From 28210410e43c43b11dab9a7a088ccc5d34d649f9 Mon Sep 17 00:00:00 2001 From: vincentsarago Date: Wed, 29 Oct 2025 13:26:17 +0100 Subject: [PATCH 1/7] switch titiler.xarray to obstore+zarr and add default application --- CONTRIBUTING.md | 3 + pyproject.toml | 3 +- .../xarray/examples/templates/landing.html | 42 - src/titiler/xarray/pyproject.toml | 22 +- src/titiler/xarray/tests/test_factory.py | 150 ++- src/titiler/xarray/tests/test_io_tools.py | 42 +- .../xarray/titiler/xarray/extensions.py | 6 +- src/titiler/xarray/titiler/xarray/io.py | 180 ++- .../{examples => titiler/xarray}/main.py | 12 +- .../xarray}/templates/conformance.html | 0 .../xarray}/templates/header.html | 0 .../titiler/xarray/templates/landing.html | 49 + uv.lock | 1147 ++++------------- 13 files changed, 599 insertions(+), 1057 deletions(-) delete mode 100644 src/titiler/xarray/examples/templates/landing.html rename src/titiler/xarray/{examples => titiler/xarray}/main.py (97%) rename src/titiler/xarray/{examples => titiler/xarray}/templates/conformance.html (100%) rename src/titiler/xarray/{examples => titiler/xarray}/templates/header.html (100%) create mode 100644 src/titiler/xarray/titiler/xarray/templates/landing.html diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md index 17e81c18e..a283b1126 100644 --- a/CONTRIBUTING.md +++ b/CONTRIBUTING.md @@ -39,6 +39,9 @@ uv run pytest src/titiler/extensions --cov=titiler.extensions --cov-report=xml - # titiler.mosaic uv run pytest src/titiler/mosaic --cov=titiler.mosaic --cov-report=xml --cov-append --cov-report=term-missing +# titiler.xarray +uv run pytest src/titiler/xarray --cov=titiler.xarray --cov-report=xml --cov-append --cov-report=term-missing + # titiler.application uv run pytest src/titiler/application --cov=titiler.application --cov-report=xml --cov-append --cov-report=term-missing ``` diff --git a/pyproject.toml b/pyproject.toml index cbbe5a7af..53570a836 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -43,7 +43,8 @@ dev = [ "pytest-cov", "pytest-asyncio", "httpx", - "zarr!=3.0.9", + "obstore", + "zarr>=3,<4.0", "h5netcdf", "fsspec", "s3fs", diff --git a/src/titiler/xarray/examples/templates/landing.html b/src/titiler/xarray/examples/templates/landing.html deleted file mode 100644 index 715d91d5b..000000000 --- a/src/titiler/xarray/examples/templates/landing.html +++ /dev/null @@ -1,42 +0,0 @@ -{% include "header.html" %} -{% if params %} - {% set urlq = url + '?' + params + '&' %} - {% else %} - {% set urlq = url + '?' %} -{% endif %} - - - -

{{ response.title }}

-

- {{ response.description }} -

- -
-  ______   __     ______   __     __         ______     ______
-/\__  _\ /\ \   /\__  _\ /\ \   /\ \       /\  ___\   /\  == \
-\/_/\ \/ \ \ \  \/_/\ \/ \ \ \  \ \ \____  \ \  __\   \ \  __<
-    \ \_\  \ \_\    \ \_\  \ \_\  \ \_____\  \ \_____\  \ \_\ \_\
-    \/_/   \/_/     \/_/   \/_/   \/_____/   \/_____/   \/_/ /_/
-
-  
- -

Links

- - -{% include "footer.html" %} diff --git a/src/titiler/xarray/pyproject.toml b/src/titiler/xarray/pyproject.toml index 04c6c2bef..bda7f2cb2 100644 --- a/src/titiler/xarray/pyproject.toml +++ b/src/titiler/xarray/pyproject.toml @@ -36,38 +36,26 @@ dependencies = [ "rio-tiler>=7.6.1,<8.0", "xarray", "rioxarray", + "obstore", + "zarr>=3.0,<4.0", ] [project.optional-dependencies] -full = [ - "zarr!=3.0.9", +fs = [ "h5netcdf", "fsspec", "s3fs", "aiohttp", "gcsfs", + "requests", ] -minimal = [ - "zarr!=3.0.9", - "h5netcdf", - "fsspec", -] -gcs = [ - "gcsfs", -] -s3 = [ - "s3fs", -] -http = [ - "aiohttp", -] + [dependency-groups] test = [ "pytest", "pytest-cov", "pytest-asyncio", "httpx", - "zarr!