Merge branch 'develop'

.github/workflows/test.yml

@@ -28,7 +28,7 @@ jobs:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        python-version: [3.6, 3.9]
+        python-version: [3.7, 3.11]
         os: [ubuntu-latest]
     steps:
     - name: Checkout the repo

.pre-commit-config.yaml

@@ -3,7 +3,7 @@ fail_fast: false
 repos:
 
 -   repo: https://github.com/pre-commit/pre-commit-hooks.git
-    rev: v3.4.0
+    rev: v4.4.0
     hooks:
     -   id: trailing-whitespace
     -   id: end-of-file-fixer
@@ -17,23 +17,23 @@ repos:
     -   id: debug-statements
     -   id: check-merge-conflict
 
--   repo: 'https://gitlab.com/pycqa/flake8'
-    rev: 3.9.0
+-   repo: 'https://github.com/PyCQA/flake8'
+    rev: 5.0.4 # needed for py < 3.8.1
     hooks:
     -   id: flake8
 
 -   repo: 'https://github.com/ambv/black'
-    rev: 20.8b1
+    rev: 22.12.0
     hooks:
     -   id: black
         args: ['--safe']
 
--   repo: 'https://github.com/chewse/pre-commit-mirrors-pydocstyle'
-    rev: v2.1.1
+-   repo: https://github.com/pycqa/pydocstyle
+    rev: 6.1.1
     hooks:
     -   id: pydocstyle
 
 -   repo: https://github.com/pre-commit/mirrors-isort
-    rev: v5.7.0
+    rev: v5.10.1
     hooks:
     -   id: isort

CHANGES.rst

@@ -1,6 +1,14 @@
 Release history
 ---------------
 
+0.3.0 (2023-03-17)
+++++++++++++++++++
+
+- New Generic driver (#26)
+- `get_data()` `crs` and `resampling` parameters are now facultative (#25)
+- Support python versions from `3.7` to `3.11` (#34)
+- `pre-commit` and dependencies updates (#33)
+
 0.2.1 (2021-08-11)
 ++++++++++++++++++
 

eodag_cube/__init__.py

@@ -19,9 +19,9 @@
 
 __title__ = "eodag-cube"
 __description__ = "Data access for EODAG"
-__version__ = "0.2.1"
+__version__ = "0.3.0"
 __author__ = "CS GROUP - France (CSSI)"
-__author_email__ = "admin@geostorm.eu"
+__author_email__ = "eodag@csgroup.space"
 __url__ = "https://github.com/CS-SI/eodag-cube"
 __license__ = "Apache 2.0"
 __copyright__ = "Copyright 2021, CS GROUP - France, http://www.c-s.fr"

eodag_cube/api/product/_product.py

@@ -16,19 +16,19 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 import logging
+from contextlib import contextmanager
 
 import numpy as np
 import rasterio
 import rioxarray
 import xarray as xr
-from rasterio.enums import Resampling
 from rasterio.vrt import WarpedVRT
 
 from eodag.api.product._product import EOProduct as EOProduct_core
 from eodag.utils import get_geometry_from_various
 from eodag.utils.exceptions import DownloadError, UnsupportedDatasetAddressScheme
 
-logger = logging.getLogger("eodag_cube.api.product")
+logger = logging.getLogger("eodag.api.product")
 
 
 class EOProduct(EOProduct_core):
@@ -59,19 +59,26 @@ class EOProduct(EOProduct_core):
     def __init__(self, *args, **kwargs):
         super(EOProduct, self).__init__(*args, **kwargs)
 
-    def get_data(self, band, crs, resolution=None, extent=None, **rioxr_kwargs):
+    def get_data(
+        self,
+        band,
+        crs=None,
+        resolution=None,
+        extent=None,
+        resampling=None,
+        **rioxr_kwargs,
+    ):
         """Retrieves all or part of the raster data abstracted by the :class:`EOProduct`
 
         :param band: The band of the dataset to retrieve (e.g.: 'B01')
         :type band: str
-        :param crs: The coordinate reference system in which the dataset should be
-                    returned
+        :param crs: (optional) The coordinate reference system in which the dataset should be returned
         :type crs: str
-        :param resolution: The resolution in which the dataset should be returned
+        :param resolution: (optional) The resolution in which the dataset should be returned
                             (given in the unit of the crs)
         :type resolution: float
-        :param extent: The coordinates on which to zoom, matching the given CRS. Can be defined in different ways
-                    (its bounds will be used):
+        :param extent: (optional) The coordinates on which to zoom, matching the given CRS. Can be defined in
+                    different ways (its bounds will be used):
 
