diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 00f7ca57..b059bc53 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -10,19 +10,25 @@ permissions: contents: read jobs: - pre-commit: + lint: runs-on: ubuntu-latest steps: - - uses: actions/checkout@df4cb1c069e1874edd31b4311f1884172cec0e10 # v6.0.3 - with: - persist-credentials: false - - uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405 # v6 - with: - python-version: '3.12' - - name: Install pre-commit - run: pip install pre-commit - - name: Run pre-commit - run: pre-commit run --all-files + - uses: actions/checkout@df4cb1c069e1874edd31b4311f1884172cec0e10 # v6.0.3 + with: + persist-credentials: false + - name: Set up Python + uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405 # v6.2.0 + with: + python-version: "3.12" + - name: Install uv + uses: astral-sh/setup-uv@fac544c07dec837d0ccb6301d7b5580bf5edae39 # v8.2.0 + with: + enable-cache: true + - name: Install dependencies + # The pyright pre-commit hook runs `uv run --frozen pyright`, so the + # project environment must be present. + run: uv sync --group dev --group test + - uses: j178/prek-action@bdca6f102f98e2b4c7029491a53dfd366469e33d # v2.0.4 test: runs-on: ${{ matrix.os }} diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index f19c8a37..52e24ad7 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -11,13 +11,12 @@ repos: args: ["--fix", "--show-fixes"] - id: ruff-format - - repo: https://github.com/pre-commit/mirrors-mypy - rev: v1.17.0 + - repo: local hooks: - - id: mypy - language_version: python - exclude: tests/.* - additional_dependencies: - - types-attrs - - typing-extensions>=4.15.0 - - pydantic>=2.12 + - id: pyright + name: pyright + language: system + entry: uv run --frozen pyright + pass_filenames: false + always_run: true + types_or: [python, pyi] diff --git a/pyproject.toml b/pyproject.toml index 2d371778..bd22dce3 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -36,7 +36,7 @@ dependencies = [ "rioxarray>=0.13.0", "cf-xarray>=0.8.0", "typing-extensions>=4.15.0", - "zarr-cm>=0.2.0", + "zarr-cm>=0.4.1", "aiohttp>=3.14.0", "s3fs>=2024.6.0", "boto3>=1.34.0", @@ -48,7 +48,7 @@ dependencies = [ dev = [ "pytest>=7.0.0", "pytest-cov>=4.0.0", - "mypy>=1.0.0", + "pyright>=1.1.390", "pre-commit>=3.0.0", "bandit[toml]>=1.7.0", ] @@ -149,40 +149,19 @@ ignore = [ "TRY003", # Long exception messages outside class - common pattern ] -[tool.mypy] -python_version = "3.12" -warn_return_any = true -warn_unused_configs = true -disallow_untyped_defs = true -disallow_incomplete_defs = true -check_untyped_defs = true -disallow_untyped_decorators = true -no_implicit_optional = true -warn_redundant_casts = true -warn_unused_ignores = true -warn_no_return = true -warn_unreachable = true -strict_equality = true -plugins = ["pydantic.mypy"] - -[tool.pydantic-mypy] -init_forbid_extra = true -init_typed = true -warn_required_dynamic_aliases = true -warn_untyped_fields = true - -[[tool.mypy.overrides]] -module = ["zarr.*", "xarray.*", "rioxarray.*", "cf_xarray.*", "dask.*"] -ignore_missing_imports = true - -[[tool.mypy.overrides]] -module = [ - "eopf_geozarr.data_api.s1", - "eopf_geozarr.data_api.s2", - "eopf_geozarr.data_api.geozarr.v2", - "eopf_geozarr.data_api.geozarr.store", -] -disable_error_code = ["valid-type"] +[tool.pyright] +include = ["src", "tests"] +pythonVersion = "3.12" +typeCheckingMode = "standard" +# Several runtime deps ship no type stubs; we can't fix their types here, so +# don't report missing stubs/sources for them. (Imports still resolve because +# the packages are installed in the environment.) +reportMissingTypeStubs = false +reportMissingModuleSource = false +# Match the strictness we relied on under mypy. +reportUnnecessaryTypeIgnoreComment = true +reportReturnType = "error" +reportUnnecessaryCast = "error" [tool.pytest.ini_options] minversion = "7.0" diff --git a/src/eopf_geozarr/cli.py b/src/eopf_geozarr/cli.py index 53c3ee21..805c9237 100755 --- a/src/eopf_geozarr/cli.py +++ b/src/eopf_geozarr/cli.py @@ -354,7 +354,7 @@ def format_data_vars(data_vars: dict[str, xr.DataArray]) -> str: # Fallback to simple format if xarray HTML fails vars_html = [] for name, var in data_vars.items(): - dims_str = format_dimensions(dict(zip(var.dims, var.shape, strict=True))) + dims_str = format_dimensions(dict(zip(map(str, var.dims), var.shape, strict=True))) dtype_str = str(var.dtype) vars_html.append( f""" @@ -450,7 +450,7 @@ def render_node(node: xr.DataTree, path: str = "", level: int = 0) -> str:

Variables

- {format_data_vars(node.ds.data_vars)} + {format_data_vars({str(k): v for k, v in node.ds.data_vars.items()})}
""" diff --git a/src/eopf_geozarr/conversion/fs_utils.py b/src/eopf_geozarr/conversion/fs_utils.py index f55a3ab0..b31ed878 100644 --- a/src/eopf_geozarr/conversion/fs_utils.py +++ b/src/eopf_geozarr/conversion/fs_utils.py @@ -3,7 +3,7 @@ import json import os from collections.abc import Mapping -from typing import TYPE_CHECKING, Any +from typing import TYPE_CHECKING, Any, Final, Literal, cast from urllib.parse import urlparse import s3fs @@ -16,6 +16,8 @@ if TYPE_CHECKING: import xarray as xr +ZarrOpenMode = Literal["r", "r+", "a", "w", "w-"] + _MISSING = object() # sentinel for missing optional attrs @@ -52,18 +54,44 @@ def replace_json_invalid_floats(obj: object) -> object: return obj +def _sanitize_attrs(attrs: Mapping[str, object]) -> dict[str, object]: + """Sanitize an attributes mapping, returning a typed ``dict``. + + Wraps :func:`replace_json_invalid_floats` (which is typed ``object -> object``) + and verifies the dict-in/dict-out invariant at runtime instead of casting. + """ + sanitized = replace_json_invalid_floats(dict(attrs)) + if not isinstance(sanitized, dict): # pragma: no cover - invariant guard + raise TypeError(f"expected a dict after sanitizing attrs, got {type(sanitized).__name__}") + return sanitized + + +_ZARR_MODES: Final = ("r", "r+", "a", "w", "w-") + + +def _zarr_mode(mode: str) -> ZarrOpenMode: + """Validate *mode* against zarr's accepted access modes and narrow its type. + + Checks the value at runtime instead of casting a bare ``str`` to the + ``Literal`` zarr expects. + """ + if mode not in _ZARR_MODES: + raise ValueError(f"Invalid zarr access mode {mode!r}; expected one of {_ZARR_MODES}") + return mode + + class NanCompatibleJSONEncoder(json.JSONEncoder): """ Custom JSON encoder that converts NaN, Inf, -Inf values to JSON-safe equivalents to ensure valid JSON output. """ - def encode(self, obj: Any) -> str: + def encode(self, o: Any) -> str: """ Encode object to JSON string, converting NaN values to "NaN". """ - converted_obj = replace_json_invalid_floats(obj) + converted_obj = replace_json_invalid_floats(o) return super().encode(converted_obj) @@ -87,7 +115,7 @@ def sanitize_dataset_attributes(ds: "xr.Dataset") -> "xr.Dataset": ds_clean = ds.copy() # Sanitize dataset attributes - ds_clean.attrs = replace_json_invalid_floats(ds_clean.attrs) + ds_clean.attrs = _sanitize_attrs(ds_clean.attrs) # Sanitize variable attributes for var_name in ds_clean.data_vars: @@ -95,14 +123,14 @@ def sanitize_dataset_attributes(ds: "xr.Dataset") -> "xr.Dataset": # Preserve _FillValue as-is — xarray encodes it via FillValueCoder on write; # converting np.nan to the string "NaN" would break FillValueCoder.encode. fill_value = var.attrs.get("_FillValue", _MISSING) - var.attrs = replace_json_invalid_floats(var.attrs) + var.attrs = _sanitize_attrs(var.attrs) if fill_value is not _MISSING: var.attrs["_FillValue"] = fill_value # Sanitize coordinate attributes for coord_name in ds_clean.coords: coord = ds_clean[coord_name] - coord.attrs = replace_json_invalid_floats(coord.attrs) + coord.attrs = _sanitize_attrs(coord.attrs) return ds_clean @@ -405,7 +433,12 @@ def open_s3_zarr_group(s3_path: str, mode: str = "r", **s3_kwargs: Any) -> zarr. Zarr group """ storage_options = get_s3_storage_options(s3_path, **s3_kwargs) - return zarr.open_group(s3_path, mode=mode, zarr_format=3, storage_options=storage_options) + return zarr.open_group( + s3_path, + mode=_zarr_mode(mode), + zarr_format=3, + storage_options=cast("dict[str, object]", storage_options), + ) def get_s3_credentials_info() -> S3Credentials: @@ -589,4 +622,9 @@ def open_zarr_group(path: str, mode: str = "r", **kwargs: Any) -> zarr.Group: Zarr group """ storage_options = get_storage_options(path, **kwargs) - return zarr.open_group(path, mode=mode, zarr_format=3, storage_options=storage_options) + return zarr.open_group( + path, + mode=_zarr_mode(mode), + zarr_format=3, + storage_options=cast("dict[str, object] | None", storage_options), + ) diff --git a/src/eopf_geozarr/conversion/geozarr.py b/src/eopf_geozarr/conversion/geozarr.py index e2a13b37..8f9c68f4 100644 --- a/src/eopf_geozarr/conversion/geozarr.py +++ b/src/eopf_geozarr/conversion/geozarr.py @@ -18,25 +18,23 @@ import os import time from collections.abc import Hashable, Iterable, Mapping, Sequence -from typing import Any +from typing import TYPE_CHECKING, Any, cast import numpy as np import structlog import xarray as xr import zarr +import zarr.core.common +import zarr.core.group from pyproj import CRS from rasterio.warp import calculate_default_transform from zarr.codecs import BloscCodec from zarr.core.sync import sync from zarr.storage import StoreLike from zarr.storage._common import make_store_path -from zarr_cm import geo_proj -from zarr_cm import multiscales as multiscales_cm -from zarr_cm import spatial as spatial_cm from eopf_geozarr.data_api.geozarr.multiscales import zcm from eopf_geozarr.data_api.geozarr.multiscales.geozarr import ( - MultiscaleGroupAttrs, MultiscaleMeta, ) from eopf_geozarr.types import ( @@ -52,6 +50,10 @@ from .fs_utils import sanitize_dataset_attributes from .sentinel1_reprojection import reproject_sentinel1_with_gcps +if TYPE_CHECKING: + from zarr.core.common import JSON + from zarr_cm import MultiscalesAttrs + log = structlog.get_logger() @@ -372,7 +374,8 @@ def iterative_copy( consolidated=False, zarr_format=3, encoding=encoding, - storage_options=storage_options, + # xarray stubs type storage_options as dict[str, str]; S3FsOptions is broader + storage_options=storage_options, # pyright: ignore[reportArgumentType] ) dt_result[relative_path] = xr.DataTree(ds) @@ -507,7 +510,7 @@ def write_geozarr_group( # Create GeoZarr-spec compliant multiscales if _is_sentinel1(dt_input): assert gcp_group is not None, "GCP group required for processing Sentinel-1" - ds_gcp = dt_input[gcp_group].to_dataset() + ds_gcp: xr.Dataset | None = dt_input[gcp_group].to_dataset() # For Sentinel-1, ds_gcp is set to None since data is now reprojected and doesn't need GCP handling ds_gcp = None else: @@ -585,7 +588,7 @@ def create_geozarr_compliant_multiscales( compressor = BloscCodec(cname="zstd", clevel=3, shuffle="shuffle") # Get spatial information from the first data variable - data_vars = [var for var in ds.data_vars if not utils.is_grid_mapping_variable(ds, var)] + data_vars = [var for var in ds.data_vars if not utils.is_grid_mapping_variable(ds, str(var))] if not data_vars: return {} @@ -672,26 +675,27 @@ def _spatial_transform_for( scale_level_data["spatial:transform"] = spatial_tf layout.append(zcm.ScaleLevel(**scale_level_data)) - multiscale_attrs = MultiscaleGroupAttrs( - zarr_conventions=(multiscales_cm.CMO, spatial_cm.CMO, geo_proj.CMO), - multiscales=MultiscaleMeta( - layout=layout, - resampling_method="average", - ), + # Validate + serialize the multiscales block via the project model (which + # also covers the ZCM/TMS duality), then hand all conventions to zarr-cm, + # which validates each and emits the matching CMOs in order (multiscales, + # spatial, proj). proj is included only when a CRS is available. + multiscales_data = cast( + "MultiscalesAttrs", + MultiscaleMeta(layout=tuple(layout), resampling_method="average").model_dump(), + ) + attrs_to_write = utils.build_convention_attrs( + multiscales=multiscales_data, + spatial={ + "spatial:dimensions": ["y", "x"], + "spatial:bbox": list(native_bounds), + "spatial:registration": "pixel", + }, + crs=native_crs or None, ) - attrs_to_write = multiscale_attrs.model_dump() - if native_crs and native_bounds: - attrs_to_write["spatial:dimensions"] = ["y", "x"] - attrs_to_write["spatial:bbox"] = list(native_bounds) - attrs_to_write["spatial:registration"] = "pixel" - if hasattr(native_crs, "to_epsg") and native_crs.to_epsg(): - attrs_to_write["proj:code"] = f"EPSG:{native_crs.to_epsg()}" - elif hasattr(native_crs, "to_wkt"): - attrs_to_write["proj:wkt2"] = native_crs.to_wkt() group_path = fs_utils.normalize_path(f"{output_path}/{group_name.lstrip('/')}") zarr_group = fs_utils.open_zarr_group(group_path, mode="r+") - zarr_group.attrs.update(attrs_to_write) + zarr_group.attrs.update(cast("dict[str, JSON]", attrs_to_write)) log.info("Added multiscales metadata to group %s", group_name) @@ -756,7 +760,8 @@ def _spatial_transform_for( zarr_format=3, encoding=encoding, align_chunks=align_chunks_flag, - storage_options=storage_options, + # xarray stubs type storage_options as dict[str, str]; S3FsOptions is broader + storage_options=storage_options, # pyright: ignore[reportArgumentType] ) overview_datasets[asset_name] = overview_ds @@ -1011,7 +1016,7 @@ def write_dataset_band_by_band_with_validation( ) # Get data variables - data_vars = [var for var in ds.data_vars if not utils.is_grid_mapping_variable(ds, var)] + data_vars = [var for var in ds.data_vars if not utils.is_grid_mapping_variable(ds, str(var))] successful_vars = [] failed_vars = [] @@ -1044,9 +1049,10 @@ def cleanup_prefix(prefix: str) -> None: for var in data_vars: # Check if this variable already exists and is valid if not force_overwrite and store_exists: - if utils.validate_existing_band_data(existing_dataset, var, ds): + assert existing_dataset is not None # guaranteed by store_exists + if utils.validate_existing_band_data(existing_dataset, str(var), ds): ds.drop_vars(str(var)) - ds[var] = existing_dataset[var] # type: ignore[index] + ds[var] = existing_dataset[var] log.info("✅ Band %s already exists and is valid, skipping.", var) skipped_vars.append(var) successful_vars.append(var) @@ -1114,7 +1120,8 @@ def cleanup_prefix(prefix: str) -> None: consolidated=False, zarr_format=3, encoding=var_encoding, - storage_options=store_storage_options, + # xarray stubs type storage_options as dict[str, str]; S3FsOptions is broader + storage_options=store_storage_options, # pyright: ignore[reportArgumentType] ) log.info(" ✅ Successfully wrote", var=var) @@ -1388,15 +1395,17 @@ def _create_encoding( for var in ds.data_vars: if hasattr(ds[var].data, "chunks"): current_chunks = ds[var].chunks + assert current_chunks is not None # guaranteed by hasattr(..., "chunks") if len(current_chunks) >= 2: chunking = tuple( current_chunks[i][0] if len(current_chunks[i]) > 0 else ds[var].shape[i] for i in range(len(current_chunks)) ) else: - chunking = ( - current_chunks[0][0] if len(current_chunks[0]) > 0 else ds[var].shape[0], - ) + chunks_list = list(current_chunks) + first_chunks = list(chunks_list[0]) + first_shape = list(ds[var].shape) + chunking = (first_chunks[0] if len(first_chunks) > 0 else first_shape[0],) else: data_shape = ds[var].shape if len(data_shape) >= 2: @@ -1404,7 +1413,7 @@ def _create_encoding( chunk_x = min(spatial_chunk, data_shape[-1]) chunking = (1, chunk_y, chunk_x) if len(data_shape) == 3 else (chunk_y, chunk_x) else: - chunking = (min(spatial_chunk, data_shape[-1]),) + chunking = (min(spatial_chunk, list(data_shape)[-1]),) var_encoding: XarrayEncodingJSON = { "compressors": [compressor], @@ -1429,7 +1438,7 @@ def _create_geozarr_encoding( encoding: dict[Hashable, XarrayEncodingJSON] = {} chunks: tuple[int, ...] for var in ds.data_vars: - if utils.is_grid_mapping_variable(ds, var): + if utils.is_grid_mapping_variable(ds, str(var)): encoding[var] = {"compressors": None} else: data_shape = ds[var].shape @@ -1480,7 +1489,7 @@ def _create_geozarr_encoding( ) else: # For 1D data, use the full dimension - shards = (data_shape[0],) + shards = (next(iter(data_shape)),) log.info( " 🔧 Sharding config", var=var, @@ -1641,7 +1650,7 @@ def _add_grid_mapping_variable( # Ensure all data variables have the grid_mapping attribute for var_name in overview_ds.data_vars: if ( - not utils.is_grid_mapping_variable(overview_ds, var_name) + not utils.is_grid_mapping_variable(overview_ds, str(var_name)) and "grid_mapping" not in overview_ds[var_name].attrs ): overview_ds[var_name].attrs["grid_mapping"] = grid_mapping_var_name @@ -1695,4 +1704,16 @@ def _is_sentinel1(dt: xr.DataTree) -> bool: def get_zarr_group(data: xr.DataTree) -> zarr.Group: - return data._close.__self__.zarr_group + # `_close` is a bound method of the backend store on an opened DataTree; + # `__self__` retrieves that store, which exposes `zarr_group`. These are + # xarray/zarr internals without public type information, so resolve them + # defensively and verify the result is actually a zarr.Group. + close = data._close + store = getattr(close, "__self__", None) + group = getattr(store, "zarr_group", None) + if not isinstance(group, zarr.Group): + raise TypeError( + "Could not resolve a zarr.Group from the DataTree backend " + f"(got {type(group).__name__}); the xarray/zarr internals may have changed." + ) + return group diff --git a/src/eopf_geozarr/conversion/sentinel1_reprojection.py b/src/eopf_geozarr/conversion/sentinel1_reprojection.py index be90abe3..7681e931 100644 --- a/src/eopf_geozarr/conversion/sentinel1_reprojection.py +++ b/src/eopf_geozarr/conversion/sentinel1_reprojection.py @@ -5,8 +5,11 @@ to geographic coordinates (lat/lon) using Ground Control Points (GCPs). """ +from typing import Any + import numpy as np import rasterio +import rasterio.control # Import submodule for GroundControlPoint attribute access import rioxarray # noqa: F401 # Import to enable .rio accessor import structlog import xarray as xr @@ -74,6 +77,9 @@ def reproject_sentinel1_with_gcps( gcps=gcps, ) + # calculate_default_transform sizes the grid, so width and height are populated + assert width is not None + assert height is not None log.info("Calculated target dimensions", width=width, height=height) log.info("Transform", transform=str(transform)) @@ -101,8 +107,13 @@ def reproject_sentinel1_with_gcps( data_vars=reprojected_data_vars, coords=target_coords, attrs=ds.attrs.copy() ) - # Set CRS information + # Set CRS information. `rio.write_crs` is untyped (returns Any), so verify + # the result is a Dataset rather than asserting it with a cast. reprojected_ds = reprojected_ds.rio.write_crs(target_crs) + if not isinstance(reprojected_ds, xr.Dataset): + raise TypeError( + f"expected an xarray.Dataset after write_crs, got {type(reprojected_ds).__name__}" + ) log.info("✅ Successfully reprojected Sentinel-1 data", target_crs=target_crs) return reprojected_ds @@ -178,7 +189,7 @@ def _create_target_coordinates( } -def _determine_nodata_value(data_var: xr.DataArray) -> float | np.floating: +def _determine_nodata_value(data_var: xr.DataArray) -> float: """ Determine appropriate nodata value based on data type and existing attributes. @@ -289,7 +300,7 @@ def _reproject_2d_array( # Initialize destination array with nodata values if np.isnan(nodata_value): dst_array = np.full((dst_height, dst_width), np.nan, dtype=np.float32) - dst_dtype = np.float32 + dst_dtype: np.dtype[Any] | type[np.floating[Any]] = np.float32 else: dst_array = np.full((dst_height, dst_width), nodata_value, dtype=src_array.dtype) dst_dtype = src_array.dtype diff --git a/src/eopf_geozarr/conversion/utils.py b/src/eopf_geozarr/conversion/utils.py index e7125c97..ff5e8d2c 100644 --- a/src/eopf_geozarr/conversion/utils.py +++ b/src/eopf_geozarr/conversion/utils.py @@ -1,15 +1,77 @@ """Utility functions for GeoZarr conversion.""" -from typing import Any +from typing import Any, Protocol, cast, runtime_checkable import numpy as np import rasterio # noqa: F401 # Import to enable .rio accessor import structlog import xarray as xr +import zarr_cm +from zarr_cm import GeoProjAttrs, MultiConventionAttrs, MultiscalesAttrs, SpatialAttrs log = structlog.get_logger() +@runtime_checkable +class CRSLike(Protocol): + """A coordinate reference system that can serialize to EPSG/WKT2. + + Both ``pyproj.CRS`` and ``rasterio.crs.CRS`` satisfy this; the conversion + code accepts either, so we depend on the shared interface rather than a + concrete class. + """ + + def to_epsg(self) -> int | None: ... + + def to_wkt(self) -> str: ... + + +def proj_attrs_for_crs(crs: CRSLike | None) -> GeoProjAttrs: + """Build the ``proj`` convention data keys for a CRS. + + Prefers an EPSG code (``proj:code``) and falls back to WKT2 + (``proj:wkt2``). Returns an empty mapping when *crs* is ``None`` or exposes + no EPSG code. + """ + if crs is None: + return GeoProjAttrs() + epsg = crs.to_epsg() + if epsg: + return GeoProjAttrs({"proj:code": f"EPSG:{epsg}"}) + return GeoProjAttrs({"proj:wkt2": crs.to_wkt()}) + + +def build_convention_attrs( + *, + spatial: SpatialAttrs, + crs: CRSLike | None, + multiscales: MultiscalesAttrs | None = None, +) -> MultiConventionAttrs: + """Build validated multiscales + ``spatial`` + ``proj`` convention attributes. + + Delegates to :func:`zarr_cm.create_many`, which validates each convention's + data and emits the matching convention-metadata objects into a combined + ``zarr_conventions`` array. The CMOs are ordered multiscales (if present), + then spatial, then proj. *spatial* holds the ``spatial:*`` keys; the proj + keys are derived from *crs* via :func:`proj_attrs_for_crs`. + + The proj convention is only included when *crs* yields a usable CRS + representation; otherwise only the other conventions are emitted (a proj + convention with no CRS field is invalid). + """ + conventions: dict[zarr_cm.ConventionName, MultiscalesAttrs | SpatialAttrs | GeoProjAttrs] = {} + if multiscales is not None: + conventions["multiscales"] = multiscales + conventions["spatial"] = spatial + proj = proj_attrs_for_crs(crs) + if proj: + conventions["geo-proj"] = proj + # create_many validates each convention and emits its CMO. It returns a + # generic JSON dict; narrow to the combined convention TypedDict. + result = zarr_cm.create_many(conventions) + return cast("MultiConventionAttrs", result) + + # Sentinel: distinguish "no explicit fill_value" from a legitimate `None`. UNSET: Any = object() diff --git a/src/eopf_geozarr/data_api/geozarr/common.py b/src/eopf_geozarr/data_api/geozarr/common.py index 8236611e..cbbbd90c 100644 --- a/src/eopf_geozarr/data_api/geozarr/common.py +++ b/src/eopf_geozarr/data_api/geozarr/common.py @@ -80,7 +80,7 @@ class BaseDataArrayAttrs(BaseModel, extra="allow"): ---------- """ - grid_mapping: str | MISSING = MISSING # type: ignore[valid-type] + grid_mapping: str | MISSING = MISSING class GridMappingAttrs(BaseModel, extra="allow"): diff --git a/src/eopf_geozarr/data_api/geozarr/multiscales/geozarr.py b/src/eopf_geozarr/data_api/geozarr/multiscales/geozarr.py index d1a5efd3..e507ae3e 100644 --- a/src/eopf_geozarr/data_api/geozarr/multiscales/geozarr.py +++ b/src/eopf_geozarr/data_api/geozarr/multiscales/geozarr.py @@ -5,6 +5,9 @@ from pydantic import BaseModel, model_validator from pydantic.experimental.missing_sentinel import MISSING from typing_extensions import TypedDict + +# Runtime import (not TYPE_CHECKING): pydantic resolves this annotation when +# building MultiscaleGroupAttrs, so the name must exist at runtime. from zarr_cm import ConventionMetadataObject # noqa: TC002 from . import tms, zcm @@ -16,17 +19,17 @@ class MultiscaleMeta(BaseModel): or ZCM multiscale metadata """ - layout: tuple[zcm.ScaleLevel, ...] | MISSING = MISSING # type: ignore[valid-type] - resampling_method: str | MISSING = MISSING # type: ignore[valid-type] - tile_matrix_set: tms.TileMatrixSet | MISSING = MISSING # type: ignore[valid-type] - tile_matrix_limits: dict[str, tms.TileMatrixLimit] | MISSING = MISSING # type: ignore[valid-type] + layout: tuple[zcm.ScaleLevel, ...] | MISSING = MISSING + resampling_method: str | MISSING = MISSING + tile_matrix_set: tms.TileMatrixSet | MISSING = MISSING + tile_matrix_limits: dict[str, tms.TileMatrixLimit] | MISSING = MISSING @model_validator(mode="after") def valid_zcm(self) -> Self: """ Ensure that the ZCM metadata, if present, is valid """ - if self.layout is not MISSING: # type: ignore[comparison-overlap] + if self.layout is not MISSING: zcm.Multiscales(**self.model_dump()) return self @@ -36,7 +39,7 @@ def valid_tms(self) -> Self: """ Ensure that the TMS metadata, if present, is valid """ - if self.tile_matrix_set is not MISSING: # type: ignore[comparison-overlap] + if self.tile_matrix_set is not MISSING: tms.Multiscales(**self.model_dump()) return self @@ -55,7 +58,7 @@ class MultiscaleGroupAttrs(BaseModel): multiscales: MultiscaleAttrs """ - zarr_conventions: tuple[ConventionMetadataObject, ...] | MISSING = MISSING # type: ignore[valid-type] + zarr_conventions: tuple[ConventionMetadataObject, ...] | MISSING = MISSING multiscales: MultiscaleMeta _zcm_multiscales: zcm.Multiscales | None = None @@ -67,15 +70,18 @@ def valid_zcm_and_tms(self) -> Self: Ensure that the ZCM metadata, if present, is valid, and that TMS metadata, if present, is valid, and that at least one of the two is present. """ - if self.zarr_conventions is not MISSING: # type: ignore[comparison-overlap] + if self.zarr_conventions is not MISSING: self._zcm_multiscales = zcm.Multiscales( layout=self.multiscales.layout, resampling_method=self.multiscales.resampling_method, ) - if