From db792e175f621bc055b2f867120feac9ae08110a Mon Sep 17 00:00:00 2001 From: tomsail Date: Fri, 24 May 2024 10:32:54 +0200 Subject: [PATCH] [telemac] addressed reviews and added docs --- .pre-commit-config.yaml | 4 - README.md | 3 +- docs/index.md | 1 + docs/installation.md | 5 + poetry.lock | 191 +++++++++++++++--------------- pyproject.toml | 5 +- requirements/requirements-dev.txt | 20 ++-- requirements/requirements.txt | 16 +-- thalassa/api.py | 2 +- 9 files changed, 118 insertions(+), 129 deletions(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 0b43371..e49bedd 100644 --- a/.pre-commit-config.yaml +++ b/.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", diff --git a/README.md b/README.md index 510304b..738b674 100644 --- a/README.md +++ b/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 diff --git a/docs/index.md b/docs/index.md index b8108e2..366a5b1 100644 --- 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 index c01ac33..d8807f4 100644 --- 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 index 9e3087d..5f50244 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1449,13 +1449,13 @@ dev = ["flake8", "markdown", "twine", "wheel"] [[package]] name = "griffe" -version = "0.45.1" +version = "0.45.2" description = "Signatures for entire Python programs. 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-optional = true +version = "0.1.6" +description = "" +optional = false python-versions = ">=3.9" files = [ - {file = "xarray-selafin-0.1.5.tar.gz", hash = "sha256:a1467323aa3df600dadfe25bfab9042c8eef7d61d72d194cfd2237140ef34371"}, - {file = "xarray_selafin-0.1.5-py3-none-any.whl", hash = "sha256:a7148c907408c99e899667389f27a4165506e203f66e9dab9a29f22b0f2bb203"}, + {file = "xarray_selafin-0.1.6-py3-none-any.whl", hash = "sha256:e484ae6e26ceb3c91f6a7a4975b171146a94171bf6472dea33a09c90a4e15ad5"}, + {file = "xarray_selafin-0.1.6.tar.gz", hash = "sha256:4fab755eb3089571c1d43b3d84491e4ffa80cdbb0977aa893a63f156be44b493"}, ] [package.dependencies] netcdf4 = "*" numpy = "*" -pytest = "*" scipy = "*" shapely = "*" xarray = "*" -[package.extras] -dask = ["dask"] -dev = ["matplotlib"] - [[package]] name = "xyzservices" version = "2024.4.0" @@ -4717,10 +4715,7 @@ files = [ docs = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"] testing = ["big-O", "jaraco.functools", "jaraco.itertools", "jaraco.test", "more-itertools", "pytest (>=6,!=8.1.*)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-ignore-flaky", "pytest-mypy", "pytest-ruff (>=0.2.1)"] -[extras] -selafin = ["xarray-selafin"] - [metadata] lock-version = "2.0" python-versions = ">=3.9, <4.0" -content-hash = "ad231bcdf63d9633a186c5693bf80bd034fa936568370edfa915849aab349b2a" +content-hash = "34abafe09252a6314c18832a0c53ff4a80cbeb13249ed940c43f3f4a82ea90af" diff --git a/pyproject.toml b/pyproject.toml index ef4e990..9351c4c 100644 --- a/pyproject.toml +++ b/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 = "*" diff --git a/requirements/requirements-dev.txt b/requirements/requirements-dev.txt index 34ef612..0b536c1 100644 --- a/requirements/requirements-dev.txt +++ b/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" diff --git a/requirements/requirements.txt b/requirements/requirements.txt index c23a715..77eac06 100644 --- a/requirements/requirements.txt +++ b/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" diff --git a/thalassa/api.py b/thalassa/api.py index c17adf7..564a03b 100644 --- a/thalassa/api.py +++ b/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``. """