=3.0.9", "h5netcdf", "fsspec", "s3fs", diff --git a/src/titiler/xarray/tests/test_factory.py b/src/titiler/xarray/tests/test_factory.py index e7aca5f12..42ba0e1f6 100644 --- a/src/titiler/xarray/tests/test_factory.py +++ b/src/titiler/xarray/tests/test_factory.py @@ -9,6 +9,7 @@ from titiler.xarray.extensions import DatasetMetadataExtension, VariablesExtension from titiler.xarray.factory import TilerFactory +from titiler.xarray.io import FsReader, fs_open_dataset prefix = os.path.join(os.path.dirname(__file__), "fixtures") @@ -61,7 +62,30 @@ def test_tiler_factory(): @pytest.fixture def app(): """App fixture.""" - md = TilerFactory(router_prefix="/md", extensions=[DatasetMetadataExtension()]) + md = TilerFactory( + router_prefix="/md", + extensions=[ + DatasetMetadataExtension(dataset_opener=fs_open_dataset), + ], + reader=FsReader, + ) + assert len(md.router.routes) == 22 + + app = FastAPI() + app.include_router(md.router, prefix="/md") + with TestClient(app) as client: + yield client + + +@pytest.fixture +def app_zarr(): + """App fixture.""" + md = TilerFactory( + router_prefix="/md", + extensions=[ + DatasetMetadataExtension(), + ], + ) assert len(md.router.routes) == 22 app = FastAPI() @@ -393,7 +417,7 @@ def test_zarr_group(group, app): def test_preview(filename): """App fixture.""" with pytest.warns(UserWarning): - md = TilerFactory(add_preview=True) + md = TilerFactory(add_preview=True, reader=FsReader) app = FastAPI() app.include_router(md.router) @@ -437,3 +461,125 @@ def test_preview(filename): with mem.open() as dst: assert dst.width == 1024 assert dst.height == 1024 + + +@pytest.mark.parametrize( + "filename", + [dataset_3d_zarr], +) +def test_app_zarr(filename, app_zarr): + """Test endpoints with Zarr Reader.""" + resp = app_zarr.get("/md/dataset/keys", params={"url": filename}) + assert resp.status_code == 200 + assert resp.headers["content-type"] == "application/json" + assert resp.json() == ["dataset"] + + resp = app_zarr.get("/md/dataset/dict", params={"url": filename}) + assert resp.status_code == 200 + assert resp.headers["content-type"] == "application/json" + assert resp.json()["data_vars"]["dataset"] + + resp = app_zarr.get("/md/dataset/", params={"url": filename}) + assert resp.status_code == 200 + assert "text/html" in resp.headers["content-type"] + + resp = app_zarr.get("/md/bounds", params={"url": filename, "variable": "dataset"}) + assert resp.status_code == 200 + assert resp.headers["content-type"] == "application/json" + + resp = app_zarr.get("/md/info", params={"url": filename, "variable": "dataset"}) + assert resp.status_code == 200 + assert resp.headers["content-type"] == "application/json" + + resp = app_zarr.get( + "/md/tiles/WebMercatorQuad/0/0/0", + params={"url": filename, "variable": "dataset", "rescale": "0,500", "bidx": 1}, + ) + assert resp.status_code == 200 + assert resp.headers["content-type"] == "image/png" + + resp = app_zarr.get( + "/md/WebMercatorQuad/tilejson.json", + params={"url": filename, "variable": "dataset", "rescale": "0,500", "bidx": 1}, + ) + assert resp.status_code == 200 + assert resp.headers["content-type"] == "application/json" + + resp = app_zarr.get( + "/md/point/0,0", params={"url": filename, "variable": "dataset"} + ) + assert resp.status_code == 200 + assert resp.headers["content-type"] == "application/json" + + feat = { + "type": "Feature", + "properties": {}, + "geometry": { + "type": "Polygon", + "coordinates": [ + [ + (-100.0, -25.0), + (40.0, -25.0), + (40.0, 60.0), + (-100.0, 60.0), + (-100.0, -25.0), + ] + ], + }, + } + + resp = app_zarr.post( + "/md/statistics", params={"url": filename, "variable": "dataset"}, json=feat + ) + assert resp.status_code == 200 + assert resp.headers["content-type"] == "application/geo+json" + + feat = { + "type": "Feature", + "properties": {}, + "geometry": { + "type": "Polygon", + "coordinates": [ + [ + (-100.0, -25.0), + (40.0, -25.0), + (40.0, 60.0), + (-100.0, 60.0), + (-100.0, -25.0), + ] + ], + }, + } + + resp = app_zarr.post( + "/md/feature", + params={"url": filename, "variable": "dataset", "rescale": "0,500", "bidx": 1}, + json=feat, + ) + assert resp.status_code == 200 + assert resp.headers["content-type"] == "image/jpeg" + + +@pytest.mark.parametrize( + "group", + [0, 1, 2], +) +def test_group_open_zarr(group, app_zarr): + """Test /tiles endpoints.""" + resp = app_zarr.get( + f"/md/tiles/WebMercatorQuad/{group}/0/0.tif", + params={"url": zarr_pyramid, "variable": "dataset", "group": str(group)}, + ) + assert resp.status_code == 200 + # see src/titiler/xarray/tests/fixtures/generate_fixtures.ipynb + # for structure of zarr pyramid + with MemoryFile(resp.content) as mem: + with mem.open() as dst: + arr = dst.read(1) + assert arr.max() == group * 2 + 1 + + resp = app_zarr.get( + "/md/point/0,0", + params={"url": zarr_pyramid, "variable": "dataset", "group": str(group)}, + ) + assert resp.json()["values"] == [group * 2 + 1] diff --git a/src/titiler/xarray/tests/test_io_tools.py b/src/titiler/xarray/tests/test_io_tools.py index 28e224908..2581a30a0 100644 --- a/src/titiler/xarray/tests/test_io_tools.py +++ b/src/titiler/xarray/tests/test_io_tools.py @@ -9,7 +9,7 @@ import pytest import xarray -from titiler.xarray.io import Reader, get_variable, xarray_open_dataset +from titiler.xarray.io import Reader, fs_open_dataset, get_variable, open_zarr prefix = os.path.join(os.path.dirname(__file__), "fixtures") @@ -220,7 +220,11 @@ def test_get_variable_datetime_tz(): def test_reader(protocol, filename): """test reader.""" src_path = protocol + os.path.join(protocol, prefix, filename) - with Reader(src_path, variable="dataset") as src: + with Reader(src_path, variable="dataset", opener=fs_open_dataset) as src: + assert src.info() + assert src.tile(0, 0, 0) + + with Reader(src_path, variable="dataset", group="/", opener=fs_open_dataset) as src: assert src.info() assert src.tile(0, 0, 0) @@ -267,7 +271,6 @@ def custom_netcdf_opener( # noqa: C901 fs = fsspec.filesystem(protocol) ds = xarray.open_dataset(fs.open(src_path), **xr_open_args) - return ds with Reader( @@ -303,14 +306,33 @@ def test_zarr_group(group): @pytest.mark.parametrize( - "src_path", + "src_path,options", + [ + ("s3://mur-sst/zarr-v1", {"anon": True}), + ( + "https://nasa-power.s3.amazonaws.com/syn1deg/temporal/power_syn1deg_monthly_temporal_lst.zarr", + {}, + ), + (os.path.join(prefix, "dataset_3d.zarr"), {}), + ], +) +def test_io_fs_open_dataset(src_path, options): + """test fs_open_dataset with cloud hosted files.""" + with fs_open_dataset(src_path, **options) as ds: + assert list(ds.data_vars) + + +@pytest.mark.parametrize( + "src_path,options", [ - # "s3://mur-sst/zarr-v1", - "https://nasa-power.s3.amazonaws.com/syn1deg/temporal/power_syn1deg_monthly_temporal_lst.zarr", - os.path.join(prefix, "dataset_3d.zarr"), + ("s3://mur-sst/zarr-v1", {"skip_signature": True}), + ("s3://mur-sst/zarr-v1", {"skip_signature": True, "region": "us-west-2"}), + # obstore.exceptions.GenericError: Generic S3 error: URL did not match any known pattern for scheme: https://nasa-power.s3.amazonaws.com/syn1deg/temporal/power_syn1deg_monthly_temporal_lst.zarr + # ("https://nasa-power.s3.amazonaws.com/syn1deg/temporal/power_syn1deg_monthly_temporal_lst.zarr", {}), + (os.path.join(prefix, "dataset_3d.zarr"), {}), ], ) -def test_io_xarray_open_dataset(src_path): - """test xarray_open_dataset with cloud hosted files.""" - with xarray_open_dataset(src_path) as ds: +def test_io_open_zarr(src_path, options): + """test open_zarr with cloud hosted files.""" + with open_zarr(src_path, **options) as ds: assert list(ds.data_vars) diff --git a/src/titiler/xarray/titiler/xarray/extensions.py b/src/titiler/xarray/titiler/xarray/extensions.py index 0f3515279..3c53727a4 100644 --- a/src/titiler/xarray/titiler/xarray/extensions.py +++ b/src/titiler/xarray/titiler/xarray/extensions.py @@ -13,7 +13,7 @@ from titiler.core.resources.enums import MediaType from titiler.xarray.dependencies import XarrayIOParams from titiler.xarray.factory import TilerFactory -from titiler.xarray.io import xarray_open_dataset +from titiler.xarray.io import open_zarr @define @@ -22,7 +22,7 @@ class VariablesExtension(FactoryExtension): # Custom dependency for /variables io_dependency: Type[DefaultDependency] = XarrayIOParams - dataset_opener: Callable[..., xarray.Dataset] = xarray_open_dataset + dataset_opener: Callable[..., xarray.Dataset] = open_zarr def __attrs_post_init__(self): """raise deprecation warning.""" @@ -54,7 +54,7 @@ class DatasetMetadataExtension(FactoryExtension): """Add dataset metadata endpoints to a Xarray TilerFactory.""" io_dependency: Type[DefaultDependency] = XarrayIOParams - dataset_opener: Callable[..., xarray.Dataset] = xarray_open_dataset + dataset_opener: Callable[..., xarray.Dataset] = open_zarr def register(self, factory: TilerFactory): """Register endpoint to the tiler factory.""" diff --git a/src/titiler/xarray/titiler/xarray/io.py b/src/titiler/xarray/titiler/xarray/io.py index 631519121..b422c747e 100644 --- a/src/titiler/xarray/titiler/xarray/io.py +++ b/src/titiler/xarray/titiler/xarray/io.py @@ -1,20 +1,39 @@ """titiler.xarray.io""" +from __future__ import annotations + +import os +from functools import cache +from pathlib import Path from typing import Any, Callable, Dict, List, Literal, Optional, Union from urllib.parse import urlparse import attr +import httpx +import obstore import xarray +import zarr from morecantile import TileMatrixSet from rio_tiler.constants import WEB_MERCATOR_TMS from rio_tiler.io.xarray import XarrayReader -from xarray.namedarray.utils import module_available +from zarr.storage import ObjectStore + +def _find_bucket_region(bucket: str, use_https: bool = True) -> str | None: + prefix = "https" if use_https else "http" + response = httpx.get(f"{prefix}://{bucket}.s3.amazonaws.com") + return response.headers.get("x-amz-bucket-region") -def xarray_open_dataset( # noqa: C901 + +@cache +def open_zarr( # noqa: C901 src_path: str, group: Optional[str] = None, decode_times: bool = True, + decode_coords: str = "all", + consolidated: bool = True, + infer_region: bool = True, + **kwargs: Any, ) -> xarray.Dataset: """Open Xarray dataset with fsspec. @@ -27,36 +46,15 @@ def xarray_open_dataset( # noqa: C901 xarray.Dataset """ - import fsspec # noqa - - try: - import h5netcdf - except ImportError: # pragma: nocover - h5netcdf = None # type: ignore - - try: - import zarr - except ImportError: # pragma: nocover - zarr = None # type: ignore - parsed = urlparse(src_path) - protocol = parsed.scheme or "file" - - if any(src_path.lower().endswith(ext) for ext in [".nc", ".nc4"]): - assert ( - h5netcdf is not None - ), "'h5netcdf' must be installed to read NetCDF dataset" - - xr_engine = "h5netcdf" - - else: - assert zarr is not None, "'zarr' must be installed to read Zarr dataset" - xr_engine = "zarr" + if not parsed.scheme: + src_path = str(Path(src_path).resolve()) + src_path = "file://" + src_path # Arguments for xarray.open_dataset # Default args xr_open_args: Dict[str, Any] = { - "decode_coords": "all", + "decode_coords": decode_coords, "decode_times": decode_times, } @@ -64,27 +62,32 @@ def xarray_open_dataset( # noqa: C901 if group is not None: xr_open_args["group"] = group - # NetCDF arguments - if xr_engine == "h5netcdf": - xr_open_args.update( - { - "engine": "h5netcdf", - "lock": False, - } - ) - fs = fsspec.filesystem(protocol) - ds = xarray.open_dataset(fs.open(src_path), **xr_open_args) + xr_open_args.update( + { + "engine": "zarr", + "consolidated": consolidated, + } + ) - # Fallback to Zarr - else: - if module_available("zarr", minversion="3.0"): - store = zarr.storage.FsspecStore.from_url( - src_path, storage_options={"asynchronous": True} + config = {**kwargs} + # We can't expect the users to pass a REGION so we guess it + if parsed.scheme == "s3": + if "region" not in kwargs and infer_region: + # infer region or fallback to env variables + region_name_env = ( + os.environ.get("AWS_REGION", os.environ.get("AWS_DEFAULT_REGION")) + or None ) - else: - store = fsspec.filesystem(protocol).get_mapper(src_path) + config["region"] = _find_bucket_region(parsed.netloc) or region_name_env + + store = obstore.store.from_url( + src_path, + config=config, + ) + + zarr_store = ObjectStore(store=store, read_only=True) + ds = xarray.open_dataset(zarr_store, **xr_open_args) - ds = xarray.open_zarr(store, **xr_open_args) return ds @@ -195,7 +198,7 @@ class Reader(XarrayReader): variable: str = attr.ib() # xarray.Dataset options - opener: Callable[..., xarray.Dataset] = attr.ib(default=xarray_open_dataset) + opener: Callable[..., xarray.Dataset] = attr.ib(default=open_zarr) opener_options: Dict = attr.ib(factory=dict) group: Optional[str] = attr.ib(default=None) @@ -216,13 +219,13 @@ class Reader(XarrayReader): def __attrs_post_init__(self): """Set bounds and CRS.""" - self.ds = self.opener( - self.src_path, - group=self.group, - decode_times=self.decode_times, + opener_options = { + "group": self.group, + "decode_times": self.decode_times, **self.opener_options, - ) + } + self.ds = self.opener(self.src_path, **opener_options) self.input = get_variable( self.ds, self.variable, @@ -238,3 +241,78 @@ def close(self): def __exit__(self, exc_type, exc_value, traceback): """Support using with Context Managers.""" self.close() + + +def fs_open_dataset( # noqa: C901 + src_path: str, + group: Optional[str] = None, + decode_times: bool = True, + decode_coords: str = "all", + **kwargs, +) -> xarray.Dataset: + """Open Xarray dataset with fsspec. + + Args: + src_path (str): dataset path. + group (Optional, str): path to the netCDF/Zarr group in the given file to open given as a str. + decode_times (bool): If True, decode times encoded in the standard NetCDF datetime format into datetime objects. Otherwise, leave them encoded as numbers. + + Returns: + xarray.Dataset + + """ + import fsspec # noqa + + try: + import h5netcdf + except ImportError: # pragma: nocover + h5netcdf = None # type: ignore + + parsed = urlparse(src_path) + protocol = parsed.scheme or "file" + + # Arguments for xarray.open_dataset + # Default args + xr_open_args: Dict[str, Any] = { + "decode_coords": decode_coords, + "decode_times": decode_times, + } + + # Argument if we're opening a datatree + if group is not None: + xr_open_args["group"] = group + + # NetCDF arguments + if any(src_path.lower().endswith(ext) for ext in [".nc", ".nc4"]): + assert ( + h5netcdf is not None + ), "'h5netcdf' must be installed to read NetCDF dataset" + + xr_open_args.update( + { + "engine": "h5netcdf", + "lock": False, + } + ) + fs = fsspec.filesystem(protocol, **kwargs) + ds = xarray.open_dataset(fs.open(src_path), **xr_open_args) + + # Fallback to Zarr + else: + store = zarr.storage.FsspecStore.from_url( + src_path, storage_options={"asynchronous": True, **kwargs} + ) + ds = xarray.open_zarr(store, **xr_open_args) + + return ds + + +# Compat +xarray_open_dataset = fs_open_dataset + + +@attr.s +class FsReader(Reader): + """Reader with fs_open_dataset opener""" + + opener: Callable[..., xarray.Dataset] = attr.ib(default=fs_open_dataset) diff --git a/src/titiler/xarray/examples/main.py b/src/titiler/xarray/titiler/xarray/main.py similarity index 97% rename from src/titiler/xarray/examples/main.py rename to src/titiler/xarray/titiler/xarray/main.py index 201bf91d8..86066c21d 100644 --- a/src/titiler/xarray/examples/main.py +++ b/src/titiler/xarray/titiler/xarray/main.py @@ -48,8 +48,8 @@ class ApiSettings(BaseSettings): """FASTAPI application settings.""" - name: str = "TiTiler with support of Multidimensional dataset" - description: str = """A modern dynamic tile server built on top of FastAPI and Rasterio/GDAL/Xarray for Zarr/NetCDF dataset. + name: str = "TiTiler with support of Zarr dataset" + description: str = """A modern dynamic tile server built on top of FastAPI and Rasterio/GDAL/Xarray for Zarr dataset. --- @@ -332,7 +332,7 @@ def landing( """TiTiler landing page.""" data = { "title": "TiTiler + Xarray", - "description": "A modern dynamic tile server built on top of FastAPI and Rasterio/GDAL/Xarray for Zarr/NetCDF dataset.", + "description": "A modern dynamic tile server built on top of FastAPI and Rasterio/GDAL/Xarray for Zarr dataset.", "links": [ { "title": "Landing page", @@ -492,9 +492,3 @@ def conformance( provider.add_span_processor(processor) trace.set_tracer_provider(provider) - - -if __name__ == "__main__": - import uvicorn - - uvicorn.run(app=app, host="127.0.0.1", port=8080, log_level="info") diff --git a/src/titiler/xarray/examples/templates/conformance.html b/src/titiler/xarray/titiler/xarray/templates/conformance.html similarity index 100% rename from src/titiler/xarray/examples/templates/conformance.html rename to src/titiler/xarray/titiler/xarray/templates/conformance.html diff --git a/src/titiler/xarray/examples/templates/header.html b/src/titiler/xarray/titiler/xarray/templates/header.html similarity index 100% rename from src/titiler/xarray/examples/templates/header.html rename to src/titiler/xarray/titiler/xarray/templates/header.html diff --git a/src/titiler/xarray/titiler/xarray/templates/landing.html b/src/titiler/xarray/titiler/xarray/templates/landing.html new file mode 100644 index 000000000..f9696c6b8 --- /dev/null +++ b/src/titiler/xarray/titiler/xarray/templates/landing.html @@ -0,0 +1,49 @@ +{% include "header.html" %} +{% if params %} + {% set urlq = url + '?' + params + '&' %} + {% else %} + {% set urlq = url + '?' %} +{% endif %} + + + +

{{ response.title }}

+

+ {{ response.description }} +

+ +
+   __     __   __     __ __                                                                                
+  |  \   |  \ |  \   |  \  \                                                                               
+ _| ▓▓_   \▓▓_| ▓▓_   \▓▓ ▓▓ ______   ______         __    __  ______   ______   ______   ______  __    __ 
+|   ▓▓ \ |  \   ▓▓ \ |  \ ▓▓/      \ /      \       |  \  /  \|      \ /      \ /      \ |      \|  \  |  \
+ \▓▓▓▓▓▓ | ▓▓\▓▓▓▓▓▓ | ▓▓ ▓▓  ▓▓▓▓▓▓\  ▓▓▓▓▓▓\      \\▓▓\/  ▓▓ \▓▓▓▓▓▓\  ▓▓▓▓▓▓\  ▓▓▓▓▓▓\ \▓▓▓▓▓▓\ ▓▓  | ▓▓
+  | ▓▓ __| ▓▓ | ▓▓ __| ▓▓ ▓▓ ▓▓    ▓▓ ▓▓              >▓▓  ▓▓ /      ▓▓ ▓▓   \▓▓ ▓▓   \▓▓/      ▓▓ ▓▓  | ▓▓
+  | ▓▓|  \ ▓▓ | ▓▓|  \ ▓▓ ▓▓ ▓▓▓▓▓▓▓▓ ▓▓      ▓▓▓▓▓▓ /  ▓▓▓▓\|  ▓▓▓▓▓▓▓ ▓▓     | ▓▓     |  ▓▓▓▓▓▓▓ ▓▓__/ ▓▓
+   \▓▓  ▓▓ ▓▓  \▓▓  ▓▓ ▓▓ ▓▓\▓▓     \ ▓▓            |  ▓▓ \▓▓\\▓▓    ▓▓ ▓▓     | ▓▓      \▓▓    ▓▓\▓▓    ▓▓
+    \▓▓▓▓ \▓▓   \▓▓▓▓ \▓▓\▓▓ \▓▓▓▓▓▓▓\▓▓             \▓▓   \▓▓ \▓▓▓▓▓▓▓\▓▓      \▓▓       \▓▓▓▓▓▓▓_\▓▓▓▓▓▓▓
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Links

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src/titiler/xarray/titiler/xarray/io.py | 30 +++++++++++++++++------ 2 files changed, 31 insertions(+), 10 deletions(-) diff --git a/src/titiler/xarray/tests/test_io_tools.py b/src/titiler/xarray/tests/test_io_tools.py index 2581a30a0..a90867b65 100644 --- a/src/titiler/xarray/tests/test_io_tools.py +++ b/src/titiler/xarray/tests/test_io_tools.py @@ -327,8 +327,15 @@ def test_io_fs_open_dataset(src_path, options): [ ("s3://mur-sst/zarr-v1", {"skip_signature": True}), ("s3://mur-sst/zarr-v1", {"skip_signature": True, "region": "us-west-2"}), - # obstore.exceptions.GenericError: Generic S3 error: URL did not match any known