self.multiscales.tile_matrix_limits is not MISSING: # type: ignore[comparison-overlap] + if self.multiscales.tile_matrix_limits is not MISSING: self._tms_multiscales = tms.Multiscales( tile_matrix_limits=self.multiscales.tile_matrix_limits, - resampling_method=self.multiscales.resampling_method, # type: ignore[arg-type] + # ``resampling_method`` is typed ``str | MISSING`` here but tms.Multiscales + # constrains it to the ``ResamplingMethod`` literal; pydantic validates the + # value at runtime. + resampling_method=self.multiscales.resampling_method, # pyright: ignore[reportArgumentType] tile_matrix_set=self.multiscales.tile_matrix_set, ) if self._tms_multiscales is None and self._zcm_multiscales is None: diff --git a/src/eopf_geozarr/data_api/geozarr/multiscales/zcm.py b/src/eopf_geozarr/data_api/geozarr/multiscales/zcm.py index 650ea07c..1c8f07cd 100644 --- a/src/eopf_geozarr/data_api/geozarr/multiscales/zcm.py +++ b/src/eopf_geozarr/data_api/geozarr/multiscales/zcm.py @@ -9,8 +9,12 @@ CONVENTION_ID = multiscales_cm.UUID CONVENTION_SCHEMA_URL = multiscales_cm.SCHEMA_URL CONVENTION_SPEC_URL = multiscales_cm.SPEC_URL -CONVENTION_NAME = multiscales_cm.CMO["name"] -CONVENTION_DESCRIPTION = multiscales_cm.CMO["description"] +_CONVENTION_NAME = multiscales_cm.CMO.get("name") +assert _CONVENTION_NAME is not None +CONVENTION_NAME = _CONVENTION_NAME +_CONVENTION_DESCRIPTION = multiscales_cm.CMO.get("description") +assert _CONVENTION_DESCRIPTION is not None +CONVENTION_DESCRIPTION = _CONVENTION_DESCRIPTION # Re-export zarr-cm TypedDicts TransformJSON = multiscales_cm.Transform @@ -26,22 +30,22 @@ class ZarrConventionAttrs(BaseModel): class Transform(BaseModel): - scale: tuple[float, ...] | MISSING = MISSING # type: ignore[valid-type] - translation: tuple[float, ...] | MISSING = MISSING # type: ignore[valid-type] + scale: tuple[float, ...] | MISSING = MISSING + translation: tuple[float, ...] | MISSING = MISSING class ScaleLevel(BaseModel): asset: str - derived_from: str | MISSING = MISSING # type: ignore[valid-type] - transform: Transform | MISSING = MISSING # type: ignore[valid-type] - resampling_method: str | MISSING = MISSING # type: ignore[valid-type] + derived_from: str | MISSING = MISSING + transform: Transform | MISSING = MISSING + resampling_method: str | MISSING = MISSING model_config = {"extra": "allow"} class Multiscales(BaseModel): layout: tuple[ScaleLevel, ...] - resampling_method: str | MISSING = MISSING # type: ignore[valid-type] + resampling_method: str | MISSING = MISSING model_config = {"extra": "allow"} @@ -59,8 +63,9 @@ def ensure_multiscales_convention( Iterate over the elements of zarr_conventions and check that at least one of them is multiscales """ - expected_uuid = multiscales_cm.CMO["uuid"] - if not any(c["uuid"] == expected_uuid for c in value): + expected_uuid = multiscales_cm.CMO.get("uuid") + assert expected_uuid is not None + if not any(c.get("uuid") == expected_uuid for c in value): raise ValueError( f"Multiscales convention (uuid={expected_uuid}) not found in zarr_conventions" ) diff --git a/src/eopf_geozarr/data_api/geozarr/store.py b/src/eopf_geozarr/data_api/geozarr/store.py index 61a6a443..0835ed25 100644 --- a/src/eopf_geozarr/data_api/geozarr/store.py +++ b/src/eopf_geozarr/data_api/geozarr/store.py @@ -91,13 +91,19 @@ class GeoZarrScaleLevel(ScaleLevel): class GeoZarrMultiscaleMeta(MultiscaleMeta): """Multiscale metadata where every layout entry is a `GeoZarrScaleLevel`.""" - layout: tuple[GeoZarrScaleLevel, ...] + # Intentionally tightens the base ``layout`` field: ``GeoZarrScaleLevel`` is a + # subclass of ``ScaleLevel`` and the optional ``MISSING`` default is dropped to make + # the field mandatory in this store-level profile. pyright flags the narrowed, + # now-required override on a mutable (invariant) field. + layout: tuple[GeoZarrScaleLevel, ...] # pyright: ignore[reportGeneralTypeIssues, reportIncompatibleVariableOverride] class GeoZarrMultiscaleGroupAttrs(MultiscaleGroupAttrs): """Multiscale group attributes with a mandatory `spatial:bbox`.""" - multiscales: GeoZarrMultiscaleMeta + # Intentionally tightens the base ``multiscales`` field to the ``GeoZarrMultiscaleMeta`` + # subclass; pyright flags the narrowed override on a mutable (invariant) field. + multiscales: GeoZarrMultiscaleMeta # pyright: ignore[reportIncompatibleVariableOverride] spatial_bbox: list[float] = Field(alias="spatial:bbox", min_length=4, max_length=4) model_config = ConfigDict( diff --git a/src/eopf_geozarr/data_api/geozarr/v2.py b/src/eopf_geozarr/data_api/geozarr/v2.py index 6e889db7..772f13d0 100644 --- a/src/eopf_geozarr/data_api/geozarr/v2.py +++ b/src/eopf_geozarr/data_api/geozarr/v2.py @@ -2,7 +2,7 @@ from __future__ import annotations -from typing import TYPE_CHECKING, Any, Literal, Self +from typing import TYPE_CHECKING, Any, Literal, Self, cast from pydantic import ConfigDict, Field, model_validator from pydantic_zarr.v2 import ArraySpec, GroupSpec, auto_attributes @@ -10,7 +10,9 @@ from eopf_geozarr.data_api.geozarr.common import ( BaseDataArrayAttrs, DatasetAttrs, + DatasetLike, GridMappingAttrs, + GroupLike, check_grid_mapping, check_valid_coordinates, ) @@ -52,8 +54,11 @@ class DataArray(ArraySpec[DataArrayAttrs]): https://github.com/zarr-developers/geozarr-spec/blob/main/geozarr-spec.md#geozarr-dataarray """ + # The override intentionally widens the accepted argument types (e.g. plain mappings for + # ``attributes``) and adds a ``dimension_names`` parameter, so the signature is not a strict + # subtype of the parent's. This is by design and does not change runtime behavior. @classmethod - def from_array( + def from_array( # type: ignore[override] cls, array: Any, chunks: tuple[int, ...] | Literal["auto"] = "auto", @@ -71,13 +76,15 @@ def from_array( auto_attrs = dict(auto_attributes(array)) if attributes == "auto" else dict(attributes) if dimension_names != "auto": auto_attrs = auto_attrs | {XARRAY_DIMS_KEY: tuple(dimension_names)} - return super().from_array( # type: ignore[no-any-return] + # ``auto_attrs``/``fill_value``/``filters`` are validated/coerced by pydantic at + # construction time; cast to the parent's declared types to satisfy the static checker. + return super().from_array( array=array, chunks=chunks, - attributes=auto_attrs, - fill_value=fill_value, + attributes=cast("Literal['auto'] | DataArrayAttrs", auto_attrs), + fill_value=cast("Literal['auto'] | float | None", fill_value), order=order, - filters=filters, + filters=cast("Literal['auto'] | list[dict[str, Any]] | None", filters), dimension_separator=dimension_separator, compressor=compressor, ) @@ -94,7 +101,7 @@ def check_array_dimensions(self) -> Self: @property def array_dimensions(self) -> tuple[str, ...]: - return self.attributes.array_dimensions # type: ignore[no-any-return] + return self.attributes.array_dimensions class GridMappingVariable(ArraySpec[GridMappingAttrs]): @@ -127,11 +134,17 @@ def check_valid_coordinates(self) -> Self: GroupSpec[Any, Any] The validated GeoZarr DataSet. """ - return check_valid_coordinates(self) + # ``self`` structurally satisfies the ``GroupLike`` protocol, but mypy cannot bind the + # helper's TypeVar to ``Self``; cast through the protocol and back to ``Self`` (the helper + # returns the same object). + check_valid_coordinates(cast("GroupLike", self)) + return self @model_validator(mode="after") def check_grid_mapping(self) -> Self: - return check_grid_mapping(self) + # See note above: ``self`` satisfies ``DatasetLike`` but the TypeVar can't bind to ``Self``. + check_grid_mapping(cast("DatasetLike", self)) + return self class MultiscaleGroup(GroupSpec[MultiscaleGroupAttrs, DataArray | GroupSpec[Any, Any]]): diff --git a/src/eopf_geozarr/data_api/geozarr/v3.py b/src/eopf_geozarr/data_api/geozarr/v3.py index 9359b22d..ee2a487c 100644 --- a/src/eopf_geozarr/data_api/geozarr/v3.py +++ b/src/eopf_geozarr/data_api/geozarr/v3.py @@ -2,7 +2,7 @@ from __future__ import annotations -from typing import Any, Self +from typing import Any, Self, cast from pydantic import model_validator from pydantic_zarr.v3 import ArraySpec, GroupSpec @@ -10,6 +10,8 @@ from eopf_geozarr.data_api.geozarr.common import ( BaseDataArrayAttrs, DatasetAttrs, + DatasetLike, + GroupLike, check_grid_mapping, check_valid_coordinates, ) @@ -29,8 +31,9 @@ class DataArray(ArraySpec[BaseDataArrayAttrs]): https://github.com/zarr-developers/geozarr-spec/blob/main/geozarr-spec.md#geozarr-dataarray """ - # The dimension names must be a tuple of strings - dimension_names: tuple[str, ...] + # GeoZarr requires dimension names, so tighten the parent's optional + # `tuple[str | None, ...] | None` field to a required tuple of strings. + dimension_names: tuple[str, ...] # pyright: ignore[reportGeneralTypeIssues, reportIncompatibleVariableOverride] @property def array_dimensions(self) -> tuple[str, ...]: @@ -55,11 +58,17 @@ def check_valid_coordinates(self) -> Self: GroupSpec[Any, Any] The validated GeoZarr DataSet. """ - return check_valid_coordinates(self) + # ``self`` structurally satisfies the ``GroupLike`` protocol, but mypy cannot bind the + # helper's TypeVar to ``Self``; cast through the protocol and back to ``Self`` (the helper + # returns the same object). + check_valid_coordinates(cast("GroupLike", self)) + return self @model_validator(mode="after") def validate_grid_mapping(self) -> Self: - return check_grid_mapping(self) + # See note above: ``self`` satisfies ``DatasetLike`` but the TypeVar can't bind to ``Self``. + check_grid_mapping(cast("DatasetLike", self)) + return self class MultiscaleGroup(GroupSpec[MultiscaleGroupAttrs, DataArray | GroupSpec[Any, Any]]): diff --git a/src/eopf_geozarr/data_api/s1.py b/src/eopf_geozarr/data_api/s1.py index d8bb91f1..00f0bed5 100644 --- a/src/eopf_geozarr/data_api/s1.py +++ b/src/eopf_geozarr/data_api/s1.py @@ -47,7 +47,7 @@ class Sentinel1DataArray(ArraySpec[Sentinel1DataArrayAttrs]): # Conditions groups -class Sentinel1AntennaPatternMembers(TypedDict, closed=True, total=False): # type: ignore[call-arg] +class Sentinel1AntennaPatternMembers(TypedDict, closed=True, total=False): """Members for antenna_pattern group. All fields are optional to support different product variants. @@ -64,53 +64,75 @@ class Sentinel1AntennaPatternMembers(TypedDict, closed=True, total=False): # ty terrain_height: ArraySpec[Any] -class Sentinel1AntennaPatternGroup( - GroupSpec[DatasetAttrs, Sentinel1AntennaPatternMembers] # type: ignore[type-var] -): +class Sentinel1AntennaPatternGroup(GroupSpec[DatasetAttrs, Sentinel1AntennaPatternMembers]): """Antenna pattern group containing antenna characteristics.""" @property def azimuth_time(self) -> ArraySpec[Any]: """Get azimuth_time array.""" - return self.members["azimuth_time"] + value = self.members.get("azimuth_time") + if value is None: + raise KeyError("azimuth_time") + return value @property def count(self) -> ArraySpec[Any]: """Get count array.""" - return self.members["count"] + value = self.members.get("count") + if value is None: + raise KeyError("count") + return value @property def elevation_angle(self) -> ArraySpec[Any]: """Get elevation_angle array.""" - return self.members["elevation_angle"] + value = self.members.get("elevation_angle") + if value is None: + raise KeyError("elevation_angle") + return value @property def incidence_angle(self) -> ArraySpec[Any]: """Get incidence_angle array.""" - return self.members["incidence_angle"] + value = self.members.get("incidence_angle") + if value is None: + raise KeyError("incidence_angle") + return value @property def roll(self) -> ArraySpec[Any]: """Get roll array.""" - return self.members["roll"] + value = self.members.get("roll") + if value is None: + raise KeyError("roll") + return value @property def slant_range_time_ap(self) -> ArraySpec[Any]: """Get slant_range_time_ap array.""" - return self.members["slant_range_time_ap"] + value = self.members.get("slant_range_time_ap") + if value is None: + raise KeyError("slant_range_time_ap") + return value @property def swath(self) -> ArraySpec[Any]: """Get swath array.""" - return self.members["swath"] + value = self.members.get("swath") + if value is None: + raise KeyError("swath") + return value @property def terrain_height(self) -> ArraySpec[Any]: """Get terrain_height array.""" - return self.members["terrain_height"] + value = self.members.get("terrain_height") + if value is None: + raise KeyError("terrain_height") + return value -class Sentinel1AttitudeMembers(TypedDict, closed=True, total=False): # type: ignore[call-arg] +class Sentinel1AttitudeMembers(TypedDict, closed=True, total=False): """Members for attitude group.""" azimuth_time: ArraySpec[Any] @@ -126,66 +148,99 @@ class Sentinel1AttitudeMembers(TypedDict, closed=True, total=False): # type: ig yaw: ArraySpec[Any] -class Sentinel1AttitudeGroup(GroupSpec[DatasetAttrs, Sentinel1AttitudeMembers]): # type: ignore[type-var] +class Sentinel1AttitudeGroup(GroupSpec[DatasetAttrs, Sentinel1AttitudeMembers]): """Attitude group containing spacecraft attitude data.""" @property def azimuth_time(self) -> ArraySpec[Any]: """Get azimuth_time array.""" - return self.members["azimuth_time"] + value = self.members.get("azimuth_time") + if value is None: + raise KeyError("azimuth_time") + return value @property def pitch(self) -> ArraySpec[Any]: """Get pitch array.""" - return self.members["pitch"] + value = self.members.get("pitch") + if value is None: + raise KeyError("pitch") + return value @property def q0(self) -> ArraySpec[Any]: """Get q0 array.""" - return self.members["q0"] + value = self.members.get("q0") + if value is None: + raise KeyError("q0") + return value @property def q1(self) -> ArraySpec[Any]: """Get q1 array.""" - return self.members["q1"] + value = self.members.get("q1") + if value is None: + raise KeyError("q1") + return value @property def q2(self) -> ArraySpec[Any]: """Get q2 array.""" - return self.members["q2"] + value = self.members.get("q2") + if value is None: + raise KeyError("q2") + return value @property def q3(self) -> ArraySpec[Any]: """Get q3 array.""" - return self.members["q3"] + value = self.members.get("q3") + if value is None: + raise KeyError("q3") + return value @property def roll(self) -> ArraySpec[Any]: """Get roll array.""" - return self.members["roll"] + value = self.members.get("roll") + if value is None: + raise KeyError("roll") + return value @property def wx(self) -> ArraySpec[Any]: """Get wx array.""" - return self.members["wx"] + value = self.members.get("wx") + if value is None: + raise KeyError("wx") + return value @property def wy(self) -> ArraySpec[Any]: """Get wy array.""" - return self.members["wy"] + value = self.members.get("wy") + if value is None: + raise KeyError("wy") + return value @property def wz(self) -> ArraySpec[Any]: """Get wz array.""" - return self.members["wz"] + value = self.members.get("wz") + if value is None: + raise KeyError("wz") + return value @property def yaw(self) -> ArraySpec[Any]: """Get yaw array.""" - return self.members["yaw"] + value = self.members.get("yaw") + if value is None: + raise KeyError("yaw") + return value -class Sentinel1AzimuthFmRateMembers(TypedDict, closed=True, total=False): # type: ignore[call-arg] +class Sentinel1AzimuthFmRateMembers(TypedDict, closed=True, total=False): """Members for azimuth_fm_rate group.""" azimuth_fm_rate_polynomial: ArraySpec[Any] @@ -193,28 +248,35 @@ class Sentinel1AzimuthFmRateMembers(TypedDict, closed=True, total=False): # typ t0: ArraySpec[Any] -class Sentinel1AzimuthFmRateGroup( - GroupSpec[DatasetAttrs, Sentinel1AzimuthFmRateMembers] # type: ignore[type-var] -): +class Sentinel1AzimuthFmRateGroup(GroupSpec[DatasetAttrs, Sentinel1AzimuthFmRateMembers]): """Azimuth FM rate group.""" @property def azimuth_fm_rate_polynomial(self) -> ArraySpec[Any]: """Get azimuth_fm_rate_polynomial array.""" - return self.members["azimuth_fm_rate_polynomial"] + value = self.members.get("azimuth_fm_rate_polynomial") + if value is None: + raise KeyError("azimuth_fm_rate_polynomial") + return value @property def azimuth_time(self) -> ArraySpec[Any]: """Get azimuth_time array.""" - return self.members["azimuth_time"] + value = self.members.get("azimuth_time") + if value is None: + raise KeyError("azimuth_time") + return value @property def t0(self) -> ArraySpec[Any]: """Get t0 array.""" - return self.members["t0"] + value = self.members.get("t0") + if value is None: + raise KeyError("t0") + return value -class Sentinel1CoordinateConversionMembers(TypedDict, closed=True, total=False): # type: ignore[call-arg] +class Sentinel1CoordinateConversionMembers(TypedDict, closed=True, total=False): """Members for coordinate_conversion group.""" azimuth_time: ArraySpec[Any] @@ -226,42 +288,60 @@ class Sentinel1CoordinateConversionMembers(TypedDict, closed=True, total=False): class Sentinel1CoordinateConversionGroup( - GroupSpec[DatasetAttrs, Sentinel1CoordinateConversionMembers] # type: ignore[type-var] + GroupSpec[DatasetAttrs, Sentinel1CoordinateConversionMembers] ): """Coordinate conversion group.""" @property def azimuth_time(self) -> ArraySpec[Any]: """Get azimuth_time array.""" - return self.members["azimuth_time"] + value = self.members.get("azimuth_time") + if value is None: + raise KeyError("azimuth_time") + return value @property def gr0(self) -> ArraySpec[Any]: """Get gr0 array.""" - return self.members["gr0"] + value = self.members.get("gr0") + if value is None: + raise KeyError("gr0") + return value @property def grsr_coefficients(self) -> ArraySpec[Any]: """Get grsr_coefficients array.""" - return self.members["grsr_coefficients"] + value = self.members.get("grsr_coefficients") + if value is None: + raise KeyError("grsr_coefficients") + return value @property def slant_range_time(self) -> ArraySpec[Any]: """Get slant_range_time array.""" - return self.members["slant_range_time"] + value = self.members.get("slant_range_time") + if value is None: + raise KeyError("slant_range_time") + return value @property def sr0(self) -> ArraySpec[Any]: """Get sr0 array.""" - return self.members["sr0"] + value = self.members.get("sr0") + if value is None: + raise KeyError("sr0") + return value @property def srgr_coefficients(self) -> ArraySpec[Any]: """Get srgr_coefficients array.""" - return self.members["srgr_coefficients"] + value = self.members.get("srgr_coefficients") + if value is None: + raise KeyError("srgr_coefficients") + return value -class Sentinel1DopplerCentroidMembers(TypedDict, closed=True, total=False): # type: ignore[call-arg] +class Sentinel1DopplerCentroidMembers(TypedDict, closed=True, total=False): """Members for doppler_centroid group.""" azimuth_time: ArraySpec[Any] @@ -275,58 +355,83 @@ class Sentinel1DopplerCentroidMembers(TypedDict, closed=True, total=False): # t t0: ArraySpec[Any] -class Sentinel1DopplerCentroidGroup( - GroupSpec[DatasetAttrs, Sentinel1DopplerCentroidMembers] # type: ignore[type-var] -): +class Sentinel1DopplerCentroidGroup(GroupSpec[DatasetAttrs, Sentinel1DopplerCentroidMembers]): """Doppler centroid group.""" @property def azimuth_time(self) -> ArraySpec[Any]: """Get azimuth_time array.""" - return self.members["azimuth_time"] + value = self.members.get("azimuth_time") + if value is None: + raise KeyError("azimuth_time") + return value @property def data_dc_polynomial(self) -> ArraySpec[Any]: """Get data_dc_polynomial array.""" - return self.members["data_dc_polynomial"] + value = self.members.get("data_dc_polynomial") + if value is None: + raise KeyError("data_dc_polynomial") + return value @property def data_dc_rms_error(self) -> ArraySpec[Any]: """Get data_dc_rms_error array.""" - return self.members["data_dc_rms_error"] + value = self.members.get("data_dc_rms_error") + if value is None: + raise KeyError("data_dc_rms_error") + return value @property def data_dc_rms_error_above_threshold(self) -> ArraySpec[Any]: """Get data_dc_rms_error_above_threshold array.""" - return self.members["data_dc_rms_error_above_threshold"] + value = self.members.get("data_dc_rms_error_above_threshold") + if value is None: + raise KeyError("data_dc_rms_error_above_threshold") + return value @property def degree(self) -> ArraySpec[Any]: """Get degree array.""" - return self.members["degree"] + value = self.members.get("degree") + if value is None: + raise KeyError("degree") + return value @property def fine_dce_azimuth_start_time(self) -> ArraySpec[Any]: """Get fine_dce_azimuth_start_time array.""" - return self.members["fine_dce_azimuth_start_time"] + value = self.members.get("fine_dce_azimuth_start_time") + if value is None: + raise KeyError("fine_dce_azimuth_start_time") + return value @property def fine_dce_azimuth_stop_time(self) -> ArraySpec[Any]: """Get fine_dce_azimuth_stop_time array.""" - return self.members["fine_dce_azimuth_stop_time"] + value = self.members.get("fine_dce_azimuth_stop_time") + if value is None: + raise KeyError("fine_dce_azimuth_stop_time") + return value @property def geometry_dc_polynomial(self) -> ArraySpec[Any]: """Get geometry_dc_polynomial array.""" - return self.members["geometry_dc_polynomial"] + value = self.members.get("geometry_dc_polynomial") + if value is None: + raise KeyError("geometry_dc_polynomial") + return value @property def t0(self) -> ArraySpec[Any]: """Get t0 array.""" - return self.members["t0"] + value = self.members.get("t0") + if value is None: + raise KeyError("t0") + return value -class Sentinel1GcpMembers(TypedDict, closed=True, total=False): # type: ignore[call-arg] +class Sentinel1GcpMembers(TypedDict, closed=True, total=False): """Members for GCP (Ground Control Points) group. All fields are optional to support different product variants (S1A, S1C). @@ -346,66 +451,99 @@ class Sentinel1GcpMembers(TypedDict, closed=True, total=False): # type: ignore[ slant_range_time_gcp: ArraySpec[Any] -class Sentinel1GcpGroup(GroupSpec[DatasetAttrs, Sentinel1GcpMembers]): # type: ignore[type-var] +class Sentinel1GcpGroup(GroupSpec[DatasetAttrs, Sentinel1GcpMembers]): """Ground Control Points (GCP) group.""" @property def azimuth_time(self) -> ArraySpec[Any]: """Get azimuth_time array.""" - return self.members["azimuth_time"] + value = self.members.get("azimuth_time") + if value is None: + raise KeyError("azimuth_time") + return value @property def azimuth_time_gcp(self) -> ArraySpec[Any]: """Get azimuth_time_gcp array.""" - return self.members["azimuth_time_gcp"] + value = self.members.get("azimuth_time_gcp") + if value is None: + raise KeyError("azimuth_time_gcp") + return value @property def elevation_angle(self) -> ArraySpec[Any]: """Get elevation_angle array.""" - return self.members["elevation_angle"] + value = self.members.get("elevation_angle") + if value is None: + raise KeyError("elevation_angle") + return value @property def ground_range(self) -> ArraySpec[Any]: """Get ground_range array.""" - return self.members["ground_range"] + value = self.members.get("ground_range") + if value is None: + raise KeyError("ground_range") + return value @property def height(self) -> ArraySpec[Any]: """Get height array.""" - return self.members["height"] + value = self.members.get("height") + if value is None: + raise KeyError("height") + return value @property def incidence_angle(self) -> ArraySpec[Any]: """Get incidence_angle array.""" - return self.members["incidence_angle"] + value = self.members.get("incidence_angle") + if value is None: + raise KeyError("incidence_angle") + return value @property def latitude(self) -> ArraySpec[Any]: """Get latitude array.""" - return self.members["latitude"] + value = self.members.get("latitude") + if value is None: + raise KeyError("latitude") + return value @property def line(self) -> ArraySpec[Any]: """Get line array.""" - return self.members["line"] + value = self.members.get("line") + if value is None: + raise KeyError("line") + return value @property def longitude(self) -> ArraySpec[Any]: """Get longitude array.""" - return self.members["longitude"] + value = self.members.get("longitude") + if value is None: + raise KeyError("longitude") + return value @property def pixel(self) -> ArraySpec[Any]: """Get pixel array.""" - return self.members["pixel"] + value = self.members.get("pixel") + if value is None: + raise KeyError("pixel") + return value @property def slant_range_time_gcp(self) -> ArraySpec[Any]: """Get slant_range_time_gcp array.""" - return self.members["slant_range_time_gcp"] + value = self.members.get("slant_range_time_gcp") + if value is None: + raise KeyError("slant_range_time_gcp") + return value -class Sentinel1OrbitMembers(TypedDict, closed=True, total=False): # type: ignore[call-arg] +class Sentinel1OrbitMembers(TypedDict, closed=True, total=False): """Members for orbit group.""" axis: ArraySpec[Any] @@ -414,31 +552,43 @@ class Sentinel1OrbitMembers(TypedDict, closed=True, total=False): # type: ignor velocity: ArraySpec[Any] -class Sentinel1OrbitGroup(GroupSpec[DatasetAttrs, Sentinel1OrbitMembers]): # type: ignore[type-var] +class Sentinel1OrbitGroup(GroupSpec[DatasetAttrs, Sentinel1OrbitMembers]): """Orbit group containing spacecraft position and velocity.""" @property def axis(self) -> ArraySpec[Any]: """Get axis array.""" - return self.members["axis"] + value = self.members.get("axis") + if value is None: + raise KeyError("axis") + return value @property def azimuth_time(self) -> ArraySpec[Any]: """Get azimuth_time array.""" - return self.members["azimuth_time"] + value = self.members.get("azimuth_time") + if value is None: + raise KeyError("azimuth_time") + return value @property