Update to support geopandas with pyproj.CRS (#18)

corteva · Mar 10, 2020 · 680cb3f · 680cb3f
1 parent 27620a3
commit 680cb3f
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diff --git a/.travis.yml b/.travis.yml
@@ -38,7 +38,7 @@ before_install:
 - conda config --add channels conda-forge
 - conda config --set channel_priority strict
 # Create conda environment for geocube
-- conda create -n test python=$PYTHON_VERSION $CONDA_COMPILER datacube gdal=2.4.* geopandas  libgdal=2.4.* rasterio=1.0.* scipy xarray
+- conda create -n test python=$PYTHON_VERSION $CONDA_COMPILER datacube gdal=2.4 geopandas  libgdal=2.4 rasterio scipy xarray
 - source activate test
 
 install:

diff --git a/appveyor.yml b/appveyor.yml
@@ -18,7 +18,7 @@ install:
 #-----------------------------------------------------------------------------
 # Create conda environment for geocube
 #-----------------------------------------------------------------------------
-  - conda create -n test python=%PYTHON_VERSION% datacube gdal=2.4.* geopandas  libgdal=2.4.* rasterio=1.0.* scipy xarray
+  - conda create -n test python=%PYTHON_VERSION% datacube gdal=2.4 geopandas  libgdal=2.4 rasterio scipy xarray
   - activate test
 
 #-------------------------------------------------------------------------------

diff --git a/docs/examples/categorical.ipynb b/docs/examples/categorical.ipynb
diff --git a/docs/examples/resample_point_data.ipynb b/docs/examples/resample_point_data.ipynb
@@ -33,8 +33,10 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "gdf = gpd.read_file(\"../../test/test_data/input/time_vector_data.geojson\")\n",
-    "gdf.crs = {'init': 'epsg:4326'}"
+    "gdf = gpd.read_file(\n",
+    "    \"../../test/test_data/input/time_vector_data.geojson\",\n",
+    "    crs=\"epsg:4326\",\n",
+    ")"
    ]
   },
   {
@@ -388,9 +390,9 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.6.7"
+   "version": "3.6.10"
   }
  },
  "nbformat": 4,
  "nbformat_minor": 4
-}
+}
diff --git a/docs/examples/timestamp_missing_data.ipynb b/docs/examples/timestamp_missing_data.ipynb
diff --git a/docs/history.rst b/docs/history.rst
@@ -1,6 +1,11 @@
 History
 =======
 
+0.0.12
+------
+- ENH: Update to support geopandas with pyproj.CRS (pull #18)
+- BUG: Update timestamp handling to ensure correct format for dtype (pull #18)
+
 0.0.11
 ------
 - Drop Python 3.5 Support (issue #12)

diff --git a/docs/installation.rst b/docs/installation.rst
@@ -8,7 +8,20 @@ Installation
 Stable release
 --------------
 
-. Use pip to install from `PyPI <https://pypi.org/project/geocube/>`__:
+Use pip to install from `PyPI <https://pypi.org/project/geocube/>`__:
+
+
+Step 1: Install python GDAL version associated with your GDAL version. 
+
+Here is a Linux example with GDAL installed in your system:
+
+  .. code-block:: bash
+
+      export CPLUS_INCLUDE_PATH=/usr/include/gdal
+      export C_INCLUDE_PATH=/usr/include/gdal  
+      pip install GDAL~=$(gdal-config --version | awk -F'[.]' '{print $1"."$2}').0
+
+Step 2: Install from pip:
 
   .. code-block:: bash
     

diff --git a/geocube/cli/commands/make_geocube.py b/geocube/cli/commands/make_geocube.py
@@ -69,7 +69,7 @@
     "-c",
     "--output-crs",
     help=(
-        "The CRS of the returned data. (e.x. +init=epsg:4326). "
+        "The CRS of the returned data. (e.g. epsg:4326). "
         "If no CRS is supplied, the CRS of the input data is used."
     ),
     required=False,

diff --git a/geocube/geo_utils/crs.py b/geocube/geo_utils/crs.py
diff --git a/geocube/geo_utils/geobox.py b/geocube/geo_utils/geobox.py
@@ -7,11 +7,10 @@
 import geopandas as gpd
 import rioxarray  # noqa
 from datacube.utils import geometry
-from rasterio.crs import CRS
+from rioxarray.crs import crs_to_wkt
 from shapely.geometry import box, mapping
 
 from geocube.exceptions import VectorDataError
-from geocube.geo_utils.crs import crs_to_wkt
 from geocube.logger import get_logger
 
