meteodata-lab 0.3.0__tar.gz

meteodata_lab-0.3.0/AUTHORS.md

@@ -0,0 +1,13 @@
+# Credits
+
+## Development Lead
+
+Carlos Osuna <carlos.osuna@meteoswiss.ch>
+
+## Contributors
+
+- Petra Baumann <petra.baumann@meteoswiss.ch>
+- Nina Burgdorfer <nina.burgdorfer@meteoswiss.ch>
+- Victoria Cherkas <victoria.cherkas@meteoswiss.ch>
+- Christian Kanesan <christian.kanesan@meteoswiss.ch>
+- Tobias Wicky <tobias.wicky@meteoswiss.ch>

meteodata_lab-0.3.0/LICENSE

@@ -0,0 +1,19 @@
+Copyright (c) 2023 Federal Office of Meteorlogy and Climatology MeteoSwiss
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

meteodata_lab-0.3.0/PKG-INFO

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+Metadata-Version: 2.3
+Name: meteodata-lab
+Version: 0.3.0
+Summary: A data post-processing framework on the basis of xarray.
+Keywords: Icon,Data Processing
+Author: Carlos Osuna
+Author-email: carlos.osuna@meteoswiss.ch
+Requires-Python: >=3.10,<3.13
+Classifier: Development Status :: 2 - Pre-Alpha
+Classifier: Intended Audience :: Developers
+Classifier: Natural Language :: English
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Provides-Extra: polytope
+Provides-Extra: regrid
+Requires-Dist: click (>=8.1.7,<9.0.0)
+Requires-Dist: earthkit-data[covjsonkit] (>=0.11,<1)
+Requires-Dist: eccodes (>=2.38,<2.39)
+Requires-Dist: eccodes-cosmo-resources-python (>=2.38,<2.39)
+Requires-Dist: numpy (>=1.26.4,<2.0.0)
+Requires-Dist: polytope-client (>=0.7.4,<0.8.0) ; extra == "polytope"
+Requires-Dist: pydantic
+Requires-Dist: pyproj (>=3.6.1,<4.0.0) ; extra == "regrid"
+Requires-Dist: pyyaml (>=6.0.1,<7.0.0)
+Requires-Dist: rasterio (>=1.3.10,<2.0.0) ; extra == "regrid"
+Requires-Dist: scipy (>=1.13,<2.0) ; extra == "regrid"
+Requires-Dist: setuptools
+Requires-Dist: xarray (>=2024)
+Project-URL: documentation, https://meteoswiss.github.io/meteodata-lab/
+Project-URL: source, https://github.com/MeteoSwiss/meteodata-lab
+Description-Content-Type: text/markdown
+
+<p align="center">
+  <picture>
+    <img src="meteodata_lab_logo_with_name-optimized.gif" height="160" alt="meteodata-lab animated logo showing a cloud partially hiding the sun in a shape of a gear">
+  </picture>
+</p>
+
+<p align="center">
+    <a href="https://pypi.org/project/meteodata-lab/">
+    <img src="https://img.shields.io/pypi/v/meteodata-lab.svg?color=ff69b4" alt="PyPI version">
+    </a>
+    <a href="https://github.com/meteoswiss/meteodata-lab/releases">
+    <img src="https://img.shields.io/github/v/release/meteoswiss/meteodata-lab?color=purple&label=Release" alt="Latest Release">
+    </a>
+    <a href="https://opensource.org/licenses/mit">
+    <img src="https://img.shields.io/badge/licence-MIT-blue.svg" alt="Licence">
+    </a>
+</p>
+
+<p align="center">
+    <a href="#installation">Installation</a> •
+    <a href="https://meteoswiss.github.io/meteodata-lab/">Documentation</a>
+</p>
+
+> [!WARNING]
+> This project is in BETA and under active development. Interfaces and functionality are subject to change.
+
+**Meteodata-lab** is a NumPy/Xarray-based Python library for processing and analyzing gridded meteorological data. It supports GRIB (read/write) and is tailored to common workflows that require data interpolation, regridding to custom grids (e.g., Swiss grid or rotated lat/lon), and the computation of advanced meteorological fields. One of the key features of meteodata-lab is its use of operators that ensure the integrity of GRIB metadata is maintained throughout processing, allowing for consistent writing back to GRIB format.
+
+## Installation
+
+
+### For Users
+
+To install the latest release from PyPI:
+
+```bash
+pip install meteodata-lab
+```
+#### Optional Extras
+To install optional extras:
+```bash
+pip install "meteodata-lab[polytope,regrid]"
+```
+**Note**: The `fdb` extra is currently disabled because its dependency `pyfdb` is not available on PyPI. As an alternative the development setup can be used.
+
+### For Development
+To set up the project for local development, clone the repository and use the provided Poetry setup script:
+```bash
+git clone git@github.com:MeteoSwiss/meteodata-lab.git
+cd meteodata-lab
+./scripts/setup_poetry.sh
+```
+This will install Poetry (if not already available), set up the virtual environment, and install all dependencies with extras.
+