def position(self) -> ArraySpec[Any]: """Get position array.""" - return self.members["position"] + value = self.members.get("position") + if value is None: + raise KeyError("position") + return value @property def velocity(self) -> ArraySpec[Any]: """Get velocity array.""" - return self.members["velocity"] + value = self.members.get("velocity") + if value is None: + raise KeyError("velocity") + return value -class Sentinel1ReferenceReplicaMembers(TypedDict, closed=True, total=False): # type: ignore[call-arg] +class Sentinel1ReferenceReplicaMembers(TypedDict, closed=True, total=False): """Members for reference_replica group. Closed TypedDict - only reference replica coefficient array keys are allowed. @@ -450,28 +600,35 @@ class Sentinel1ReferenceReplicaMembers(TypedDict, closed=True, total=False): # reference_replica_phase_coefficients: ArraySpec[Any] -class Sentinel1ReferenceReplicaGroup( - GroupSpec[DatasetAttrs, Sentinel1ReferenceReplicaMembers] # type: ignore[type-var] -): +class Sentinel1ReferenceReplicaGroup(GroupSpec[DatasetAttrs, Sentinel1ReferenceReplicaMembers]): """Reference replica group.""" @property def azimuth_time(self) -> ArraySpec[Any]: """Get azimuth_time array.""" - return self.members["azimuth_time"] + value = self.members.get("azimuth_time") + if value is None: + raise KeyError("azimuth_time") + return value @property def reference_replica_amplitude_coefficients(self) -> ArraySpec[Any]: """Get reference_replica_amplitude_coefficients array.""" - return self.members["reference_replica_amplitude_coefficients"] + value = self.members.get("reference_replica_amplitude_coefficients") + if value is None: + raise KeyError("reference_replica_amplitude_coefficients") + return value @property def reference_replica_phase_coefficients(self) -> ArraySpec[Any]: """Get reference_replica_phase_coefficients array.""" - return self.members["reference_replica_phase_coefficients"] + value = self.members.get("reference_replica_phase_coefficients") + if value is None: + raise KeyError("reference_replica_phase_coefficients") + return value -class Sentinel1ReplicaMembers(TypedDict, closed=True, total=False): # type: ignore[call-arg] +class Sentinel1ReplicaMembers(TypedDict, closed=True, total=False): """Members for replica group. Closed TypedDict - only pulse replica data array keys are allowed. @@ -491,89 +648,126 @@ class Sentinel1ReplicaMembers(TypedDict, closed=True, total=False): # type: ign relative_pg_product_valid_flag: ArraySpec[Any] -class Sentinel1ReplicaGroup(GroupSpec[DatasetAttrs, Sentinel1ReplicaMembers]): # type: ignore[type-var] +class Sentinel1ReplicaGroup(GroupSpec[DatasetAttrs, Sentinel1ReplicaMembers]): """Replica group containing pulse replica data.""" @property def absolute_pg_product_valid_flag(self) -> ArraySpec[Any]: """Get absolute_pg_product_valid_flag array.""" - return self.members["absolute_pg_product_valid_flag"] + value = self.members.get("absolute_pg_product_valid_flag") + if value is None: + raise KeyError("absolute_pg_product_valid_flag") + return value @property def azimuth_time(self) -> ArraySpec[Any]: """Get azimuth_time array.""" - return self.members["azimuth_time"] + value = self.members.get("azimuth_time") + if value is None: + raise KeyError("azimuth_time") + return value @property def cross_correlation_peak_location(self) -> ArraySpec[Any]: """Get cross_correlation_peak_location array.""" - return self.members["cross_correlation_peak_location"] + value = self.members.get("cross_correlation_peak_location") + if value is None: + raise KeyError("cross_correlation_peak_location") + return value @property def cross_correlation_pslr(self) -> ArraySpec[Any]: """Get cross_correlation_pslr array.""" - return self.members["cross_correlation_pslr"] + value = self.members.get("cross_correlation_pslr") + if value is None: + raise KeyError("cross_correlation_pslr") + return value @property def internal_time_delay(self) -> ArraySpec[Any]: """Get internal_time_delay array.""" - return self.members["internal_time_delay"] + value = self.members.get("internal_time_delay") + if value is None: + raise KeyError("internal_time_delay") + return value @property def model_pg_product_amplitude(self) -> ArraySpec[Any]: """Get model_pg_product_amplitude array.""" - return self.members["model_pg_product_amplitude"] + value = self.members.get("model_pg_product_amplitude") + if value is None: + raise KeyError("model_pg_product_amplitude") + return value @property def model_pg_product_phase(self) -> ArraySpec[Any]: """Get model_pg_product_phase array.""" - return self.members["model_pg_product_phase"] + value = self.members.get("model_pg_product_phase") + if value is None: + raise KeyError("model_pg_product_phase") + return value @property def pg_product_amplitude(self) -> ArraySpec[Any]: """Get pg_product_amplitude array.""" - return self.members["pg_product_amplitude"] + value = self.members.get("pg_product_amplitude") + if value is None: + raise KeyError("pg_product_amplitude") + return value @property def pg_product_phase(self) -> ArraySpec[Any]: """Get pg_product_phase array.""" - return self.members["pg_product_phase"] + value = self.members.get("pg_product_phase") + if value is None: + raise KeyError("pg_product_phase") + return value @property def reconstructed_replica_valid_flag(self) -> ArraySpec[Any]: """Get reconstructed_replica_valid_flag array.""" - return self.members["reconstructed_replica_valid_flag"] + value = self.members.get("reconstructed_replica_valid_flag") + if value is None: + raise KeyError("reconstructed_replica_valid_flag") + return value @property def relative_pg_product_valid_flag(self) -> ArraySpec[Any]: """Get relative_pg_product_valid_flag array.""" - return self.members["relative_pg_product_valid_flag"] + value = self.members.get("relative_pg_product_valid_flag") + if value is None: + raise KeyError("relative_pg_product_valid_flag") + return value -class Sentinel1TerrainHeightMembers(TypedDict, closed=True, total=False): # type: ignore[call-arg] +class Sentinel1TerrainHeightMembers(TypedDict, closed=True, total=False): """Members for terrain_height group.""" azimuth_time: ArraySpec[Any] terrain_height: ArraySpec[Any] -class Sentinel1TerrainHeightGroup( - GroupSpec[DatasetAttrs, Sentinel1TerrainHeightMembers] # type: ignore[type-var] -): +class Sentinel1TerrainHeightGroup(GroupSpec[DatasetAttrs, Sentinel1TerrainHeightMembers]): """Terrain height group.""" @property def azimuth_time(self) -> ArraySpec[Any]: """Get azimuth_time array.""" - return self.members["azimuth_time"] + value = self.members.get("azimuth_time") + if value is None: + raise KeyError("azimuth_time") + return value @property def terrain_height(self) -> ArraySpec[Any]: """Get terrain_height array.""" - return self.members["terrain_height"] + value = self.members.get("terrain_height") + if value is None: + raise KeyError("terrain_height") + return value -class Sentinel1ConditionsMembers(TypedDict, closed=True): # type: ignore[call-arg] +class Sentinel1ConditionsMembers(TypedDict, closed=True): """Members for conditions group. Closed TypedDict - only antenna_pattern, attitude, azimuth_fm_rate, etc. keys are allowed. @@ -591,7 +785,7 @@ class Sentinel1ConditionsMembers(TypedDict, closed=True): # type: ignore[call-a terrain_height: Sentinel1TerrainHeightGroup -class Sentinel1ConditionsGroup(GroupSpec[DatasetAttrs, Sentinel1ConditionsMembers]): # type: ignore[type-var] +class Sentinel1ConditionsGroup(GroupSpec[DatasetAttrs, Sentinel1ConditionsMembers]): """Conditions group containing acquisition and processing metadata.""" def get_antenna_pattern(self) -> Sentinel1AntennaPatternGroup | None: @@ -636,7 +830,7 @@ def get_terrain_height(self) -> Sentinel1TerrainHeightGroup | None: # Quality groups -class Sentinel1CalibrationMembers(TypedDict, closed=True, total=False): # type: ignore[call-arg] +class Sentinel1CalibrationMembers(TypedDict, closed=True, total=False): """Members for calibration group.""" azimuth_time: ArraySpec[Any] @@ -649,51 +843,75 @@ class Sentinel1CalibrationMembers(TypedDict, closed=True, total=False): # type: sigma_nought: ArraySpec[Any] -class Sentinel1CalibrationGroup(GroupSpec[DatasetAttrs, Sentinel1CalibrationMembers]): # type: ignore[type-var] +class Sentinel1CalibrationGroup(GroupSpec[DatasetAttrs, Sentinel1CalibrationMembers]): """Calibration group containing radiometric calibration data.""" @property def azimuth_time(self) -> ArraySpec[Any]: """Get azimuth_time array.""" - return self.members["azimuth_time"] + value = self.members.get("azimuth_time") + if value is None: + raise KeyError("azimuth_time") + return value @property def beta_nought(self) -> ArraySpec[Any]: """Get beta_nought array.""" - return self.members["beta_nought"] + value = self.members.get("beta_nought") + if value is None: + raise KeyError("beta_nought") + return value @property def dn(self) -> ArraySpec[Any]: """Get dn array.""" - return self.members["dn"] + value = self.members.get("dn") + if value is None: + raise KeyError("dn") + return value @property def gamma(self) -> ArraySpec[Any]: """Get gamma array.""" - return self.members["gamma"] + value = self.members.get("gamma") + if value is None: + raise KeyError("gamma") + return value @property def ground_range(self) -> ArraySpec[Any]: """Get ground_range array.""" - return self.members["ground_range"] + value = self.members.get("ground_range") + if value is None: + raise KeyError("ground_range") + return value @property def line(self) -> ArraySpec[Any]: """Get line array.""" - return self.members["line"] + value = self.members.get("line") + if value is None: + raise KeyError("line") + return value @property def pixel(self) -> ArraySpec[Any]: """Get pixel array.""" - return self.members["pixel"] + value = self.members.get("pixel") + if value is None: + raise KeyError("pixel") + return value @property def sigma_nought(self) -> ArraySpec[Any]: """Get sigma_nought array.""" - return self.members["sigma_nought"] + value = self.members.get("sigma_nought") + if value is None: + raise KeyError("sigma_nought") + return value -class Sentinel1NoiseMembers(TypedDict, closed=True, total=False): # type: ignore[call-arg] +class Sentinel1NoiseMembers(TypedDict, closed=True, total=False): """Members for noise group.""" azimuth_time: ArraySpec[Any] @@ -701,26 +919,35 @@ class Sentinel1NoiseMembers(TypedDict, closed=True, total=False): # type: ignor number_of_noise_lines: ArraySpec[Any] -class Sentinel1NoiseGroup(GroupSpec[DatasetAttrs, Sentinel1NoiseMembers]): # type: ignore[type-var] +class Sentinel1NoiseGroup(GroupSpec[DatasetAttrs, Sentinel1NoiseMembers]): """Noise group containing noise estimation data.""" @property def azimuth_time(self) -> ArraySpec[Any]: """Get azimuth_time array.""" - return self.members["azimuth_time"] + value = self.members.get("azimuth_time") + if value is None: + raise KeyError("azimuth_time") + return value @property def noise_power_correction_factor(self) -> ArraySpec[Any]: """Get noise_power_correction_factor array.""" - return self.members["noise_power_correction_factor"] + value = self.members.get("noise_power_correction_factor") + if value is None: + raise KeyError("noise_power_correction_factor") + return value @property def number_of_noise_lines(self) -> ArraySpec[Any]: """Get number_of_noise_lines array.""" - return self.members["number_of_noise_lines"] + value = self.members.get("number_of_noise_lines") + if value is None: + raise KeyError("number_of_noise_lines") + return value -class Sentinel1NoiseAzimuthMembers(TypedDict, closed=True, total=False): # type: ignore[call-arg] +class Sentinel1NoiseAzimuthMembers(TypedDict, closed=True, total=False): """Members for noise_azimuth group.""" first_azimuth_time: ArraySpec[Any] @@ -732,46 +959,67 @@ class Sentinel1NoiseAzimuthMembers(TypedDict, closed=True, total=False): # type swath: ArraySpec[Any] -class Sentinel1NoiseAzimuthGroup(GroupSpec[DatasetAttrs, Sentinel1NoiseAzimuthMembers]): # type: ignore[type-var] +class Sentinel1NoiseAzimuthGroup(GroupSpec[DatasetAttrs, Sentinel1NoiseAzimuthMembers]): """Noise azimuth group containing azimuth noise vectors.""" @property def first_azimuth_time(self) -> ArraySpec[Any]: """Get first_azimuth_time array.""" - return self.members["first_azimuth_time"] + value = self.members.get("first_azimuth_time") + if value is None: + raise KeyError("first_azimuth_time") + return value @property def first_range_sample(self) -> ArraySpec[Any]: """Get first_range_sample array.""" - return self.members["first_range_sample"] + value = self.members.get("first_range_sample") + if value is None: + raise KeyError("first_range_sample") + return value @property def last_azimuth_time(self) -> ArraySpec[Any]: """Get last_azimuth_time array.""" - return self.members["last_azimuth_time"] + value = self.members.get("last_azimuth_time") + if value is None: + raise KeyError("last_azimuth_time") + return value @property def last_range_sample(self) -> ArraySpec[Any]: """Get last_range_sample array.""" - return self.members["last_range_sample"] + value = self.members.get("last_range_sample") + if value is None: + raise KeyError("last_range_sample") + return value @property def line(self) -> ArraySpec[Any]: """Get line array.""" - return self.members["line"] + value = self.members.get("line") + if value is None: + raise KeyError("line") + return value @property def noise_azimuth_lut(self) -> ArraySpec[Any]: """Get noise_azimuth_lut array.""" - return self.members["noise_azimuth_lut"] + value = self.members.get("noise_azimuth_lut") + if value is None: + raise KeyError("noise_azimuth_lut") + return value @property def swath(self) -> ArraySpec[Any]: """Get swath array.""" - return self.members["swath"] + value = self.members.get("swath") + if value is None: + raise KeyError("swath") + return value -class Sentinel1NoiseRangeMembers(TypedDict, closed=True, total=False): # type: ignore[call-arg] +class Sentinel1NoiseRangeMembers(TypedDict, closed=True, total=False): """Members for noise_range group.""" azimuth_time: ArraySpec[Any] @@ -781,36 +1029,51 @@ class Sentinel1NoiseRangeMembers(TypedDict, closed=True, total=False): # type: pixel: ArraySpec[Any] -class Sentinel1NoiseRangeGroup(GroupSpec[DatasetAttrs, Sentinel1NoiseRangeMembers]): # type: ignore[type-var] +class Sentinel1NoiseRangeGroup(GroupSpec[DatasetAttrs, Sentinel1NoiseRangeMembers]): """Noise range group containing range noise vectors.""" @property def azimuth_time(self) -> ArraySpec[Any]: """Get azimuth_time array.""" - return self.members["azimuth_time"] + value = self.members.get("azimuth_time") + if value is None: + raise KeyError("azimuth_time") + return value @property def ground_range(self) -> ArraySpec[Any]: """Get ground_range array.""" - return self.members["ground_range"] + value = self.members.get("ground_range") + if value is None: + raise KeyError("ground_range") + return value @property def line(self) -> ArraySpec[Any]: """Get line array.""" - return self.members["line"] + value = self.members.get("line") + if value is None: + raise KeyError("line") + return value @property def noise_range_lut(self) -> ArraySpec[Any]: """Get noise_range_lut array.""" - return self.members["noise_range_lut"] + value = self.members.get("noise_range_lut") + if value is None: + raise KeyError("noise_range_lut") + return value @property def pixel(self) -> ArraySpec[Any]: """Get pixel array.""" - return self.members["pixel"] + value = self.members.get("pixel") + if value is None: + raise KeyError("pixel") + return value -class Sentinel1QualityMembers(TypedDict, closed=True, total=False): # type: ignore[call-arg] +class Sentinel1QualityMembers(TypedDict, closed=True, total=False): """Members for quality group. Closed TypedDict with optional fields to support different product variants: @@ -824,7 +1087,7 @@ class Sentinel1QualityMembers(TypedDict, closed=True, total=False): # type: ign noise_range: Sentinel1NoiseRangeGroup -class Sentinel1QualityGroup(GroupSpec[DatasetAttrs, Sentinel1QualityMembers]): # type: ignore[type-var] +class Sentinel1QualityGroup(GroupSpec[DatasetAttrs, Sentinel1QualityMembers]): """Quality group containing quality assurance and calibration data. Supports both S1A (with noise_azimuth, noise_range) and S1C (without them) products. @@ -848,7 +1111,7 @@ def get_noise_range(self) -> Sentinel1NoiseRangeGroup | None: # Measurements -class Sentinel1MeasurementsMembers(TypedDict, closed=True, total=False): # type: ignore[call-arg] +class Sentinel1MeasurementsMembers(TypedDict, closed=True, total=False): """Members for measurements group.""" azimuth_time: ArraySpec[Any] @@ -858,37 +1121,52 @@ class Sentinel1MeasurementsMembers(TypedDict, closed=True, total=False): # type pixel: ArraySpec[Any] -class Sentinel1MeasurementsGroup(GroupSpec[DatasetAttrs, Sentinel1MeasurementsMembers]): # type: ignore[type-var] +class Sentinel1MeasurementsGroup(GroupSpec[DatasetAttrs, Sentinel1MeasurementsMembers]): """Measurements group containing SAR imagery data.""" @property def azimuth_time(self) -> ArraySpec[Any]: """Get azimuth_time array.""" - return self.members["azimuth_time"] + value = self.members.get("azimuth_time") + if value is None: + raise KeyError("azimuth_time") + return value @property def grd(self) -> ArraySpec[Any]: """Get grd array.""" - return self.members["grd"] + value = self.members.get("grd") + if value is None: + raise KeyError("grd") + return value @property def ground_range(self) -> ArraySpec[Any]: """Get ground_range array.""" - return self.members["ground_range"] + value = self.members.get("ground_range") + if value is None: + raise KeyError("ground_range") + return value @property def line(self) -> ArraySpec[Any]: """Get line array.""" - return self.members["line"] + value = self.members.get("line") + if value is None: + raise KeyError("line") + return value @property def pixel(self) -> ArraySpec[Any]: """Get pixel array.""" - return self.members["pixel"] + value = self.members.get("pixel") + if value is None: + raise KeyError("pixel") + return value # Polarization group -class Sentinel1PolarizationMembers(TypedDict, closed=True): # type: ignore[call-arg] +class Sentinel1PolarizationMembers(TypedDict, closed=True): """Members for polarization group. Closed TypedDict - only conditions, measurements, quality keys are allowed. @@ -899,7 +1177,7 @@ class Sentinel1PolarizationMembers(TypedDict, closed=True): # type: ignore[call quality: Sentinel1QualityGroup -class Sentinel1PolarizationGroup(GroupSpec[DatasetAttrs, Sentinel1PolarizationMembers]): # type: ignore[type-var] +class Sentinel1PolarizationGroup(GroupSpec[DatasetAttrs, Sentinel1PolarizationMembers]): """Polarization-specific group containing all data for one polarization.""" @property diff --git a/src/eopf_geozarr/data_api/s2.py b/src/eopf_geozarr/data_api/s2.py index 3cfdbd02..c86c48a7 100644 --- a/src/eopf_geozarr/data_api/s2.py +++ b/src/eopf_geozarr/data_api/s2.py @@ -222,7 +222,7 @@ class Sentinel2ArrayAttributes(BaseModel): # Resolution-level members for probability data arrays -class ProbabilityArrayMembers(TypedDict, closed=True, total=False): # type: ignore[call-arg] +class ProbabilityArrayMembers(TypedDict, closed=True, total=False): """Members for probability arrays at a specific resolution (r10m, r20m, r60m). Closed TypedDict - contains probability arrays (cld, snw) and per-band/coordinate arrays. @@ -237,20 +237,20 @@ class ProbabilityArrayMembers(TypedDict, closed=True, total=False): # type: ign # Probability resolution groups (r10m, r20m, r60m) -class ProbabilityResolutionMembers(TypedDict, closed=True, total=False): # type: ignore[call-arg] +class ProbabilityResolutionMembers(TypedDict, closed=True, total=False): """Members for probability data containing resolution-level groups (r10m, r20m, r60m). Closed TypedDict - contains resolution groups as subgroups. All fields are optional since not all resolutions are always present. """ - r10m: GroupSpec[Any, ProbabilityArrayMembers] # type: ignore[type-var] - r20m: GroupSpec[Any, ProbabilityArrayMembers] # type: ignore[type-var] - r60m: GroupSpec[Any, ProbabilityArrayMembers] # type: ignore[type-var] + r10m: GroupSpec[Any, ProbabilityArrayMembers] + r20m: GroupSpec[Any, ProbabilityArrayMembers] + r60m: GroupSpec[Any, ProbabilityArrayMembers] # Resolution-level members for quicklook data arrays -class QuicklookArrayMembers(TypedDict, closed=True, total=False): # type: ignore[call-arg] +class QuicklookArrayMembers(TypedDict, closed=True, total=False): """Members for quicklook arrays at a specific resolution. Closed TypedDict - typically contains TCI (True Color Image) and optional band/coordinate arrays. @@ -264,20 +264,20 @@ class QuicklookArrayMembers(TypedDict, closed=True, total=False): # type: ignor # Quicklook resolution groups (r10m, r20m, r60m) -class QuicklookResolutionMembers(TypedDict, closed=True, total=False): # type: ignore[call-arg] +class QuicklookResolutionMembers(TypedDict, closed=True, total=False): """Members for quicklook data containing resolution-level groups (r10m, r20m, r60m). Closed TypedDict - contains resolution groups as subgroups. All fields are optional since not all resolutions are always present. """ - r10m: GroupSpec[Any, QuicklookArrayMembers] # type: ignore[type-var] - r20m: GroupSpec[Any, QuicklookArrayMembers] # type: ignore[type-var] - r60m: GroupSpec[Any, QuicklookArrayMembers] # type: ignore[type-var] + r10m: GroupSpec[Any, QuicklookArrayMembers] + r20m: GroupSpec[Any, QuicklookArrayMembers] + r60m: GroupSpec[Any, QuicklookArrayMembers] # Mask members - contains resolution-level groups or various classification/detector groups -class ConditionsMaskMembers(TypedDict, closed=True, total=False): # type: ignore[call-arg] +class ConditionsMaskMembers(TypedDict, closed=True, total=False): """Members for mask subgroup in conditions. Closed TypedDict - can contain either: @@ -297,7 +297,7 @@ class ConditionsMaskMembers(TypedDict, closed=True, total=False): # type: ignor # Geometry members - contains angle and orientation groups/arrays -class GeometryMembers(TypedDict, closed=True, total=False): # type: ignore[call-arg] +class GeometryMembers(TypedDict, closed=True, total=False): """Members for geometry group containing sun and viewing angles. Closed TypedDict - contains angle and geometry groups/arrays with flexible internal structure. @@ -321,7 +321,7 @@ class GeometryMembers(TypedDict, closed=True, total=False): # type: ignore[call # Meteorology members - contains CAMS and ECMWF atmospheric data -class MeteorologyMembers(TypedDict, closed=True, total=False): # type: ignore[call-arg] +class MeteorologyMembers(TypedDict, closed=True, total=False): """Members for meteorology group containing CAMS and ECMWF atmospheric data. Closed TypedDict - contains subgroups for different meteorological data sources. @@ -458,7 +458,7 @@ class Sentinel2CoordinateArray(ArraySpec[Sentinel2DataArrayAttrs]): # TypedDict definitions for members structure -class Sentinel2ResolutionMembers(TypedDict, closed=True, total=False): # type: ignore[call-arg] +class Sentinel2ResolutionMembers(TypedDict, closed=True, total=False): """Members dict for a resolution dataset (r10m, r20m, r60m). Closed TypedDict - no extra keys are allowed beyond those explicitly defined. @@ -483,11 +483,11 @@ class Sentinel2ResolutionMembers(TypedDict, closed=True, total=False): # type: b12: ArraySpec[Any] -class Sentinel2ResolutionDataset(GroupSpec[DatasetAttrs, Sentinel2ResolutionMembers]): # type: ignore[type-var] +class Sentinel2ResolutionDataset(GroupSpec[DatasetAttrs, Sentinel2ResolutionMembers]): """A single resolution dataset within reflectance (r10m, r20m, r60m).""" -class Sentinel2ReflectanceMembers(TypedDict, closed=True, total=False): # type: ignore[call-arg] +class Sentinel2ReflectanceMembers(TypedDict, closed=True, total=False): """Members for reflectance group. Closed TypedDict - only r10m, r20m, r60m keys are allowed. @@ -498,11 +498,11 @@ class Sentinel2ReflectanceMembers(TypedDict, closed=True, total=False): # type: r60m: Sentinel2ResolutionDataset -class Sentinel2ReflectanceGroup(GroupSpec[DatasetAttrs, Sentinel2ReflectanceMembers]): # type: ignore[type-var] +class Sentinel2ReflectanceGroup(GroupSpec[DatasetAttrs, Sentinel2ReflectanceMembers]): """Reflectance data organized by resolution.""" -class Sentinel2MeasurementsMembers(TypedDict, closed=True): # type: ignore[call-arg] +class Sentinel2MeasurementsMembers(TypedDict, closed=True): """Members for measurements group. Closed TypedDict - only 'reflectance' key is allowed. @@ -511,7 +511,7 @@ class Sentinel2MeasurementsMembers(TypedDict, closed=True): # type: ignore[call reflectance: Sentinel2ReflectanceGroup -class Sentinel2MeasurementsGroup(GroupSpec[DatasetAttrs, Sentinel2MeasurementsMembers]): # type: ignore[type-var] +class Sentinel2MeasurementsGroup(GroupSpec[DatasetAttrs, Sentinel2MeasurementsMembers]): """Measurements group containing reflectance data.""" @property @@ -523,7 +523,7 @@ def reflectance(self) -> Sentinel2ReflectanceGroup: # Quality data groups - need resolution-level typed groups -class Sentinel2AtmosphereResolutionMembers(TypedDict, closed=True, total=False): # type: ignore[call-arg] +class Sentinel2AtmosphereResolutionMembers(TypedDict, closed=True, total=False): """Members for atmosphere data at a specific resolution. Closed TypedDict - may contain aot and/or wvp arrays depending on available data. @@ -537,12 +537,12 @@ class Sentinel2AtmosphereResolutionMembers(TypedDict, closed=True, total=False): class