defair-data 0.4.0rc2__tar.gz

defair_data-0.4.0rc2/LICENSE

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+
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defair_data-0.4.0rc2/PKG-INFO

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+Metadata-Version: 2.4
+Name: defair-data
+Version: 0.4.0rc2
+Summary: Destination Earth Framework for preparing AI-Ready data
+Keywords: eumetsat,defair,destine,destination earth,machine learning,earth observation
+Author: Dusan Figala, Erwan Fassot
+Author-email: Dusan Figala <dusan@oxidian.com>, Erwan Fassot <erwan@oxidian.com>
+License-Expression: Apache-2.0
+License-File: LICENSE
+Classifier: Development Status :: 3 - Alpha
+Classifier: Intended Audience :: Developers
+Classifier: License :: OSI Approved :: Apache Software License
+Classifier: Intended Audience :: Education
+Classifier: Intended Audience :: Science/Research
+Classifier: Topic :: Scientific/Engineering
+Classifier: Topic :: Scientific/Engineering :: GIS
+Classifier: Topic :: Software Development
+Classifier: Topic :: Software Development :: Libraries
+Classifier: Topic :: Software Development :: Libraries :: Python Modules
+Classifier: Programming Language :: Python :: 3 :: Only
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Requires-Dist: defair
+Requires-Dist: defair-ops
+Requires-Dist: fsspec>=2025.9.0
+Requires-Dist: xarray>=2025.6.1
+Requires-Dist: loguru>=0.7.3
+Requires-Dist: numpy>=1.24.0
+Requires-Dist: pandas>=2.0.0,<=3.0.3
+Requires-Dist: dask[distributed]>=2023.8.0,<=2025.3.0
+Requires-Dist: pyproj>=3.0.0
+Requires-Dist: rioxarray>=0.15.0
+Requires-Dist: rasterio>=1.3.0
+Requires-Dist: typing-extensions>=4.15.0
+Requires-Dist: numcodecs>=0.12.0
+Requires-Dist: zarr>=2.18.0
+Requires-Dist: earthkit-data>=0.17.0,<1
+Requires-Dist: earthkit-utils>=0.1.1,<0.2
+Requires-Dist: h5netcdf>=1.7.3
+Requires-Dist: boto3>=1.34.0
+Requires-Dist: s3fs>=2025.9.0
+Requires-Dist: cf-xarray>=0.9.0
+Requires-Dist: psutil>=7.1.1
+Requires-Dist: scipy>=1.15.3
+Requires-Dist: gribscan>=0.0.14
+Requires-Dist: python-dotenv>=1.2.1
+Requires-Dist: h5py>=3.16
+Requires-Dist: eccodes>=2.38.0
+Requires-Dist: eccodeslib>=2.38.0
+Requires-Dist: cfgrib>=0.9.14
+Requires-Dist: pystac>=1.14.3
+Requires-Dist: destinelab>=1.14
+Requires-Dist: aiohttp>=3.10.0
+Requires-Dist: tenacity>=9.0.0
+Requires-Dist: filelock>=3.20.0
+Requires-Dist: hdf5plugin>=6.0.0
+Requires-Dist: pyarrow>=18.0.0
+Requires-Python: >=3.10
+Description-Content-Type: text/markdown
+
+# Defair Data