pattern for scheme: https://nasa-power.s3.amazonaws.com/syn1deg/temporal/power_syn1deg_monthly_temporal_lst.zarr - # ("https://nasa-power.s3.amazonaws.com/syn1deg/temporal/power_syn1deg_monthly_temporal_lst.zarr", {}), + # https://github.com/developmentseed/obstore/pull/590 + # ( + # "https://nasa-power.s3.amazonaws.com/syn1deg/temporal/power_syn1deg_monthly_temporal_lst.zarr", + # {"skip_signature": True}, + # ), + ( + "https://nasa-power.s3.us-west-2.amazonaws.com/syn1deg/temporal/power_syn1deg_monthly_temporal_lst.zarr", + {"skip_signature": True}, + ), (os.path.join(prefix, "dataset_3d.zarr"), {}), ], ) diff --git a/src/titiler/xarray/titiler/xarray/io.py b/src/titiler/xarray/titiler/xarray/io.py index b422c747e..3cce75265 100644 --- a/src/titiler/xarray/titiler/xarray/io.py +++ b/src/titiler/xarray/titiler/xarray/io.py @@ -3,6 +3,7 @@ from __future__ import annotations import os +import re from functools import cache from pathlib import Path from typing import Any, Callable, Dict, List, Literal, Optional, Union @@ -71,20 +72,33 @@ def open_zarr( # noqa: C901 config = {**kwargs} # We can't expect the users to pass a REGION so we guess it - if parsed.scheme == "s3": - if "region" not in kwargs and infer_region: - # infer region or fallback to env variables + if parsed.scheme == "s3" or "amazonaws.com" in parsed.netloc: + if "region" not in config and infer_region: region_name_env = ( os.environ.get("AWS_REGION", os.environ.get("AWS_DEFAULT_REGION")) or None ) - config["region"] = _find_bucket_region(parsed.netloc) or region_name_env - store = obstore.store.from_url( - src_path, - config=config, - ) + # s3:// urls + if parsed.scheme == "s3": + config["region"] = _find_bucket_region(parsed.netloc) or region_name_env + # https://{bucket}.s3.{region}?.amazonaws.com urls + else: + if expr := re.compile( + r"(?P[a-z0-9\.\-_]+)\.s3" + r"(\.dualstack)?" + r"(\.(?P[a-z0-9\-_]+))?" + r"\.amazonaws\.(com|cn)", + re.IGNORECASE, + ).match(parsed.netloc): + bucket = expr.groupdict()["bucket"] + if not expr.groupdict().get("region"): + config["region"] = ( + _find_bucket_region(bucket) or region_name_env + ) + + store = obstore.store.from_url(src_path, config=config) zarr_store = ObjectStore(store=store, read_only=True) ds = xarray.open_dataset(zarr_store, **xr_open_args) From 9277098243a8ebe98168689e58bb6ba8c82afe98 Mon Sep 17 00:00:00 2001 From: vincentsarago Date: Thu, 30 Oct 2025 12:22:12 +0100 Subject: [PATCH 4/7] update from comment --- src/titiler/xarray/titiler/xarray/io.py | 9 ++------- 1 file changed, 2 insertions(+), 7 deletions(-) diff --git a/src/titiler/xarray/titiler/xarray/io.py b/src/titiler/xarray/titiler/xarray/io.py index 3cce75265..2f1138c55 100644 --- a/src/titiler/xarray/titiler/xarray/io.py +++ b/src/titiler/xarray/titiler/xarray/io.py @@ -55,6 +55,8 @@ def open_zarr( # noqa: C901 # Arguments for xarray.open_dataset # Default args xr_open_args: Dict[str, Any] = { + "engine": "zarr", + "consolidated": consolidated, "decode_coords": decode_coords, "decode_times": decode_times, } @@ -63,13 +65,6 @@ def open_zarr( # noqa: C901 if group is not None: xr_open_args["group"] = group - xr_open_args.update( - { - "engine": "zarr", - "consolidated": consolidated, - } - ) - config = {**kwargs} # We can't expect the users to 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}, + { name = "s3fs", specifier = ">=2025.2.0" }, { name = "zarr", specifier = ">=3,<4.0" }, ] docs = [ From 5d12df261fe24a601d4bbc71df37ecf006f2e9db Mon Sep 17 00:00:00 2001 From: vincentsarago Date: Thu, 30 Oct 2025 14:40:27 +0100 Subject: [PATCH 6/7] assume https s3 object are public --- src/titiler/xarray/tests/test_io_tools.py | 9 ++++++--- src/titiler/xarray/titiler/xarray/io.py | 4 ++++ uv.lock | 2 +- 3 files changed, 11 insertions(+), 4 deletions(-) diff --git