Sentinel2AtmosphereResolutionDataset( - GroupSpec[DatasetAttrs, Sentinel2AtmosphereResolutionMembers] # type: ignore[type-var] + GroupSpec[DatasetAttrs, Sentinel2AtmosphereResolutionMembers] ): """Atmosphere data at a single resolution.""" -class Sentinel2AtmosphereMembers(TypedDict, closed=True, total=False): # type: ignore[call-arg] +class Sentinel2AtmosphereMembers(TypedDict, closed=True, total=False): """Members for atmosphere group containing resolution datasets.""" r10m: Sentinel2AtmosphereResolutionDataset @@ -550,25 +550,23 @@ class Sentinel2AtmosphereMembers(TypedDict, closed=True, total=False): # type: r60m: Sentinel2AtmosphereResolutionDataset -class Sentinel2AtmosphereDataset(GroupSpec[DatasetAttrs, Sentinel2AtmosphereMembers]): # type: ignore[type-var] +class Sentinel2AtmosphereDataset(GroupSpec[DatasetAttrs, Sentinel2AtmosphereMembers]): """Atmosphere quality data (AOT, WVP) at multiple resolutions.""" -class Sentinel2ProbabilityDataset( - GroupSpec[DatasetAttrs, ProbabilityResolutionMembers] # type: ignore[type-var] -): +class Sentinel2ProbabilityDataset(GroupSpec[DatasetAttrs, ProbabilityResolutionMembers]): """Probability data (cloud, snow) at multiple resolutions.""" -class Sentinel2QuicklookDataset(GroupSpec[DatasetAttrs, QuicklookResolutionMembers]): # type: ignore[type-var] +class Sentinel2QuicklookDataset(GroupSpec[DatasetAttrs, QuicklookResolutionMembers]): """True Color Image (TCI) quicklook data at multiple resolutions.""" -class Sentinel2MaskDataset(GroupSpec[DatasetAttrs, ConditionsMaskMembers]): # type: ignore[type-var] +class Sentinel2MaskDataset(GroupSpec[DatasetAttrs, ConditionsMaskMembers]): """Mask data containing classification and detector footprints.""" -class Sentinel2QualityMembers(TypedDict, closed=True, total=False): # type: ignore[call-arg] +class Sentinel2QualityMembers(TypedDict, closed=True, total=False): """Members for quality group. Closed TypedDict with optional fields to accommodate different product levels: @@ -583,7 +581,7 @@ class Sentinel2QualityMembers(TypedDict, closed=True, total=False): # type: ign mask: Sentinel2MaskDataset -class Sentinel2QualityGroup(GroupSpec[DatasetAttrs, Sentinel2QualityMembers]): # type: ignore[type-var] +class Sentinel2QualityGroup(GroupSpec[DatasetAttrs, Sentinel2QualityMembers]): """Quality group containing atmosphere, probability, classification, and quicklook data. Supports both L2A products (Sentinel-2A, 2C) and L1C products (Sentinel-2B). @@ -607,19 +605,19 @@ def mask(self) -> Sentinel2MaskDataset | None: # Conditions groups -class Sentinel2GeometryGroup(GroupSpec[DatasetAttrs, GeometryMembers]): # type: ignore[type-var] +class Sentinel2GeometryGroup(GroupSpec[DatasetAttrs, GeometryMembers]): """Geometry group containing sun and viewing angles.""" -class Sentinel2MeteorologyGroup(GroupSpec[DatasetAttrs, MeteorologyMembers]): # type: ignore[type-var] +class Sentinel2MeteorologyGroup(GroupSpec[DatasetAttrs, MeteorologyMembers]): """Meteorology group containing CAMS and ECMWF atmospheric data.""" -class Sentinel2ConditionsMaskGroup(GroupSpec[DatasetAttrs, ConditionsMaskMembers]): # type: ignore[type-var] +class Sentinel2ConditionsMaskGroup(GroupSpec[DatasetAttrs, ConditionsMaskMembers]): """Mask subgroup in conditions.""" -class Sentinel2ConditionsMembers(TypedDict, closed=True): # type: ignore[call-arg] +class Sentinel2ConditionsMembers(TypedDict, closed=True): """Members for conditions group. Closed TypedDict - only geometry, mask, meteorology keys are allowed. @@ -630,7 +628,7 @@ class Sentinel2ConditionsMembers(TypedDict, closed=True): # type: ignore[call-a meteorology: Sentinel2MeteorologyGroup -class Sentinel2ConditionsGroup(GroupSpec[DatasetAttrs, Sentinel2ConditionsMembers]): # type: ignore[type-var] +class Sentinel2ConditionsGroup(GroupSpec[DatasetAttrs, Sentinel2ConditionsMembers]): """Conditions group containing geometry and meteorology data.""" def geometry(self) -> Sentinel2GeometryGroup | None: @@ -647,7 +645,7 @@ def meteorology(self) -> Sentinel2MeteorologyGroup | None: # Root model -class Sentinel2RootMembers(TypedDict, closed=True): # type: ignore[call-arg] +class Sentinel2RootMembers(TypedDict, closed=True): """Members for Sentinel-2 root group. Closed TypedDict - only measurements, quality, conditions keys are allowed. @@ -658,7 +656,7 @@ class Sentinel2RootMembers(TypedDict, closed=True): # type: ignore[call-arg] conditions: Sentinel2ConditionsGroup -class Sentinel2Root(GroupSpec[Sentinel2RootAttrs, Sentinel2RootMembers]): # type: ignore[type-var] +class Sentinel2Root(GroupSpec[Sentinel2RootAttrs, Sentinel2RootMembers]): """Complete Sentinel-2 EOPF Zarr hierarchy. The hierarchy follows EOPF organization: diff --git a/src/eopf_geozarr/pyz/common.py b/src/eopf_geozarr/pyz/common.py index 3b5bee04..fd21b00f 100644 --- a/src/eopf_geozarr/pyz/common.py +++ b/src/eopf_geozarr/pyz/common.py @@ -103,7 +103,7 @@ def _format_array_html(arr: Any) -> str: if value is None: continue dtype_str = str(value).strip() - value_str = dtype_str if dtype_str else "(not set)" + value_str = dtype_str or "(not set)" # Skip data_type if we already handled it via dtype elif prop_name == "data_type": if getattr(arr, "dtype", None) is not None: @@ -149,13 +149,12 @@ def _format_array_html(arr: Any) -> str: "
" ) - # Get items based on type - if is_dict_attrs: - attrs_dict = attributes - items = list(attrs_dict.items()) - else: # is_model_attrs - attrs_dict = attributes.model_dump() - items = list(attrs_dict.items()) + # Get items based on type. Use direct isinstance checks (not the + # boolean flags) so the type checker narrows `attributes`. + if isinstance(attributes, dict): + items = list(attributes.items()) + else: + items = list(attributes.model_dump().items()) for key, value in items: if isinstance(value, dict): diff --git a/src/eopf_geozarr/pyz/v2.py b/src/eopf_geozarr/pyz/v2.py index 052834fb..52605eb1 100644 --- a/src/eopf_geozarr/pyz/v2.py +++ b/src/eopf_geozarr/pyz/v2.py @@ -40,9 +40,13 @@ class MyGroup(GroupSpec[Any, MyMembers]) TArraySpecType = TypeVar("TArraySpecType") -class GroupSpec(GroupSpecV2[TAttr, TMembers]): +class GroupSpec(GroupSpecV2[TAttr, TMembers]): # type: ignore[type-var] + # TMembers is bound to the full members mapping (e.g. a TypedDict) by design, + # whereas the parent's second type parameter expects a single member item type. attributes: TAttr - members: TMembers + # members holds the full mapping (TMembers) rather than the parent's + # Mapping[str, TItem] | None; this is the intended structure for this subclass. + members: TMembers # type: ignore[assignment] def __repr__(self) -> str: """Return a condensed text representation of the GroupSpec.""" diff --git a/src/eopf_geozarr/pyz/v3.py b/src/eopf_geozarr/pyz/v3.py index fabdf4e6..0613e507 100644 --- a/src/eopf_geozarr/pyz/v3.py +++ b/src/eopf_geozarr/pyz/v3.py @@ -41,8 +41,12 @@ class MyGroup(GroupSpec[Any, MyMembers]) class GroupSpec(GroupSpecV3[TAttr, TMembers]): + # TMembers is bound to the full members mapping (e.g. a TypedDict) by design, + # whereas the parent's second type parameter expects a single member item type. attributes: TAttr - members: TMembers + # members holds the full mapping (TMembers) rather than the parent's + # Mapping[str, TItem] | None; this is the intended structure for this subclass. + members: TMembers # type: ignore[assignment] def __repr__(self) -> str: """Return a condensed text representation of the GroupSpec.""" diff --git a/src/eopf_geozarr/s2_optimization/s2_converter.py b/src/eopf_geozarr/s2_optimization/s2_converter.py index fd303b69..6a868087 100644 --- a/src/eopf_geozarr/s2_optimization/s2_converter.py +++ b/src/eopf_geozarr/s2_optimization/s2_converter.py @@ -5,7 +5,7 @@ from __future__ import annotations import time -from typing import Any, TypedDict +from typing import TYPE_CHECKING, TypedDict import structlog import xarray as xr @@ -20,6 +20,9 @@ from .s2_multiscale import create_multiscale_from_datatree +if TYPE_CHECKING: + from collections.abc import Mapping + log = structlog.get_logger() @@ -66,13 +69,16 @@ def initialize_crs_from_dataset(dt_input: xr.DataTree) -> CRS | None: continue dataset = group_node.ds - # Check if dataset has rio accessor with CRS + # Check if dataset has rio accessor with CRS. rioxarray returns a + # rasterio CRS; convert it to a pyproj CRS (the declared return type), + # which also validates the value at runtime. if hasattr(dataset, "rio"): try: - crs = dataset.rio.crs - if crs is not None: - log.info("Initialized CRS from dataset", crs=str(crs)) - return crs + rio_crs = dataset.rio.crs + if rio_crs is not None: + ds_crs = CRS.from_user_input(rio_crs) + log.info("Initialized CRS from dataset", crs=str(ds_crs)) + return ds_crs except Exception: log.debug("Failed to get CRS from dataset rio accessor") @@ -80,10 +86,11 @@ def initialize_crs_from_dataset(dt_input: xr.DataTree) -> CRS | None: for var in dataset.data_vars.values(): if hasattr(var, "rio"): try: - crs = var.rio.crs - if crs is not None: - log.info("Initialized CRS from variable", crs=str(crs)) - return crs + rio_crs = var.rio.crs + if rio_crs is not None: + var_crs = CRS.from_user_input(rio_crs) + log.info("Initialized CRS from variable", crs=str(var_crs)) + return var_crs except Exception: log.debug("Failed to get CRS from variable rio accessor") @@ -263,7 +270,7 @@ def convert_s2_optimized( return result_dt -def simple_root_consolidation(output_path: str, datasets: dict[str, dict]) -> None: +def simple_root_consolidation(output_path: str, datasets: Mapping[str, object]) -> None: """Simple root-level metadata consolidation with proper zarr group creation.""" # create missing intermediary groups (/conditions, /quality, etc.) # using the keys of the datasets dict @@ -318,6 +325,19 @@ def simple_root_consolidation(output_path: str, datasets: dict[str, dict]) -> No zarr.consolidate_metadata(output_path, zarr_format=3) +def _as_bbox(value: object) -> tuple[float, float, float, float] | None: + """Return *value* as a 4-tuple of floats, or ``None`` if it is not one. + + ``spatial:bbox`` is read from stored metadata, so its type is not known + statically; this verifies the shape at runtime rather than asserting it. + """ + if not isinstance(value, (list, tuple)) or len(value) != 4: + return None + if not all(isinstance(v, (int, float)) for v in value): + return None + return (float(value[0]), float(value[1]), float(value[2]), float(value[3])) + + def write_store_root_bbox(output_path: str) -> None: """Write `spatial:bbox` and `proj:code` at the store root. @@ -336,14 +356,18 @@ def _walk(group: zarr.Group) -> None: attrs = dict(group.attrs) bbox = attrs.get("spatial:bbox") code = attrs.get("proj:code") - if bbox is not None and len(bbox) == 4: + # spatial:bbox comes from stored metadata; verify it is a 4-element + # numeric sequence before use rather than trusting the type. + corners = _as_bbox(bbox) + if corners is not None: + x0, y0, x1, y1 = corners if code and code != "EPSG:4326": transformer = Transformer.from_crs(code, "EPSG:4326", always_xy=True) - xmin, ymin = transformer.transform(bbox[0], bbox[1]) - xmax, ymax = transformer.transform(bbox[2], bbox[3]) + xmin, ymin = transformer.transform(x0, y0) + xmax, ymax = transformer.transform(x1, y1) bboxes_4326.append((xmin, ymin, xmax, ymax)) else: - bboxes_4326.append(tuple(float(v) for v in bbox)) # type: ignore[arg-type] + bboxes_4326.append((x0, y0, x1, y1)) for child in group.groups(): _walk(child[1]) @@ -408,7 +432,7 @@ def create_result_datatree(output_path: str) -> xr.DataTree: def is_sentinel2_dataset(group: zarr.Group) -> bool: from eopf_geozarr.pyz.v2 import GroupSpec - adapter = TypeAdapter(Sentinel1Root | Sentinel2Root) # type: ignore[var-annotated] + adapter = TypeAdapter(Sentinel1Root | Sentinel2Root) try: model = adapter.validate_python(GroupSpec.from_zarr(group).model_dump()) except ValueError as e: @@ -418,7 +442,16 @@ def is_sentinel2_dataset(group: zarr.Group) -> bool: return isinstance(model, Sentinel2Root) -def validate_optimized_dataset(dataset_path: str) -> dict[str, Any]: +class ValidationResult(TypedDict): + """Result of validating an optimized Sentinel-2 dataset.""" + + is_valid: bool + issues: list[str] + warnings: list[str] + summary: dict[str, object] + + +def validate_optimized_dataset(dataset_path: str) -> ValidationResult: """ Validate an optimized Sentinel-2 dataset. diff --git a/src/eopf_geozarr/s2_optimization/s2_data_consolidator.py b/src/eopf_geozarr/s2_optimization/s2_data_consolidator.py index 7ca56db5..67cf071c 100644 --- a/src/eopf_geozarr/s2_optimization/s2_data_consolidator.py +++ b/src/eopf_geozarr/s2_optimization/s2_data_consolidator.py @@ -159,7 +159,7 @@ def _extract_geometry_data(self) -> None: # Consolidate all geometry variables for var_name in ds.data_vars: - self.geometry_data[var_name] = ds[var_name] + self.geometry_data[str(var_name)] = ds[var_name] def _extract_meteorology_data(self) -> None: """Extract meteorological data (CAMS and ECMWF).""" diff --git a/src/eopf_geozarr/s2_optimization/s2_multiscale.py b/src/eopf_geozarr/s2_optimization/s2_multiscale.py index d9743069..35a06520 100644 --- a/src/eopf_geozarr/s2_optimization/s2_multiscale.py +++ b/src/eopf_geozarr/s2_optimization/s2_multiscale.py @@ -6,25 +6,22 @@ from __future__ import annotations from itertools import pairwise -from typing import TYPE_CHECKING, Any, Literal +from typing import TYPE_CHECKING, Any, Literal, cast import numpy as np import structlog import xarray as xr -from dask import delayed +import zarr from dask.array import from_delayed +from dask.delayed import delayed from pydantic.experimental.missing_sentinel import MISSING from pyproj import CRS from zarr.codecs import CastValue -from zarr_cm import geo_proj -from zarr_cm import multiscales as multiscales_cm -from zarr_cm import spatial as spatial_cm from eopf_geozarr.conversion import utils from eopf_geozarr.conversion.fs_utils import sanitize_dataset_attributes from eopf_geozarr.data_api.geozarr.multiscales import zcm from eopf_geozarr.data_api.geozarr.multiscales.geozarr import ( - MultiscaleGroupAttrs, MultiscaleMeta, ) from eopf_geozarr.data_api.geozarr.types import ( @@ -40,7 +37,8 @@ if TYPE_CHECKING: from collections.abc import Hashable, Mapping - import zarr + from zarr_cm import MultiscalesAttrs + from zarr_cm import spatial as spatial_cm from eopf_geozarr.types import OverviewLevelJSON @@ -107,7 +105,9 @@ def _preferred_spatial_transform( rio_value = dataset.rio.transform if callable(rio_value): rio_value = rio_value() - rio_values = tuple(float(value) for value in tuple(rio_value)[:6]) + # rio transform value is dynamically typed; it is iterable at runtime. + rio_iter = cast("tuple[float, ...]", tuple(rio_value)) # pyright: ignore[reportArgumentType] + rio_values = tuple(float(value) for value in rio_iter[:6]) if len(rio_values) == 6: rio_transform = ( rio_values[0], @@ -139,11 +139,13 @@ def _coarsen_variable(var_name: str, var_data: xr.DataArray, factor: int) -> xr. var_type = determine_variable_type(var_name, var_data) coarsened = var_data.coarsen({"x": factor, "y": factor}, boundary="trim") if var_type in ("reflectance", "probability"): - result = coarsened.mean() + # xarray stubs omit reduction methods on DataArrayCoarsen. + result = coarsened.mean() # type: ignore[attr-defined] elif var_type == "classification": result = coarsened.reduce(subsample_2) elif var_type == "quality_mask": - result = coarsened.max() + # xarray stubs omit reduction methods on DataArrayCoarsen. + result = coarsened.max() # type: ignore[attr-defined] else: raise ValueError(f"Unknown variable type {var_type}") @@ -152,9 +154,9 @@ def _coarsen_variable(var_name: str, var_data: xr.DataArray, factor: int) -> xr. # inspects encoding (e.g. to push CF scale-offset into a codec pipeline) # would see an empty encoding on every coarsened level. encoding = var_data.encoding - result = result.astype(var_data.dtype) - result.encoding = encoding - return result + cast_result: xr.DataArray = result.astype(var_data.dtype) + cast_result.encoding = encoding + return cast_result def inject_missing_bands( @@ -255,7 +257,7 @@ def create_multiscale_from_datatree( Returns: Dictionary of processed groups """ - processed_groups = {} + processed_groups: dict[str, Any] = {} # The scale levels in the output data. 10, 20, 60 already exist in the source data. # Step 1: Copy all original groups as-is @@ -409,14 +411,20 @@ def create_multiscale_from_datatree( # Step 3: Add multiscales metadata to parent groups log.info("Adding multiscales metadata to parent groups") - # Get the parent group (it was created when writing the resolution groups) + # Get the parent group (it was created when writing the resolution groups). + # `output_group[base_path]` is typed `Array | Group`; `base_path` always + # addresses a group (the reflectance parent), so verify that at runtime. parent_group = output_group[base_path] + if not isinstance(parent_group, zarr.Group): + raise TypeError( + f"expected a zarr.Group at {base_path!r}, got {type(parent_group).__name__}" + ) - dt_multiscale = add_multiscales_metadata_to_parent( + add_multiscales_metadata_to_parent( parent_group, resolution_groups, ) - processed_groups[base_path] = dt_multiscale + processed_groups[base_path] = None return processed_groups @@ -533,7 +541,7 @@ def create_measurements_encoding( for key in keep_keys: if key in var_data.encoding: - var_encoding[key] = var_data.encoding[key] # type: ignore[literal-required] + var_encoding[key] = var_data.encoding[key] if len(set(var_data.encoding.keys()) - XARRAY_ENCODING_KEYS) > 0: log.warning( @@ -546,13 +554,13 @@ def create_measurements_encoding( # otherwise leak into the output). is_float = np.issubdtype(var_data.dtype, np.floating) var_data.attrs = utils.sanitize_array_attrs(var_data.attrs, is_decoded_float=is_float) - encoding[var_name] = var_encoding + encoding[str(var_name)] = var_encoding # Add coordinate encoding and sanitize coord attrs (e.g. drop # ``_eopf_attrs`` from datetime coords carried in from the source). for coord_name, coord_data in dataset.coords.items(): coord_data.attrs = utils.sanitize_array_attrs(coord_data.attrs) - encoding[coord_name] = {"compressors": []} # type: ignore[typeddict-item] + encoding[str(coord_name)] = {"compressors": []} # type: ignore[typeddict-item] return encoding @@ -613,8 +621,12 @@ def calculate_simple_shard_dimensions( def add_multiscales_metadata_to_parent( group: zarr.Group, res_groups: Mapping[str, xr.Dataset], -) -> xr.DataTree: - """Add GeoZarr-compliant multiscales metadata to parent group.""" +) -> None: + """Add GeoZarr-compliant multiscales metadata to parent group. + + Returns ``None`` in all cases: metadata is written directly to ``group`` + via ``group.attrs.update`` rather than returned as a DataTree. + """ # Sort by resolution (finest to coarsest) res_order = { "r10m": 10, @@ -632,7 +644,7 @@ def add_multiscales_metadata_to_parent( "Skipping {} - only one resolution available", base_path=group.path, ) - return None + return # Get CRS and bounds from first available dataset (load from output path) first_res = all_resolutions[0] @@ -642,14 +654,14 @@ def add_multiscales_metadata_to_parent( native_crs = first_dataset.rio.crs if hasattr(first_dataset, "rio") else None if native_crs is None: log.info("No CRS found, skipping multiscales metadata", base_path=group.path) - return None + return # Calculate bounds directly from coordinates for consistency with the data arrays if "x" not in first_dataset.coords or "y" not in first_dataset.coords: log.error( "Missing x/y coordinates in dataset, cannot determine bounds", base_path=group.path ) - return None + return x_coords = first_dataset.x.values y_coords = first_dataset.y.values @@ -668,6 +680,8 @@ def add_multiscales_metadata_to_parent( dataset = res_groups[res_name] + # Defensive guard retained for runtime safety even though the typed + # contract (Mapping[str, xr.Dataset]) means mypy proves it unreachable. if dataset is None: continue @@ -771,9 +785,9 @@ def add_multiscales_metadata_to_parent( if len(overview_levels) < 2: log.info(" Could not create overview levels for {}", base_path=group.path) - return None + return - layout: list[zcm.ScaleLevel] | MISSING = MISSING # type: ignore[valid-type] + layout: list[zcm.ScaleLevel] | MISSING = MISSING layout = [] @@ -804,6 +818,7 @@ def add_multiscales_metadata_to_parent( scale_level_data["transform"] = multiscale_transform # Add spatial properties + assert "spatial_shape" in overview_level # always populated by the producer above scale_level_data["spatial:shape"] = overview_level["spatial_shape"] if "spatial_transform" in overview_level: spatial_transform = overview_level["spatial_transform"] @@ -813,42 +828,35 @@ def add_multiscales_metadata_to_parent( scale_level = zcm.ScaleLevel(**scale_level_data) layout.append(scale_level) - # Create convention metadata for all three conventions - multiscale_attrs = MultiscaleGroupAttrs( - zarr_conventions=( - multiscales_cm.CMO, - spatial_cm.CMO, - geo_proj.CMO, - ), - multiscales=MultiscaleMeta( - layout=layout, - resampling_method="average", - ), - ) - # Write multiscale attributes directly to the parent group - attrs_to_write = multiscale_attrs.model_dump() + # Validate + serialize the multiscales block via the project model (which + # also covers the ZCM/TMS duality), then hand all three conventions to + # zarr-cm, which validates each and emits the matching CMOs in order + # (multiscales, spatial, proj). + multiscales_data = cast( + "MultiscalesAttrs", + MultiscaleMeta(layout=tuple(layout), resampling_method="average").model_dump(), + ) - # Add spatial and proj attributes at group level following specifications + attrs_to_write: dict[str, Any] = {} if native_crs and native_bounds: - # Add spatial convention attributes - attrs_to_write["spatial:dimensions"] = ["y", "x"] # Required field - attrs_to_write["spatial:bbox"] = list(native_bounds) # [xmin, ymin, xmax, ymax] - attrs_to_write["spatial:registration"] = "pixel" # Default registration type - - # Add proj convention attributes - if hasattr(native_crs, "to_epsg") and native_crs.to_epsg(): - attrs_to_write["proj:code"] = f"EPSG:{native_crs.to_epsg()}" - elif hasattr(native_crs, "to_wkt"): - attrs_to_write["proj:wkt2"] = native_crs.to_wkt() + attrs_to_write.update( + utils.build_convention_attrs( + multiscales=multiscales_data, + spatial={ + "spatial:dimensions": ["y", "x"], + "spatial:bbox": list(native_bounds), # [xmin, ymin, xmax, ymax] + "spatial:registration": "pixel", + }, + crs=native_crs, + ) + ) # Write attributes directly to the zarr group group.attrs.update(attrs_to_write) log.info("Added %s multiscale levels to %s", len(overview_levels), group.path) - return None # No DataTree to return since we wrote directly to the group - def create_original_encoding(dataset: xr.Dataset) -> dict[str, XarrayDataArrayEncoding]: """Write a group preserving its original chunking and encoding.""" @@ -856,7 +864,7 @@ def create_original_encoding(dataset: xr.Dataset) -> dict[str, XarrayDataArrayEn # Simple encoding that preserves original structure compressor = BloscCodec(cname="zstd", clevel=3, shuffle="shuffle", blocksize=0) - encoding = {} + encoding: dict[str, XarrayDataArrayEncoding] = {} for var_name in dataset.data_vars: # start with the original encoding @@ -865,7 +873,7 @@ def create_original_encoding(dataset: xr.Dataset) -> dict[str, XarrayDataArrayEn var_encoding["compressors"] = (compressor,) for key in XARRAY_ENCODING_KEYS - {"compressors", "fill_value"}: if key in var_data.encoding: - var_encoding[key] = var_data.encoding[key] # type: ignore[literal-required] + var_encoding[key] = var_data.encoding[key] # Set the zarr-level `fill_value` explicitly rather than letting xarray # decide — different xarray versions infer different defaults from the # variable's `_FillValue`. See `explicit_fill_value` for the rationale. @@ -881,11 +889,11 @@ def create_original_encoding(dataset: xr.Dataset) -> dict[str, XarrayDataArrayEn # Sanitize source-only attributes (replace dict — ``.update`` cannot # remove keys, so stale ``_eopf_attrs`` would otherwise leak through). var_data.attrs = utils.sanitize_array_attrs(var_data.attrs) - encoding[var_name] = var_encoding + encoding[str(var_name)] = var_encoding for coord_name, coord_data in dataset.coords.items(): coord_data.attrs = utils.sanitize_array_attrs(coord_data.attrs) - encoding[coord_name] = {"compressors": None} + encoding[str(coord_name)] = {"compressors": None} return encoding @@ -912,7 +920,7 @@ def create_downsampled_resolution_group(source_dataset: xr.Dataset, factor: int) for var_name, var_data in source_dataset.data_vars.items(): if var_data.ndim < 2: continue - lazy_vars[var_name] = _coarsen_variable(var_name, var_data, factor) + lazy_vars[var_name] = _coarsen_variable(str(var_name), var_data, factor) if not lazy_vars: return xr.Dataset() @@ -962,7 +970,7 @@ def create_downsampled_coordinates( # Copy any other coordinates that might exist coords.update( { - coord_name: coord_data + str(coord_name): coord_data for coord_name, coord_data in level_2_dataset.coords.items() if coord_name not in ["x", "y"] } @@ -976,9 +984,9 @@ def create_lazy_downsample_operation_from_existing( ) -> xr.DataArray: """Create lazy downsampling operation from existing data.""" - @delayed # type: ignore[misc] + @delayed def downsample_operation() -> Any: - var_type = determine_variable_type(source_data.name, source_data) + var_type = determine_variable_type(str(source_data.name), source_data) return downsample_variable(source_data, target_height, target_width, var_type) # Create delayed operation @@ -1040,8 +1048,14 @@ def stream_write_dataset( "Level path {} already exists. Skipping write.", dataset_path=path, ) + # The zarr backend accepts a zarr `Store` here at runtime, but xarray's + # `open_dataset` stub only types the first arg as path/buffer/datastore. return xr.open_dataset( - group.store, engine="zarr", chunks={}, decode_coords="all", group=path + group.store, # type: ignore[arg-type] + engine="zarr", + chunks={}, + decode_coords="all", + group=path, ) log.info("Streaming computation and write to {}", dataset_path=path) @@ -1079,8 +1093,11 @@ def stream_write_dataset( # Try to get current client for better status monitoring try: client = distributed.Client.current() - # Use client.compute to get a proper Future with status + # client.compute is untyped (returns Any); verify we got a + # Future rather than asserting it with a cast. future = client.compute(write_job) + if not isinstance(future, distributed.Future): + raise TypeError(f"expected a distributed.Future, got {type(future).