defair_data-0.4.0rc2/README.md

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+# Defair Data

defair_data-0.4.0rc2/pyproject.toml

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+# Copyright 2025 EUMETSAT
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+[project]
+name = "defair-data"
+version = "0.4.0rc2"
+description = "Destination Earth Framework for preparing AI-Ready data"
+readme = "README.md"
+authors = [
+    { name = "Dusan Figala", email = "dusan@oxidian.com" },
+    { name = "Erwan Fassot", email = "erwan@oxidian.com" }
+]
+classifiers = [
+    "Development Status :: 3 - Alpha",
+    "Intended Audience :: Developers",
+    "License :: OSI Approved :: Apache Software License",
+    "Intended Audience :: Education",
+    "Intended Audience :: Science/Research",
+    "Topic :: Scientific/Engineering",
+    "Topic :: Scientific/Engineering :: GIS",
+    "Topic :: Software Development",
+    "Topic :: Software Development :: Libraries",
+    "Topic :: Software Development :: Libraries :: Python Modules",
+    "Programming Language :: Python :: 3 :: Only",
+    "Programming Language :: Python :: 3.10",
+    "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
+    "Programming Language :: Python :: 3.13",
+]
+keywords = ["eumetsat", "defair", "destine", "destination earth", "machine learning", "earth observation"]
+license = "Apache-2.0"
+license-files = ["LICENSE"]
+requires-python = ">=3.10"
+dependencies = [
+    "defair",
+    "defair-ops",
+    "fsspec>=2025.9.0",
+    "xarray>=2025.6.1",
+    "loguru>=0.7.3",
+    "numpy>=1.24.0",
+    "pandas>=2.0.0,<=3.0.3",
+    "dask[distributed]>=2023.8.0,<=2025.3.0",
+    "pyproj>=3.0.0",
+    "rioxarray>=0.15.0",
+    "rasterio>=1.3.0",
+    "typing-extensions>=4.15.0",
+    "numcodecs>=0.12.0",
+    "zarr>=2.18.0",
+    # earthkit-data <1 imports array_to_numpy, which earthkit-utils removed after
+    # 0.1.x, and declares no upper bound on it; pin both until the coordinated
+    # earthkit 1.0 upgrade (data + meteo + utils together).
+    "earthkit-data>=0.17.0,<1",
+    "earthkit-utils>=0.1.1,<0.2",
+    "h5netcdf>=1.7.3",
+    "boto3>=1.34.0",
+    "s3fs>=2025.9.0",
+    "cf-xarray>=0.9.0",
+    "psutil>=7.1.1",
+    "scipy>=1.15.3",
+    "gribscan>=0.0.14",
+    "python-dotenv>=1.2.1",
+    # h5py 3.15.1 shares a libhdf5_hl soname with netCDF4 wheels, breaking HDF5 readers (DEFAIR-548)
+    "h5py>=3.16",
+    "eccodes>=2.38.0",
+    "eccodeslib>=2.38.0",
+    "cfgrib>=0.9.14",
+    "pystac>=1.14.3",
+    "destinelab>=1.14",
+    "aiohttp>=3.10.0",
+    "tenacity>=9.0.0",
+    "filelock>=3.20.0",
+    "hdf5plugin>=6.0.0",
+    # Column output (Parquet/GeoParquet/CSV). Floor 18 rather than dask's
+    # 14.0.1 because 18 is the first release with wheels across the full
+    # Python 3.10-3.13 range this package supports.
+    "pyarrow>=18.0.0",
+]
+
+[build-system]
+requires = ["uv_build>=0.8.11,<0.9.0"]
+build-backend = "uv_build"
+
+[project.entry-points."defair_data.sources"]
+local = "defair_data.sources.local.local_filesystem_plugin:LocalFilesystemPlugin"
+s3 = "defair_data.sources.s3.s3_fsspec_plugin:S3FsspecPlugin"
+s3boto = "defair_data.sources.s3.s3_boto3_plugin:S3Boto3Plugin"
