From d0a221bd318c34e60acb85fa91cb85a34772be9d Mon Sep 17 00:00:00 2001 From: Panos Mavrogiorgos Date: Thu, 6 Jun 2024 00:10:53 +0300 Subject: [PATCH 1/2] feat: Add telemac support fixes #27 --- .github/workflows/run_tests.yml | 24 +- .pre-commit-config.yaml | 43 +- Makefile | 2 +- README.md | 48 +- ci/conda-lock-Linux-64-py3.10 | 170 +- ci/conda-lock-Linux-64-py3.11 | 171 +- ci/conda-lock-Linux-64-py3.9 | 169 +- ci/conda-lock-macOS-64-py3.10 | 155 +- ci/conda-lock-macOS-64-py3.11 | 156 +- ci/conda-lock-macOS-64-py3.9 | 154 +- ci/conda-lock-py3.10.yml | 3874 ++++++++++++------------- ci/conda-lock-py3.11.yml | 3902 +++++++++++++------------- ci/conda-lock-py3.9.yml | 3860 ++++++++++++------------- inspectds/cli.py | 70 +- poetry.lock | 621 ++-- pyproject.toml | 5 +- requirements/requirements-dev.txt | 51 +- requirements/requirements-extras.txt | 41 +- requirements/requirements.txt | 30 +- tests/cli_test.py | 6 +- tests/data/iceland.slf | Bin 0 -> 306052 bytes 21 files changed, 7067 insertions(+), 6485 deletions(-) create mode 100644 tests/data/iceland.slf diff --git a/.github/workflows/run_tests.yml b/.github/workflows/run_tests.yml index bf53296..d120938 100644 --- a/.github/workflows/run_tests.yml +++ b/.github/workflows/run_tests.yml @@ -7,20 +7,20 @@ on: - main - master paths: - - '**.py' - - '.github/workflows/test*.yml' - - 'pyproject.toml' - - 'poetry.lock' - - 'conda-lock.yml' - - 'requirements/*' + - "**.py" + - ".github/workflows/test*.yml" + - "pyproject.toml" + - "poetry.lock" + - "conda-lock.yml" + - "requirements/*" pull_request: paths: - - '**.py' - - '.github/workflows/test*.yml' - - 'pyproject.toml' - - 'poetry.lock' - - 'conda-lock.yml' - - 'requirements/*' + - "**.py" + - ".github/workflows/test*.yml" + - "pyproject.toml" + - "poetry.lock" + - "conda-lock.yml" + - "requirements/*" jobs: run_tests: diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 0a3513d..576c302 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -1,4 +1,3 @@ - --- ci: skip: ["mypy"] @@ -54,7 +53,7 @@ repos: - repo: "https://github.com/charliermarsh/ruff-pre-commit" # Ruff version. - rev: 'v0.4.7' + rev: "v0.4.7" hooks: - id: "ruff" @@ -70,18 +69,44 @@ repos: - id: "poetry-lock" args: ["--check"] - id: "poetry-export" - name: 'poetry export main' - args: ["--without-hashes", "-f", "requirements.txt", "-o", "requirements/requirements.txt"] + name: "poetry export main" + args: + [ + "--without-hashes", + "-f", + "requirements.txt", + "-o", + "requirements/requirements.txt", + ] - id: "poetry-export" - name: 'poetry export main + grib' - args: ["--without-hashes", "-E", "grib", "-f", "requirements.txt", "-o", "requirements/requirements-extras.txt"] + name: "poetry export main + grib" + args: + [ + "--without-hashes", + "-E", + "all", + "-f", + "requirements.txt", + "-o", + "requirements/requirements-extras.txt", + ] - id: "poetry-export" - name: 'poetry export dev' - args: ["--without-hashes", "--with", "dev", "-E", "grib", "-f", "requirements.txt", "-o", "requirements/requirements-dev.txt"] + name: "poetry export dev" + args: + [ + "--without-hashes", + "--with", + "dev", + "-E", + "all", + "-f", + "requirements.txt", + "-o", + "requirements/requirements-dev.txt", + ] - repo: "local" hooks: - - id: "mypy" name: "mypy" entry: "make mypy" 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/README.md b/README.md index 83350a5..0d90c36 100644 --- a/README.md +++ b/README.md @@ -5,14 +5,14 @@ A CLI utility to print metadata of datasets in various formats (e.g. NetCDF, zarr, GRIB etc) -*powered by [xarray](https://github.com/pydata/xarray)* +_powered by [xarray](https://github.com/pydata/xarray)_ ## Prerequisites You need the following binary dependencies: - Python >= 3.9 -- Optionally, [eccodes](https://github.com/ecmwf/eccodes), which is necessary for GRIB support. +- Optionally, [eccodes](https://github.com/ecmwf/eccodes), which is necessary for GRIB support. ## Installation @@ -20,20 +20,26 @@ The recommended way of installation is [pipx](https://github.com/pypa/pipx): ``` pipx install inspectds +``` -# or if you want support for GRIB +or if you want support for GRIB, SELAFIN or both: +``` pipx install 'inspectds[grib]' +pipx install 'inspectds[selafin]' +pipx install 'inspectds[all]' ``` If you want to install the latest development version from git, then use: + ``` -pipx install 'git+https://github.com/pmav99/inspectds.git#egg=inspectds[grib]' +pipx install 'git+https://github.com/pmav99/inspectds.git#egg=inspectds[all]' ``` ## Usage ### Netcdf + ``` $ inspectds tests/data/example_1.nc @@ -63,6 +69,7 @@ Data variables: ``` ### GRIB + ``` $ inspectds tests/data/example.grib @@ -80,10 +87,41 @@ Data variables: t (number, time, isobaricInhPa, latitude, longitude) float32 ... ``` +### SELAFIN + +``` +$ inspectds tests/data/iceland.slf +Dimensions: (time: 13, node: 3526) +Coordinates: + x (node) float32 14kB -13.99 -14.97 -15.89 ... -13.52 -16.31 -12.28 + y (node) float32 14kB 57.38 60.19 69.79 63.11 ... 66.37 69.34 63.52 + * time (time) datetime64[ns] 104B 2017-10-01 ... 2017-10-01T12:00:00 +Data variables: + S (time, node) float32 183kB ... +``` + ### More info: ``` -inspectds --help +$ inspectds --help + + Usage: inspectds [OPTIONS] PATH + +╭─ Arguments ─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╮ +│ * path PATH The path to the dataset [default: None] [required] │ +╰─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╯ +╭─ Options ───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╮ +│ --dataset-type [auto|netcdf|zarr|grib|selafin] The dataset type. If 'auto', then it gets inferred from PATH [default: auto] │ +│ --mask-and-scale --no-mask-and-scale Whether to mask and scale the dataset [default: no-mask-and-scale] │ +│ --dimensions --no-dimensions Whether to include 'Dimensions' in the output [default: dimensions] │ +│ --coordinates --no-coordinates Whether to include 'Coordinates' in the output [default: coordinates] │ +│ --variables --no-variables Whether to include 'Variables' in the output [default: variables] │ +│ --variable-attributes --no-variable-attributes Whether to include the variable attributes in the output [default: no-variable-attributes] │ +│ --global-attributes --no-global-attributes Whether to include the global attributes in the output [default: no-global-attributes] │ +│ --full --no-full Display full output. Overrides any other option [default: no-full] │ +│ --version Display the version │ +│ --help Show this message and exit. │ +╰─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╯ ``` ## Development diff --git a/ci/conda-lock-Linux-64-py3.10 b/ci/conda-lock-Linux-64-py3.10 index 1931c21..7ce92b1 100644 --- a/ci/conda-lock-Linux-64-py3.10 +++ b/ci/conda-lock-Linux-64-py3.10 @@ -1,108 +1,112 @@ # Generated by conda-lock. # platform: linux-64 -# input_hash: f5660fb756d34bc7542d45d9604342460f16ab264624e0753a135ff6e6e873c7 +# input_hash: 79c07e4b566ab7a56ae9351bef089646a801010e0f8e2a3debad58b2d364a915 @EXPLICIT https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81 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DO NOT EDIT! +# This lock file was generated by conda-lock (https://github.com/conda/conda-lock). DO NOT EDIT! # # A "lock file" contains a concrete list of package versions (with checksums) to be installed. 