meteodata_lab-0.3.0/README.md

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+<p align="center">
+  <picture>
+    <img src="meteodata_lab_logo_with_name-optimized.gif" height="160" alt="meteodata-lab animated logo showing a cloud partially hiding the sun in a shape of a gear">
+  </picture>
+</p>
+
+<p align="center">
+    <a href="https://pypi.org/project/meteodata-lab/">
+    <img src="https://img.shields.io/pypi/v/meteodata-lab.svg?color=ff69b4" alt="PyPI version">
+    </a>
+    <a href="https://github.com/meteoswiss/meteodata-lab/releases">
+    <img src="https://img.shields.io/github/v/release/meteoswiss/meteodata-lab?color=purple&label=Release" alt="Latest Release">
+    </a>
+    <a href="https://opensource.org/licenses/mit">
+    <img src="https://img.shields.io/badge/licence-MIT-blue.svg" alt="Licence">
+    </a>
+</p>
+
+<p align="center">
+    <a href="#installation">Installation</a> •
+    <a href="https://meteoswiss.github.io/meteodata-lab/">Documentation</a>
+</p>
+
+> [!WARNING]
+> This project is in BETA and under active development. Interfaces and functionality are subject to change.
+
+**Meteodata-lab** is a NumPy/Xarray-based Python library for processing and analyzing gridded meteorological data. It supports GRIB (read/write) and is tailored to common workflows that require data interpolation, regridding to custom grids (e.g., Swiss grid or rotated lat/lon), and the computation of advanced meteorological fields. One of the key features of meteodata-lab is its use of operators that ensure the integrity of GRIB metadata is maintained throughout processing, allowing for consistent writing back to GRIB format.
+
+## Installation
+
+
+### For Users
+
+To install the latest release from PyPI:
+
+```bash
+pip install meteodata-lab
+```
+#### Optional Extras
+To install optional extras:
+```bash
+pip install "meteodata-lab[polytope,regrid]"
+```
+**Note**: The `fdb` extra is currently disabled because its dependency `pyfdb` is not available on PyPI. As an alternative the development setup can be used.
+
+### For Development
+To set up the project for local development, clone the repository and use the provided Poetry setup script:
+```bash
+git clone git@github.com:MeteoSwiss/meteodata-lab.git
+cd meteodata-lab
+./scripts/setup_poetry.sh
+```
+This will install Poetry (if not already available), set up the virtual environment, and install all dependencies with extras.