+hda = "defair_data.sources.hda.hda_stac_plugin:HdaStacPlugin"
+
+[project.entry-points."defair_data.readers"]
+msg15nat = "defair_data.readers.msg15.msg15_native_reader_plugin:MSG15NativeReaderPlugin"
+era5grib = "defair_data.readers.era5_grib.era5_grib_reader_plugin:ERA5GribReaderPlugin"
+mtg_fci_l1c_nc = "defair_data.readers.mtg_fci.mtg_fci_l1c_nc_reader_plugin:MTGFCIL1cNCReaderPlugin"
+mtg_l2_clm = "defair_data.readers.mtg_fci.mtg_l2_clm_reader_plugin:MTGL2CLMReaderPlugin"
+mtg_l2_oca = "defair_data.readers.mtg_fci.mtg_l2_oca_reader_plugin:MTGL2OCAReaderPlugin"
+mtg_l2_olr = "defair_data.readers.mtg_fci.mtg_l2_olr_reader_plugin:MTGL2OLRReaderPlugin"
+mtg_fci_l2_amv = "defair_data.readers.mtg_fci.mtg_l2_amv_reader_plugin:MTGFCIAMVReaderPlugin"
+mtg_l2_gii = "defair_data.readers.mtg_fci.mtg_l2_gii_reader_plugin:MTGL2GIIReaderPlugin"
+mtg_l2_asr = "defair_data.readers.mtg_fci.mtg_l2_asr_reader_plugin:MTGL2ASRReaderPlugin"
+mtg_li_af = "defair_data.readers.mtg_li.mtg_li_af_reader_plugin:MTGLIAFReaderPlugin"
+mtg_li_afa = "defair_data.readers.mtg_li.mtg_li_afa_reader_plugin:MTGLIAFAReaderPlugin"
+mtg_li_afr = "defair_data.readers.mtg_li.mtg_li_afr_reader_plugin:MTGLIAFRReaderPlugin"
+mtg_li_lef = "defair_data.readers.mtg_li.mtg_li_lef_reader_plugin:MTGLILEFReaderPlugin"
+mtg_li_lfl = "defair_data.readers.mtg_li.mtg_li_lfl_reader_plugin:MTGLILFLReaderPlugin"
+mtg_li_lgr = "defair_data.readers.mtg_li.mtg_li_lgr_reader_plugin:MTGLILGRReaderPlugin"
+metop_osi150a = "defair_data.readers.metop.metop_osi150a_reader_plugin:MetopOSI150AReaderPlugin"
+metop_osi150b = "defair_data.readers.metop.metop_osi150b_reader_plugin:MetopOSI150BReaderPlugin"
+metop_osi104 = "defair_data.readers.metop.metop_osi104_reader_plugin:MetopOSI104ReaderPlugin"
+metop_hirs_fdr = "defair_data.readers.metop.metop_hirs_fdr_reader_plugin:MetopHIRSFDRReaderPlugin"
+metop_glbsst = "defair_data.readers.metop.metop_glbsst_reader_plugin:MetopGLBSSTReaderPlugin"
+metop_avhrr_amv = "defair_data.readers.metop.metop_avhrr_amv_reader_plugin:MetopAVHRRAMVReaderPlugin"
+metop_ascszfr02 = "defair_data.readers.metop.metop_ascszfr02_reader_plugin:MetopASCSZFR02ReaderPlugin"
+metop_ascszrr02 = "defair_data.readers.metop.metop_ascszrr02_reader_plugin:MetopASCSZRR02ReaderPlugin"
+metop_ascszf1b = "defair_data.readers.metop.metop_ascszf1b_reader_plugin:MetopASCSZF1BReaderPlugin"
+metop_amsul1 = "defair_data.readers.metop.metop_amsul1_reader_plugin:MetopAMSUL1ReaderPlugin"
+metop_ascszo1b = "defair_data.readers.metop.metop_ascszo1b_reader_plugin:MetopASCSZO1BReaderPlugin"
+metop_ascszor02 = "defair_data.readers.metop.metop_ascszor02_reader_plugin:MetopASCSZOR02ReaderPlugin"
+metop_ascszr1b = "defair_data.readers.metop.metop_ascszr1b_reader_plugin:MetopASCSZR1BReaderPlugin"
+metop_mhsl1 = "defair_data.readers.metop.metop_mhsl1_reader_plugin:MetopMHSL1ReaderPlugin"
+metop_hirsl1 = "defair_data.readers.metop.metop_hirsl1_reader_plugin:MetopHIRSL1ReaderPlugin"
+metop_somo25 = "defair_data.readers.metop.metop_somo25_reader_plugin:MetopSOMO25ReaderPlugin"
+metop_somo12 = "defair_data.readers.metop.metop_somo12_reader_plugin:MetopSOMO12ReaderPlugin"
+metop_gomel1 = "defair_data.readers.metop.metop_gomel1_reader_plugin:MetopGOMEL1ReaderPlugin"
