" and python_version < "4.0" +ipykernel==6.29.4 ; python_version >= "3.9" and python_version < "4.0" ipython==8.18.1 ; python_version >= "3.9" and python_version < "4.0" jedi==0.19.1 ; python_version >= "3.9" and python_version < "4.0" -jinja2==3.1.3 ; 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==4.21.1 ; python_version >= "3.9" and python_version < "4.0" -jupyter-client==8.6.0 ; python_version >= "3.9" and python_version < "4.0" -jupyter-core==5.7.1 ; 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-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" 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-inline==0.1.6 ; 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-inline==0.1.7 ; 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" mergedeep==1.3.4 ; python_version >= "3.9" and python_version < "4.0" -mkdocs-autorefs==0.5.0 ; 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==9.5.7 ; python_version >= "3.9" and python_version < "4.0" -mkdocs==1.5.3 ; python_version >= "3.9" and python_version < "4.0" -mkdocstrings-python==1.8.0 ; python_version >= "3.9" and python_version < "4.0" -mkdocstrings==0.24.0 ; python_version >= "3.9" and python_version < "4.0" -msgpack==1.0.7 ; python_version >= "3.9" and python_version < "4.0" +mkdocs-material==9.5.23 ; 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==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" multipledispatch==1.0.0 ; python_version >= "3.9" and python_version < "4.0" mypy-extensions==1.0.0 ; python_version >= "3.9" and python_version < "4.0" -mypy==1.8.0 ; python_version >= "3.9" and python_version < "4.0" -nbclient==0.9.0 ; python_version >= "3.9" and python_version < "4.0" -nbformat==5.9.2 ; python_version >= "3.9" and python_version < "4.0" +mypy==1.10.0 ; python_version >= "3.9" and python_version < "4.0" +nbclient==0.10.0 ; python_version >= "3.9" and python_version < "4.0" +nbformat==5.10.4 ; python_version >= "3.9" and python_version < "4.0" nest-asyncio==1.6.0 ; 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" +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==2.1.4.231227 ; 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" -papermill==2.5.0 ; python_version >= "3.9" and python_version < "4.0" -param==2.0.2 ; python_version >= "3.9" and python_version < "4.0" -parso==0.8.3 ; python_version >= "3.9" and python_version < "4.0" -partd==1.4.1 ; 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" +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" +partd==1.4.2 ; python_version >= "3.9" and python_version < "4.0" pathspec==0.12.1 ; python_version >= "3.9" and python_version < "4.0" pexpect==4.9.0 ; python_version >= "3.9" and python_version < "4.0" and sys_platform != "win32" -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" -pluggy==1.4.0 ; python_version >= "3.9" and python_version < "4.0" -pooch==1.8.0 ; 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" prompt-toolkit==3.0.43 ; python_version >= "3.9" and python_version < "4.0" psutil==5.9.8 ; python_version >= "3.9" and python_version < "4.0" ptyprocess==0.7.0 ; python_version >= "3.9" and python_version < "4.0" and sys_platform != "win32" pure-eval==0.2.2 ; 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" -pycparser==2.21 ; python_version >= "3.9" and python_version < "4.0" and implementation_name == "pypy" +pyarrow==16.1.0 ; python_version >= "3.9" and python_version < "4.0" +pycparser==2.22 ; python_version >= "3.9" and python_version < "4.0" and implementation_name == "pypy" 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" -pygments==2.17.2 ; python_version >= "3.9" and python_version < "4.0" -pymdown-extensions==10.7 ; python_version >= "3.9" and python_version < "4.0" -pyparsing==3.1.1 ; python_version >= "3.9" and python_version < "4.0" +pygments==2.18.0 ; python_version >= "3.9" and python_version < "4.0" +pymdown-extensions==10.8.1 ; 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" -pytest-cov==4.1.0 ; python_version >= "3.9" and python_version < "4.0" -pytest==8.0.0 ; python_version >= "3.9" and python_version < "4.0" -python-dateutil==2.8.2 ; python_version >= "3.9" and python_version < "4.0" +pytest-cov==5.0.0 ; python_version >= "3.9" and python_version < "4.0" +pytest==8.2.0 ; 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" pywin32==306 ; sys_platform == "win32" and platform_python_implementation != "PyPy" and python_version >= "3.9" and python_version < "4.0" pyyaml-env-tag==0.1 ; python_version >= "3.9" and python_version < "4.0" pyyaml==6.0.1 ; python_version >= "3.9" and python_version < "4.0" -pyzmq==25.1.2 ; python_version >= "3.9" and python_version < "4.0" -referencing==0.33.0 ; python_version >= "3.9" and python_version < "4.0" -regex==2023.12.25 ; 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" -rpds-py==0.17.1 ; 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" +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" +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" stack-data==0.6.3 ; python_version >= "3.9" and python_version < "4.0" tblib==3.0.0 ; python_version >= "3.9" and python_version < "4.0" -tenacity==8.2.3 ; python_version >= "3.9" and python_version < "4.0" +tenacity==8.3.0 ; python_version >= "3.9" and python_version < "4.0" tomli==2.0.1 ; python_version >= "3.9" and python_full_version <= "3.11.0a6" 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" -traitlets==5.14.1 ; python_version >= "3.9" and python_version < "4.0" -types-decorator==5.1.8.20240106 ; python_version >= "3.9" and python_version < "4.0" -types-pytz==2024.1.0.20240203 ; 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" -watchdog==3.0.0 ; python_version >= "3.9" and python_version < "4.0" +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" +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" 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==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" +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" yarl==1.9.4 ; python_version == "3.12" -zarr==2.16.1 ; 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/requirements/requirements.txt b/requirements/requirements.txt index ce1db99..384087c 100644 --- 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" @@ -12,91 +12,97 @@ 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" -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" +colorama==0.4.6 ; python_version >= "3.9" and python_version < "4.0" and (platform_system == "Windows" or sys_platform == "win32") +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" +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" +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" +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" 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==1.4.2 ; 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" -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" +pytest==8.2.0 ; 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" +scipy==1.13.0 ; 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==4.66.1 ; 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==4.11.0 ; 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-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" +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 index 92aa6a1..63e1dfd 100644 --- a/tests/api_test.py +++ b/tests/api_test.py @@ -9,11 +9,19 @@ from thalassa import normalization ADCIRC_NC = DATA_DIR / "fort.63.nc" +SELAFIN = DATA_DIR / "r3d_tidal_flats.slf" +@pytest.mark.parametrize( + "file,variable", + [ + pytest.param(ADCIRC_NC, "zeta"), + pytest.param(SELAFIN, "U"), + ], +) -def test_main_api(): - variable = "zeta" - ds = api.open_dataset(ADCIRC_NC) + +def test_main_api(file, variable): + ds = api.open_dataset(file) assert normalization.is_generic(ds) # Create objects diff --git a/tests/normalization_test.py b/tests/normalization_test.py index 3786c78..0bb30cb 100644 --- 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 / "r3d_tidal_flats.