a/src/titiler/xarray/tests/test_io_tools.py b/src/titiler/xarray/tests/test_io_tools.py index a90867b65..bc0ae063e 100644 --- a/src/titiler/xarray/tests/test_io_tools.py +++ b/src/titiler/xarray/tests/test_io_tools.py @@ -325,16 +325,19 @@ def test_io_fs_open_dataset(src_path, options): @pytest.mark.parametrize( "src_path,options", [ + # Let's assume we don't have S3 Credentials ("s3://mur-sst/zarr-v1", {"skip_signature": True}), ("s3://mur-sst/zarr-v1", {"skip_signature": True, "region": "us-west-2"}), - # https://github.com/developmentseed/obstore/pull/590 + # HTTS url are considered public + ("https://mur-sst.s3.us-west-2.amazonaws.com/zarr-v1", {}), + # NOTE: https://github.com/developmentseed/obstore/pull/590 # ( # "https://nasa-power.s3.amazonaws.com/syn1deg/temporal/power_syn1deg_monthly_temporal_lst.zarr", - # {"skip_signature": True}, + # {}, # ), ( "https://nasa-power.s3.us-west-2.amazonaws.com/syn1deg/temporal/power_syn1deg_monthly_temporal_lst.zarr", - {"skip_signature": True}, + {}, ), (os.path.join(prefix, "dataset_3d.zarr"), {}), ], diff --git a/src/titiler/xarray/titiler/xarray/io.py b/src/titiler/xarray/titiler/xarray/io.py index 2f1138c55..46ddf0d95 100644 --- a/src/titiler/xarray/titiler/xarray/io.py +++ b/src/titiler/xarray/titiler/xarray/io.py @@ -80,6 +80,10 @@ def open_zarr( # noqa: C901 # https://{bucket}.s3.{region}?.amazonaws.com urls else: + # We assume that https:// url are public object + config["skip_signature"] = True + + # Get Region from URL or guess if needed if expr := re.compile( r"(?P[a-z0-9\.\-_]+)\.s3" r"(\.dualstack)?" diff --git a/uv.lock b/uv.lock index 320a9e0ea..401ff90e6 100644 --- a/uv.lock +++ b/uv.lock @@ -4371,7 +4371,7 @@ requires-dist = [ { name = "requests", marker = "extra == 'fs'" }, { name = "rio-tiler", specifier = ">=7.6.1,<8.0" }, { name = "rioxarray" }, - { name = "s3fs", marker = "extra == 'fs'" }, + { name = "s3fs", marker = "extra == 'fs'", specifier = ">=2025.2.0" }, { name = "titiler-core", editable = "src/titiler/core" }, { name = "xarray" }, { name = "zarr", specifier = ">=3.0,<4.0" }, From 02546d1752b4586b8161e3ebacde2cc8b77c7182 Mon Sep 17 00:00:00 2001 From: vincentsarago Date: Thu, 6 Nov 2025 18:48:39 +0100 Subject: [PATCH 7/7] update dependencies and remove consolidated --- src/titiler/xarray/pyproject.toml | 2 +- src/titiler/xarray/titiler/xarray/io.py | 2 -- uv.lock | 2 +- 3 files changed, 2 insertions(+), 4 deletions(-) diff --git a/src/titiler/xarray/pyproject.toml b/src/titiler/xarray/pyproject.toml index 37a61dfe7..bc59ca692 100644 --- a/src/titiler/xarray/pyproject.toml +++ b/src/titiler/xarray/pyproject.toml @@ -37,7 +37,7 @@ dependencies = [ "xarray", "rioxarray", "obstore", - "zarr>=3.0,<4.0", + "zarr>=3.1,<4.0", ] [project.optional-dependencies] diff --git a/src/titiler/xarray/titiler/xarray/io.py b/src/titiler/xarray/titiler/xarray/io.py index 46ddf0d95..ebbfe3476 100644 --- a/src/titiler/xarray/titiler/xarray/io.py +++ b/src/titiler/xarray/titiler/xarray/io.py @@ -32,7 +32,6 @@ def open_zarr( # noqa: C901 group: Optional[str] = None, decode_times: bool = True, decode_coords: str = "all", - consolidated: bool = True, infer_region: bool = True, **kwargs: Any, ) -> xarray.Dataset: @@ -56,7 +55,6 @@ def open_zarr( # noqa: C901 # Default args xr_open_args: Dict[str, Any] = { "engine": "zarr", - "consolidated": consolidated, "decode_coords": decode_coords, "decode_times": decode_times, } diff --git a/uv.lock b/uv.lock index 401ff90e6..9d4224fdd 100644 --- a/uv.lock +++ b/uv.lock @@ -4374,7 +4374,7 @@ requires-dist = [ { name = "s3fs", marker = "extra == 'fs'", specifier = ">=2025.2.0" }, { name = "titiler-core", editable = "src/titiler/core" }, { name = "xarray" }, - { name = "zarr", specifier = ">=3.0,<4.0" }, + { name = "zarr", specifier = ">=3.1,<4.0" }, ] provides-extras = ["fs"]