__name__}") log.info("Using distributed client for write job monitoring") try: @@ -1146,9 +1163,11 @@ def write_geo_metadata( # TODO : Remove once rioxarray supports writing these conventions directly # https://github.com/corteva/rioxarray/pull/883 - # Add spatial convention attributes - dataset.attrs["spatial:dimensions"] = ["y", "x"] # Required field - dataset.attrs["spatial:registration"] = "pixel" # Default registration type + # Assemble spatial convention data + spatial_data: spatial_cm.SpatialAttrs = { + "spatial:dimensions": ["y", "x"], # Required field + "spatial:registration": "pixel", # Default registration type + } # Calculate and add spatial bbox if coordinates are available if "x" in dataset.coords and "y" in dataset.coords: @@ -1156,33 +1175,23 @@ def write_geo_metadata( y_coords = dataset.coords["y"].values x_min, x_max = float(x_coords.min()), float(x_coords.max()) y_min, y_max = float(y_coords.min()), float(y_coords.max()) - dataset.attrs["spatial:bbox"] = [x_min, y_min, x_max, y_max] + spatial_data["spatial:bbox"] = [x_min, y_min, x_max, y_max] spatial_transform = _preferred_spatial_transform(dataset) # Only add spatial:transform if we have valid transform data (not all zeros) if spatial_transform is not None and not all(t == 0 for t in spatial_transform): - dataset.attrs["spatial:transform"] = list(spatial_transform) + spatial_data["spatial:transform"] = list(spatial_transform) # Add spatial shape if data variables exist if dataset.data_vars: first_var = next(iter(dataset.data_vars.values())) if first_var.ndim >= 2: height, width = first_var.shape[-2:] - dataset.attrs["spatial:shape"] = [height, width] - - # Add proj convention attributes - if hasattr(crs, "to_epsg") and crs.to_epsg(): - dataset.attrs["proj:code"] = f"EPSG:{crs.to_epsg()}" - elif hasattr(crs, "to_wkt"): - dataset.attrs["proj:wkt2"] = crs.to_wkt() + spatial_data["spatial:shape"] = [height, width] - # Add zarr convention declarations - conventions = [ - spatial_cm.CMO, - geo_proj.CMO, - ] - dataset.attrs["zarr_conventions"] = conventions + # Build validated spatial + proj convention attrs (data + CMOs) via zarr-cm + dataset.attrs.update(utils.build_convention_attrs(spatial=spatial_data, crs=crs)) def rechunk_dataset_for_encoding( @@ -1194,11 +1203,11 @@ def rechunk_dataset_for_encoding( When using Zarr v3 sharding, Dask chunks must align with shard dimensions to avoid checksum validation errors. """ - rechunked_vars = {} + rechunked_vars: dict[Hashable, xr.DataArray] = {} for var_name, var_data in dataset.data_vars.items(): - if var_name in encoding: - var_encoding = encoding[var_name] + if str(var_name) in encoding: + var_encoding = encoding[str(var_name)] # If sharding is enabled, rechunk based on shard dimensions if "shards" in var_encoding and var_encoding["shards"] is not None: diff --git a/tests/_test_data/geozarr_examples/S2A_MSIL2A_20251008T100041_N0511_R122_T32TQM_20251008T122613.json b/tests/_test_data/geozarr_examples/S2A_MSIL2A_20251008T100041_N0511_R122_T32TQM_20251008T122613.json index 48a69cc8..8bc9e17a 100644 --- a/tests/_test_data/geozarr_examples/S2A_MSIL2A_20251008T100041_N0511_R122_T32TQM_20251008T122613.json +++ b/tests/_test_data/geozarr_examples/S2A_MSIL2A_20251008T100041_N0511_R122_T32TQM_20251008T122613.json @@ -4117,22 +4117,22 @@ "zarr_conventions": [ { "uuid": "d35379db-88df-4056-af3a-620245f8e347", - "schema_url": "https://raw.githubusercontent.com/zarr-conventions/multiscales/refs/tags/v1/schema.json", - "spec_url": "https://github.com/zarr-conventions/multiscales/blob/v1/README.md", + "schema_url": "https://raw.githubusercontent.com/zarr-conventions/multiscales/refs/tags/v0.1/schema.json", + "spec_url": "https://github.com/zarr-conventions/multiscales/blob/v0.1/README.md", "name": "multiscales", "description": "Multiscale layout of zarr datasets" }, { "uuid": "689b58e2-cf7b-45e0-9fff-9cfc0883d6b4", - "schema_url": "https://raw.githubusercontent.com/zarr-conventions/spatial/refs/tags/v1/schema.json", - "spec_url": "https://github.com/zarr-conventions/spatial/blob/v1/README.md", + "schema_url": "https://raw.githubusercontent.com/zarr-conventions/spatial/54d81b7ced0376e63ee10f34db31db7d08dcc28d/schema.json", + "spec_url": "https://github.com/zarr-conventions/spatial/blob/54d81b7ced0376e63ee10f34db31db7d08dcc28d/README.md", "name": "spatial:", "description": "Spatial coordinate information" }, { "uuid": "f17cb550-5864-4468-aeb7-f3180cfb622f", - "schema_url": "https://raw.githubusercontent.com/zarr-experimental/geo-proj/refs/tags/v1/schema.json", - "spec_url": "https://github.com/zarr-experimental/geo-proj/blob/v1/README.md", + "schema_url": "https://raw.githubusercontent.com/zarr-conventions/proj/5ca5b2f92e5c7245f957d9128b289ee535f0720d/schema.json", + "spec_url": "https://github.com/zarr-conventions/proj/blob/5ca5b2f92e5c7245f957d9128b289ee535f0720d/README.md", "name": "proj:", "description": "Coordinate reference system information for geospatial data" } @@ -4277,15 +4277,15 @@ "zarr_conventions": [ { "uuid": "689b58e2-cf7b-45e0-9fff-9cfc0883d6b4", - "schema_url": "https://raw.githubusercontent.com/zarr-conventions/spatial/refs/tags/v1/schema.json", - "spec_url": "https://github.com/zarr-conventions/spatial/blob/v1/README.md", + "schema_url": "https://raw.githubusercontent.com/zarr-conventions/spatial/54d81b7ced0376e63ee10f34db31db7d08dcc28d/schema.json", + "spec_url": "https://github.com/zarr-conventions/spatial/blob/54d81b7ced0376e63ee10f34db31db7d08dcc28d/README.md", "name": "spatial:", "description": "Spatial coordinate information" }, { "uuid": "f17cb550-5864-4468-aeb7-f3180cfb622f", - "schema_url": "https://raw.githubusercontent.com/zarr-experimental/geo-proj/refs/tags/v1/schema.json", - "spec_url": "https://github.com/zarr-experimental/geo-proj/blob/v1/README.md", + "schema_url": "https://raw.githubusercontent.com/zarr-conventions/proj/5ca5b2f92e5c7245f957d9128b289ee535f0720d/schema.json", + "spec_url": "https://github.com/zarr-conventions/proj/blob/5ca5b2f92e5c7245f957d9128b289ee535f0720d/README.md", "name": "proj:", "description": "Coordinate reference system information for geospatial data" } @@ -4752,15 +4752,15 @@ "zarr_conventions": [ { "uuid": "689b58e2-cf7b-45e0-9fff-9cfc0883d6b4", - "schema_url": "https://raw.githubusercontent.com/zarr-conventions/spatial/refs/tags/v1/schema.json", - "spec_url": "https://github.com/zarr-conventions/spatial/blob/v1/README.md", + "schema_url": "https://raw.githubusercontent.com/zarr-conventions/spatial/54d81b7ced0376e63ee10f34db31db7d08dcc28d/schema.json", + "spec_url": "https://github.com/zarr-conventions/spatial/blob/54d81b7ced0376e63ee10f34db31db7d08dcc28d/README.md", "name": "spatial:", "description": "Spatial coordinate information" }, { "uuid": "f17cb550-5864-4468-aeb7-f3180cfb622f", - "schema_url": "https://raw.githubusercontent.com/zarr-experimental/geo-proj/refs/tags/v1/schema.json", - "spec_url": "https://github.com/zarr-experimental/geo-proj/blob/v1/README.md", + "schema_url": "https://raw.githubusercontent.com/zarr-conventions/proj/5ca5b2f92e5c7245f957d9128b289ee535f0720d/schema.json", + "spec_url": "https://github.com/zarr-conventions/proj/blob/5ca5b2f92e5c7245f957d9128b289ee535f0720d/README.md", "name": "proj:", "description": "Coordinate reference system information for geospatial data" } @@ -5842,15 +5842,15 @@ "zarr_conventions": [ { "uuid": "689b58e2-cf7b-45e0-9fff-9cfc0883d6b4", - "schema_url": "https://raw.githubusercontent.com/zarr-conventions/spatial/refs/tags/v1/schema.json", - "spec_url": "https://github.com/zarr-conventions/spatial/blob/v1/README.md", + "schema_url": "https://raw.githubusercontent.com/zarr-conventions/spatial/54d81b7ced0376e63ee10f34db31db7d08dcc28d/schema.json", + "spec_url": "https://github.com/zarr-conventions/spatial/blob/54d81b7ced0376e63ee10f34db31db7d08dcc28d/README.md", "name": "spatial:", "description": "Spatial coordinate information" }, { "uuid": "f17cb550-5864-4468-aeb7-f3180cfb622f", - "schema_url": "https://raw.githubusercontent.com/zarr-experimental/geo-proj/refs/tags/v1/schema.json", - "spec_url": "https://github.com/zarr-experimental/geo-proj/blob/v1/README.md", + "schema_url": "https://raw.githubusercontent.com/zarr-conventions/proj/5ca5b2f92e5c7245f957d9128b289ee535f0720d/schema.json", + "spec_url": "https://github.com/zarr-conventions/proj/blob/5ca5b2f92e5c7245f957d9128b289ee535f0720d/README.md", "name": "proj:", "description": "Coordinate reference system information for geospatial data" } @@ -6856,15 +6856,15 @@ "zarr_conventions": [ { "uuid": "689b58e2-cf7b-45e0-9fff-9cfc0883d6b4", - "schema_url": "https://raw.githubusercontent.com/zarr-conventions/spatial/refs/tags/v1/schema.json", - "spec_url": "https://github.com/zarr-conventions/spatial/blob/v1/README.md", + "schema_url": "https://raw.githubusercontent.com/zarr-conventions/spatial/54d81b7ced0376e63ee10f34db31db7d08dcc28d/schema.json", + "spec_url": "https://github.com/zarr-conventions/spatial/blob/54d81b7ced0376e63ee10f34db31db7d08dcc28d/README.md", "name": "spatial:", "description": "Spatial coordinate information" }, { "uuid": "f17cb550-5864-4468-aeb7-f3180cfb622f", - "schema_url": "https://raw.githubusercontent.com/zarr-experimental/geo-proj/refs/tags/v1/schema.json", - "spec_url": "https://github.com/zarr-experimental/geo-proj/blob/v1/README.md", + "schema_url": "https://raw.githubusercontent.com/zarr-conventions/proj/5ca5b2f92e5c7245f957d9128b289ee535f0720d/schema.json", + "spec_url": "https://github.com/zarr-conventions/proj/blob/5ca5b2f92e5c7245f957d9128b289ee535f0720d/README.md", "name": "proj:", "description": "Coordinate reference system information for geospatial data" } @@ -7946,15 +7946,15 @@ "zarr_conventions": [ { "uuid": "689b58e2-cf7b-45e0-9fff-9cfc0883d6b4", - "schema_url": "https://raw.githubusercontent.com/zarr-conventions/spatial/refs/tags/v1/schema.json", - "spec_url": "https://github.com/zarr-conventions/spatial/blob/v1/README.md", + "schema_url": "https://raw.githubusercontent.com/zarr-conventions/spatial/54d81b7ced0376e63ee10f34db31db7d08dcc28d/schema.json", + "spec_url": "https://github.com/zarr-conventions/spatial/blob/54d81b7ced0376e63ee10f34db31db7d08dcc28d/README.md", "name": "spatial:", "description": "Spatial coordinate information" }, { "uuid": "f17cb550-5864-4468-aeb7-f3180cfb622f", - "schema_url": "https://raw.githubusercontent.com/zarr-experimental/geo-proj/refs/tags/v1/schema.json", - "spec_url": "https://github.com/zarr-experimental/geo-proj/blob/v1/README.md", + "schema_url": "https://raw.githubusercontent.com/zarr-conventions/proj/5ca5b2f92e5c7245f957d9128b289ee535f0720d/schema.json", + "spec_url": "https://github.com/zarr-conventions/proj/blob/5ca5b2f92e5c7245f957d9128b289ee535f0720d/README.md", "name": "proj:", "description": "Coordinate reference system information for geospatial data" } @@ -9037,15 +9037,15 @@ "zarr_conventions": [ { "uuid": "689b58e2-cf7b-45e0-9fff-9cfc0883d6b4", - "schema_url": "https://raw.githubusercontent.com/zarr-conventions/spatial/refs/tags/v1/schema.json", - "spec_url": "https://github.com/zarr-conventions/spatial/blob/v1/README.md", + "schema_url": "https://raw.githubusercontent.com/zarr-conventions/spatial/54d81b7ced0376e63ee10f34db31db7d08dcc28d/schema.json", + "spec_url": "https://github.com/zarr-conventions/spatial/blob/54d81b7ced0376e63ee10f34db31db7d08dcc28d/README.md", "name": "spatial:", "description": "Spatial coordinate information" }, { "uuid": "f17cb550-5864-4468-aeb7-f3180cfb622f", - "schema_url": "https://raw.githubusercontent.com/zarr-experimental/geo-proj/refs/tags/v1/schema.json", - "spec_url": "https://github.com/zarr-experimental/geo-proj/blob/v1/README.md", + "schema_url": "https://raw.githubusercontent.com/zarr-conventions/proj/5ca5b2f92e5c7245f957d9128b289ee535f0720d/schema.json", + "spec_url": "https://github.com/zarr-conventions/proj/blob/5ca5b2f92e5c7245f957d9128b289ee535f0720d/README.md", "name": "proj:", "description": "Coordinate reference system information for geospatial data" } @@ -10141,15 +10141,15 @@ "zarr_conventions": [ { "uuid": "689b58e2-cf7b-45e0-9fff-9cfc0883d6b4", - "schema_url": "https://raw.githubusercontent.com/zarr-conventions/spatial/refs/tags/v1/schema.json", - "spec_url": "https://github.com/zarr-conventions/spatial/blob/v1/README.md", + "schema_url": "https://raw.githubusercontent.com/zarr-conventions/spatial/54d81b7ced0376e63ee10f34db31db7d08dcc28d/schema.json", + "spec_url": "https://github.com/zarr-conventions/spatial/blob/54d81b7ced0376e63ee10f34db31db7d08dcc28d/README.md", "name": "spatial:", "description": "Spatial coordinate information" }, { "uuid": "f17cb550-5864-4468-aeb7-f3180cfb622f", - "schema_url": "https://raw.githubusercontent.com/zarr-experimental/geo-proj/refs/tags/v1/schema.json", - "spec_url": "https://github.com/zarr-experimental/geo-proj/blob/v1/README.md", + "schema_url": "https://raw.githubusercontent.com/zarr-conventions/proj/5ca5b2f92e5c7245f957d9128b289ee535f0720d/schema.json", + "spec_url": "https://github.com/zarr-conventions/proj/blob/5ca5b2f92e5c7245f957d9128b289ee535f0720d/README.md", "name": "proj:", "description": "Coordinate reference system information for geospatial data" } @@ -10457,15 +10457,15 @@ 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}, { "uuid": "f17cb550-5864-4468-aeb7-f3180cfb622f", - "schema_url": "https://raw.githubusercontent.com/zarr-experimental/geo-proj/refs/tags/v1/schema.json", - "spec_url": "https://github.com/zarr-experimental/geo-proj/blob/v1/README.md", + "schema_url": "https://raw.githubusercontent.com/zarr-conventions/proj/5ca5b2f92e5c7245f957d9128b289ee535f0720d/schema.json", + "spec_url": "https://github.com/zarr-conventions/proj/blob/5ca5b2f92e5c7245f957d9128b289ee535f0720d/README.md", "name": "proj:", "description": "Coordinate reference system information for geospatial data" } @@ -11636,15 +11636,15 @@ "zarr_conventions": [ { "uuid": "689b58e2-cf7b-45e0-9fff-9cfc0883d6b4", - "schema_url": "https://raw.githubusercontent.com/zarr-conventions/spatial/refs/tags/v1/schema.json", - "spec_url": "https://github.com/zarr-conventions/spatial/blob/v1/README.md", + "schema_url": "https://raw.githubusercontent.com/zarr-conventions/spatial/54d81b7ced0376e63ee10f34db31db7d08dcc28d/schema.json", + 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"https://github.com/zarr-conventions/spatial/blob/v1/README.md", + "schema_url": "https://raw.githubusercontent.com/zarr-conventions/spatial/54d81b7ced0376e63ee10f34db31db7d08dcc28d/schema.json", + "spec_url": "https://github.com/zarr-conventions/spatial/blob/54d81b7ced0376e63ee10f34db31db7d08dcc28d/README.md", "name": "spatial:", "description": "Spatial coordinate information" }, { "uuid": "f17cb550-5864-4468-aeb7-f3180cfb622f", - "schema_url": "https://raw.githubusercontent.com/zarr-experimental/geo-proj/refs/tags/v1/schema.json", - "spec_url": "https://github.com/zarr-experimental/geo-proj/blob/v1/README.md", + "schema_url": "https://raw.githubusercontent.com/zarr-conventions/proj/5ca5b2f92e5c7245f957d9128b289ee535f0720d/schema.json", + "spec_url": "https://github.com/zarr-conventions/proj/blob/5ca5b2f92e5c7245f957d9128b289ee535f0720d/README.md", "name": "proj:", "description": "Coordinate reference system information for geospatial data" } @@ -12816,15 +12816,15 @@ "zarr_conventions": [ { "uuid": "689b58e2-cf7b-45e0-9fff-9cfc0883d6b4", - "schema_url": "https://raw.githubusercontent.com/zarr-conventions/spatial/refs/tags/v1/schema.json", - "spec_url": "https://github.com/zarr-conventions/spatial/blob/v1/README.md", + "schema_url": "https://raw.githubusercontent.com/zarr-conventions/spatial/54d81b7ced0376e63ee10f34db31db7d08dcc28d/schema.json", + "spec_url": "https://github.com/zarr-conventions/spatial/blob/54d81b7ced0376e63ee10f34db31db7d08dcc28d/README.md", "name": "spatial:", "description": "Spatial coordinate information" }, { "uuid": "f17cb550-5864-4468-aeb7-f3180cfb622f", - "schema_url": "https://raw.githubusercontent.com/zarr-experimental/geo-proj/refs/tags/v1/schema.json", - "spec_url": "https://github.com/zarr-experimental/geo-proj/blob/v1/README.md", + "schema_url": "https://raw.githubusercontent.com/zarr-conventions/proj/5ca5b2f92e5c7245f957d9128b289ee535f0720d/schema.json", + "spec_url": 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"https://raw.githubusercontent.com/zarr-conventions/multiscales/refs/tags/v0.1/schema.json", + "spec_url": "https://github.com/zarr-conventions/multiscales/blob/v0.1/README.md", "name": "multiscales", "description": "Multiscale layout of zarr datasets" }, { "uuid": "689b58e2-cf7b-45e0-9fff-9cfc0883d6b4", - "schema_url": "https://raw.githubusercontent.com/zarr-conventions/spatial/refs/tags/v1/schema.json", - "spec_url": "https://github.com/zarr-conventions/spatial/blob/v1/README.md", + "schema_url": "https://raw.githubusercontent.com/zarr-conventions/spatial/54d81b7ced0376e63ee10f34db31db7d08dcc28d/schema.json", + "spec_url": "https://github.com/zarr-conventions/spatial/blob/54d81b7ced0376e63ee10f34db31db7d08dcc28d/README.md", "name": "spatial:", "description": "Spatial coordinate information" }, { "uuid": "f17cb550-5864-4468-aeb7-f3180cfb622f", - "schema_url": "https://raw.githubusercontent.com/zarr-experimental/geo-proj/refs/tags/v1/schema.json", - "spec_url": 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"https://raw.githubusercontent.com/zarr-conventions/multiscales/refs/tags/v0.1/schema.json", + "spec_url": "https://github.com/zarr-conventions/multiscales/blob/v0.1/README.md", "name": "multiscales", "description": "Multiscale layout of zarr datasets" }, { "uuid": "689b58e2-cf7b-45e0-9fff-9cfc0883d6b4", - "schema_url": "https://raw.githubusercontent.com/zarr-conventions/spatial/refs/tags/v1/schema.json", - "spec_url": "https://github.com/zarr-conventions/spatial/blob/v1/README.md", + "schema_url": "https://raw.githubusercontent.com/zarr-conventions/spatial/54d81b7ced0376e63ee10f34db31db7d08dcc28d/schema.json", + "spec_url": "https://github.com/zarr-conventions/spatial/blob/54d81b7ced0376e63ee10f34db31db7d08dcc28d/README.md", "name": "spatial:", "description": "Spatial coordinate information" }, { "uuid": "f17cb550-5864-4468-aeb7-f3180cfb622f", - "schema_url": "https://raw.githubusercontent.com/zarr-experimental/geo-proj/refs/tags/v1/schema.json", - "spec_url": 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"spec_url": "https://github.com/zarr-conventions/spatial/blob/54d81b7ced0376e63ee10f34db31db7d08dcc28d/README.md", "name": "spatial:", "description": "Spatial coordinate information" }, { "uuid": "f17cb550-5864-4468-aeb7-f3180cfb622f", - "schema_url": "https://raw.githubusercontent.com/zarr-experimental/geo-proj/refs/tags/v1/schema.json", - "spec_url": "https://github.com/zarr-experimental/geo-proj/blob/v1/README.md", + "schema_url": "https://raw.githubusercontent.com/zarr-conventions/proj/5ca5b2f92e5c7245f957d9128b289ee535f0720d/schema.json", + "spec_url": "https://github.com/zarr-conventions/proj/blob/5ca5b2f92e5c7245f957d9128b289ee535f0720d/README.md", "name": "proj:", "description": "Coordinate reference system information for geospatial data" } @@ -12816,15 +12816,15 @@ "zarr_conventions": [ { "uuid": "689b58e2-cf7b-45e0-9fff-9cfc0883d6b4", - "schema_url": "https://raw.githubusercontent.com/zarr-conventions/spatial/refs/tags/v1/schema.json", - "spec_url": 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a/tests/_test_data/optimized_geozarr_examples/S2A_MSIL2A_20251008T100041_N0511_R122_T32TQM_20251008T122613.json b/tests/_test_data/optimized_geozarr_examples/S2A_MSIL2A_20251008T100041_N0511_R122_T32TQM_20251008T122613.json index fa20e80d..5b335149 100644 --- a/tests/_test_data/optimized_geozarr_examples/S2A_MSIL2A_20251008T100041_N0511_R122_T32TQM_20251008T122613.json +++ b/tests/_test_data/optimized_geozarr_examples/S2A_MSIL2A_20251008T100041_N0511_R122_T32TQM_20251008T122613.json @@ -4218,22 +4218,22 @@ { "description": "Multiscale layout of zarr datasets", "name": "multiscales", - "schema_url": "https://raw.githubusercontent.com/zarr-conventions/multiscales/refs/tags/v1/schema.json", - "spec_url": "https://github.com/zarr-conventions/multiscales/blob/v1/README.md", + "schema_url": "https://raw.githubusercontent.com/zarr-conventions/multiscales/refs/tags/v0.1/schema.json", + "spec_url": "https://github.com/zarr-conventions/multiscales/blob/v0.1/README.md", "uuid": 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b/tests/_test_data/optimized_geozarr_examples/S2C_MSIL2A_20250811T112131_N0511_R037_T29TPF_20250811T152216.json index 9ed8a49e..7eb259c3 100644 --- a/tests/_test_data/optimized_geozarr_examples/S2C_MSIL2A_20250811T112131_N0511_R037_T29TPF_20250811T152216.json +++ b/tests/_test_data/optimized_geozarr_examples/S2C_MSIL2A_20250811T112131_N0511_R037_T29TPF_20250811T152216.json @@ -4218,22 +4218,22 @@ { "description": "Multiscale layout of zarr datasets", "name": "multiscales", - "schema_url": "https://raw.githubusercontent.com/zarr-conventions/multiscales/refs/tags/v1/schema.json", - "spec_url": "https://github.com/zarr-conventions/multiscales/blob/v1/README.md", + "schema_url": "https://raw.githubusercontent.com/zarr-conventions/multiscales/refs/tags/v0.1/schema.json", + "spec_url": "https://github.com/zarr-conventions/multiscales/blob/v0.1/README.md", "uuid": "d35379db-88df-4056-af3a-620245f8e347" }, { "description": "Spatial coordinate information", "name": "spatial:", - "schema_url": 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"https://raw.githubusercontent.com/zarr-experimental/geo-proj/refs/tags/v1/schema.json", - "spec_url": "https://github.com/zarr-experimental/geo-proj/blob/v1/README.md", + "schema_url": "https://raw.githubusercontent.com/zarr-conventions/proj/5ca5b2f92e5c7245f957d9128b289ee535f0720d/schema.json", + "spec_url": "https://github.com/zarr-conventions/proj/blob/5ca5b2f92e5c7245f957d9128b289ee535f0720d/README.md", "uuid": "f17cb550-5864-4468-aeb7-f3180cfb622f" } ] @@ -14250,15 +14250,15 @@ { "description": "Spatial coordinate information", "name": "spatial:", - "schema_url": "https://raw.githubusercontent.com/zarr-conventions/spatial/refs/tags/v1/schema.json", - "spec_url": "https://github.com/zarr-conventions/spatial/blob/v1/README.md", + "schema_url": "https://raw.githubusercontent.com/zarr-conventions/spatial/54d81b7ced0376e63ee10f34db31db7d08dcc28d/schema.json", + "spec_url": "https://github.com/zarr-conventions/spatial/blob/54d81b7ced0376e63ee10f34db31db7d08dcc28d/README.md", "uuid": "689b58e2-cf7b-45e0-9fff-9cfc0883d6b4" }, { "description": "Coordinate reference system information for geospatial data", "name": "proj:", - "schema_url": "https://raw.githubusercontent.com/zarr-experimental/geo-proj/refs/tags/v1/schema.json", - "spec_url": "https://github.com/zarr-experimental/geo-proj/blob/v1/README.md", + "schema_url": "https://raw.githubusercontent.com/zarr-conventions/proj/5ca5b2f92e5c7245f957d9128b289ee535f0720d/schema.json", + "spec_url": "https://github.com/zarr-conventions/proj/blob/5ca5b2f92e5c7245f957d9128b289ee535f0720d/README.md", "uuid": "f17cb550-5864-4468-aeb7-f3180cfb622f" } ] diff --git a/tests/conftest.py b/tests/conftest.py index c08bade3..59746f8f 100644 --- a/tests/conftest.py +++ b/tests/conftest.py @@ -28,7 +28,9 @@ def read_json(path: pathlib.Path) -> dict[str, object]: """ Read the contents of path as JSON """ - return json.loads(path.read_text()) + obj = json.loads(path.read_text()) + assert isinstance(obj, dict) + return obj def get_stem(p: pathlib.Path) -> str: @@ -40,8 +42,9 @@ def create_group_from_json(source_path: pathlib.Path, out_path: pathlib.Path) -> Create a Zarr V2 group from a JSON model """ out_dir = out_path / (source_path.stem + ".zarr") - g = GroupSpecV2(**read_json(source_path)) - g.to_zarr(out_dir, path="") + g: GroupSpecV2 = GroupSpecV2.model_validate(read_json(source_path)) + # to_zarr is annotated to take a Store but accepts a path-like at runtime. + g.to_zarr(out_dir, path="") # type: ignore[arg-type] return out_dir @@ -87,8 +90,9 @@ def s2_geozarr_group_example(request: pytest.FixtureRequest) -> zarr.Group: Return a memory-backed Zarr V3 Group based on a sentinel 2 product converted to geozarr """ source_path: pathlib.Path = request.param - store = {} - return GroupSpecV3(**read_json(source_path)).to_zarr(store, path="") + store: dict[str, bytes] = {} + # to_zarr is annotated to take a Store but accepts a dict-backed store at runtime. + return GroupSpecV3.model_validate(read_json(source_path)).to_zarr(store, path="") # type: ignore[arg-type] @pytest.fixture(params=optimized_geozarr_example_paths, ids=get_stem) @@ -97,8 +101,9 @@ def s2_optimized_geozarr_group_example(request: pytest.FixtureRequest) -> zarr.G Return a memory-backed Zarr V3 Group based on a sentinel 2 product converted to geozarr """ source_path: pathlib.Path = request.param - store = {} - return GroupSpecV3(**read_json(source_path)).to_zarr(store, path="") + store: dict[str, bytes] = {} + # to_zarr is annotated to take a Store but accepts a dict-backed store at runtime. + return GroupSpecV3.model_validate(read_json(source_path)).to_zarr(store, path="") # type: ignore[arg-type] @pytest.fixture(params=zcm_multiscales_example_paths, ids=get_stem) @@ -207,7 +212,7 @@ def _verify_geozarr_spec_compliance(output_path: pathlib.Path, group: str) -> No # Check coordinates for coord_name in ds.coords: - if coord_name not in ["spatial_ref"]: # Skip CRS coordinate + if coord_name != "spatial_ref": # Skip CRS coordinate assert "_ARRAY_DIMENSIONS" in ds[coord_name].attrs, ( f"Missing _ARRAY_DIMENSIONS for coordinate {coord_name} in {group}" ) diff --git a/tests/test_array_attrs.py b/tests/test_array_attrs.py index 53ef3e0a..a4234a11 100644 --- a/tests/test_array_attrs.py +++ b/tests/test_array_attrs.py @@ -46,7 +46,8 @@ def _is_float_array(node: dict) -> bool: @pytest.fixture(params=_SNAPSHOTS, ids=lambda p: p.stem) def snapshot(request: pytest.FixtureRequest) -> dict: - return json.loads(request.param.read_text()) + loaded: dict = json.loads(request.param.read_text()) + return loaded def test_no_eopf_attrs(snapshot: dict) -> None: @@ -163,7 +164,9 @@ def test_fill_value_masking_roundtrip(tmp_path: pathlib.Path) -> None: "NaN cells in converter output should be masked when opened with " "use_zarr_fill_value_as_mask=True" ) - assert masked.mask[0, 0], "nodata corner cell must be masked" - assert not masked.mask[-1, -1], "valid cell must not be masked" + mask = masked.mask + assert isinstance(mask, np.ndarray), "mask must be an array, not a scalar" + assert mask[0, 0], "nodata corner cell must be masked" + assert not mask[-1, -1], "valid cell must not be masked" finally: reopened.close() diff --git a/tests/test_cli_e2e.py b/tests/test_cli_e2e.py index 6b11b120..b91ce2b9 100644 --- a/tests/test_cli_e2e.py +++ b/tests/test_cli_e2e.py @@ -140,7 +140,7 @@ def test_cli_convert_real_sentinel2_data(s2_group_example: Path, tmp_path: Path) GroupSpec.from_zarr(zarr.open_group(output_path)).model_dump() ) assert expected_structure_json == observed_structure_json, view_json_diff( - expected_structure_json, observed_structure_json + dict(expected_structure_json), dict(observed_structure_json) ) @@ -206,7 +206,7 @@ def test_cli_crs_groups_option() -> None: assert "Groups that need CRS information added" in result.stdout, "Help text should be present" -def test_cli_convert_with_crs_groups(s2_group_example, tmp_path: Path) -> None: +def test_cli_convert_with_crs_groups(s2_group_example: Path, tmp_path: Path) -> None: """ Test CLI conversion with --crs-groups option using real Sentinel-2 data. diff --git a/tests/test_convention_attrs.py b/tests/test_convention_attrs.py new file mode 100644 index 00000000..f3ddf576 --- /dev/null +++ b/tests/test_convention_attrs.py @@ -0,0 +1,142 @@ +"""Tests for the zarr-cm convention-attribute helpers in conversion.utils.""" + +from __future__ import annotations + +from typing import cast + +import pytest +from pyproj import CRS +from zarr_cm import geo_proj +from zarr_cm import multiscales as multiscales_cm +from zarr_cm import spatial as spatial_cm + +from eopf_geozarr.conversion.utils import ( + build_convention_attrs, + proj_attrs_for_crs, +) + + +def test_proj_attrs_for_crs_epsg() -> None: + """A CRS with an EPSG code yields proj:code.""" + crs = CRS.from_epsg(32632) + assert proj_attrs_for_crs(crs) == {"proj:code": "EPSG:32632"} + + +def test_proj_attrs_for_crs_wkt_fallback() -> None: + """A CRS without an EPSG code falls back to proj:wkt2.""" + # A bare WKT-defined CRS with no authority code. + crs = CRS.from_wkt(CRS.from_epsg(4326).to_wkt()) + out = proj_attrs_for_crs(crs) + # from_wkt of an EPSG CRS still resolves an epsg in most pyproj versions, so + # accept either, but the key must be one of the two proj CRS keys. + assert set(out) <= {"proj:code", "proj:wkt2"} + assert len(out) == 1 + + +def test_proj_attrs_for_crs_none() -> None: + """No CRS yields an empty dict (no proj keys).""" + assert proj_attrs_for_crs(None) == {} + + +def test_build_convention_attrs_data_and_cmos() -> None: + """The helper emits spatial+proj data keys plus their CMOs, in order.""" + bbox = [300000.0, 4990200.0, 409800.0, 5100000.0] + out = build_convention_attrs( + spatial={ + "spatial:dimensions": ["y", "x"], + "spatial:bbox": bbox, + "spatial:registration": "pixel", + }, + crs=CRS.from_epsg(32632), + ) + data: dict[str, object] = dict(out) + assert data["spatial:dimensions"] == ["y", "x"] + assert data["spatial:bbox"] == bbox + assert data["spatial:registration"] == "pixel" + assert data["proj:code"] == "EPSG:32632" + conventions = out.get("zarr_conventions") + assert conventions is not None + names = [c.get("name") for c in conventions] + assert names == [spatial_cm.CMO.get("name"), geo_proj.CMO.get("name")] + + +def test_build_convention_attrs_matches_handwritten() -> None: + """Output is byte-equivalent to the previous hand-assembled dict.""" + bbox = [300000.0, 4990200.0, 409800.0, 5100000.0] + hand: dict[str, object] = { + "spatial:dimensions": ["y", "x"], + "spatial:bbox": bbox, + "spatial:registration": "pixel", + "proj:code": "EPSG:32632", + } + out = build_convention_attrs( + spatial={ + "spatial:dimensions": ["y", "x"], + "spatial:bbox": bbox, + "spatial:registration": "pixel", + }, + crs=CRS.from_epsg(32632), + ) + data = {k: v for k, v in out.items() if k != "zarr_conventions"} + assert data == hand + + +def test_build_convention_attrs_validates() -> None: + """Invalid spatial data is rejected by zarr-cm validation.""" + with pytest.raises(ValueError, match="spatial:dimensions"): + build_convention_attrs( + # missing required dimensions — exercises runtime validation + spatial=cast("spatial_cm.SpatialAttrs", {"spatial:registration": "pixel"}), + crs=CRS.from_epsg(32632), + ) + + +def test_build_convention_attrs_with_multiscales() -> None: + """With multiscales, CMOs are ordered [multiscales, spatial, proj].""" + out = build_convention_attrs( + multiscales=cast( + "multiscales_cm.MultiscalesAttrs", + { + "layout": [ + {"asset": "r10m", "spatial:shape": [10980, 10980]}, + { + "asset": "r20m", + "derived_from": "r10m", + "transform": {"scale": [2.0, 2.0], "translation": [0.0, 0.0]}, + "spatial:shape": [5490, 5490], + }, + ], + "resampling_method": "average", + }, + ), + spatial={"spatial:dimensions": ["y", "x"]}, + crs=CRS.from_epsg(32632), + ) + conventions = out.get("zarr_conventions") + assert conventions is not None + names = [c.get("name") for c in conventions] + assert names == [ + multiscales_cm.CMO.get("name"), + spatial_cm.CMO.get("name"), + geo_proj.CMO.get("name"), + ] + # extra layout keys (spatial:shape) survive the round-trip + multiscales = out.get("multiscales") + assert multiscales is not None + layout = multiscales["layout"] + assert isinstance(layout, list) + first_layout: dict[str, object] = dict(layout[0]) + assert first_layout["spatial:shape"] == [10980, 10980] + + +def test_build_convention_attrs_multiscales_validation() -> None: + """zarr-cm rejects a layout entry with derived_from but no transform.""" + with pytest.raises(ValueError, match="transform"): + build_convention_attrs( + multiscales={ + "layout": [{"asset": "r20m", "derived_from": "r10m"}], # no transform + "resampling_method": "average", + }, + spatial={"spatial:dimensions": ["y", "x"]}, + crs=CRS.from_epsg(32632), + ) diff --git a/tests/test_data_api/conftest.py b/tests/test_data_api/conftest.py index be567726..03537803 100644 --- a/tests/test_data_api/conftest.py +++ b/tests/test_data_api/conftest.py @@ -5,13 +5,9 @@ import re from collections.abc import Mapping from pathlib import Path -from typing import TYPE_CHECKING import pytest -if TYPE_CHECKING: - from typing import Any - def extract_json_code_blocks( markdown_content: str, @@ -53,7 +49,8 @@ def extract_json_code_blocks( end_line: int = i # Line with closing ``` raw_json: str = "\n".join(json_lines) - parsed_json: Any = json.loads(raw_json) + parsed_json: object = json.loads(raw_json) + assert isinstance(parsed_json, dict) code_blocks[(start_line + 1, end_line)] = parsed_json i += 1 diff --git a/tests/test_data_api/test_geoproj.py b/tests/test_data_api/test_geoproj.py index 5949099c..c9f734ce 100644 --- a/tests/test_data_api/test_geoproj.py +++ b/tests/test_data_api/test_geoproj.py @@ -14,7 +14,7 @@ class TestProj: def test_proj_with_epsg_code(self) -> None: """Test creation with EPSG code.""" - proj = Proj(**{"proj:code": "EPSG:4326"}) + proj = Proj.model_validate({"proj:code": "EPSG:4326"}) assert proj.code == "EPSG:4326" assert proj.wkt2 is None @@ -23,7 +23,7 @@ def test_proj_with_epsg_code(self) -> None: def test_proj_with_wkt2(self) -> None: """Test creation with WKT2 string.""" wkt2_example = 'GEOGCRS["WGS 84",DATUM["World Geodetic System 1984"]]' - proj = Proj(**{"proj:wkt2": wkt2_example}) + proj = Proj.model_validate({"proj:wkt2": wkt2_example}) assert proj.wkt2 == wkt2_example assert proj.code is None @@ -36,7 +36,7 @@ def test_proj_with_projjson(self) -> None: "type": "GeographicCRS", "name": "WGS 84", } - proj = Proj(**{"proj:projjson": projjson_data}) + proj = Proj.model_validate({"proj:projjson": projjson_data}) assert proj.projjson is not None assert proj.code is None @@ -45,7 +45,7 @@ def test_proj_with_projjson(self) -> None: def test_proj_validation_error_no_crs(self) -> None: """Test that missing all CRS fields raises ValidationError.""" with pytest.raises(ValidationError) as exc_info: - Proj() + Proj() # pyright: ignore[reportCallIssue] # no-args construction tests the validation error assert "At least one of proj:code, proj:wkt2, or proj:projjson must be provided" in str( exc_info.value @@ -54,7 +54,7 @@ def test_proj_validation_error_no_crs(self) -> None: def test_proj_multiple_crs_fields(self) -> None: """Test that multiple CRS fields can be provided.""" wkt2_example = 'GEOGCRS["WGS 84",DATUM["World Geodetic System 1984"]]' - proj = Proj(**{"proj:code": "EPSG:4326", "proj:wkt2": wkt2_example}) + proj = Proj.model_validate({"proj:code": "EPSG:4326", "proj:wkt2": wkt2_example}) assert proj.code == "EPSG:4326" assert proj.wkt2 == wkt2_example @@ -62,7 +62,7 @@ def test_proj_multiple_crs_fields(self) -> None: def test_proj_serialization_by_alias(self) -> None: """Test that serialization uses aliases (proj: prefixes).""" - proj = Proj(**{"proj:code": "EPSG:32633"}) + proj = Proj.model_validate({"proj:code": "EPSG:32633"}) result = proj.model_dump() # Should serialize with proj: prefix @@ -74,7 +74,7 @@ def test_proj_serialization_by_alias(self) -> None: def test_proj_none_fields_excluded(self) -> None: """Test that None fields are excluded from serialization.""" - proj = Proj(**{"proj:code": "EPSG:4326"}) + proj = Proj.model_validate({"proj:code": "EPSG:4326"}) result = proj.model_dump() # None fields should be excluded @@ -86,8 +86,8 @@ def test_proj_none_fields_excluded(self) -> None: def test_proj_extra_fields_allowed(self) -> None: """Test that extra fields are allowed.""" - proj = Proj( - **{ + proj = Proj.model_validate( + { "proj:code": "EPSG:4326", "custom_field": "custom_value", "proj:custom": "also_allowed", @@ -104,7 +104,7 @@ def test_proj_roundtrip_serialization(self) -> None: original_data = {"proj:code": "EPSG:32633", "proj:wkt2": 'PROJCRS["WGS 84 / UTM zone 33N"]'} # Create model, serialize, then recreate - proj1 = Proj(**original_data) + proj1 = Proj.model_validate(original_data) serialized = proj1.model_dump() proj2 = Proj(**serialized) @@ -124,8 +124,8 @@ def test_geoproj_is_proj_alias(self) -> None: def test_geoproj_functionality(self) -> None: """Test that GeoProj works exactly like Proj.""" # Create using both classes - proj_instance = Proj(**{"proj:code": "EPSG:4326"}) - geoproj_instance = GeoProj(**{"proj:code": "EPSG:4326"}) + proj_instance = Proj.model_validate({"proj:code": "EPSG:4326"}) + geoproj_instance = GeoProj.model_validate({"proj:code": "EPSG:4326"}) # Should be instances of the same class assert type(proj_instance) is type(geoproj_instance) diff --git a/tests/test_data_api/test_geozarr/test_common.py b/tests/test_data_api/test_geozarr/test_common.py index fa54ffb8..e7286726 100644 --- a/tests/test_data_api/test_geozarr/test_common.py +++ b/tests/test_data_api/test_geozarr/test_common.py @@ -1,11 +1,14 @@ from __future__ import annotations -from typing import TYPE_CHECKING, Any +from collections.abc import Mapping +from typing import TYPE_CHECKING import numpy as np import pytest from pydantic_zarr.core import tuplify_json +from pydantic_zarr.v2 import AnyGroupSpec as AnyGroupSpec_V2 from pydantic_zarr.v2 import GroupSpec as GroupSpec_V2 +from pydantic_zarr.v3 import AnyGroupSpec as AnyGroupSpec_V3 from pydantic_zarr.v3 import GroupSpec as GroupSpec_V3 from eopf_geozarr.data_api.geozarr.common import ( @@ -33,7 +36,7 @@ DataArray_V3.from_array(np.arange(10), dimension_names=("time",)), ], ) -def test_datarraylike(obj: DataArray_V2 | DataArray_V3) -> None: +def test_datarraylike(obj: object) -> None: """ Test that the DataArrayLike protocol works correctly """ @@ -41,7 +44,7 @@ def test_datarraylike(obj: DataArray_V2 | DataArray_V3) -> None: @pytest.mark.parametrize("obj", [GroupSpec_V2(attributes={}), GroupSpec_V3(attributes={})]) -def test_grouplike(obj: GroupSpec_V3[Any, Any] | GroupSpec_V2[Any, Any]) -> None: +def test_grouplike(obj: AnyGroupSpec_V3 | AnyGroupSpec_V2) -> None: """ Test that the GroupLike protocol works correctly """ @@ -80,9 +83,12 @@ def test_multiscales_round_trip(s2_optimized_geozarr_group_example: zarr.Group) """ Ensure that we can round-trip multiscale metadata through the `Multiscales` model. """ - source_untyped = GroupSpec_V3.from_zarr(s2_optimized_geozarr_group_example) + source_untyped: AnyGroupSpec_V3 = GroupSpec_V3.from_zarr(s2_optimized_geozarr_group_example) flat = source_untyped.to_flat() - meta = flat["/measurements/reflectance"].attributes["multiscales"] + attributes = flat["/measurements/reflectance"].attributes + assert isinstance(attributes, Mapping) + meta = attributes["multiscales"] + assert isinstance(meta, Mapping) # pull out the multiscales keys, ignore extra submodel = tuplify_json({k: meta[k] for k in ZCMMultiscales.model_fields if k in meta}) assert ZCMMultiscales(**submodel).model_dump() == submodel @@ -95,11 +101,11 @@ def test_projattrs_crs_required() -> None: with pytest.raises( ValueError, match=r"One of 'code', 'wkt2', or 'projjson' must be provided\." ): - ProjAttrs() + ProjAttrs() # pyright: ignore[reportCallIssue] # no-args construction tests the validation error def test_projattrs_json_examples( - proj_attrs_examples: dict[tuple[int, int], dict[str, Any]], + proj_attrs_examples: dict[tuple[int, int], dict[str, object]], ) -> None: """ Test that proj attributes in the JSON examples of the proj extension README are valid. @@ -108,19 +114,22 @@ def test_projattrs_json_examples( for json_block in proj_attrs_examples.values(): # Check if this JSON block contains geo.proj attributes - if "attributes" in json_block and isinstance(json_block["attributes"], dict): - geo: Any = json_block["attributes"].get("geo") + attributes = json_block.get("attributes") + if isinstance(attributes, dict): + geo: object = attributes.get("geo") if geo and isinstance(geo, dict) and "proj" in geo: proj_examples_found += 1 - proj_data: dict[str, Any] = geo["proj"] + proj_data_obj: object = geo["proj"] + assert isinstance(proj_data_obj, dict) + proj_data: dict[str, object] = proj_data_obj # Validate that ProjAttrs can parse this data - proj_attrs: ProjAttrs = ProjAttrs(**proj_data) + proj_attrs: ProjAttrs = ProjAttrs.model_validate(proj_data) # Verify that all fields from the original data are present in the model for key, value in proj_data.items(): if value is not None: - model_value: Any = getattr(proj_attrs, key) + model_value: object = getattr(proj_attrs, key) # Handle tuple/list comparison for transform and bbox fields if isinstance(value, list) and isinstance(model_value, tuple): assert tuple(value) == model_value, f"Field {key} mismatch" diff --git a/tests/test_data_api/test_geozarr/test_multiscales/test_geozarr.py b/tests/test_data_api/test_geozarr/test_multiscales/test_geozarr.py index a9c9418c..3391d796 100644 --- a/tests/test_data_api/test_geozarr/test_multiscales/test_geozarr.py +++ b/tests/test_data_api/test_geozarr/test_multiscales/test_geozarr.py @@ -1,7 +1,8 @@ -from typing import Any, Literal +from typing import Literal import pytest from pydantic.experimental.missing_sentinel import MISSING +from zarr_cm import ConventionMetadataObject from zarr_cm import multiscales as multiscales_cm from eopf_geozarr.data_api.geozarr.multiscales import tms, zcm @@ -18,13 +19,13 @@ def test_multiscale_group_attrs(multiscale_flavor: set[Literal["zcm", "tms"]]) - """ zcm_meta: dict[str, object] = {} tms_meta: dict[str, object] = {} - zarr_conventions_meta: MISSING | tuple[Any, ...] = MISSING + zarr_conventions_meta: tuple[ConventionMetadataObject, ...] | MISSING = MISSING if "zcm" in multiscale_flavor: layout = ( zcm.ScaleLevel( asset="level_0", - transform={"scale": (1.0, 1.0), "translation": (0.0, 0.0)}, + transform=zcm.Transform(scale=(1.0, 1.0), translation=(0.0, 0.0)), ), ) zcm_meta = zcm.Multiscales(layout=layout, resampling_method="nearest").model_dump() @@ -58,13 +59,17 @@ def test_multiscale_group_attrs(multiscale_flavor: set[Literal["zcm", "tms"]]) - ) }, ).model_dump() - multiscale_meta = MultiscaleMeta(**{**zcm_meta, **tms_meta}) + multiscale_meta = MultiscaleMeta.model_validate({**zcm_meta, **tms_meta}) multiscale_group_attrs = MultiscaleGroupAttrs( zarr_conventions=zarr_conventions_meta, multiscales=multiscale_meta ) if "zcm" in multiscale_flavor: assert "zcm" in multiscale_group_attrs.multiscale_meta - assert multiscale_group_attrs.multiscale_meta["zcm"] == zcm.Multiscales(**zcm_meta) + assert multiscale_group_attrs.multiscale_meta["zcm"] == zcm.Multiscales.model_validate( + zcm_meta + ) if "tms" in multiscale_flavor: assert "tms" in multiscale_group_attrs.multiscale_meta - assert multiscale_group_attrs.multiscale_meta["tms"] == tms.Multiscales(**tms_meta) + assert multiscale_group_attrs.multiscale_meta["tms"] == tms.Multiscales.model_validate( + tms_meta + ) diff --git a/tests/test_data_api/test_geozarr/test_multiscales/test_zcm.py b/tests/test_data_api/test_geozarr/test_multiscales/test_zcm.py index 32d3dc4c..52be4251 100644 --- a/tests/test_data_api/test_geozarr/test_multiscales/test_zcm.py +++ b/tests/test_data_api/test_geozarr/test_multiscales/test_zcm.py @@ -30,7 +30,7 @@ def test_scale_level_from_group() -> None: """ meta = {"group": "1", "from_group": "0"} with pytest.raises(ValidationError): - ScaleLevel(**meta) + ScaleLevel.model_validate(meta) def test_scalelevel_json() -> None: @@ -46,4 +46,4 @@ def test_scalelevel_json() -> None: }, "resampling_method": "nearest", } - assert ScaleLevel(**x).model_dump() == x + assert ScaleLevel.model_validate(x).model_dump() == x diff --git a/tests/test_data_api/test_projjson.py b/tests/test_data_api/test_projjson.py index ada54398..ae2214f8 100644 --- a/tests/test_data_api/test_projjson.py +++ b/tests/test_data_api/test_projjson.py @@ -7,8 +7,6 @@ from __future__ import annotations -from typing import Any - import pytest from pydantic import ValidationError @@ -39,51 +37,52 @@ class TestBasicModels: def test_id_model(self) -> None: """Test Id model validation""" # Valid ID with required fields - id_data: dict[str, Any] = {"authority": "EPSG", "code": 4326} - id_obj: Id = Id(**id_data) + id_data: dict[str, object] = {"authority": "EPSG", "code": 4326} + id_obj: Id = Id.model_validate(id_data) assert id_obj.authority == "EPSG" assert id_obj.code == 4326 # ID with string code - id_data_str: dict[str, Any] = {"authority": "EPSG", "code": "4326"} - id_obj_str: Id = Id(**id_data_str) + id_data_str: dict[str, object] = {"authority": "EPSG", "code": "4326"} + id_obj_str: Id = Id.model_validate(id_data_str) assert id_obj_str.code == "4326" # ID with optional fields - id_full: dict[str, Any] = { + id_full: dict[str, object] = { "authority": "EPSG", "code": 4326, "version": "10.095", "authority_citation": "EPSG Geodetic Parameter Dataset", "uri": "urn:ogc:def:crs:EPSG::4326", } - id_obj_full: Id = Id(**id_full) + id_obj_full: Id = Id.model_validate(id_full) assert id_obj_full.version == "10.095" assert id_obj_full.uri == "urn:ogc:def:crs:EPSG::4326" # Missing required field should raise ValidationError with pytest.raises(ValidationError): - Id(authority="EPSG") # missing code + Id(authority="EPSG") # type: ignore[call-arg] # missing code (intentional) def test_unit_model(self) -> None: """Test Unit model validation""" - unit_data: dict[str, Any] = { + unit_data: dict[str, object] = { "type": "Unit", "name": "metre", "conversion_factor": 1.0, } - unit: Unit = Unit(**unit_data) + unit: Unit = Unit.model_validate(unit_data) assert unit.name == "metre" assert unit.conversion_factor == 1.0 # With ID - unit_with_id: dict[str, Any] = { + unit_with_id: dict[str, object] = { "type": "Unit", "name": "degree", "conversion_factor": 0.017453292519943295, "id": {"authority": "EPSG", "code": 9122}, } - unit = Unit(**unit_with_id) + unit = Unit.model_validate(unit_with_id) + assert unit.id is not None assert unit.id.authority == "EPSG" assert unit.id.code == 9122 @@ -101,17 +100,18 @@ def test_bbox_model(self) -> None: # Missing required field with pytest.raises(ValidationError): - BBox(east_longitude=180.0, west_longitude=-180.0) # missing latitude fields + # missing latitude fields (intentional) + BBox(east_longitude=180.0, west_longitude=-180.0) # type: ignore[call-arg] def test_axis_model(self) -> None: """Test Axis model validation""" - axis_data: dict[str, str] = { + axis_data: dict[str, object] = { "type": "Axis", "name": "Geodetic latitude", "abbreviation": "Lat", "direction": "north", } - axis: Axis = Axis(**axis_data) + axis: Axis = Axis.model_validate(axis_data) assert axis.name == "Geodetic latitude" assert axis.direction == "north" @@ -121,7 +121,7 @@ def test_axis_model(self) -> None: type="Axis", name="Invalid", abbreviation="Inv", - direction="invalid_direction", + direction="invalid_direction", # type: ignore[arg-type] # invalid direction (intentional) ) @@ -130,35 +130,35 @@ class TestEllipsoidModel: def test_ellipsoid_with_semi_axes(self) -> None: """Test ellipsoid with semi-major and semi-minor axes""" - ellipsoid_data: dict[str, Any] = { + ellipsoid_data: dict[str, object] = { "type": "Ellipsoid", "name": "WGS 84", "semi_major_axis": 6378137.0, "semi_minor_axis": 6356752.314245179, } - ellipsoid: Ellipsoid = Ellipsoid(**ellipsoid_data) + ellipsoid: Ellipsoid = Ellipsoid.model_validate(ellipsoid_data) assert ellipsoid.name == "WGS 84" assert ellipsoid.semi_major_axis == 6378137.0 def test_ellipsoid_with_inverse_flattening(self) -> None: """Test ellipsoid with inverse flattening""" - ellipsoid_data: dict[str, Any] = { + ellipsoid_data: dict[str, object] = { "type": "Ellipsoid", "name": "WGS 84", "semi_major_axis": 6378137.0, "inverse_flattening": 298.257223563, } - ellipsoid: Ellipsoid = Ellipsoid(**ellipsoid_data) + ellipsoid: Ellipsoid = Ellipsoid.model_validate(ellipsoid_data) assert ellipsoid.inverse_flattening == 298.257223563 def test_ellipsoid_sphere(self) -> None: """Test spherical ellipsoid (equal radii)""" - ellipsoid_data: dict[str, Any] = { + ellipsoid_data: dict[str, object] = { "type": "Ellipsoid", "name": "Sphere", "radius": 6371000.0, } - ellipsoid: Ellipsoid = Ellipsoid(**ellipsoid_data) + ellipsoid: Ellipsoid = Ellipsoid.model_validate(ellipsoid_data) assert ellipsoid.radius == 6371000.0 @@ -167,7 +167,7 @@ class TestCoordinateSystemModel: def test_ellipsoidal_coordinate_system(self) -> None: """Test ellipsoidal coordinate system""" - cs_data: dict[str, Any] = { + cs_data: dict[str, object] = { "type": "CoordinateSystem", "subtype": "ellipsoidal", "axis": [ @@ -195,14 +195,14 @@ def test_ellipsoidal_coordinate_system(self) -> None: }, ], } - cs: CoordinateSystem = CoordinateSystem(**cs_data) + cs: CoordinateSystem = CoordinateSystem.model_validate(cs_data) assert cs.subtype == "ellipsoidal" assert len(cs.axis) == 2 assert cs.axis[0].name == "Geodetic latitude" def test_cartesian_coordinate_system(self) -> None: """Test Cartesian coordinate system""" - cs_data: dict[str, Any] = { + cs_data: dict[str, object] = { "type": "CoordinateSystem", "subtype": "Cartesian", "axis": [ @@ -222,7 +222,7 @@ def test_cartesian_coordinate_system(self) -> None: }, ], } - cs: CoordinateSystem = CoordinateSystem(**cs_data) + cs: CoordinateSystem = CoordinateSystem.model_validate(cs_data) assert cs.subtype == "Cartesian" assert cs.axis[0].direction == "east" assert cs.axis[1].direction == "north" @@ -233,7 +233,7 @@ class TestCRSModels: def test_geodetic_crs_wgs84(self) -> None: """Test WGS 84 geodetic CRS""" - wgs84_data: dict[str, Any] = { + wgs84_data: dict[str, object] = { "type": "GeographicCRS", "name": "WGS 84", "datum": { @@ -276,14 +276,16 @@ def test_geodetic_crs_wgs84(self) -> None: }, "id": {"authority": "EPSG", "code": 4326}, } - crs: GeodeticCRS = GeodeticCRS(**wgs84_data) + crs: GeodeticCRS = GeodeticCRS.model_validate(wgs84_data) assert crs.name == "WGS 84" + assert crs.datum is not None assert crs.datum.name == "World Geodetic System 1984" + assert crs.id is not None assert crs.id.code == 4326 def test_projected_crs_utm(self) -> None: """Test UTM projected CRS""" - utm_data: dict[str, Any] = { + utm_data: dict[str, object] = { "type": "ProjectedCRS", "name": "WGS 84 / UTM zone 33N", "base_crs": { @@ -356,14 +358,14 @@ def test_projected_crs_utm(self) -> None: ], }, } - crs: ProjectedCRS = ProjectedCRS(**utm_data) + crs: ProjectedCRS = ProjectedCRS.model_validate(utm_data) assert crs.name == "WGS 84 / UTM zone 33N" assert crs.base_crs.name == "WGS 84" assert crs.conversion.name == "UTM zone 33N" def test_compound_crs(self) -> None: """Test compound CRS with horizontal and vertical components""" - compound_data: dict[str, Any] = { + compound_data: dict[str, object] = { "type": "CompoundCRS", "name": "WGS 84 + EGM96 height", "components": [ @@ -388,11 +390,15 @@ def test_compound_crs(self) -> None: }, ], } - crs: CompoundCRS = CompoundCRS(**compound_data) + crs: CompoundCRS = CompoundCRS.model_validate(compound_data) assert crs.name == "WGS 84 + EGM96 height" assert len(crs.components) == 2 - assert crs.components[0].name == "WGS 84" - assert crs.components[1].name == "EGM96 height" + component_0 = crs.components[0] + component_1 = crs.components[1] + assert isinstance(component_0, GeodeticCRS) + assert isinstance(component_1, VerticalCRS) + assert component_0.name == "WGS 84" + assert component_1.name == "EGM96 height" class TestDatumEnsemble: @@ -400,7 +406,7 @@ class TestDatumEnsemble: def test_datum_ensemble_creation(self) -> None: """Test creation of datum ensemble""" - ensemble_data: dict[str, Any] = { + ensemble_data: dict[str, object] = { "type": "DatumEnsemble", "name": "World Geodetic System 1984 ensemble", "members": [ @@ -416,7 +422,7 @@ def test_datum_ensemble_creation(self) -> None: }, "accuracy": "2.0", } - ensemble: DatumEnsemble = DatumEnsemble(**ensemble_data) + ensemble: DatumEnsemble = DatumEnsemble.model_validate(ensemble_data) assert ensemble.name == "World Geodetic System 1984 ensemble" assert len(ensemble.members) == 3 assert ensemble.accuracy == "2.0" @@ -427,7 +433,7 @@ class TestOperations: def test_coordinate_metadata(self) -> None: """Test coordinate metadata""" - metadata_data: dict[str, Any] = { + metadata_data: dict[str, object] = { "type": "CoordinateMetadata", "crs": { "type": "GeographicCRS", @@ -445,13 +451,14 @@ def test_coordinate_metadata(self) -> None: }, "coordinateEpoch": 2020.0, } - metadata: CoordinateMetadata = CoordinateMetadata(**metadata_data) + metadata: CoordinateMetadata = CoordinateMetadata.model_validate(metadata_data) assert metadata.coordinateEpoch == 2020.0 + assert isinstance(metadata.crs, GeodeticCRS) assert metadata.crs.name == "WGS 84" def test_single_operation(self) -> None: """Test single operation (transformation)""" - operation_data: dict[str, Any] = { + operation_data: dict[str, object] = { "type": "Transformation", "name": "NAD27 to NAD83 (1)", "method": {"type": "OperationMethod", "name": "NADCON"}, @@ -469,9 +476,10 @@ def test_single_operation(self) -> None: ], "accuracy": "0.15", } - operation: SingleOperation = SingleOperation(**operation_data) + operation: SingleOperation = SingleOperation.model_validate(operation_data) assert operation.name == "NAD27 to NAD83 (1)" assert operation.accuracy == "0.15" + assert operation.parameters is not None assert len(operation.parameters) == 2 @@ -480,27 +488,28 @@ class TestValidationEdgeCases: def test_invalid_crs_type(self) -> None: """Test invalid CRS type raises ValidationError""" - invalid_data: dict[str, Any] = { + invalid_data: dict[str, object] = { "type": "InvalidCRS", # Invalid type "name": "Invalid CRS", } with pytest.raises(ValidationError): - GeodeticCRS(**invalid_data) + GeodeticCRS(**invalid_data) # type: ignore[arg-type] # building model from dict[str, object] (intentional) def test_missing_required_fields(self) -> None: """Test missing required fields raise ValidationError""" # Missing name for CRS with pytest.raises(ValidationError): - GeodeticCRS(type="GeographicCRS") + GeodeticCRS(type="GeographicCRS") # type: ignore[call-arg] # missing name (intentional) # Missing ellipsoid for geodetic reference frame with pytest.raises(ValidationError): - GeodeticReferenceFrame(type="GeodeticReferenceFrame", name="Test Datum") + # missing ellipsoid (intentional) + GeodeticReferenceFrame(type="GeodeticReferenceFrame", name="Test Datum") # type: ignore[call-arg] def test_mutually_exclusive_fields(self) -> None: """Test that mutually exclusive fields are properly validated""" # Cannot have both id and ids - invalid_data: dict[str, Any] = { + invalid_data: dict[str, object] = { "type": "Unit", "name": "metre", "conversion_factor": 1.0, @@ -511,27 +520,27 @@ def test_mutually_exclusive_fields(self) -> None: # For now, we'll just ensure the model can be created with either field with pytest.raises(ValidationError): - Unit(**invalid_data) + Unit(**invalid_data) # type: ignore[arg-type] # building model from dict[str, object] (intentional) # Valid with id only - valid_with_id: dict[str, Any] = { + valid_with_id: dict[str, object] = { "type": "Unit", "name": "metre", "conversion_factor": 1.0, "id": {"authority": "EPSG", "code": 9001}, } - unit: Unit = Unit(**valid_with_id) + unit: Unit = Unit.model_validate(valid_with_id) assert unit.id is not None assert unit.ids is None # Valid with ids only - valid_with_ids: dict[str, Any] = { + valid_with_ids: dict[str, object] = { "type": "Unit", "name": "metre", "conversion_factor": 1.0, "ids": [{"authority": "EPSG", "code": 9001}], } - unit = Unit(**valid_with_ids) + unit = Unit.model_validate(valid_with_ids) assert unit.ids is not None assert unit.id is None @@ -542,7 +551,7 @@ class TestSerializationDeserialization: def test_round_trip_serialization(self) -> None: """Test that models can be serialized to JSON and back""" # Create a simple CRS - crs_data: dict[str, Any] = { + crs_data: dict[str, object] = { "type": "GeographicCRS", "name": "WGS 84", "datum": { @@ -558,14 +567,16 @@ def test_round_trip_serialization(self) -> None: } # Create model instance - original_crs: GeodeticCRS = GeodeticCRS(**crs_data) + original_crs: GeodeticCRS = GeodeticCRS.model_validate(crs_data) # Deserialize back to model - json_data: dict[str, Any] = original_crs.model_dump() - reconstructed_crs: GeodeticCRS = GeodeticCRS(**json_data) + json_data: dict[str, object] = original_crs.model_dump() + reconstructed_crs: GeodeticCRS = GeodeticCRS.model_validate(json_data) # Verify they're equivalent assert reconstructed_crs.name == original_crs.name + assert reconstructed_crs.datum is not None + assert original_crs.datum is not None assert reconstructed_crs.datum.name == original_crs.datum.name assert reconstructed_crs.datum.ellipsoid.name == original_crs.datum.ellipsoid.name @@ -574,17 +585,17 @@ def test_projjson_union_type(self) -> None: # Test with different types that should all be valid ProjJSON # Ellipsoid - ellipsoid_data: dict[str, Any] = { + ellipsoid_data: dict[str, object] = { "type": "Ellipsoid", "name": "WGS 84", "semi_major_axis": 6378137.0, "inverse_flattening": 298.257223563, } - ellipsoid: Ellipsoid = Ellipsoid(**ellipsoid_data) + ellipsoid: Ellipsoid = Ellipsoid.model_validate(ellipsoid_data) assert ellipsoid.name == "WGS 84" # CRS - crs_data: dict[str, Any] = { + crs_data: dict[str, object] = { "type": "GeographicCRS", "name": "WGS 84", "datum": { @@ -593,26 +604,26 @@ def test_projjson_union_type(self) -> None: "ellipsoid": ellipsoid_data, }, } - crs: GeodeticCRS = GeodeticCRS(**crs_data) + crs: GeodeticCRS = GeodeticCRS.model_validate(crs_data) assert crs.name == "WGS 84" class TestRoundTripSerialization: """Test round-trip serialization with real PROJ JSON examples.""" - def test_projected_crs_round_trip(self, projected_crs_json: dict[str, Any]) -> None: + def test_projected_crs_round_trip(self, projected_crs_json: dict[str, object]) -> None: """Test round-trip serialization of projected CRS example.""" # Parse JSON to Pydantic model from eopf_geozarr.data_api.geozarr.projjson import ProjectedCRS # Create model from JSON - original_crs: ProjectedCRS = ProjectedCRS(**projected_crs_json) + original_crs: ProjectedCRS = ProjectedCRS.model_validate(projected_crs_json) # Serialize back to dict - serialized: dict[str, Any] = original_crs.model_dump(exclude_none=True) + serialized: dict[str, object] = original_crs.model_dump(exclude_none=True) # Create model from serialized data - round_trip_crs: ProjectedCRS = ProjectedCRS(**serialized) + round_trip_crs: ProjectedCRS = ProjectedCRS.model_validate(serialized) # Verify key properties are preserved assert round_trip_crs.name == original_crs.name @@ -620,88 +631,100 @@ def test_projected_crs_round_trip(self, projected_crs_json: dict[str, Any]) -> N assert round_trip_crs.base_crs.name == original_crs.base_crs.name assert round_trip_crs.conversion.name == original_crs.conversion.name if original_crs.id: + assert round_trip_crs.id is not None assert round_trip_crs.id.authority == original_crs.id.authority assert round_trip_crs.id.code == original_crs.id.code - def test_bound_crs_round_trip(self, bound_crs_json: dict[str, Any]) -> None: + def test_bound_crs_round_trip(self, bound_crs_json: dict[str, object]) -> None: """Test round-trip serialization of bound CRS example.""" from eopf_geozarr.data_api.geozarr.projjson import BoundCRS # Create model from JSON - original_crs: BoundCRS = BoundCRS(**bound_crs_json) + original_crs: BoundCRS = BoundCRS.model_validate(bound_crs_json) # Serialize back to dict - serialized: dict[str, Any] = original_crs.model_dump(exclude_none=True) + serialized: dict[str, object] = original_crs.model_dump(exclude_none=True) # Create model from serialized data - round_trip_crs: BoundCRS = BoundCRS(**serialized) + round_trip_crs: BoundCRS = BoundCRS.model_validate(serialized) # Verify key properties are preserved assert round_trip_crs.type == original_crs.type + # A nested BoundCRS has no "name"; this example's source/target are named CRSs. + assert not isinstance(round_trip_crs.source_crs, BoundCRS) + assert not isinstance(round_trip_crs.target_crs, BoundCRS) + assert not isinstance(original_crs.source_crs, BoundCRS) + assert not isinstance(original_crs.target_crs, BoundCRS) assert round_trip_crs.source_crs.name == original_crs.source_crs.name assert round_trip_crs.target_crs.name == original_crs.target_crs.name assert round_trip_crs.transformation.name == original_crs.transformation.name - def test_compound_crs_round_trip(self, compound_crs_json: dict[str, Any]) -> None: + def test_compound_crs_round_trip(self, compound_crs_json: dict[str, object]) -> None: """Test round-trip serialization of compound CRS example.""" from eopf_geozarr.data_api.geozarr.projjson import CompoundCRS # Create model from JSON - original_crs: CompoundCRS = CompoundCRS(**compound_crs_json) + original_crs: CompoundCRS = CompoundCRS.model_validate(compound_crs_json) # Serialize back to dict - serialized: dict[str, Any] = original_crs.model_dump(exclude_none=True) + serialized: dict[str, object] = original_crs.model_dump(exclude_none=True) # Create model from serialized data - round_trip_crs: CompoundCRS = CompoundCRS(**serialized) + round_trip_crs: CompoundCRS = CompoundCRS.model_validate(serialized) # Verify key properties are preserved assert round_trip_crs.name == original_crs.name assert round_trip_crs.type == original_crs.type assert len(round_trip_crs.components) == len(original_crs.components) for i, component in enumerate(round_trip_crs.components): - assert component.name == original_crs.components[i].name + # Compound components are named CRSs, never a nested BoundCRS. + assert not isinstance(component, BoundCRS) + original_component = original_crs.components[i] + assert not isinstance(original_component, BoundCRS) + assert component.name == original_component.name - def test_datum_ensemble_round_trip(self, datum_ensemble_json: dict[str, Any]) -> None: + def test_datum_ensemble_round_trip(self, datum_ensemble_json: dict[str, object]) -> None: """Test round-trip serialization of datum ensemble example.""" from eopf_geozarr.data_api.geozarr.projjson import GeodeticCRS # Create model from JSON - original_crs: GeodeticCRS = GeodeticCRS(**datum_ensemble_json) + original_crs: GeodeticCRS = GeodeticCRS.model_validate(datum_ensemble_json) # Serialize back to dict - serialized: dict[str, Any] = original_crs.model_dump(exclude_none=True) + serialized: dict[str, object] = original_crs.model_dump(exclude_none=True) # Create model from serialized data - round_trip_crs: GeodeticCRS = GeodeticCRS(**serialized) + round_trip_crs: GeodeticCRS = GeodeticCRS.model_validate(serialized) # Verify key properties are preserved assert round_trip_crs.name == original_crs.name assert round_trip_crs.type == original_crs.type if original_crs.datum_ensemble: + assert round_trip_crs.datum_ensemble is not None assert round_trip_crs.datum_ensemble.name == original_crs.datum_ensemble.name assert len(round_trip_crs.datum_ensemble.members) == len( original_crs.datum_ensemble.members ) - def test_transformation_round_trip(self, transformation_json: dict[str, Any]) -> None: + def test_transformation_round_trip(self, transformation_json: dict[str, object]) -> None: """Test round-trip serialization of transformation example.""" from eopf_geozarr.data_api.geozarr.projjson import SingleOperation # Create model from JSON - original_op: SingleOperation = SingleOperation(**transformation_json) + original_op: SingleOperation = SingleOperation.model_validate(transformation_json) # Serialize back to dict - serialized: dict[str, Any] = original_op.model_dump(exclude_none=True) + serialized: dict[str, object] = original_op.model_dump(exclude_none=True) # Create model from serialized data - round_trip_op: SingleOperation = SingleOperation(**serialized) + round_trip_op: SingleOperation = SingleOperation.model_validate(serialized) # Verify key properties are preserved assert round_trip_op.name == original_op.name assert round_trip_op.type == original_op.type assert round_trip_op.method.name == original_op.method.name if original_op.parameters: + assert round_trip_op.parameters is not None assert len(round_trip_op.parameters) == len(original_op.parameters) def test_all_examples_round_trip(self, projjson_example: dict[str, object]) -> None: @@ -726,6 +749,7 @@ def test_all_examples_round_trip(self, projjson_example: dict[str, object]) -> N # Get the model class based on type obj_type = projjson_example.get("type") + assert isinstance(obj_type, str) model_class = type_mapping[obj_type] diff --git a/tests/test_data_api/test_s1.py b/tests/test_data_api/test_s1.py index 98d9917e..5e7ce77d 100644 --- a/tests/test_data_api/test_s1.py +++ b/tests/test_data_api/test_s1.py @@ -15,7 +15,7 @@ def test_sentinel1_roundtrip(s1_json_example: dict[str, object]) -> None: """Test that we can round-trip JSON data without loss""" - model1 = Sentinel1Root(**s1_json_example) + model1 = Sentinel1Root.model_validate(s1_json_example) dumped = model1.model_dump() - model2 = Sentinel1Root(**dumped) + model2 = Sentinel1Root.model_validate(dumped) assert model1.model_dump() == model2.model_dump() diff --git a/tests/test_data_api/test_s2.py b/tests/test_data_api/test_s2.py index a17fa138..ad7c45c7 100644 --- a/tests/test_data_api/test_s2.py +++ b/tests/test_data_api/test_s2.py @@ -15,7 +15,7 @@ def test_sentinel2_roundtrip(s2_json_example: dict[str, object]) -> None: """Test that we can round-trip JSON data without loss""" - model1 = Sentinel2Root(**s2_json_example) + model1 = Sentinel2Root.model_validate(s2_json_example) dumped = model1.model_dump() - model2 = Sentinel2Root(**dumped) + model2 = Sentinel2Root.model_validate(dumped) assert model1.model_dump() == model2.model_dump() diff --git a/tests/test_data_api/test_spatial.py b/tests/test_data_api/test_spatial.py index aa757644..0ee7464f 100644 --- a/tests/test_data_api/test_spatial.py +++ b/tests/test_data_api/test_spatial.py @@ -13,7 +13,8 @@ class TestSpatial: def test_minimal_required_fields(self) -> None: """Test creation with only required fields.""" - spatial = Spatial(**{"spatial:dimensions": ["y", "x"]}) + data: dict[str, object] = {"spatial:dimensions": ["y", "x"]} + spatial = Spatial.model_validate(data) assert spatial.dimensions == ["y", "x"] assert spatial.bbox is None @@ -25,13 +26,13 @@ def test_minimal_required_fields(self) -> None: def test_missing_required_dimensions(self) -> None: """Test that missing dimensions field raises ValidationError.""" with pytest.raises(ValidationError) as exc_info: - Spatial() + Spatial() # type: ignore[call-arg] # intentionally missing required field assert "spatial:dimensions" in str(exc_info.value) def test_full_spatial_metadata(self) -> None: """Test creation with all fields populated.""" - data = { + data: dict[str, object] = { "spatial:dimensions": ["y", "x"], "spatial:bbox": [500000.0, 4900000.0, 600000.0, 5000000.0], "spatial:transform_type": "affine", @@ -40,7 +41,7 @@ def test_full_spatial_metadata(self) -> None: "spatial:registration": "pixel", } - spatial = Spatial(**data) + spatial = Spatial.model_validate(data) assert spatial.dimensions == ["y", "x"] assert spatial.bbox == [500000.0, 4900000.0, 600000.0, 5000000.0] @@ -51,13 +52,13 @@ def test_full_spatial_metadata(self) -> None: def test_3d_spatial_data(self) -> None: """Test spatial model with 3D data.""" - data = { + data: dict[str, object] = { "spatial:dimensions": ["z", "y", "x"], "spatial:bbox": [500000.0, 4900000.0, 0.0, 600000.0, 5000000.0, 100.0], "spatial:shape": [10, 1000, 1000], } - spatial = Spatial(**data) + spatial = Spatial.model_validate(data) assert spatial.dimensions == ["z", "y", "x"] assert spatial.bbox == [500000.0, 4900000.0, 0.0, 600000.0, 5000000.0, 100.0] @@ -65,14 +66,14 @@ def test_3d_spatial_data(self) -> None: def test_serialization_by_alias(self) -> None: """Test that serialization uses aliases (spatial: prefixes).""" - data = { + data: dict[str, object] = { "spatial:dimensions": ["y", "x"], "spatial:bbox": [0.0, 0.0, 100.0, 100.0], "spatial:transform": [1.0, 0.0, 0.0, 0.0, -1.0, 100.0], "spatial:shape": [100, 100], } - spatial = Spatial(**data) + spatial = Spatial.model_validate(data) result = spatial.model_dump() # Should serialize with spatial: prefixes @@ -91,7 +92,8 @@ def test_serialization_by_alias(self) -> None: def test_none_fields_excluded(self) -> None: """Test that None fields are excluded from serialization.""" - spatial = Spatial(**{"spatial:dimensions": ["y", "x"]}) + data: dict[str, object] = {"spatial:dimensions": ["y", "x"]} + spatial = Spatial.model_validate(data) result = spatial.model_dump() # None fields should be excluded @@ -105,27 +107,30 @@ def test_none_fields_excluded(self) -> None: def test_node_registration(self) -> None: """Test node registration type.""" - data = {"spatial:dimensions": ["y", "x"], "spatial:registration": "node"} + data: dict[str, object] = {"spatial:dimensions": ["y", "x"], "spatial:registration": "node"} - spatial = Spatial(**data) + spatial = Spatial.model_validate(data) assert spatial.registration == "node" def test_non_affine_transform_type(self) -> None: """Test non-affine transform types.""" - data = {"spatial:dimensions": ["y", "x"], "spatial:transform_type": "rpc"} + data: dict[str, object] = { + "spatial:dimensions": ["y", "x"], + "spatial:transform_type": "rpc", + } - spatial = Spatial(**data) + spatial = Spatial.model_validate(data) assert spatial.transform_type == "rpc" def test_extra_fields_allowed(self) -> None: """Test that extra fields are allowed.""" - data = { + data: dict[str, object] = { "spatial:dimensions": ["y", "x"], "custom_field": "custom_value", "spatial:custom": "also_allowed", } - spatial = Spatial(**data) + spatial = Spatial.model_validate(data) result = spatial.model_dump() assert result["custom_field"] == "custom_value" @@ -133,7 +138,7 @@ def test_extra_fields_allowed(self) -> None: def test_roundtrip_serialization(self) -> None: """Test that serialization and deserialization preserves data.""" - original_data = { + original_data: dict[str, object] = { "spatial:dimensions": ["y", "x"], "spatial:bbox": [500000.0, 4900000.0, 600000.0, 5000000.0], "spatial:transform": [10.0, 0.0, 500000.0, 0.0, -10.0, 5000000.0], @@ -143,7 +148,7 @@ def test_roundtrip_serialization(self) -> None: } # Create model, serialize, then recreate - spatial1 = Spatial(**original_data) + spatial1 = Spatial.model_validate(original_data) serialized = spatial1.model_dump() spatial2 = Spatial(**serialized) @@ -157,23 +162,26 @@ def test_roundtrip_serialization(self) -> None: def test_invalid_dimensions_none(self) -> None: """Test that None dimensions raise ValidationError.""" + data: dict[str, object] = {"spatial:dimensions": None} # intentionally invalid value with pytest.raises(ValidationError): - Spatial(**{"spatial:dimensions": None}) + Spatial.model_validate(data) def test_empty_dimensions_not_allowed(self) -> None: """Test that empty dimensions raise ValidationError.""" + empty_data: dict[str, object] = {"spatial:dimensions": []} with pytest.raises(ValidationError) as exc_info: - Spatial(**{"spatial:dimensions": []}) + Spatial.model_validate(empty_data) assert "spatial:dimensions must contain at least one dimension" in str(exc_info.value) - data = { + data: dict[str, object] = { "spatial:dimensions": ["y", "x"], "spatial:transform_type": "affine", "spatial:transform": [10.0, 0.0, 500000.0, 0.0, -10.0], # Only 5 elements } # Currently this will pass, but in the future we might want validation - spatial = Spatial(**data) + spatial = Spatial.model_validate(data) + assert spatial.transform is not None assert len(spatial.transform) == 5 # Current behavior # Future: might want to validate for exactly 6 elements for affine diff --git a/tests/test_data_api/test_v2.py b/tests/test_data_api/test_v2.py index a3386033..78bdc161 100644 --- a/tests/test_data_api/test_v2.py +++ b/tests/test_data_api/test_v2.py @@ -1,6 +1,7 @@ from __future__ import annotations -from typing import Any +from collections.abc import Mapping +from typing import TYPE_CHECKING, cast import numpy as np import pytest @@ -12,6 +13,9 @@ check_valid_coordinates, ) +if TYPE_CHECKING: + from eopf_geozarr.data_api.geozarr.common import GroupLike + def test_invalid_dimension_names() -> None: msg = r"The _ARRAY_DIMENSIONS attribute has length 3, which does not match the number of dimensions for this array \(got 2\)" @@ -35,10 +39,13 @@ def test_valid(data_shape: tuple[int, ...]) -> None: f"dim_{idx}": DataArray.from_array(np.arange(s), dimension_names=(f"dim_{idx}",)) for idx, s in enumerate(data_shape) } - group = GroupSpec[Any, DataArray]( + group = GroupSpec[Mapping[str, object], DataArray]( attributes={}, members={"base": base_array, **coords_arrays} ) - assert check_valid_coordinates(group) == group + # ``group`` structurally satisfies ``GroupLike``, but mypy cannot bind the + # invariant ``Mapping`` value type, mirroring the cast used in the source. + group_like = cast("GroupLike", group) + assert check_valid_coordinates(group_like) == group_like @staticmethod @pytest.mark.parametrize("data_shape", [(10,), (10, 12)]) @@ -59,9 +66,9 @@ def test_invalid_coordinates( f"dim_{idx}": DataArray.from_array(np.arange(s + 1), dimension_names=(f"dim_{idx}",)) for idx, s in enumerate(data_shape) } - group = GroupSpec[Any, DataArray]( + group = GroupSpec[Mapping[str, object], DataArray]( attributes={}, members={"base": base_array, **coords_arrays} ) msg = "Dimension .* for array 'base' has a shape mismatch:" with pytest.raises(ValueError, match=msg): - check_valid_coordinates(group) + check_valid_coordinates(cast("GroupLike", group)) diff --git a/tests/test_data_api/test_v3.py b/tests/test_data_api/test_v3.py index 09771b01..c2a16fa4 100644 --- a/tests/test_data_api/test_v3.py +++ b/tests/test_data_api/test_v3.py @@ -1,4 +1,5 @@ -from typing import Any +from collections.abc import Mapping +from typing import TYPE_CHECKING, cast import numpy as np import pytest @@ -12,6 +13,9 @@ check_valid_coordinates, ) +if TYPE_CHECKING: + from eopf_geozarr.data_api.geozarr.common import GroupLike + class TestCheckValidCoordinates: @staticmethod @@ -29,10 +33,13 @@ def test_valid(data_shape: tuple[int, ...]) -> None: f"dim_{idx}": DataArray.from_array(np.arange(s), dimension_names=(f"dim_{idx}",)) for idx, s in enumerate(data_shape) } - group = GroupSpec[Any, DataArray]( + group = GroupSpec[Mapping[str, object], DataArray]( attributes={}, members={"base": base_array, **coords_arrays} ) - assert check_valid_coordinates(group) == group + # ``group`` structurally satisfies ``GroupLike``, but mypy cannot bind the + # invariant ``Mapping`` value type, mirroring the cast used in the source. + group_like = cast("GroupLike", group) + assert check_valid_coordinates(group_like) == group_like @staticmethod @pytest.mark.parametrize("data_shape", [(10,), (10, 12)]) @@ -53,19 +60,19 @@ def test_invalid_coordinates( f"dim_{idx}": DataArray.from_array(np.arange(s + 1), dimension_names=(f"dim_{idx}",)) for idx, s in enumerate(data_shape) } - group = GroupSpec[Any, DataArray]( + group = GroupSpec[Mapping[str, object], DataArray]( attributes={}, members={"base": base_array, **coords_arrays} ) msg = "Dimension .