                     * with a Shapely geometry object:
                       :class:`shapely.geometry.base.BaseGeometry`
@@ -82,6 +89,8 @@ def get_data(self, band, crs, resolution=None, extent=None, **rioxr_kwargs):
                     * with a WKT str
 
         :type extent: Union[str, dict, shapely.geometry.base.BaseGeometry]
+        :param resampling: (optional) Warp resampling algorithm passed to :class:`rasterio.vrt.WarpedVRT`
+        :type resampling: Resampling
         :param rioxr_kwargs: kwargs passed to ``rioxarray.open_rasterio()``
         :type rioxr_kwargs: dict
         :returns: The numeric matrix corresponding to the sub dataset or an empty
@@ -90,6 +99,7 @@ def get_data(self, band, crs, resolution=None, extent=None, **rioxr_kwargs):
         """
         fail_value = xr.DataArray(np.empty(0))
         try:
+            logger.debug("Getting data address")
             dataset_address = self.driver.get_data_address(self, band)
         except UnsupportedDatasetAddressScheme:
             logger.warning(
@@ -98,7 +108,7 @@ def get_data(self, band, crs, resolution=None, extent=None, **rioxr_kwargs):
                 "data..."
             )
             try:
-                path_of_downloaded_file = self.download()
+                path_of_downloaded_file = self.download(extract=True)
             except (RuntimeError, DownloadError):
                 import traceback
 
@@ -125,24 +135,51 @@ def get_data(self, band, crs, resolution=None, extent=None, **rioxr_kwargs):
         # rasterio/gdal needed env variables for auth
         gdal_env = self._get_rio_env(dataset_address)
 
-        with rasterio.Env(**gdal_env):
-            with rasterio.open(dataset_address) as src:
-                with WarpedVRT(src, crs=crs, resampling=Resampling.bilinear) as vrt:
-
-                    da = rioxarray.open_rasterio(vrt, **rioxr_kwargs)
-                    if extent:
-                        da = da.rio.clip_box(minx=minx, miny=miny, maxx=maxx, maxy=maxy)
-                    if resolution:
-                        height = int((maxy - miny) / resolution)
-                        width = int((maxx - minx) / resolution)
-                        out_shape = (height, width)
-
-                        da = da.rio.reproject(
-                            dst_crs=crs,
-                            shape=out_shape,
-                            resampling=Resampling.bilinear,
-                        )
-                    return da
+        warped_vrt_args = {}
+        if crs is not None:
+            warped_vrt_args["crs"] = crs
+        if resampling is not None:
+            warped_vrt_args["resampling"] = resampling
+
+        @contextmanager
+        def pass_resource(resource, **kwargs):
+            yield resource
+
+        if warped_vrt_args:
+            warped_vrt_class = WarpedVRT
+        else:
+            warped_vrt_class = pass_resource
+
+        logger.debug(f"Getting data from {dataset_address}")
+
+        try:
+            with rasterio.Env(**gdal_env):
+                with rasterio.open(dataset_address) as src:
+                    with warped_vrt_class(src, **warped_vrt_args) as vrt:
+                        da = rioxarray.open_rasterio(vrt, **rioxr_kwargs)
+                        if extent:
+                            da = da.rio.clip_box(
+                                minx=minx, miny=miny, maxx=maxx, maxy=maxy
+                            )
+                        if resolution:
+                            height = int((maxy - miny) / resolution)
+                            width = int((maxx - minx) / resolution)
+                            out_shape = (height, width)
+
+                            reproject_args = {}
+                            if crs is not None:
+                                reproject_args["dst_crs"] = crs
+                            if resampling is not None:
+                                reproject_args["resampling"] = resampling
+
+                            da = da.rio.reproject(
+                                shape=out_shape,
+                                **reproject_args,
+                            )
+                        return da
+        except Exception as e:
+            logger.error(e)
+            return fail_value
 
     def _get_rio_env(self, dataset_address):
         """Get rasterio environement variables needed for data access.

eodag_cube/api/product/drivers/__init__.py

@@ -17,6 +17,7 @@
 # limitations under the License.
 """EODAG drivers package"""
 from eodag.api.product.drivers.base import NoDriver  # noqa
+from eodag_cube.api.product.drivers.generic import GenericDriver
 from eodag_cube.api.product.drivers.sentinel2_l1c import Sentinel2L1C
 from eodag_cube.api.product.drivers.stac_assets import StacAssets
 