+metop_gomel1r03 = "defair_data.readers.metop.metop_gomel1r03_reader_plugin:MetopGOMEL1R03ReaderPlugin"
+metop_avhrrl1 = "defair_data.readers.metop.metop_avhrrl1_reader_plugin:MetopAVHRRL1ReaderPlugin"
+metop_edlst = "defair_data.readers.metop.metop_edlst_reader_plugin:MetopEDLSTReaderPlugin"
+metop_iasil1c_all = "defair_data.readers.metop.metop_iasil1c_all_reader_plugin:MetopIASIL1CAllReaderPlugin"
+metop_iasisnd02 = "defair_data.readers.metop.metop_iasisnd02_reader_plugin:MetopIASISND02ReaderPlugin"
+metop_iasthr011 = "defair_data.readers.metop.metop_iasthr011_reader_plugin:MetopIASTHR011ReaderPlugin"
+# Sentinel-3 SLSTR
+sentinel3_aod = "defair_data.readers.sentinel3.sentinel3_aod_reader_plugin:Sentinel3AODReaderPlugin"
+sentinel3_frp = "defair_data.readers.sentinel3.sentinel3_frp_reader_plugin:Sentinel3FRPReaderPlugin"
+sentinel3_sl_1_rbt = "defair_data.readers.sentinel3.sentinel3_sl_1_rbt_reader_plugin:Sentinel3SL1RBTReaderPlugin"
+sentinel3_wst = "defair_data.readers.sentinel3.sentinel3_wst_reader_plugin:Sentinel3WSTReaderPlugin"
+# Sentinel-3 OLCI
+sentinel3_ol_1_efr = "defair_data.readers.sentinel3.sentinel3_ol_1_efr_reader_plugin:Sentinel3OL1EFRReaderPlugin"
+sentinel3_ol_1_err = "defair_data.readers.sentinel3.sentinel3_ol_1_err_reader_plugin:Sentinel3OL1ERRReaderPlugin"
+sentinel3_ol_2_wfr = "defair_data.readers.sentinel3.sentinel3_ol_2_wfr_reader_plugin:Sentinel3OL2WFRReaderPlugin"
+sentinel3_ol_2_wrr = "defair_data.readers.sentinel3.sentinel3_ol_2_wrr_reader_plugin:Sentinel3OL2WRRReaderPlugin"
+# Sentinel-3 SRAL
+sentinel3_sr1_sra_a = "defair_data.readers.sentinel3.sentinel3_sr1_sra_a_reader_plugin:Sentinel3SR1SRAAReaderPlugin"
+sentinel3_sr1_sra = "defair_data.readers.sentinel3.sentinel3_sr1_sra_reader_plugin:Sentinel3SR1SRAReaderPlugin"
+sentinel3_sr1_sra_bs = "defair_data.readers.sentinel3.sentinel3_sr1_sra_bs_reader_plugin:Sentinel3SR1SRABSReaderPlugin"
+sentinel3_sr2_wat = "defair_data.readers.sentinel3.sentinel3_sr2_wat_reader_plugin:Sentinel3SR2WATReaderPlugin"
+
+[project.entry-points."defair_data.writers"]
+netcdf4 = "defair_data.writers.netcdf4.netcdf4_writer:NetCDF4Writer"
+hdf5 = "defair_data.writers.hdf5.hdf5_writer:HDF5Writer"
+zarrv2 = "defair_data.writers.zarr.zarr_writer:ZarrV2Writer"
+zarrv3 = "defair_data.writers.zarr.zarr_writer:ZarrV3Writer"
+geotiff = "defair_data.writers.geotiff.geotiff_writer:GeoTIFFWriter"
+png = "defair_data.writers.png.png_writer:PNGWriter"
+jpeg = "defair_data.writers.jpeg.jpeg_writer:JPEGWriter"
+parquet = "defair_data.writers.parquet.parquet_writer:ParquetWriter"
+# Claims no extension, so it never competes with parquet for auto-detection.
+geoparquet = "defair_data.writers.parquet.parquet_writer:GeoParquetWriter"
+csv = "defair_data.writers.csv.csv_writer:CSVWriter"
+
+[project.entry-points."xarray.backends"]
+msg15 = "defair_data.readers.msg15._msg15_xarray_backend:MSG15BackendEntrypoint"
+
+[tool.pytest.ini_options]
+markers = [
+    "real_s3: Tests requiring S3 access and credentials",
+]
+
+[tool.uv.sources]
+defair = { workspace = true }
+defair-ops = { workspace = true }
+
+[dependency-groups]
+dev = [
+    "moto[s3]>=5.0.0",
+    "pytest-asyncio>=0.23.0",
+]