meteodata_lab-0.3.0/pyproject.toml

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+[build-system]
+requires = ["poetry-core>=1.0.0"]
+build-backend = "poetry.core.masonry.api"
+
+[tool.poetry]
+name = "meteodata-lab"
+version = "0.3.0"
+description = "A data post-processing framework on the basis of xarray."
+readme = "README.md"
+keywords = ["Icon", "Data Processing"]
+classifiers = [
+    "Development Status :: 2 - Pre-Alpha",
+    "Intended Audience :: Developers",
+    "Natural Language :: English",
+    "Programming Language :: Python :: 3",
+    "Programming Language :: Python :: 3.10",
+]
+authors = [
+    "Carlos Osuna <carlos.osuna@meteoswiss.ch>",
+    "Petra Baumann <petra.baumanna@meteoswiss.ch>",
+    "Nina Burgdorfer <nina.burgdorfer@meteoswiss.ch>",
+    "Victoria Cherkas <victoria.cherkas@meteoswiss.ch>",
+    "Christian Kanesan <christian.kanesan@meteoswiss.ch>",
+    "Tobias Wicky <tobias.wicky@meteoswiss.ch>",
+]
+packages = [
+    { include = "meteodatalab", from = "src" },
+]
+
+[tool.poetry.dependencies]
+python = ">=3.10,<3.13"
+click = "^8.1.7"
+earthkit-data = { version = ">=0.11,<1", extras = ["covjsonkit"] }
+eccodes = "~2.38"
+eccodes-cosmo-resources-python = "~2.38"
+numpy = "^1.26.4"
+polytope-client = { version = "^0.7.4", optional = true }
+pydantic = "*"
+pyproj = { version = "^3.6.1", optional = true }
+pyyaml = "^6.0.1"
+rasterio = { version = "^1.3.10", optional = true }
+scipy = { version = "^1.13", optional = true }
+setuptools = "*"
+xarray = ">=2024"
+
+[tool.poetry.extras]
+# fdb = ["pyfdb"]
+polytope = ["polytope-client"]
+regrid = ["pyproj", "rasterio", "scipy"]
+
+[tool.poetry.group.dev.dependencies]
+black = "*"
+codespell = "*"
+flake8 = "*"
+Flake8-pyproject = "*"
+ipykernel = "*"
+isort = "*"
+mypy = "*"
+pandas-stubs = "*"
+pre-commit = "*"
+pydocstyle = "*"
+pyfdb = { url = "https://github.com/ecmwf/pyfdb/archive/refs/tags/0.0.3.zip" }
+pytest = "*"
+rstcheck = { version = "*", extras = ["sphinx"] }
+types-requests = "*"
+types-PyYAML = "*"
+
+[tool.poetry.urls]
+source = "https://github.com/MeteoSwiss/meteodata-lab"
+documentation = "https://meteoswiss.github.io/meteodata-lab/"
+
+[tool.poetry.scripts]
+# Format: <command> = "<package>.<module>:<function>"
+meteodata-lab = "meteodatalab.cli:main"
+
+[tool.pytest.ini_options]
+testpaths = ["tests"]
+addopts = [
+    "-ra",
+    "--pdbcls=IPython.terminal.debugger:TerminalPdb",
+    "--tb=short",
+    # "--cov=meteodatalab",
+    # "--mypy",
+]
+markers = [
+    "ifs",   # marks tests that use IFS grib definitions
+    "cosmo", # marks tests that use COSMO grib definitions
+    "data",  # marks tests that depend on specific test data
+]
+
+[tool.black]
+
+[tool.isort]
+default_section = "THIRDPARTY"
+profile = "black"
+# Headings
+import_heading_stdlib = "Standard library"
+import_heading_thirdparty = "Third-party"
+import_heading_firstparty = "First-party"
+import_heading_localfolder = "Local"
+# Known modules to avoid misclassification
+known_standard_library = [
+    # Add standard library modules that may be misclassified by isort
+]
+known_third_party = [
+    # Add third-party modules that may be misclassified by isort
+]
+known_first_party = [
+    # Add first-party modules that may be misclassified by isort
+    "meteodatalab",
+]
+
+[tool.mypy]
+plugins = ["pydantic.mypy"]
+
+[[tool.mypy.overrides]]
+# Note: Only globally ignore missing imports as a matter of last resort!
+# See https://blog.wolt.com/engineering/2021/09/30/professional-grade-mypy-configuration/