@@ -37,4 +38,8 @@
         ],
         "driver": Sentinel2L1C(),
     },
+    {
+        "criteria": [lambda prod: True],
+        "driver": GenericDriver(),
+    },
 ]

eodag_cube/api/product/drivers/generic.py

@@ -0,0 +1,52 @@
+# -*- coding: utf-8 -*-
+# Copyright 2021, CS GROUP - France, http://www.c-s.fr
+#
+# This file is part of EODAG project
+#     https://www.github.com/CS-SI/EODAG
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+from pathlib import Path
+
+import rasterio
+
+from eodag.api.product.drivers.base import DatasetDriver
+from eodag.utils import uri_to_path
+from eodag.utils.exceptions import AddressNotFound, UnsupportedDatasetAddressScheme
+
+
+class GenericDriver(DatasetDriver):
+    """Generic Driver for products that need to be downloaded"""
+
+    def get_data_address(self, eo_product, band):
+        """Get the address of a product subdataset.
+
+        See :func:`~eodag.api.product.drivers.base.DatasetDriver.get_data_address` to get help on the formal
+        parameters.
+        """
+        product_location_scheme = eo_product.location.split("://")[0]
+        if product_location_scheme == "file":
+
+            filenames = Path(uri_to_path(eo_product.location)).glob(f"**/*{band}*")
+
+            for filename in filenames:
+                try:
+                    # return the first file readable by rasterio
+                    rasterio.drivers.driver_from_extension(filename)
+                    return str(filename)
+                except ValueError:
+                    pass
+            raise AddressNotFound
+        raise UnsupportedDatasetAddressScheme(
+            "eo product {} is accessible through a location scheme that is not yet "
+            "supported by eodag: {}".format(eo_product, product_location_scheme)
+        )

eodag_cube/api/product/protobuf/__init__.py

@@ -16,3 +16,11 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 """EODAG product protobuf package"""
+import os
+
+# Fixes: descriptors cannot not be created directly.
+# If this call came from a _pb2.py file, your generated code is out of date and must be regenerated with protoc >= 3.19.0.
+# If you cannot immediately regenerate your protos, some other possible workarounds are:
+#  1. Downgrade the protobuf package to 3.20.x or lower.
+#  2. Set PROTOCOL_BUFFERS_PYTHON_IMPLEMENTATION=python (but this will use pure-Python parsing and will be much slower).
+os.environ["PROTOCOL_BUFFERS_PYTHON_IMPLEMENTATION"] = "python"

eodag_cube/rpc/protocol/__init__.py

@@ -16,3 +16,11 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 """EODAG rpc.protocol package"""
+import os
+
+# Fixes: descriptors cannot not be created directly.
+# If this call came from a _pb2.py file, your generated code is out of date and must be regenerated with protoc >= 3.19.0.
+# If you cannot immediately regenerate your protos, some other possible workarounds are:
+#  1. Downgrade the protobuf package to 3.20.x or lower.
+#  2. Set PROTOCOL_BUFFERS_PYTHON_IMPLEMENTATION=python (but this will use pure-Python parsing and will be much slower).
+os.environ["PROTOCOL_BUFFERS_PYTHON_IMPLEMENTATION"] = "python"

setup.py

@@ -27,7 +27,7 @@
         "eodag >= 2.3.2",
         "numpy",
         "rasterio",
-        "protobuf",
+        "protobuf <= 3.20",
         "grpcio",
         "xarray",
         "rioxarray",
@@ -37,7 +37,7 @@
             "flake8",
             "isort",
             "pre-commit",
-            "pytest==5.0.1",  # pytest pined to v5.0.1 to avoid issue when run from VSCode
+            "pytest",
             "pytest-cov",
             "tox",
             "nose",
@@ -57,10 +57,11 @@
         "License :: OSI Approved :: Apache Software License",
         "Programming Language :: Python",
         "Programming Language :: Python :: 3",
-        "Programming Language :: Python :: 3.6",
         "Programming Language :: Python :: 3.7",
         "Programming Language :: Python :: 3.8",
         "Programming Language :: Python :: 3.9",
+        "Programming Language :: Python :: 3.10",
+        "Programming Language :: Python :: 3.11",
         "Programming Language :: Python :: Implementation :: CPython",
         "Topic :: Scientific/Engineering :: GIS",
     ],

tests/context.py

@@ -29,6 +29,7 @@
 from eodag.api.product import EOProduct
 from eodag.api.product.drivers import DRIVERS
 from eodag.api.product.drivers.base import NoDriver
+from eodag_cube.api.product.drivers.generic import GenericDriver
 from eodag_cube.api.product.drivers.sentinel2_l1c import Sentinel2L1C
 from eodag_cube.api.product.drivers.stac_assets import StacAssets
 from eodag.api.search_result import SearchResult