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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. 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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..00edbb9 100644 --- a/requirements/requirements-dev.txt +++ b/requirements/requirements-dev.txt @@ -1,39 +1,42 @@ 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" +scipy==1.13.1 ; python_version >= "3.9" +shapely==2.0.4 ; 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-selafin==0.1.6 ; 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..68bbe80 100644 --- a/requirements/requirements-extras.txt +++ b/requirements/requirements-extras.txt @@ -1,30 +1,33 @@ 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" +scipy==1.13.1 ; python_version >= "3.9" +shapely==2.0.4 ; 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-selafin==0.1.6 ; 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..ec6d647 100644 --- a/tests/cli_test.py +++ b/tests/cli_test.py @@ -9,10 +9,14 @@ 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") + if path.suffix == ".slf": + pytest.importorskip("xarray_selafin") result = runner.invoke(app, [path.as_posix()]) assert result.exit_code == 0 assert "Dimensions" in result.stdout diff --git a/tests/data/iceland.slf b/tests/data/iceland.slf new file mode 100644 index 0000000000000000000000000000000000000000..caefc23ef54702344b5885c19ea3ff4597baae65 GIT binary patch literal 306052 zcmbTfdH8kJ{QrN>+4DpyWbCGtnNTXEIcY8`VC<NMgfM;XQGPC(}?;LqC 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zT020RzAnto&q1+<91R$%!`A2-lrle)DW(>D7Eg zyxcq<3SZlh!89RwwdM`V9#y6m9|w{!vVi=5$MK85-NE`{;oU8lqW?N)u?M Date: Fri, 14 Jun 2024 15:16:27 +0300 Subject: [PATCH 2/2] ci: Add support for python 3.12 + Only run Macos on python 3.9 --- .github/workflows/run_tests.yml | 7 +- Makefile | 5 + ci/conda-lock-Linux-64-py3.11 | 68 +- ci/conda-lock-Linux-64-py3.12 | 113 ++ ci/conda-lock-macOS-64-py3.11 | 42 +- ci/conda-lock-macOS-64-py3.12 | 90 + ci/conda-lock-py3.11.yml | 424 ++--- ci/conda-lock-py3.12.yml | 2714 +++++++++++++++++++++++++++++++ ci/py3.11.yml | 2 +- ci/py3.12.yml | 7 + 10 files changed, 3203 insertions(+), 269 deletions(-) create mode 100644 ci/conda-lock-Linux-64-py3.12 create mode 100644 ci/conda-lock-macOS-64-py3.12 create mode 100644 ci/conda-lock-py3.12.yml create mode 100644 ci/py3.12.yml diff --git a/.github/workflows/run_tests.yml b/.github/workflows/run_tests.yml index d120938..6fa0308 100644 --- a/.github/workflows/run_tests.yml +++ b/.github/workflows/run_tests.yml @@ -30,11 +30,14 @@ jobs: matrix: os: - "ubuntu" - - "macos" python-version: - "3.9" - "3.10" - "3.11" + - "3.12" + include: + - os: "macos" + python-version: "3.9" runs-on: "${{ matrix.os }}-latest" defaults: run: @@ -53,7 +56,7 @@ jobs: path: "~/conda_pkgs_dir" key: "conda-${{ runner.os }}-${{ hashFiles( env.LOCK_FILE ) }}-${{ env.CACHE_NUMBER }}" - name: "Setup conda" - uses: "conda-incubator/setup-miniconda@v2" + uses: "conda-incubator/setup-miniconda@v3" with: activate-environment: "inspectds_ci" # python-version: ${{ matrix.python-version }} diff --git a/Makefile b/Makefile index 0e3c9b6..d643cdb 100644 --- a/Makefile +++ b/Makefile @@ -27,18 +27,23 @@ conda_lock_ci: conda-lock lock --mamba --check-input-hash --platform linux-64 --platform osx-64 -f ci/py3.9.yml --lockfile ci/conda-lock-py3.9.yml conda-lock lock --mamba --check-input-hash --platform linux-64 --platform osx-64 -f ci/py3.10.yml --lockfile ci/conda-lock-py3.10.yml conda-lock lock --mamba --check-input-hash --platform linux-64 --platform osx-64 -f ci/py3.11.yml --lockfile ci/conda-lock-py3.11.yml + conda-lock lock --mamba --check-input-hash --platform linux-64 --platform osx-64 -f ci/py3.12.yml --lockfile ci/conda-lock-py3.12.yml conda-lock render --platform linux-64 --filename-template ci/conda-lock-{platform}-py3.9 ci/conda-lock-py3.9.yml conda-lock render --platform linux-64 --filename-template ci/conda-lock-{platform}-py3.10 ci/conda-lock-py3.10.yml conda-lock render --platform linux-64 --filename-template ci/conda-lock-{platform}-py3.11 ci/conda-lock-py3.11.yml + conda-lock render --platform linux-64 --filename-template ci/conda-lock-{platform}-py3.12 ci/conda-lock-py3.12.yml conda-lock render --platform osx-64 --filename-template ci/conda-lock-{platform}-py3.9 ci/conda-lock-py3.9.yml conda-lock render --platform osx-64 --filename-template ci/conda-lock-{platform}-py3.10 ci/conda-lock-py3.10.yml conda-lock render --platform osx-64 --filename-template ci/conda-lock-{platform}-py3.11 ci/conda-lock-py3.11.yml + conda-lock render --platform osx-64 --filename-template ci/conda-lock-{platform}-py3.12 ci/conda-lock-py3.12.yml mv ci/conda-lock-linux-64-py3.9 ci/conda-lock-Linux-64-py3.9 mv ci/conda-lock-linux-64-py3.10 ci/conda-lock-Linux-64-py3.10 mv ci/conda-lock-linux-64-py3.11 ci/conda-lock-Linux-64-py3.11 + mv ci/conda-lock-linux-64-py3.12 ci/conda-lock-Linux-64-py3.12 mv ci/conda-lock-osx-64-py3.9 ci/conda-lock-macOS-64-py3.9 mv ci/conda-lock-osx-64-py3.10 ci/conda-lock-macOS-64-py3.10 mv ci/conda-lock-osx-64-py3.11 ci/conda-lock-macOS-64-py3.11 + mv ci/conda-lock-osx-64-py3.12 ci/conda-lock-macOS-64-py3.12 conda_lock: conda-lock lock --mamba --check-input-hash -f pyproject.toml --lockfile conda-lock.yml diff --git a/ci/conda-lock-Linux-64-py3.11 b/ci/conda-lock-Linux-64-py3.11 index 63078ad..6f8ce00 100644 --- a/ci/conda-lock-Linux-64-py3.11 +++ b/ci/conda-lock-Linux-64-py3.11 @@ -1,40 +1,35 @@ # Generated by conda-lock. # platform: linux-64 -# input_hash: 3846b0b6eac1cdc114b498ea49f7fe5728c7ab22bde5eae4e62e8f1dc8857126 +# input_hash: d285bf94b1bd4686fa7c711591704da50b3b7f928f174855954ca063b0afd223 @EXPLICIT https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81 https://conda.anaconda.org/conda-forge/linux-64/ca-certificates-2024.6.2-hbcca054_0.conda#847c3c2905cc467cea52c24f9cfa8080 -https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.40-hf3520f5_2.conda#61b0bd5219ce7192b4e3633521a78975 -https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-ng-13.2.0-hc0a3c3a_7.conda#53ebd4c833fa01cb2c6353e99f905406 +https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.40-hf3520f5_3.conda#7c1062eaa78dec4ea8a9a988dbda6045 https://conda.anaconda.org/conda-forge/noarch/pybind11-abi-4-hd8ed1ab_3.tar.bz2#878f923dd6acc8aeb47a75da6c4098be -https://conda.anaconda.org/conda-forge/linux-64/python_abi-3.11-4_cp311.conda#d786502c97404c94d7d58d258a445a65 +https://conda.anaconda.org/conda-forge/linux-64/python_abi-3.12-4_cp312.conda#dccc2d142812964fcc6abdc97b672dff https://conda.anaconda.org/conda-forge/noarch/tzdata-2024a-h0c530f3_0.conda#161081fc7cec0bfda0d86d7cb595f8d8 -https://conda.anaconda.org/conda-forge/linux-64/libgomp-13.2.0-h77fa898_7.conda#abf3fec87c2563697defa759dec3d639 +https://conda.anaconda.org/conda-forge/linux-64/libgomp-13.2.0-h77fa898_9.conda#0d0ad0fdee21442a479005ef5f3a02e8 https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2#73aaf86a425cc6e73fcf236a5a46396d -https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-13.2.0-h77fa898_7.conda#72ec1b1b04c4d15d4204ece1ecea5978 +https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-13.2.0-h77fa898_9.conda#f23bc130bc3d2bbd9d9d6892609546ea https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-hd590300_5.conda#69b8b6202a07720f448be700e300ccf4 https://conda.anaconda.org/conda-forge/linux-64/c-ares-1.28.1-hd590300_0.conda#dcde58ff9a1f30b0037a2315d1846d1f -https://conda.anaconda.org/conda-forge/linux-64/fmt-10.2.1-h00ab1b0_0.conda#35ef8bc24bd34074ebae3c943d551728 -https://conda.anaconda.org/conda-forge/linux-64/icu-73.2-h59595ed_0.conda#cc47e1facc155f91abd89b11e48e72ff https://conda.anaconda.org/conda-forge/linux-64/keyutils-1.6.1-h166bdaf_0.tar.bz2#30186d27e2c9fa62b45fb1476b7200e3 -https://conda.anaconda.org/conda-forge/linux-64/libaec-1.1.3-h59595ed_0.conda#5e97e271911b8b2001a8b71860c32faa https://conda.anaconda.org/conda-forge/linux-64/libev-4.33-hd590300_2.conda#172bf1cd1ff8629f2b1179945ed45055 https://conda.anaconda.org/conda-forge/linux-64/libexpat-2.6.2-h59595ed_0.conda#e7ba12deb7020dd080c6c70e7b6f6a3d https://conda.anaconda.org/conda-forge/linux-64/libffi-3.4.2-h7f98852_5.tar.bz2#d645c6d2ac96843a2bfaccd2d62b3ac3 -https://conda.anaconda.org/conda-forge/linux-64/libgfortran5-13.2.0-hca663fb_7.conda#c0bd771f09a326fdcd95a60b617795bf +https://conda.anaconda.org/conda-forge/linux-64/libgfortran5-13.2.0-h3d2ce59_9.conda#2f2a59af95aed6024368b8dbaf9591d8 https://conda.anaconda.org/conda-forge/linux-64/libiconv-1.17-hd590300_2.conda#d66573916ffcf376178462f1b61c941e https://conda.anaconda.org/conda-forge/linux-64/libjpeg-turbo-3.0.0-hd590300_1.conda#ea25936bb4080d843790b586850f82b8 https://conda.anaconda.org/conda-forge/linux-64/libnsl-2.0.1-hd590300_0.conda#30fd6e37fe21f86f4bd26d6ee73eeec7 +https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-ng-13.2.0-hc0a3c3a_9.conda#2075df518ef9d09f1ae209c83116e808 https://conda.anaconda.org/conda-forge/linux-64/libuuid-2.38.1-h0b41bf4_0.conda#40b61aab5c7ba9ff276c41cfffe6b80b https://conda.anaconda.org/conda-forge/linux-64/libxcrypt-4.4.36-hd590300_1.conda#5aa797f8787fe7a17d1b0821485b5adc https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.3.1-h4ab18f5_1.conda#57d7dc60e9325e3de37ff8dffd18e814 -https://conda.anaconda.org/conda-forge/linux-64/lz4-c-1.9.4-hcb278e6_0.conda#318b08df404f9c9be5712aaa5a6f0bb0 https://conda.anaconda.org/conda-forge/linux-64/lzo-2.10-hd590300_1001.conda#ec7398d21e2651e0dcb0044d03b9a339 https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.5-h59595ed_0.conda#fcea371545eda051b6deafb24889fc69 https://conda.anaconda.org/conda-forge/linux-64/openssl-3.3.1-h4ab18f5_0.conda#a41fa0e391cc9e0d6b78ac69ca047a6c https://conda.anaconda.org/conda-forge/linux-64/pthread-stubs-0.4-h36c2ea0_1001.tar.bz2#22dad4df6e8630e8dff2428f6f6a7036 https://conda.anaconda.org/conda-forge/linux-64/reproc-14.2.4.post0-hd590300_1.conda#82ca53502dfd5a64a80dee76dae14685 -https://conda.anaconda.org/conda-forge/linux-64/snappy-1.2.0-hdb0a2a9_1.conda#843bbb8ace1d64ac50d64639ff38b014 https://conda.anaconda.org/conda-forge/linux-64/xorg-inputproto-2.3.2-h7f98852_1002.tar.bz2#bcd1b3396ec6960cbc1d2855a9e60b2b https://conda.anaconda.org/conda-forge/linux-64/xorg-kbproto-1.0.7-h7f98852_1002.tar.bz2#4b230e8381279d76131116660f5a241a https://conda.anaconda.org/conda-forge/linux-64/xorg-libxau-1.0.11-hd590300_0.conda#2c80dc38fface310c9bd81b17037fee5 @@ -42,72 +37,77 @@ https://conda.anaconda.org/conda-forge/linux-64/xorg-libxdmcp-1.1.3-h7f98852_0.t