 
@@ -71,7 +70,7 @@ def load_vector_data(vector_data):
 
     # make sure projection is set
     if not vector_data.crs:
-        vector_data.crs = {"init": "epsg:4326"}
+        vector_data.crs = "EPSG:4326"
         logger.warning(
             "Projection not defined in `vector_data`."
             " Setting to geographic (EPSG:4326)."
@@ -149,9 +148,9 @@ def from_vector(self, vector_data):
             raise RuntimeError("Must specify 'resolution' if 'like' not specified.")
 
         if self.output_crs:
-            crs = geometry.CRS(self.output_crs)
+            crs = geometry.CRS(crs_to_wkt(self.output_crs))
         else:
-            crs = geometry.CRS(crs_to_wkt(CRS.from_user_input(vector_data.crs)))
+            crs = geometry.CRS(crs_to_wkt(vector_data.crs))
 
         if self.geom is None and self.output_crs:
             geopoly = geometry.Geometry(
@@ -168,12 +167,11 @@ def from_vector(self, vector_data):
         else:
             geom_json = json.loads(self.geom)
             geom_crs = geometry.CRS(
-                "+init={}".format(
-                    geom_json["crs"]["properties"]["name"].lower()
-                    if "crs" in geom_json
-                    else "epsg:4326"
-                )
+                geom_json["crs"]["properties"]["name"]
+                if "crs" in geom_json
+                else "epsg:4326"
             )
+
             geopoly = geometry.Geometry(geom_json, crs=geom_crs)
 
         return geometry.GeoBox.from_geopolygon(

diff --git a/geocube/rasterize.py b/geocube/rasterize.py
@@ -5,8 +5,6 @@
 import numpy
 import pandas
 import rasterio.features
-import rasterio.transform
-import rasterio.warp
 from rasterio.enums import MergeAlg
 from scipy.interpolate import Rbf, griddata
 from shapely.geometry import mapping

diff --git a/geocube/vector_to_cube.py b/geocube/vector_to_cube.py
@@ -136,15 +136,13 @@ def make_geocube(
                 set(datetime_measurements) & set(measurements)
             )
         # reproject vector data to the projection of the output raster
-        vector_data = self.vector_data.to_crs(
-            self.geobox.crs._crs.ExportToProj4()
-        )  # pylint: disable=protected-access
+        vector_data = self.vector_data.to_crs(self.geobox.crs.wkt)
 
         # convert to datetime
         for datetime_measurement in self.datetime_measurements:
             vector_data[datetime_measurement] = pandas.to_datetime(
                 vector_data[datetime_measurement]
-            )
+            ).astype("datetime64[ns]")
 
         # get categorical enumerations if they exist
         self._categorical_enums = {}

diff --git a/geocube/xarray_extensions/vectorxarray.py b/geocube/xarray_extensions/vectorxarray.py
@@ -4,6 +4,7 @@
 """
 import geopandas as gpd
 import xarray
+from pyproj import CRS
 from shapely.wkb import dumps, loads
 
 
@@ -14,7 +15,7 @@ def from_geodataframe(in_geodataframe):
     geodf = in_geodataframe.copy().set_index("geometry")
     geox = xarray.Dataset.from_dataframe(geodf)
     geox.coords["crs"] = 0
-    geox.coords["crs"].attrs = geodf.crs
+    geox.coords["crs"].attrs["crs_wkt"] = CRS.from_user_input(geodf.crs).to_wkt()
     return geox
 
 
@@ -60,7 +61,7 @@ def to_geodataframe(self):
         if extra_coords:
             out_obj = out_obj.copy().reset_coords(extra_coords)
         geodf = gpd.GeoDataFrame(out_obj.to_dataframe().reset_index())
-        geodf.crs = self._obj.coords["crs"].attrs
+        geodf.crs = self._obj.coords["crs"].attrs["crs_wkt"]
         return geodf
 
     def to_netcdf(self, *args, **kwargs):

diff --git a/setup.py b/setup.py
@@ -14,10 +14,11 @@
     "appdirs",
     "Click>=6.0",
     "datacube",
-    "geopandas",
+    "geopandas>=0.6",
     "rasterio",
-    "rioxarray",
+    "rioxarray>=0.0.22",
     "xarray",
+    "pyproj>=2",
 ]
 
 test_requirements = ["pytest>=3.6", "pytest-cov", "mock"]

diff --git a/test/integration/api/test_core_integration.py b/test/integration/api/test_core_integration.py
@@ -20,7 +20,7 @@
 )
 from test.conftest import TEST_COMPARE_DATA_DIR, TEST_INPUT_DATA_DIR
 