+module = [
+    # Add external modules w/o type hints here
+    "rasterio",
+    "rasterio.crs",
+]
+ignore_missing_imports = true
+
+[tool.flake8]
+max-line-length = 88
+# max-complexity = 10
+ignore = [
+    "E203", # Allow whitespace before ':' (https://github.com/PyCQA/pycodestyle/issues/373)
+    "F811", # Allow redefinition of unused name (necessary for typing.overload)
+    "I002", # Don't check for isort configuration
+    "W503", # Allow line break before binary operator (PEP 8-compatible)
+    "E704", # Allow multiple statements on one line (def)
+]
+per-file-ignores = [
+    "__init__.py: F401", # Allow unused imports
+]
+
+[tool.pylint]
+recursive = true
+ignore-imports = true
+max-line-length = 88
+# Tweak valid name formats
+# Defaults (http://pylint-messages.wikidot.com/messages:c0103):
+#  argument-rgx  = "^[a-z_][a-z0-9_]{2,30}$"
+#  attr-rgx      = "^[a-z_][a-z0-9_]{2,30}$"
+#  function-rgx  = "^[a-z_][a-z0-9_]{2,30}$"
+#  method-rgx    = "^[a-z_][a-z0-9_]{2,30}$"
+#  variable-rgx  = "^[a-z_][a-z0-9_]{2,30}$"
+#  class-rgx     = "^[A-Z_][a-zA-Z0-9]+$"
+#  const-rgx     = "^(([A-Z_][A-Z0-9_]*)|(__.*__))$"
+#  module-rgx    = "^(([a-z_][a-z0-9_]*)|([A-Z][a-zA-Z0-9]+))$"
+argument-rgx = "^[a-z_][a-z0-9_]{,40}$"
+attr-rgx = "^[a-z_][a-z0-9_]{,40}$"
+function-rgx = "^[a-z_][a-z0-9_]{,40}$"
+method-rgx = "^[a-z_][a-z0-9_]{,40}$"
+variable-rgx = "^[a-z_][a-z0-9_]{,40}$"
+class-rgx = "^[A-Z_][a-zA-Z0-9]+$"
+const-rgx = "^(([a-z_][a-z0-9_]*)|([A-Z_][A-Z0-9_]*)|(__[a-zA-Z0-9]+__))$"
+module-rgx = "^(([a-z_][a-z0-9_]*)|([A-Z][a-zA-Z0-9]+))$"
+inlinevar-rgx = "^[A-Za-z_][A-Za-z0-9_]*$"
+# Disable selected warnings, errors etc. that conflict with style guide etc.
+# Note: To locally ignore certain errors, use "pylint: disable=XXXX" comments instead!
+disable = [
+    "C0115", # Missing class docstring
+    "C0116", # Missing function or method docstring
+    "R0903", # Too few public methods (*/2) (too-few-public-methods)
+    # "R0801", # Similar lines in 2 files (duplicate-code)
+    # -> see https://github.com/PyCQA/pylint/issues/214
+    "R1705", # Unnecessary "elif" after "return" (no-else-return)
+    "R1720", # Unnecessary "elif" after "raise" (no-else-raise)
+    "R1724", # Unnecessary "elif" after "continue" (no-else-continue)
+    "W1116", # Second argument of isinstance is not a type (isinstance-second-argument-not-valid-type)
+]
+# Ignore (sub-)modules that trigger errors like E1101 (no-member) or E0611 (no-name-in-module)
+ignored-modules = []
+
+[tool.pydocstyle]
+# All codes: http://www.pydocstyle.org/en/stable/error_codes.html
+ignore = [
+    # "D100", # Missing docstring in public module
+    "D101", # Missing docstring in public class
+    "D102", # Missing docstring in public method
+    "D103", # Missing docstring in public function
+    # "D104", # Missing docstring in public package
+    "D105", # Missing docstring in magic method
+    # "D105", # Missing docstring in public nested class
+    "D107", # Missing docstring in __init__
+    "D203", # Blank line required before class docstring
+    "D213", # Multi-line docstring summary should start at the second line
+    # "D405", # Section name should be properly capitalized
+    "D406", # Section name should end with a newline
+    "D407", # Missing dashed underline after section
+]
+
+[tool.rstcheck]
+ignore_directives = ["automodule", "mdinclude", "autosummary"]
+
+[tool.codespell]
+ignore-words-list = "aare,inout,THIRDPARTY"
+skip = "poetry.lock"