* for array 'base' has a shape mismatch:" with pytest.raises(ValueError, match=msg): - check_valid_coordinates(group) + check_valid_coordinates(cast("GroupLike", group)) -def test_dataarray_round_trip(s2_geozarr_group_example: Any) -> None: +def test_dataarray_round_trip(s2_geozarr_group_example: zarr.Group) -> None: """ Ensure that we can round-trip dataarray attributes through the `Multiscales` model. """ - source_untyped = GroupSpec.from_zarr(s2_geozarr_group_example) + source_untyped: GroupSpec = GroupSpec.from_zarr(s2_geozarr_group_example) flat = source_untyped.to_flat() for val in flat.values(): if isinstance(val, ArraySpec) and val.dimension_names is not None: @@ -73,7 +80,7 @@ def test_dataarray_round_trip(s2_geozarr_group_example: Any) -> None: assert DataArray(**model_json).model_dump() == model_json -def test_multiscale_attrs_round_trip(s2_geozarr_group_example: Any) -> None: +def test_multiscale_attrs_round_trip(s2_geozarr_group_example: zarr.Group) -> None: """ Test that multiscale datasets round-trip through the `Multiscales` model """ diff --git a/tests/test_docs.py b/tests/test_docs.py index 82763904..b9422d38 100644 --- a/tests/test_docs.py +++ b/tests/test_docs.py @@ -10,6 +10,7 @@ #> hello """ +import uuid from io import StringIO from pathlib import Path @@ -92,7 +93,7 @@ def _validate_output(example: CodeExample, captured_output: str) -> None: # Get all examples and group them by group ID _all_examples = list(find_examples("docs")) -_examples_by_group = {} +_examples_by_group: dict[uuid.UUID | None, list[CodeExample]] = {} for ex in _all_examples: if ex.prefix == "python": if ex.group not in _examples_by_group: @@ -120,7 +121,7 @@ def test_doc_example_group(group_examples: list[CodeExample]) -> None: #> hello """ # Execute all examples in the group sequentially to share state - namespace = {} + namespace: dict[str, object] = {} any_skipped = False for example in group_examples: diff --git a/tests/test_fs_utils.py b/tests/test_fs_utils.py index 872f93a9..fec0cee7 100644 --- a/tests/test_fs_utils.py +++ b/tests/test_fs_utils.py @@ -66,7 +66,7 @@ def test_get_s3_credentials_info() -> None: @patch("eopf_geozarr.conversion.fs_utils.s3fs.S3FileSystem") -def test_validate_s3_access_success(mock_s3fs) -> None: +def test_validate_s3_access_success(mock_s3fs: Mock) -> None: """Test successful S3 access validation.""" mock_fs = Mock() mock_fs.ls.return_value = ["file1", "file2"] @@ -79,7 +79,7 @@ def test_validate_s3_access_success(mock_s3fs) -> None: @patch("eopf_geozarr.conversion.fs_utils.s3fs.S3FileSystem") -def test_validate_s3_access_failure(mock_s3fs) -> None: +def test_validate_s3_access_failure(mock_s3fs: Mock) -> None: """Test failed S3 access validation.""" mock_fs = Mock() mock_fs.ls.side_effect = Exception("Access denied") @@ -87,6 +87,7 @@ def test_validate_s3_access_failure(mock_s3fs) -> None: success, error = validate_s3_access("s3://test-bucket/path") assert success is False + assert error is not None assert "Access denied" in error @@ -101,11 +102,13 @@ def test_get_s3_storage_options() -> None: ): options = get_s3_storage_options("s3://test-bucket/path") - assert options["anon"] is False - assert options["use_ssl"] is True - assert options["client_kwargs"]["region_name"] == "us-west-2" - assert options["endpoint_url"] == "https://s3.example.com" - assert options["client_kwargs"]["endpoint_url"] == "https://s3.example.com" + assert options.get("anon") is False + assert options.get("use_ssl") is True + client_kwargs = options.get("client_kwargs") + assert client_kwargs is not None + assert client_kwargs.get("region_name") == "us-west-2" + assert options.get("endpoint_url") == "https://s3.example.com" + assert client_kwargs.get("endpoint_url") == "https://s3.example.com" def test_get_storage_options() -> None: @@ -114,9 +117,11 @@ def test_get_storage_options() -> None: with patch.dict("os.environ", {"AWS_DEFAULT_REGION": "us-west-2"}): options = get_storage_options("s3://test-bucket/path") assert options is not None - assert options["anon"] is False - assert options["use_ssl"] is True - assert options["client_kwargs"]["region_name"] == "us-west-2" + assert options.get("anon") is False + assert options.get("use_ssl") is True + client_kwargs = options.get("client_kwargs") + assert client_kwargs is not None + assert client_kwargs.get("region_name") == "us-west-2" # Test local path options = get_storage_options("/local/path") @@ -142,7 +147,7 @@ def test_normalize_path() -> None: @patch("eopf_geozarr.conversion.fs_utils.get_filesystem") -def test_path_exists(mock_get_filesystem) -> None: +def test_path_exists(mock_get_filesystem: Mock) -> None: """Test unified path existence check.""" mock_fs = Mock() mock_fs.exists.return_value = True @@ -160,7 +165,7 @@ def test_path_exists(mock_get_filesystem) -> None: @patch("eopf_geozarr.conversion.fs_utils.get_filesystem") -def test_write_json_metadata(mock_get_filesystem) -> None: +def test_write_json_metadata(mock_get_filesystem: Mock) -> None: """Test unified JSON metadata writing.""" from unittest.mock import MagicMock, mock_open @@ -183,7 +188,7 @@ def test_write_json_metadata(mock_get_filesystem) -> None: @patch("eopf_geozarr.conversion.fs_utils.get_filesystem") -def test_read_json_metadata(mock_get_filesystem) -> None: +def test_read_json_metadata(mock_get_filesystem: Mock) -> None: """Test unified JSON metadata reading.""" from unittest.mock import MagicMock, mock_open diff --git a/tests/test_integration_sentinel1.py b/tests/test_integration_sentinel1.py index 137cd53b..13f20925 100644 --- a/tests/test_integration_sentinel1.py +++ b/tests/test_integration_sentinel1.py @@ -21,7 +21,7 @@ class MockSentinel1L1GRDBuilder: """Builder class to generate a sample EOPF Sentinel-1 Level 1 GRD data product for testing purpose.""" - def __init__(self, product_id) -> None: + def __init__(self, product_id: str) -> None: self.product_title = "S01SIWGRD" self.product_id = product_id @@ -32,7 +32,7 @@ def __init__(self, product_id) -> None: self.nlines = 552 self.npixels = 1131 - def create_coordinates(self, az_dim_size, gr_dim_size) -> xr.Coordinates: + def create_coordinates(self, az_dim_size: int, gr_dim_size: int) -> xr.Coordinates: coords = { self.az_dim: pd.date_range( start="2017-05-08T16:48:30", @@ -182,7 +182,7 @@ def temp_output_dir() -> Generator[str, None, None]: shutil.rmtree(temp_dir) -def test_no_gcp_group(temp_output_dir, sample_sentinel1_datatree) -> None: +def test_no_gcp_group(temp_output_dir: str, sample_sentinel1_datatree: xr.DataTree) -> None: output_path = Path(temp_output_dir) / "temp.zarr" with pytest.raises(ValueError, match=r"Detected Sentinel-1.*GCP group not provided"): @@ -193,7 +193,9 @@ def test_no_gcp_group(temp_output_dir, sample_sentinel1_datatree) -> None: ) -def test_invalid_gcp_group_raises_error(temp_output_dir, sample_sentinel1_datatree) -> None: +def test_invalid_gcp_group_raises_error( + temp_output_dir: str, sample_sentinel1_datatree: xr.DataTree +) -> None: """Test that specifying a non-existent GCP group raises an error.""" output_path = Path(temp_output_dir) / "test_s1_invalid_gcp.zarr" groups = ["measurements"] @@ -216,7 +218,7 @@ def test_invalid_gcp_group_raises_error(temp_output_dir, sample_sentinel1_datatr ], ) def test_sentinel1_gcp_conversion( - temp_output_dir, sample_sentinel1_datatree, polarization_group + temp_output_dir: str, sample_sentinel1_datatree: xr.DataTree, polarization_group: str ) -> None: """Test conversion of Sentinel-1 data with GCPs.""" # Prepare test diff --git a/tests/test_integration_sentinel2.py b/tests/test_integration_sentinel2.py index bae02360..91b6b7bc 100644 --- a/tests/test_integration_sentinel2.py +++ b/tests/test_integration_sentinel2.py @@ -230,7 +230,7 @@ def temp_output_dir() -> Generator[str, None, None]: def test_complete_sentinel2_conversion_notebook_workflow( - sample_sentinel2_datatree, temp_output_dir + sample_sentinel2_datatree: xr.DataTree, temp_output_dir: str ) -> None: """ Test complete conversion following the notebook workflow. @@ -290,7 +290,9 @@ def test_complete_sentinel2_conversion_notebook_workflow( @pytest.mark.slow -def test_performance_characteristics(sample_sentinel2_datatree, temp_output_dir) -> None: +def test_performance_characteristics( + sample_sentinel2_datatree: xr.DataTree, temp_output_dir: str +) -> None: """ Test performance characteristics following notebook analysis. diff --git a/tests/test_reprojection_validation.py b/tests/test_reprojection_validation.py index aa5bbab1..abb944ce 100755 --- a/tests/test_reprojection_validation.py +++ b/tests/test_reprojection_validation.py @@ -16,7 +16,7 @@ class MockSentinel1L1GRDBuilder: """Builder class to generate a sample EOPF Sentinel-1 Level 1 GRD data product for testing purpose.""" - def __init__(self, product_id) -> None: + def __init__(self, product_id: str) -> None: self.product_title = "S01SIWGRD" self.product_id = product_id self.az_dim = "azimuth_time" @@ -25,7 +25,7 @@ def __init__(self, product_id) -> None: self.nlines = 552 self.npixels = 1131 - def create_coordinates(self, az_dim_size, gr_dim_size) -> xr.Coordinates: + def create_coordinates(self, az_dim_size: int, gr_dim_size: int) -> xr.Coordinates: coords = { self.az_dim: pd.date_range( start="2017-05-08T16:48:30", diff --git a/tests/test_s2_converter_simplified.py b/tests/test_s2_converter_simplified.py index 69cff728..0bbf746b 100644 --- a/tests/test_s2_converter_simplified.py +++ b/tests/test_s2_converter_simplified.py @@ -254,8 +254,10 @@ def test_write_store_root_bbox_reprojects_utm_to_wgs84(tmp_path: Path) -> None: root_attrs = dict(zarr.open_group(store_path, mode="r").attrs) bbox = root_attrs["spatial:bbox"] + assert isinstance(bbox, list) + assert all(isinstance(coord, float) for coord in bbox) assert len(bbox) == 4 - xmin, ymin, xmax, ymax = bbox + xmin, ymin, xmax, ymax = (coord for coord in bbox if isinstance(coord, float)) # Roughly 7.0-8.0E, 44.1-45.1N after reprojection assert 6.0 < xmin < 8.0, bbox assert 43.0 < ymin < 45.0, bbox diff --git a/tests/test_s2_data_consolidator.py b/tests/test_s2_data_consolidator.py index 6102a25d..be82a85e 100644 --- a/tests/test_s2_data_consolidator.py +++ b/tests/test_s2_data_consolidator.py @@ -187,7 +187,7 @@ def sample_s2_datatree(self) -> MagicMock: } # Mock the dataset access - def mock_getitem(self, path: str) -> MagicMock: + def mock_getitem(self: object, path: str) -> MagicMock: mock_node = MagicMock() if "r10m" in path: if "reflectance" in path: @@ -220,7 +220,7 @@ def mock_getitem(self, path: str) -> MagicMock: mock_dt.__getitem__ = mock_getitem return mock_dt - def test_init(self, sample_s2_datatree) -> None: + def test_init(self, sample_s2_datatree: MagicMock) -> None: """Test consolidator initialization.""" consolidator = S2DataConsolidator(sample_s2_datatree) @@ -229,7 +229,7 @@ def test_init(self, sample_s2_datatree) -> None: assert consolidator.geometry_data == {} assert consolidator.meteorology_data == {} - def test_consolidate_all_data(self, sample_s2_datatree) -> None: + def test_consolidate_all_data(self, sample_s2_datatree: MagicMock) -> None: """Test complete data consolidation.""" consolidator = S2DataConsolidator(sample_s2_datatree) measurements, geometry, meteorology = consolidator.consolidate_all_data() @@ -253,7 +253,7 @@ def test_consolidate_all_data(self, sample_s2_datatree) -> None: assert "atmosphere" in measurements[resolution] assert "probability" in measurements[resolution] - def test_extract_reflectance_bands(self, sample_s2_datatree) -> None: + def test_extract_reflectance_bands(self, sample_s2_datatree: MagicMock) -> None: """Test reflectance band extraction.""" consolidator = S2DataConsolidator(sample_s2_datatree) consolidator._extract_measurements_data() @@ -274,7 +274,7 @@ def test_extract_reflectance_bands(self, sample_s2_datatree) -> None: assert "b01" in consolidator.measurements_data[60]["bands"] assert "b09" in consolidator.measurements_data[60]["bands"] - def test_extract_quality_data(self, sample_s2_datatree) -> None: + def test_extract_quality_data(self, sample_s2_datatree: MagicMock) -> None: """Test quality data extraction.""" consolidator = S2DataConsolidator(sample_s2_datatree) consolidator._extract_measurements_data() @@ -283,7 +283,7 @@ def test_extract_quality_data(self, sample_s2_datatree) -> None: assert "quality_b02" in consolidator.measurements_data[10]["quality"] assert "quality_b03" in consolidator.measurements_data[10]["quality"] - def test_extract_detector_footprints(self, sample_s2_datatree) -> None: + def test_extract_detector_footprints(self, sample_s2_datatree: MagicMock) -> None: """Test detector footprint extraction.""" consolidator = S2DataConsolidator(sample_s2_datatree) consolidator._extract_measurements_data() @@ -292,7 +292,7 @@ def test_extract_detector_footprints(self, sample_s2_datatree) -> None: assert "detector_footprint_b02" in consolidator.measurements_data[10]["detector_footprints"] assert "detector_footprint_b03" in consolidator.measurements_data[10]["detector_footprints"] - def test_extract_atmosphere_data(self, sample_s2_datatree) -> None: + def test_extract_atmosphere_data(self, sample_s2_datatree: MagicMock) -> None: """Test atmosphere data extraction.""" consolidator = S2DataConsolidator(sample_s2_datatree) consolidator._extract_measurements_data() @@ -301,7 +301,7 @@ def test_extract_atmosphere_data(self, sample_s2_datatree) -> None: assert "aot" in consolidator.measurements_data[20]["atmosphere"] assert "wvp" in consolidator.measurements_data[20]["atmosphere"] - def test_extract_classification_data(self, sample_s2_datatree) -> None: + def test_extract_classification_data(self, sample_s2_datatree: MagicMock) -> None: """Test classification data extraction.""" consolidator = S2DataConsolidator(sample_s2_datatree) consolidator._extract_measurements_data() @@ -309,7 +309,7 @@ def test_extract_classification_data(self, sample_s2_datatree) -> None: # Classification should be at 20m resolution assert "scl" in consolidator.measurements_data[20]["classification"] - def test_extract_probability_data(self, sample_s2_datatree) -> None: + def test_extract_probability_data(self, sample_s2_datatree: MagicMock) -> None: """Test probability data extraction.""" consolidator = S2DataConsolidator(sample_s2_datatree) consolidator._extract_measurements_data() @@ -318,7 +318,7 @@ def test_extract_probability_data(self, sample_s2_datatree) -> None: assert "cld" in consolidator.measurements_data[20]["probability"] assert "snw" in consolidator.measurements_data[20]["probability"] - def test_extract_geometry_data(self, sample_s2_datatree) -> None: + def test_extract_geometry_data(self, sample_s2_datatree: MagicMock) -> None: """Test geometry data extraction.""" consolidator = S2DataConsolidator(sample_s2_datatree) consolidator._extract_geometry_data() @@ -329,7 +329,7 @@ def test_extract_geometry_data(self, sample_s2_datatree) -> None: assert "view_zenith_angle" in consolidator.geometry_data assert "view_azimuth_angle" in consolidator.geometry_data - def test_extract_meteorology_data(self, sample_s2_datatree) -> None: + def test_extract_meteorology_data(self, sample_s2_datatree: MagicMock) -> None: """Test meteorology data extraction.""" consolidator = S2DataConsolidator(sample_s2_datatree) consolidator._extract_meteorology_data() @@ -412,7 +412,9 @@ def sample_data_dict(self) -> dict[str, dict[str, xr.DataArray]]: }, } - def test_create_consolidated_dataset_success(self, sample_data_dict) -> None: + def test_create_consolidated_dataset_success( + self, sample_data_dict: dict[str, dict[str, xr.DataArray]] + ) -> None: """Test successful dataset creation.""" ds = create_consolidated_dataset(sample_data_dict, resolution=10) @@ -434,14 +436,20 @@ def test_create_consolidated_dataset_success(self, sample_data_dict) -> None: def test_create_consolidated_dataset_empty_data(self) -> None: """Test dataset creation with empty data.""" - empty_data_dict = {"bands": {}, "quality": {}, "atmosphere": {}} + empty_data_dict: dict[str, dict[str, xr.DataArray]] = { + "bands": {}, + "quality": {}, + "atmosphere": {}, + } ds = create_consolidated_dataset(empty_data_dict, resolution=20) # Should return empty dataset assert isinstance(ds, xr.Dataset) assert len(ds.data_vars) == 0 - def test_create_consolidated_dataset_with_crs(self, sample_data_dict) -> None: + def test_create_consolidated_dataset_with_crs( + self, sample_data_dict: dict[str, dict[str, xr.DataArray]] + ) -> None: """Test dataset creation with CRS information.""" # Add CRS to one of the data arrays sample_data_dict["bands"]["b02"] = sample_data_dict["bands"]["b02"].rio.write_crs( @@ -513,7 +521,7 @@ def complete_s2_datatree(self) -> MagicMock: coords={"time": time, "x": x_20m, "y": y_20m}, ) - def mock_getitem(self, path: str) -> MagicMock: + def mock_getitem(self: object, path: str) -> MagicMock: mock_node = MagicMock() if "/measurements/reflectance/r10m" in path: mock_node.to_dataset.return_value = reflectance_10m @@ -526,7 +534,7 @@ def mock_getitem(self, path: str) -> MagicMock: mock_dt.__getitem__ = mock_getitem return mock_dt - def test_end_to_end_consolidation(self, complete_s2_datatree) -> None: + def test_end_to_end_consolidation(self, complete_s2_datatree: MagicMock) -> None: """Test complete end-to-end consolidation and dataset creation.""" # Step 1: Consolidate data consolidator = S2DataConsolidator(complete_s2_datatree) diff --git a/tests/test_s2_multiscale.py b/tests/test_s2_multiscale.py index a0ad955f..29c57117 100644 --- a/tests/test_s2_multiscale.py +++ b/tests/test_s2_multiscale.py @@ -4,6 +4,7 @@ import json import pathlib +from collections.abc import Mapping, Sequence from itertools import pairwise from pathlib import Path from unittest.mock import patch @@ -17,6 +18,7 @@ from structlog.testing import capture_logs from zarr.codecs import BloscCodec, CastValue, ScaleOffset from zarr.core.dtype import Int16 +from zarr.core.metadata import ArrayV3Metadata from eopf_geozarr.s2_optimization.s2_multiscale import ( _coarsen_variable, @@ -70,7 +72,9 @@ def _dataset(resolution: int, size: int, x0: float, y0: float) -> xr.Dataset: {"band": (["y", "x"], np.ones((size, size), dtype=np.uint16))}, coords={"x": x, "y": y}, ) - return ds.rio.write_crs("EPSG:32631") + crs_ds = ds.rio.write_crs("EPSG:32631") + assert isinstance(crs_ds, xr.Dataset) + return crs_ds r10m = _dataset(10, 12, 600000.0, 4900020.0) r120m = _dataset(120, 3, 600030.0, 4899990.0) @@ -86,9 +90,17 @@ def stale_transform() -> tuple[float, float, float, float, float, float]: {"r10m": r10m, "r120m": r120m}, ) - layout = parent_group.attrs["multiscales"]["layout"] - derived_level = next(level for level in layout if level["asset"] == "r120m") - assert tuple(derived_level["spatial:transform"]) == ( + multiscales = parent_group.attrs["multiscales"] + assert isinstance(multiscales, Mapping) + layout = multiscales["layout"] + assert isinstance(layout, Sequence) + derived_level = next( + level for level in layout if isinstance(level, Mapping) and level["asset"] == "r120m" + ) + assert isinstance(derived_level, Mapping) + transform = derived_level["spatial:transform"] + assert isinstance(transform, Sequence) + assert tuple(transform) == ( 120.0, 0.0, 600030.0, @@ -101,8 +113,8 @@ def stale_transform() -> tuple[float, float, float, float, float, float]: def test_calculate_simple_shard_dimensions() -> None: """Test simplified shard dimensions calculation.""" # Test 3D data (time, y, x) - shards are multiples of chunks - data_shape = (5, 1024, 1024) - chunks = (1, 256, 256) + data_shape: tuple[int, ...] = (5, 1024, 1024) + chunks: tuple[int, ...] = (1, 256, 256) shard_dims = calculate_simple_shard_dimensions(data_shape, chunks) @@ -181,8 +193,8 @@ def test_create_measurements_encoding(keep_scale_offset: bool, sample_dataset: x # Check that encoding is created for all variables for var_name in sample_dataset.data_vars: - assert var_name in encoding - var_encoding = encoding[var_name] + assert str(var_name) in encoding + var_encoding = encoding[str(var_name)] # Check basic encoding structure assert "chunks" in var_encoding @@ -194,11 +206,11 @@ def test_create_measurements_encoding(keep_scale_offset: bool, sample_dataset: x # Check coordinate encoding for coord_name in sample_dataset.coords: - if coord_name in encoding: + if str(coord_name) in encoding: # Coordinates may have either compressor or compressors set to None assert ( - encoding[coord_name].get("compressor") is None - or encoding[coord_name].get("compressors") is None + encoding[str(coord_name)].get("compressor") is None + or encoding[str(coord_name)].get("compressors") is None ) # Store data and check that we are conditionally applying the scale-offset transformation # based on the request passed to the encoding @@ -220,7 +232,8 @@ def test_create_measurements_encoding_time_chunking(sample_dataset: xr.Dataset) for var_name in sample_dataset.data_vars: if sample_dataset[var_name].ndim == 3: # 3D variable with time - chunks = encoding[var_name]["chunks"] + chunks = encoding[str(var_name)].get("chunks") + assert chunks is not None assert chunks[0] == 1 # Time dimension should be chunked to 1 @@ -240,7 +253,7 @@ def test_calculate_aligned_chunk_size() -> None: @pytest.mark.filterwarnings("ignore:.*:FutureWarning") @pytest.mark.filterwarnings("ignore:.*:UserWarning") def test_create_multiscale_from_datatree( - s2_group_example: zarr.Group, + s2_group_example: pathlib.Path, tmp_path: pathlib.Path, ) -> None: """Snapshot test: a single canonical parametrization (keep_scale_offset=False, @@ -253,7 +266,13 @@ def test_create_multiscale_from_datatree( output_path = str(tmp_path / "output.zarr") input_group = zarr.open_group(s2_group_example) output_group = zarr.create_group(output_path) - dt_input = xr.open_datatree(input_group.store, engine="zarr", chunks="auto") + # xarray's open_datatree accepts a zarr store at runtime, but its stub does + # not list Store among the accepted input types. + dt_input = xr.open_datatree( + input_group.store, # pyright: ignore[reportArgumentType] + engine="zarr", + chunks="auto", + ) # Capture log output using structlog's testing context manager with capture_logs(): @@ -291,7 +310,9 @@ def test_create_multiscale_from_datatree( # check that all multiscale levels have the same data type # this check is redundant with the later check, but it's expedient to check this here. # eventually this check should be spun out into its own test - _, res_groups = zip(*observed_group["measurements/reflectance"].groups(), strict=False) + reflectance_group = observed_group["measurements/reflectance"] + assert isinstance(reflectance_group, zarr.Group) + _, res_groups = zip(*reflectance_group.groups(), strict=False) dtype_mismatch: set[object] = set() for group_a, group_b in pairwise(res_groups): @@ -421,6 +442,7 @@ def test_create_multiscale_from_datatree_behavior( # ------------------------------------------------------------------ for group_path, var_name in _ORIGINAL_GROUPS.items(): arr = zarr.open_array(output_path, path=f"{group_path}/{var_name}") + assert isinstance(arr.metadata, ArrayV3Metadata) codec_names = [type(c).__name__ for c in arr.metadata.codecs] if keep_scale_offset: @@ -461,6 +483,7 @@ def test_create_multiscale_from_datatree_behavior( assert ds.data_vars, f"{group_path} has no variables" for name in ds.data_vars: arr = zarr.open_array(output_path, path=f"{group_path}/{name}") + assert isinstance(arr.metadata, ArrayV3Metadata) codec_names = [type(c).__name__ for c in arr.metadata.codecs] if keep_scale_offset: diff --git a/tests/test_scale_offset.py b/tests/test_scale_offset.py index 18826e0f..913c1c84 100644 --- a/tests/test_scale_offset.py +++ b/tests/test_scale_offset.py @@ -37,4 +37,4 @@ def test_scale_offset_from_cf_round_trip() -> None: ) arr[:] = unpacked_values - np.testing.assert_array_almost_equal(arr[:], unpacked_values) + np.testing.assert_array_almost_equal(np.asarray(arr[:]), unpacked_values) diff --git a/tests/test_titiler_integration.py b/tests/test_titiler_integration.py index 3d761c76..925e019e 100644 --- a/tests/test_titiler_integration.py +++ b/tests/test_titiler_integration.py @@ -9,6 +9,10 @@ - titiler-xarray, httpx installed """ +# titiler/fastapi/starlette are optional (the `downstream-titiler` group); this +# module is skipped at runtime when they're absent, so don't flag their imports. +# pyright: reportMissingImports=false + from __future__ import annotations import pathlib @@ -89,7 +93,7 @@ def _open_group(path: pathlib.Path, group: str) -> xr.Dataset: def _band_vars(ds: xr.Dataset) -> list[str]: """Get band variable names, excluding spatial_ref.""" - return [v for v in ds.data_vars if v != "spatial_ref"] + return [str(v) for v in ds.data_vars if v != "spatial_ref"] class TestTitilerInfo: diff --git a/uv.lock b/uv.lock index 6f1926ed..88d9e183 100644 --- a/uv.lock +++ b/uv.lock @@ -214,46 +214,6 @@ wheels = [ { url = "https://files.pythonhosted.org/packages/da/42/e921fccf5015463e32a3cf6ee7f980a6ed0f395ceeaa45060b61d86486c2/anyio-4.13.0-py3-none-any.whl", hash = "sha256:08b310f9e24a9594186fd75b4f73f4a4152069e3853f1ed8bfbf58369f4ad708", size = 114353, upload-time = "2026-03-24T12:59:08.246Z" }, ] -[[package]] -name = "ast-serialize" -version = "0.5.0" -source = { registry = "https://pypi.org/simple" } -sdist = { url = "https://files.pythonhosted.org/packages/81/9d/09e27731bd5864a9ce04e3244074e674bb8936bf62b45e0357248717adac/ast_serialize-0.5.0.tar.gz", hash = "sha256:5880091bfe6f4f986f22866375c2e884843e7a0b6343ae41aeea659613d879b6", size = 61157, upload-time = "2026-05-17T17:48:29.429Z" } -wheels = [ - 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