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 / "r3d_tidal_flats.slf", True, id="TELEMAC"), pytest.param(__file__, False, id="Unknown"), ], ) diff --git a/thalassa/api.py b/thalassa/api.py index f25d6bf..c17adf7 100644 --- a/thalassa/api.py +++ b/thalassa/api.py @@ -74,7 +74,7 @@ def 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, ) diff --git a/thalassa/normalization.py b/thalassa/normalization.py index cd4855f..b6eb197 100644 --- a/thalassa/normalization.py +++ b/thalassa/normalization.py @@ -19,19 +19,29 @@ class THALASSA_FORMATS(enum.Enum): UNKNOWN = "UNKNOWN" ADCIRC = "ADCIRC" SCHISM = "SCHISM" + TELEMAC = "TELEMAC" GENERIC = "GENERIC" PYPOSEIDON = "PYPOSEIDON" # fmt: off +EDGE_DIM = "edge" +FACE_DIM = "face" +NODE_DIM = "node" +VERTICAL_DIM = "layer" +CONNECTIVITY = "face_nodes" +VERTICE_DIM = "max_no_vertices" +X_DIM = "lon" +Y_DIM = "lat" + _GENERIC_DIMS = { - "node", + NODE_DIM, "triface", "three", } _GENERIC_VARS = { - "lon", - "lat", + X_DIM, + Y_DIM, "triface_nodes", } _SCHISM_DIMS = { @@ -45,6 +55,14 @@ class THALASSA_FORMATS(enum.Enum): "SCHISM_hgrid_node_y", "SCHISM_hgrid_face_nodes", } +_TELEMAC_DIMS = { + "node", +} +_TELEMAC_VARS = { + "x", + "y", + "ikle2", +} _PYPOSEIDON_DIMS = { "nSCHISM_hgrid_face", "nSCHISM_hgrid_node", @@ -76,6 +94,11 @@ def is_schism(ds: xarray.Dataset) -> bool: return _SCHISM_DIMS.issubset(ds.dims) and _SCHISM_VARS.issubset(total_vars) +def is_telemac(ds: xarray.Dataset) -> bool: + total_vars = list(ds.data_vars.keys()) + list(ds.coords.keys()) + list(ds.attrs.keys()) + return _TELEMAC_DIMS.issubset(ds.dims) and _TELEMAC_VARS.issubset(total_vars) + + def is_pyposeidon(ds: xarray.Dataset) -> bool: return _PYPOSEIDON_DIMS.issubset(ds.dims) and _PYPOSEIDON_VARS.issubset(ds.data_vars) @@ -87,6 +110,8 @@ def is_adcirc(ds: xarray.Dataset) -> bool: def infer_format(ds: xarray.Dataset) -> THALASSA_FORMATS: if is_schism(ds): fmt = THALASSA_FORMATS.SCHISM + if is_telemac(ds): + fmt = THALASSA_FORMATS.TELEMAC elif is_pyposeidon(ds): fmt = THALASSA_FORMATS.PYPOSEIDON elif is_generic(ds): @@ -120,37 +145,59 @@ def normalize_generic(ds: xarray.Dataset) -> xarray.Dataset: def normalize_schism(ds: xarray.Dataset) -> xarray.Dataset: ds = ds.rename( { - "nSCHISM_hgrid_edge": "edge", - "nSCHISM_hgrid_face": "face", - "nSCHISM_hgrid_node": "node", - "SCHISM_hgrid_face_nodes": "face_nodes", - "nMaxSCHISM_hgrid_face_nodes": "max_no_vertices", - "SCHISM_hgrid_node_x": "lon", - "SCHISM_hgrid_node_y": "lat", + "nSCHISM_hgrid_edge": EDGE_DIM, + "nSCHISM_hgrid_face": FACE_DIM, + "nSCHISM_hgrid_node": NODE_DIM, + "SCHISM_hgrid_face_nodes": CONNECTIVITY, + "nMaxSCHISM_hgrid_face_nodes": VERTICE_DIM, + "SCHISM_hgrid_node_x": X_DIM, + "SCHISM_hgrid_node_y": Y_DIM, }, ) if "nSCHISM_vgrid_layers" in ds.dims: # I.e. OLD Schism IO or "merged" new IO ds = ds.rename( { - "nSCHISM_vgrid_layers": "layer", + "nSCHISM_vgrid_layers": VERTICAL_DIM, }, ) # SCHISM output uses one-based indices for `face_nodes` # Let's ensure that we use zero-based indices everywhere. - ds["face_nodes"] -= 1 + ds[CONNECTIVITY] -= 1 + return ds + + +def normalize_telemac(ds: xarray.Dataset) -> xarray.Dataset: + ds = ds.rename( + { + "node": NODE_DIM, + "x": X_DIM, + "y": Y_DIM, + }, + ) + if "plan" in ds.dims: + # I.e. OLD Schism IO or "merged" new IO + ds = ds.rename( + { + "plan": VERTICAL_DIM, + }, + ) + + # TELEMAC output uses one-based indices for `face_nodes` + # Let's ensure that we use zero-based indices everywhere. + ds[CONNECTIVITY] = ((FACE_DIM, VERTICE_DIM), ds.attrs['ikle2'] - 1) return ds def normalize_pyposeidon(ds: xarray.Dataset) -> xarray.Dataset: ds = ds.rename( { - "nSCHISM_hgrid_face": "face", - "nSCHISM_hgrid_node": "node", - "SCHISM_hgrid_face_nodes": "face_nodes", - "nMaxSCHISM_hgrid_face_nodes": "max_no_vertices", - "SCHISM_hgrid_node_x": "lon", - "SCHISM_hgrid_node_y": "lat", + "nSCHISM_hgrid_face": FACE_DIM, + "nSCHISM_hgrid_node": NODE_DIM, + "SCHISM_hgrid_face_nodes": CONNECTIVITY, + "nMaxSCHISM_hgrid_face_nodes": VERTICE_DIM, + "SCHISM_hgrid_node_x": X_DIM, + "SCHISM_hgrid_node_y": Y_DIM, }, ) return ds @@ -159,16 +206,16 @@ def normalize_pyposeidon(ds: xarray.Dataset) -> xarray.Dataset: def normalize_adcirc(ds: xarray.Dataset) -> xarray.Dataset: ds = ds.rename( { - "x": "lon", - "y": "lat", - "element": "face_nodes", - "nvertex": "max_no_vertices", - "nele": "face", + "x": X_DIM, + "y": Y_DIM, + "element": CONNECTIVITY, + "nvertex": VERTICE_DIM, + "nele": FACE_DIM, }, ) # ADCIRC output uses one-based indices for `face_nodes` # Let's ensure that we use zero-based indices everywhere. - ds["face_nodes"] -= 1 + ds[CONNECTIVITY] -= 1 return ds @@ -176,6 +223,7 @@ def normalize_adcirc(ds: xarray.Dataset) -> xarray.Dataset: THALASSA_FORMATS.ADCIRC: normalize_adcirc, THALASSA_FORMATS.GENERIC: normalize_generic, THALASSA_FORMATS.SCHISM: normalize_schism, + THALASSA_FORMATS.TELEMAC: normalize_telemac, THALASSA_FORMATS.PYPOSEIDON: normalize_pyposeidon, }