meteodata_lab-0.3.0/src/meteodatalab/__init__.py

@@ -0,0 +1,8 @@
+"""Top-level package for meteodata-lab."""
+
+# Standard library
+import importlib.metadata
+
+__author__ = "Carlos Osuna"
+__email__ = "carlos.osuna@meteoswiss.ch"
+__version__ = importlib.metadata.version("meteodata-lab")

meteodata_lab-0.3.0/src/meteodatalab/cli.py

@@ -0,0 +1,151 @@
+"""Command line interface of meteodata-lab."""
+
+# Standard library
+from importlib.resources import files
+from pathlib import Path
+
+# Third-party
+import click
+import yaml
+
+# Local
+from . import __version__, grib_decoder
+from .metadata import is_staggered_horizontal
+from .operators import destagger, gis, regrid
+
+
+def print_version(ctx, _, value: bool) -> None:
+    """Print the version number and exit."""
+    if value:
+        click.echo(__version__)
+        ctx.exit(0)
+
+
+@click.group()
+@click.option(
+    "--version",
+    "-V",
+    help="Print version and exit.",
+    is_flag=True,
+    expose_value=False,
+    callback=print_version,
+)
+def main() -> None:
+    """Console script for test_cli_project."""
+    print("CLI for meteodatalab")
+
+
+RESAMPLING = {
+    "nearest": regrid.Resampling.nearest,
+    "bilinear": regrid.Resampling.bilinear,
+    "cubic": regrid.Resampling.cubic,
+}
+
+
+def _load_mapping():
+    mapping_path = files("meteodatalab.data").joinpath("field_mappings.yml")
+    return yaml.safe_load(mapping_path.open())
+
+
+def handle_vector_fields(ds):
+    mapping = _load_mapping()
+    names = set(ds)
+    pairs = []
+    while names:
+        name = names.pop()
+        item = mapping[name]["cosmo"]
+        if u := item.get("uComponent"):
+            if u not in names:
+                msg = f"The u-component {u} must be part of PARAMS"
+                raise click.UsageError(msg)
+            names.remove(u)
+            pairs.append((u, name))
+        elif v := item.get("vComponent"):
+            if v not in names:
+                msg = f"The v-component {v} must be part of PARAMS"
+                raise click.UsageError(msg)
+            names.remove(v)
+            pairs.append((name, v))
+
+    for u_name, v_name in pairs:
+        click.echo(f"Rotating vector field components {u_name}, {v_name} to geolatlon")
+        u, v = ds[u_name], ds[v_name]
+        if is_staggered_horizontal(u):
+            u = destagger.destagger(u, "x")
+        if is_staggered_horizontal(v):
+            v = destagger.destagger(v, "y")
+        if u.vref == "native" and v.vref == "native":
+            u_g, v_g = gis.vref_rot2geolatlon(u, v)
+            ds[u_name] = u_g
+            ds[v_name] = v_g
+        elif u.vref == "geo" and v.vref == "geo":
+            continue
+        else:
+            msg = "Differing vector references."
+            raise RuntimeError(msg)
+
+
+@main.command("regrid")
+@click.option(
+    "--crs",
+    type=click.Choice(["geolatlon"]),
+    default="geolatlon",
+    help="Coordinate reference system",
+)
+@click.option(
+    "--resampling",
+    type=click.Choice(list(RESAMPLING.keys())),
+    default="nearest",
+    help="Resampling method",
+)
+@click.option(
+    "--ref-param",
+    default="HHL",
+    help="Reference parameter with respect to staggering, default: HHL",
+)
+@click.argument(
+    "infile",
+    nargs=-1,
+    type=click.Path(exists=True, path_type=Path),
+)
+@click.argument(
+    "outfile",
+    type=click.Path(writable=True, path_type=Path),
+)
+@click.argument("params")
+def regrid_cmd(
+    crs: str,
+    resampling: str,
+    ref_param: str,
+    infile: tuple[Path, ...],
+    outfile: Path,
+    params: str,
+):
+    """Regrid the given PARAMS found in INFILE and write to OUTFILE.
+
+    PARAMS is a comma separated list of short names following the cosmo convention.
+    """
+    resampling_arg = RESAMPLING[resampling]
+    crs_str = regrid.CRS_ALIASES.get(crs, crs)
+
+    if not infile:
+        raise click.UsageError("No input files")
+
+    if outfile.exists():
+        click.confirm(f"OUTFILE {outfile} exists. Overwrite?")
+
+    reader = grib_decoder.GribReader.from_files(list(infile), ref_param=ref_param)
+    ds = reader.load_fieldnames(params.split(","))
+
+    handle_vector_fields(ds)
+
+    with outfile.open("wb") as fout:
+        for name, field in ds.items():
+            src = regrid.RegularGrid.from_field(field)
+            dst = src.to_crs(crs_str)
+
+            click.echo(f"Regridding field {name} to {dst}")
+            field_out = regrid.regrid(field, dst, resampling_arg)
+
+            click.echo(f"Writing GRIB fields to {outfile}")
+            grib_decoder.save(field_out, fout)