defair_data-0.4.0rc2/src/defair_data/__init__.py

@@ -0,0 +1,113 @@
+#
+# Copyright 2026 EUMETSAT
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+#
+
+import atexit
+import os
+import sys
+
+# CRITICAL: Must be set before ANY module imports zarr
+# Zarr checks this at import time, and xarray imports zarr
+os.environ.setdefault("ZARR_V3_EXPERIMENTAL_API", "1")
+
+# Silence noisy S3/HTTP dependency loggers BEFORE any defair / defair_data
+# submodule is imported, so the first boto3/botocore record (e.g. credential
+# discovery on Dataset.from_source) never reaches pytest's caplog or any
+# user-attached root handler. Required for consumers that never invoke
+# ``defair.logging.setup_logging`` — e.g. the vendor pytest suite.
+from defair_data import _logging_defaults as _logging_defaults  # noqa: I001  side effect: silence noisy loggers
+from importlib.metadata import version
+
+from defair.plugin_manager import load_reader
+from defair_data.constants import CF_VERSION
+from defair_data.core import Dataset
+from defair_data.dask_manager import S3CredentialsPlugin, propagate_s3_credentials
+from defair_data.data_reader_plugin import DataReaderPlugin
+from defair_data.logging import get_logger
+from defair_data.readers import (
+    ReaderInfo,
+    ReaderProduct,
+    describe_readers,
+    find_reader_for_path,
+    get_reader,
+    get_reader_info,
+    list_readers,
+)
+from defair_data.readers.msg15.msg15_native_reader_plugin import MSG15NativeReaderPlugin
+
+__version__ = version("defair-data")
+
+logger = get_logger(__name__)
+
+# The netCDF4 wheel bundles its own libhdf5 build and h5py bundles a different one. In a
+# single process the library imported first binds the shared symbols, so when netCDF4 wins
+# every HDF5-backed reader here fails with "Unspecified error in H5DSget_num_scales" and the
+# interpreter can dump core at shutdown -- a failure whose message names neither library.
+# defair-data no longer depends on netCDF4, but earthkit-data still installs it, and
+# "import netCDF4" is a common first line in an Earth-observation notebook. Saying so at the
+# only moment the clash is detectable is the whole defence a library has here.
+if sys.modules.get("netCDF4") is not None:
+    logger.warning(
+        "netCDF4 was imported before defair_data. The two bundle different libhdf5 builds and the "
+        "first import wins the shared symbols, so HDF5-backed readers (MTG FCI, MTG LI, Sentinel-3 "
+        "and others) may fail with 'Unspecified error in H5DSget_num_scales' and the process may "
+        "crash at exit. Import defair_data before netCDF4, or keep netCDF4 out of this process."
+    )
+
+
+def _close_native_handles_before_teardown() -> None:
+    """Release HDF5 and projection handles while their libraries are still alive.
+
+    xarray deliberately stops closing cached files at exit, so an h5py handle left in
+    a CachingFileManager is finalised during interpreter teardown, after libhdf5 (and,
+    in environments where pyproj and fiona each bundle a libproj, after one of those)
+    has already been torn down. A plain FCI read then exits with SIGSEGV after printing
+    a correct result. Registered here, after xarray and the HDF5 stack were imported,
+    this runs before their own exit hooks and leaves nothing for teardown to finalise.
+    """
+    import gc  # noqa: PLC0415
+
+    from xarray.backends.file_manager import FILE_CACHE  # noqa: PLC0415
+
+    from defair_data.readers.mtg_fci.mtg_fci_l1c_nc_reader_plugin import release_retired_managers  # noqa: PLC0415
+
+    try:
+        release_retired_managers(force=True)
+        FILE_CACHE.clear()
+    except Exception:  # best effort: an exit hook must never raise
+        logger.debug("exit cleanup of native handles failed", exc_info=True)
+    gc.collect()
+
+
+atexit.register(_close_native_handles_before_teardown)
+
+__all__ = [
+    "CF_VERSION",
+    "DataReaderPlugin",
+    "Dataset",
+    "MSG15NativeReaderPlugin",
+    "ReaderInfo",
+    "ReaderProduct",
+    "S3CredentialsPlugin",
+    "__version__",
+    "describe_readers",
+    "find_reader_for_path",
+    "get_logger",
+    "get_reader",
+    "get_reader_info",
+    "list_readers",
+    "load_reader",
+    "propagate_s3_credentials",
+]