https://conda.anaconda.org/conda-forge/linux-64/xorg-xextproto-7.3.0-h0b41bf4_1003.conda#bce9f945da8ad2ae9b1d7165a64d0f87 https://conda.anaconda.org/conda-forge/linux-64/xorg-xproto-7.0.31-h7f98852_1007.tar.bz2#b4a4381d54784606820704f7b5f05a15 https://conda.anaconda.org/conda-forge/linux-64/xz-5.2.6-h166bdaf_0.tar.bz2#2161070d867d1b1204ea749c8eec4ef0 -https://conda.anaconda.org/conda-forge/linux-64/yaml-cpp-0.8.0-h59595ed_0.conda#965eaacd7c18eb8361fd12bb9e7a57d7 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b/ci/conda-lock-macOS-64-py3.11 @@ -1,6 +1,6 @@ # Generated by conda-lock. # platform: osx-64 -# input_hash: aacdd01963e5c3f724296431f90e009462f382b8be641dd0e9b2d95436a0943c +# input_hash: a1de9584165fca412ddc8e339c2ed6db6b8aa0e736a474f9694507119500766e @EXPLICIT https://conda.anaconda.org/conda-forge/osx-64/bzip2-1.0.8-h10d778d_5.conda#6097a6ca9ada32699b5fc4312dd6ef18 https://conda.anaconda.org/conda-forge/osx-64/c-ares-1.28.1-h10d778d_0.conda#d5eb7992227254c0e9a0ce71151f0079 @@ -14,7 +14,7 @@ https://conda.anaconda.org/conda-forge/osx-64/libjpeg-turbo-3.0.0-h0dc2134_1.con https://conda.anaconda.org/conda-forge/osx-64/lzo-2.10-h10d778d_1001.conda#bfecd73e4a2dc18ffd5288acf8a212ab https://conda.anaconda.org/conda-forge/osx-64/ncurses-6.5-h5846eda_0.conda#02a888433d165c99bf09784a7b14d900 https://conda.anaconda.org/conda-forge/noarch/pybind11-abi-4-hd8ed1ab_3.tar.bz2#878f923dd6acc8aeb47a75da6c4098be -https://conda.anaconda.org/conda-forge/osx-64/python_abi-3.11-4_cp311.conda#fef7a52f0eca6bae9e8e2e255bc86394 +https://conda.anaconda.org/conda-forge/osx-64/python_abi-3.12-4_cp312.conda#87201ac4314b911b74197e588cca3639 https://conda.anaconda.org/conda-forge/osx-64/reproc-14.2.4.post0-h10d778d_1.conda#d7c3258e871481be5bbaf28b4729e29f https://conda.anaconda.org/conda-forge/noarch/tzdata-2024a-h0c530f3_0.conda#161081fc7cec0bfda0d86d7cb595f8d8 https://conda.anaconda.org/conda-forge/osx-64/xz-5.2.6-h775f41a_0.tar.bz2#a72f9d4ea13d55d745ff1ed594747f10 @@ -22,7 +22,7 @@ https://conda.anaconda.org/conda-forge/osx-64/jasper-4.2.4-hb10263b_0.conda#b7a6 https://conda.anaconda.org/conda-forge/osx-64/libcxx-17.0.6-h88467a6_0.conda#0fe355aecb8d24b8bc07c763209adbd9 https://conda.anaconda.org/conda-forge/osx-64/libedit-3.1.20191231-h0678c8f_2.tar.bz2#6016a8a1d0e63cac3de2c352cd40208b https://conda.anaconda.org/conda-forge/osx-64/libzlib-1.3.1-h87427d6_1.conda#b7575b5aa92108dcc9aaab0f05f2dbce 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DO NOT EDIT! +# +# A "lock file" contains a concrete list of package versions (with checksums) to be installed. Unlike +# e.g. `conda env create`, the resulting environment will not change as new package versions become +# available, unless you explicitly update the lock file. +# +# Install this environment as "YOURENV" with: +# conda-lock install -n YOURENV conda-lock-py3.12.yml +# To update a single package to the latest version compatible with the version constraints in the source: +# conda-lock lock --lockfile conda-lock-py3.12.yml --update PACKAGE +# To re-solve the entire environment, e.g. after changing a version constraint in the source file: +# conda-lock -f py3.12.yml --lockfile conda-lock-py3.12.yml +version: 1 +metadata: + content_hash: + linux-64: d285bf94b1bd4686fa7c711591704da50b3b7f928f174855954ca063b0afd223 + osx-64: a1de9584165fca412ddc8e339c2ed6db6b8aa0e736a474f9694507119500766e + channels: + - url: conda-forge + used_env_vars: [] + platforms: + - linux-64 + - osx-64 + sources: + - py3.12.yml +package: +- name: _libgcc_mutex + version: '0.1' + manager: conda + platform: 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