diff --git a/Makefile b/Makefile index 567b7ac..0e3c9b6 100644 --- a/Makefile +++ b/Makefile @@ -4,7 +4,7 @@ list: @LC_ALL=C $(MAKE) -pRrq -f $(lastword $(MAKEFILE_LIST)) : 2>/dev/null | awk -v RS= -F: '/^# File/,/^# Finished Make data base/ {if ($$1 !~ "^[#.]") {print $$1}}' | sort | grep -E -v -e '^[^[:alnum:]]' -e '^$@$$' init: - poetry install --with=dev -E grib + poetry install --with=dev -E all pre-commit install style: diff --git a/inspectds/cli.py b/inspectds/cli.py index e78196d..0428546 100644 --- a/inspectds/cli.py +++ b/inspectds/cli.py @@ -15,23 +15,41 @@ if TYPE_CHECKING: import xarray -if importlib.util.find_spec("cfgrib"): - IS_GRIB_AVAILABLE = True -else: - IS_GRIB_AVAILABLE = False +IS_GRIB_AVAILABLE = bool(importlib.util.find_spec("cfgrib")) +IS_SELAFIN_AVAILABLE = bool(importlib.util.find_spec("xarray_selafin")) + -if IS_GRIB_AVAILABLE: +if IS_GRIB_AVAILABLE and IS_SELAFIN_AVAILABLE: + SUPPORTED_DATASETS = {"netcdf", "zarr", "grib", "selafin"} + + class DATASET_TYPE(str, enum.Enum): + AUTO = "auto" + NETCDF = "netcdf" + ZARR = "zarr" + GRIB = "grib" + SELAFIN = "selafin" + +elif IS_GRIB_AVAILABLE: SUPPORTED_DATASETS = { - "grib", "netcdf", "zarr", + "grib", } - class DATASET_TYPE(str, enum.Enum): + class DATASET_TYPE(str, enum.Enum): # type: ignore[no-redef] AUTO = "auto" + NETCDF = "netcdf" + ZARR = "zarr" GRIB = "grib" + +elif IS_SELAFIN_AVAILABLE: + SUPPORTED_DATASETS = {"netcdf", "zarr", "selafin"} + + class DATASET_TYPE(str, enum.Enum): # type: ignore[no-redef] + AUTO = "auto" NETCDF = "netcdf" ZARR = "zarr" + SELAFIN = "selafin" else: SUPPORTED_DATASETS = { @@ -92,11 +110,18 @@ def echo_dataset( # 3. we want to allow the user to override the inferring # This is why we keep this function def infer_dataset_type(path: Path) -> DATASET_TYPE: - if path.suffix in (".grib", ".grib2"): + if path.suffix in (".grb", ".grib", ".grib2"): if IS_GRIB_AVAILABLE: dataset_type = DATASET_TYPE.GRIB else: - msg = "GRIB file detected, but GRIB support is not available. Please install cfgrib." + msg = "GRIB file detected, but GRIB support is not available. Please install 'cfgrib'." + typer.echo(msg) + raise typer.Exit(code=1) + elif path.suffix in (".slf", ".selafin"): + if IS_SELAFIN_AVAILABLE: + dataset_type = DATASET_TYPE.SELAFIN + else: + msg = "SELAFIN file detected, but SELAFIN support is not available. Please install 'xarray-selafin'." typer.echo(msg) raise typer.Exit(code=1) elif path.is_dir() or path.suffix == ".zarr" or path.suffix == ".zip": @@ -128,6 +153,13 @@ def get_kwargs(dataset_type: DATASET_TYPE) -> dict[str, Any]: engine="netcdf4", ) ) + elif IS_SELAFIN_AVAILABLE and dataset_type == DATASET_TYPE.SELAFIN: + open_dataset_kwargs.update( + dict( + mask_and_scale=None, + engine="selafin", + ) + ) else: raise ValueError("WTF??? Unknown Dataset type...") return open_dataset_kwargs @@ -150,7 +182,8 @@ def version_callback(value: bool) -> None: @app.command(no_args_is_help=True) def inspect_dataset( path: Path = typer.Argument(dir_okay=True, file_okay=True, exists=True, readable=True, help="The path to the dataset"), - dataset_type: DATASET_TYPE = typer.Option(default=DATASET_TYPE.AUTO, help="The dataset type. If 'auto', then it gets inferred from PATH"), + #dataset_type: DATASET_TYPE = typer.Option(default=DATASET_TYPE.AUTO.value, help="The dataset type. If 'auto', then it gets