meteodata_lab-0.3.0/src/meteodatalab/config.py

@@ -0,0 +1,61 @@
+"""global configuration for meteodatalab."""
+
+# Standard library
+from contextlib import contextmanager
+from typing import Any, Literal
+
+config: dict = {}
+
+
+@contextmanager
+def set_values(config: dict = config, **kwargs):
+    """Temporarily set configuration values within a context manager.
+
+    Parameters
+    ----------
+    config : dict, optional
+        dictionary object use to hold the configuration.
+        Default will use the config object in this module
+    **kwargs :
+        the configuration key-value pairs to set.
+
+    """
+    record: list[tuple[Literal["insert", "replace"], str, Any]] = []
+
+    for key, value in kwargs.items():
+        if key in config:
+            record.append(("replace", key, config[key]))
+        else:
+            record.append(("insert", key, None))
+
+        config[key] = value
+
+    try:
+        yield config
+    finally:
+        for op, key, value in reversed(record):
+            d = config
+            if op == "replace":
+                d[key] = value
+            else:  # insert
+                d.pop(key, None)
+
+
+def get(
+    key: str,
+    default: Any = None,
+    config: dict = config,
+) -> Any:
+    """Get values from global config.
+
+    Parameters
+    ----------
+    key: str
+        specifies the name of the key for which the value is requested
+    default: Any
+        default value to be returned in case the key does not exist in config
+    config: dict, optional
+        config object holding the mapping. Default value is the global config
+
+    """
+    return config.get(key, default)

meteodata_lab-0.3.0/src/meteodatalab/data/fdb_config_balfrin.yaml

@@ -0,0 +1,8 @@
+---
+type: local
+engine: toc
+schema: /store_new/mch/msopr/icon_workflow_2/fdb-schema
+spaces:
+- handler: Default
+  roots:
+  - path: /store_new/mch/msopr/icon_workflow_2/fdb_32_39x45_51/

meteodata_lab-0.3.0/src/meteodatalab/data/fdb_config_tsa.yaml

@@ -0,0 +1,8 @@
+---
+type: local
+engine: toc
+schema: /project/s83c/rz+/icon_data_processing_incubator/fdb_schema
+spaces:
+- handler: Default
+  roots:
+  - path: /scratch/ckanesan/fdb_32_39x45_51