inferred from PATH"), + dataset_type: DATASET_TYPE = typer.Option(default="auto", help="The dataset type. If 'auto', then it gets inferred from PATH"), mask_and_scale: bool = typer.Option(False, help="Whether to mask and scale the dataset"), dimensions: bool = typer.Option(default=True, help="Whether to include 'Dimensions' in the output"), coordinates: bool = typer.Option(default=True, help="Whether to include 'Coordinates' in the output"), @@ -161,24 +194,25 @@ def inspect_dataset( version: bool = typer.Option(False, "--version", help="Display the version", callback=version_callback, is_eager=True), ) -> int: # fmt: skip xr = lazy_imports.import_xarray() + if dataset_type == DATASET_TYPE.AUTO: dataset_type = infer_dataset_type(path) - open_dataset_kwargs = get_kwargs(dataset_type=dataset_type) - # Some netcdf files are not compatible with Xarray # More specifically you can't have a dimension as a variable too. # https://github.com/pydata/xarray/issues/1709#issuecomment-343714896 # When we find such variables we drop them: drop_variables: list[str] = [] + default_open_kwargs = { + "filename_or_obj": path, + "mask_and_scale": "mask_and_scale", + "drop_variables": "drop_variables", + } + dataset_type_open__kwargs = get_kwargs(dataset_type=dataset_type) + open_kwargs = default_open_kwargs | dataset_type_open__kwargs while True: try: - ds = xr.open_dataset( - filename_or_obj=path, - mask_and_scale=mask_and_scale, - drop_variables=drop_variables, - **open_dataset_kwargs, - ) + ds = xr.open_dataset(**open_kwargs) except Exception as exc: if "already exists as a scalar variable" in str(exc): to_be_dropped = str(exc).split("'")[-2] diff --git a/poetry.lock b/poetry.lock index 60d2ed2..37f9361 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,4 +1,4 @@ -# This file is automatically @generated by Poetry 1.7.1 and should not be changed by hand. +# This file is automatically @generated by Poetry 1.8.3 and should not be changed by hand. [[package]] name = "asciitree" @@ -12,31 +12,32 @@ files = [ [[package]] name = "attrs" -version = "23.1.0" +version = "23.2.0" description = "Classes Without Boilerplate" optional = true python-versions = ">=3.7" files = [ - {file = "attrs-23.1.0-py3-none-any.whl", hash = "sha256:1f28b4522cdc2fb4256ac1a020c78acf9cba2c6b461ccd2c126f3aa8e8335d04"}, - {file = "attrs-23.1.0.tar.gz", hash = "sha256:6279836d581513a26f1bf235f9acd333bc9115683f14f7e8fae46c98fc50e015"}, + {file = "attrs-23.2.0-py3-none-any.whl", hash = "sha256:99b87a485a5820b23b879f04c2305b44b951b502fd64be915879d77a7e8fc6f1"}, + {file = "attrs-23.2.0.tar.gz", hash = "sha256:935dc3b529c262f6cf76e50877d35a4bd3c1de194fd41f47a2b7ae8f19971f30"}, ] [package.extras] cov = ["attrs[tests]", "coverage[toml] (>=5.3)"] -dev = ["attrs[docs,tests]", "pre-commit"] +dev = ["attrs[tests]", "pre-commit"] docs = ["furo", "myst-parser", "sphinx", "sphinx-notfound-page", "sphinxcontrib-towncrier", "towncrier", "zope-interface"] tests = 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[[package]] name = "zarr" -version = "2.16.1" +version = "2.18.2" description = "An implementation of chunked, compressed, N-dimensional arrays for Python" optional = false -python-versions = ">=3.8" +python-versions = ">=3.9" files = [ - {file = "zarr-2.16.1-py3-none-any.whl", hash = "sha256:de4882433ccb5b42cc1ec9872b95e64ca3a13581424666b28ed265ad76c7056f"}, - {file = "zarr-2.16.1.tar.gz", hash = "sha256:4276cf4b4a653431042cd53ff2282bc4d292a6842411e88529964504fb073286"}, + {file = "zarr-2.18.2-py3-none-any.whl", hash = "sha256:a638754902f97efa99b406083fdc807a0e2ccf12a949117389d2a4ba9b05df38"}, + {file = "zarr-2.18.2.tar.gz", hash = "sha256:9bb393b8a0a38fb121dbb913b047d75db28de9890f6d644a217a73cf4ae74f47"}, ] [package.dependencies] asciitree = "*" -fasteners = "*" +fasteners = {version = "*", markers = "sys_platform != \"emscripten\""} numcodecs = ">=0.10.0" -numpy = ">=1.20,<1.21.0 || >1.21.0" +numpy = ">=1.23" [package.extras] -docs = ["numcodecs[msgpack]", "numpydoc", "pydata-sphinx-theme", "sphinx", "sphinx-copybutton", "sphinx-design", "sphinx-issues", "sphinx-rtd-theme"] +docs = ["numcodecs[msgpack]", "numpydoc", "pydata-sphinx-theme", "sphinx", "sphinx-automodapi", "sphinx-copybutton", "sphinx-design", "sphinx-issues"] jupyter = ["ipytree (>=0.2.2)", "ipywidgets (>=8.0.0)", "notebook"] [extras] +all = ["cfgrib", "xarray-selafin"] grib = ["cfgrib"] +selafin = ["xarray-selafin"] [metadata] lock-version = "2.0" python-versions = ">=3.9" -content-hash = "ef112372b66bed1e73ddec0fdd1542a94504c7b47b6e346c73cb4782fa09fd33" +content-hash = "37ddd602f5f9861d2517313dfb221eb7add3455ba7c5c9de06343743a0485640" diff --git a/pyproject.toml b/pyproject.toml index df3b1a3..7c8a8c9 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,6 +1,6 @@ [tool.poetry] name = "inspectds" -version = "0.1.0" +version = "0.3.0" description = "" authors = ["Panos Mavrogiorgos "] license = "Unlicense" @@ -27,10 +27,13 @@ cfgrib = { version = ">=0.9", optional = true } netcdf4 = "*" typer = {version = ">=0.9.0", extras = ["all"]} xarray = "*" +xarray-selafin = {version = "*", optional = true} zarr = ">=2.8" [tool.poetry.extras] grib = ["cfgrib"] +selafin = ["xarray-selafin"] +all = ["cfgrib", "xarray-selafin"] [tool.poetry.group.dev.dependencies] covdefaults = "*" diff --git a/requirements/requirements-dev.txt b/requirements/requirements-dev.txt index 710dc7e..fe5a1dc 100644 --- a/requirements/requirements-dev.txt +++ b/requirements/requirements-dev.txt @@ -1,39 +1,39 @@ asciitree==0.3.3 ; python_version >= "3.9" -attrs==23.1.0 ; python_version >= "3.9" -certifi==2023.7.22 ; python_version >= "3.9" +attrs==23.2.0 ; python_version >= "3.9" +certifi==2024.6.2 ; python_version >= "3.9" cffi==1.16.0 ; python_version >= "3.9" -cfgrib==0.9.10.4 ; python_version >= "3.9" +cfgrib==0.9.12.0 ; python_version >= "3.9" cftime==1.6.3 ; python_version >= "3.9" click==8.1.7 ; python_version >= "3.9" -colorama==0.4.6 ; python_version >= "3.9" +colorama==0.4.6 ; python_version >= "3.9" and (sys_platform == "win32" or platform_system == "Windows") covdefaults==2.3.0 ; python_version >= "3.9" -coverage==7.3.2 ; python_version >= "3.9" -eccodes==1.6.1 ; python_version >= "3.9" -exceptiongroup==1.1.3 ; python_version < "3.11" and python_version >= "3.9" -fasteners==0.19 ; python_version >= "3.9" +coverage==7.5.3 ; python_version >= "3.9" +eccodes==1.7.0 ; python_version >= "3.9" +exceptiongroup==1.2.1 ; python_version < "3.11" and python_version >= "3.9" +fasteners==0.19 ; sys_platform != "emscripten" and python_version >= "3.9" findlibs==0.0.5 ; python_version >= "3.9" iniconfig==2.0.0 ; python_version >= "3.9" markdown-it-py==3.0.0 ; python_version >= "3.9" mdurl==0.1.2 ; python_version >= "3.9" mypy-extensions==1.0.0 ; python_version >= "3.9" -mypy==1.7.0 ; python_version >= "3.9" +mypy==1.10.0 ; python_version >= "3.9" netcdf4==1.6.5 ; python_version >= "3.9" numcodecs==0.12.1 ; python_version >= "3.9" -numpy==1.26.2 ; python_version >= "3.9" -packaging==23.2 ; python_version >= "3.9" -pandas==2.1.3 ; python_version >= "3.9" -pluggy==1.3.0 ; python_version >= "3.9" -pycparser==2.21 ; python_version >= "3.9" -pygments==2.16.1 ; python_version >= "3.9" -pytest==7.4.3 ; python_version >= "3.9" -python-dateutil==2.8.2 ; python_version >= "3.9" -pytz==2023.3.post1 ; python_version >= "3.9" -rich==13.7.0 ; python_version >= "3.9" +numpy==1.26.4 ; python_version >= "3.9" +packaging==24.0 ; python_version >= "3.9" +pandas==2.2.2 ; python_version >= "3.9" +pluggy==1.5.0 ; python_version >= "3.9" +pycparser==2.22 ; python_version >= "3.9" +pygments==2.18.0 ; python_version >= "3.9" +pytest==8.2.2 ; python_version >= "3.9" +python-dateutil==2.9.0.post0 ; python_version >= "3.9" +pytz==2024.1 ; python_version >= "3.9" +rich==13.7.1 ; python_version >= "3.9" shellingham==1.5.4 ; python_version >= "3.9" six==1.16.0 ; python_version >= "3.9" tomli==2.0.1 ; python_version < "3.11" and python_version >= "3.9" -typer[all]==0.9.0 ; python_version >= "3.9" -typing-extensions==4.8.0 ; python_version >= "3.9" -tzdata==2023.3 ; python_version >= "3.9" -xarray==2023.11.0 ; python_version >= "3.9" -zarr==2.16.1 ; python_version >= "3.9" +typer[all]==0.12.3 ; python_version >= "3.9" +typing-extensions==4.12.1 ; python_version >= "3.9" +tzdata==2024.1 ; python_version >= "3.9" +xarray==2024.5.0 ; python_version >= "3.9" +zarr==2.18.2 ; python_version >= "3.9" diff --git a/requirements/requirements-extras.txt b/requirements/requirements-extras.txt index 0cbb071..4401c46 100644 --- a/requirements/requirements-extras.txt +++ b/requirements/requirements-extras.txt @@ -1,30 +1,30 @@ asciitree==0.3.3 ; python_version >= "3.9" -attrs==23.1.0 ; python_version >= "3.9" -certifi==2023.7.22 ; python_version >= "3.9" +attrs==23.2.0 ; python_version >= "3.9" +certifi==2024.6.2 ; python_version >= "3.9" cffi==1.16.0 ; python_version >= "3.9" -cfgrib==0.9.10.4 ; python_version >= "3.9" +cfgrib==0.9.12.0 ; python_version >= "3.9" cftime==1.6.3 ; python_version >= "3.9" click==8.1.7 ; python_version >= "3.9" -colorama==0.4.6 ; python_version >= "3.9" -eccodes==1.6.1 ; python_version >= "3.9" -fasteners==0.19 ; python_version >= "3.9" +colorama==0.4.6 ; python_version >= "3.9" and platform_system == "Windows" +eccodes==1.7.0 ; python_version >= "3.9" +fasteners==0.19 ; sys_platform != "emscripten" and python_version >= "3.9" findlibs==0.0.5 ; python_version >= "3.9" markdown-it-py==3.0.0 ; python_version >= "3.9" mdurl==0.1.2 ; python_version >= "3.9" netcdf4==1.6.5 ; python_version >= "3.9" numcodecs==0.12.1 ; python_version >= "3.9" -numpy==1.26.2 ; python_version >= "3.9" -packaging==23.2 ; python_version >= "3.9" -pandas==2.1.3 ; python_version >= "3.9" -pycparser==2.21 ; python_version >= "3.9" -pygments==2.16.1 ; python_version >= "3.9" -python-dateutil==2.8.2 ; python_version >= "3.9" -pytz==2023.3.post1 ; python_version >= "3.9" -rich==13.7.0 ; python_version >= "3.9" +numpy==1.26.4 ; python_version >= "3.9" +packaging==24.0 ; python_version >= "3.9" +pandas==2.2.2 ; python_version >= "3.9" +pycparser==2.22 ; python_version >= "3.9" +pygments==2.18.0 ; python_version >= "3.9" +python-dateutil==2.9.0.post0 ; python_version >= "3.9" +pytz==2024.1 ; python_version >= "3.9" +rich==13.7.1 ; python_version >= "3.9" shellingham==1.5.4 ; python_version >= "3.9" six==1.16.0 ; python_version >= "3.9" -typer[all]==0.9.0 ; python_version >= "3.9" -typing-extensions==4.8.0 ; python_version >= "3.9" -tzdata==2023.3 ; python_version >= "3.9" -xarray==2023.11.0 ; python_version >= "3.9" -zarr==2.16.1 ; python_version >= "3.9" +typer[all]==0.12.3 ; python_version >= "3.9" +typing-extensions==4.12.1 ; python_version >= "3.9" +tzdata==2024.1 ; python_version >= "3.9" +xarray==2024.5.0 ; python_version >= "3.9" +zarr==2.18.2 ; python_version >= "3.9" diff --git a/requirements/requirements.txt b/requirements/requirements.txt index 9ca82d7..fb53f23 100644 --- a/requirements/requirements.txt +++ b/requirements/requirements.txt @@ -1,24 +1,24 @@ asciitree==0.3.3 ; python_version >= "3.9" -certifi==2023.7.22 ; python_version >= "3.9" +certifi==2024.6.2 ; python_version >= "3.9" cftime==1.6.3 ; python_version >= "3.9" click==8.1.7 ; python_version >= "3.9" -colorama==0.4.6 ; python_version >= "3.9" -fasteners==0.19 ; python_version >= "3.9" +colorama==0.4.6 ; python_version >= "3.9" and platform_system == "Windows" +fasteners==0.19 ; sys_platform != "emscripten" and python_version >= "3.9" markdown-it-py==3.0.0 ; python_version >= "3.9" mdurl==0.1.2 ; python_version >= "3.9" netcdf4==1.6.5 ; python_version >= "3.9" numcodecs==0.12.1 ; python_version >= "3.9" -numpy==1.26.2 ; python_version >= "3.9" -packaging==23.2 ; python_version >= "3.9" -pandas==2.1.3 ; python_version >= "3.9" -pygments==2.16.1 ; python_version >= "3.9" -python-dateutil==2.8.2 ; python_version >= "3.9" -pytz==2023.3.post1 ; python_version >= "3.9" -rich==13.7.0 ; python_version >= "3.9" +numpy==1.26.4 ; python_version >= "3.9" +packaging==24.0 ; python_version >= "3.9" +pandas==2.2.2 ; python_version >= "3.9" +pygments==2.18.0 ; python_version >= "3.9" +python-dateutil==2.9.0.post0 ; python_version >= "3.9" +pytz==2024.1 ; python_version >= "3.9" +rich==13.7.1 ; python_version >= "3.9" shellingham==1.5.4 ; python_version >= "3.9" six==1.16.0 ; python_version >= "3.9" -typer[all]==0.9.0 ; python_version >= "3.9" -typing-extensions==4.8.0 ; python_version >= "3.9" -tzdata==2023.3 ; python_version >= "3.9" -xarray==2023.11.0 ; python_version >= "3.9" -zarr==2.16.1 ; python_version >= "3.9" +typer[all]==0.12.3 ; python_version >= "3.9" +typing-extensions==4.12.1 ; python_version >= "3.9" +tzdata==2024.1 ; python_version >= "3.9" +xarray==2024.5.0 ; python_version >= "3.9" +zarr==2.18.2 ; python_version >= "3.9" diff --git a/tests/cli_test.py b/tests/cli_test.py index 7eac103..5e81cef 100644 --- a/tests/cli_test.py +++ b/tests/cli_test.py @@ -9,7 +9,9 @@ runner = CliRunner() -@pytest.mark.parametrize("path", [path for path in pathlib.Path("tests/data/").glob("*")]) +@pytest.mark.parametrize( + "path", [pytest.param(path, id=path.name) for path in pathlib.Path("tests/data/").glob("*")] +) def test_grib(path: pathlib.Path) -> None: if path.suffix == ".grib": pytest.importorskip("cfgrib") diff --git a/tests/data/iceland.slf b/tests/data/iceland.slf new file mode 100644 index 0000000..caefc23 Binary files /dev/null and b/tests/data/iceland.slf differ