-TEST_GARS_PROJ = "+init=epsg:32615"
+TEST_GARS_PROJ = "epsg:32615"
 TEST_GARS_POLY = loads(
     "POLYGON (("
     "-90.58343333333333 41.48343333333334, "
@@ -257,10 +257,10 @@ def test_make_geocube__convert_time(input_geodata, tmpdir):
 @pytest.mark.parametrize(
     "load_extra_kwargs",
     [
-        {"output_crs": "+init=epsg:4326"},
+        {"output_crs": "epsg:4326"},
         {"resolution": (-10, 10)},
         {"align": (0, 0)},
-        {"output_crs": "+init=epsg:4326", "resolution": (-10, 10), "align": (0, 0)},
+        {"output_crs": "epsg:4326", "resolution": (-10, 10), "align": (0, 0)},
     ],
 )
 def test_make_geocube__like_error_invalid_args(load_extra_kwargs):
@@ -588,10 +588,10 @@ def test_make_geocube__group_by_convert_with_time(input_geodata, tmpdir):
 @pytest.mark.parametrize(
     "load_extra_kwargs",
     [
-        {"output_crs": "+init=epsg:4326"},
+        {"output_crs": "epsg:4326"},
         {"resolution": (-10, 10)},
         {"align": (0, 0)},
-        {"output_crs": "+init=epsg:4326", "resolution": (-10, 10), "align": (0, 0)},
+        {"output_crs": "epsg:4326", "resolution": (-10, 10), "align": (0, 0)},
     ],
 )
 def test_make_geocube__group_by_like_error_invalid_args(load_extra_kwargs):

diff --git a/test/integration/xarray_extensions/test_integration_xarray_extensions_vectorxarray.py b/test/integration/xarray_extensions/test_integration_xarray_extensions_vectorxarray.py
@@ -22,7 +22,7 @@ def test_from_geodataframe():
     vxd = vectorxarray.from_geodataframe(gdf)
     assert all(gdf.geometry == vxd.geometry.values)
     assert sorted(gdf.columns.tolist() + ["crs"]) == sorted(vxd.variables)
-    assert gdf.crs == vxd.crs.attrs
+    assert gdf.crs == vxd.crs.attrs["crs_wkt"]
     assert "geometry" in vxd.coords
     assert "crs" in vxd.coords
 

diff --git a/test/test_data/compare/rasterize_griddata_cubic.nc b/test/test_data/compare/rasterize_griddata_cubic.nc
diff --git a/test/test_data/compare/rasterize_griddata_cubic_nodata.nc b/test/test_data/compare/rasterize_griddata_cubic_nodata.nc
diff --git a/test/test_data/compare/rasterize_griddata_nearest.nc b/test/test_data/compare/rasterize_griddata_nearest.nc
diff --git a/test/test_data/compare/rasterize_griddata_nearest_nodata.nc b/test/test_data/compare/rasterize_griddata_nearest_nodata.nc
diff --git a/test/test_data/compare/rasterize_griddata_rescale.nc b/test/test_data/compare/rasterize_griddata_rescale.nc
diff --git a/test/test_data/compare/rasterize_image_sum.nc b/test/test_data/compare/rasterize_image_sum.nc
diff --git a/test/test_data/compare/rasterize_image_sum_nodata.nc b/test/test_data/compare/rasterize_image_sum_nodata.nc
diff --git a/test/test_data/compare/rasterize_radial_linear.nc b/test/test_data/compare/rasterize_radial_linear.nc
diff --git a/test/test_data/compare/rasterize_radial_linear_nodata.nc b/test/test_data/compare/rasterize_radial_linear_nodata.nc
diff --git a/test/unit/cli/commands/test_make_geocube.py b/test/unit/cli/commands/test_make_geocube.py
@@ -41,11 +41,8 @@ def _get_called_dict(**kwargs):
             ["-m", "measure1", "--measurements", "measure2"],
             _get_called_dict(measurements=("measure1", "measure2")),
         ),
-        (["-c", "+init=epsg:4326"], _get_called_dict(output_crs="+init=epsg:4326")),
-        (
-            ["--output-crs", "+init=epsg:4326"],
-            _get_called_dict(output_crs="+init=epsg:4326"),
-        ),
+        (["-c", "epsg:4326"], _get_called_dict(output_crs="epsg:4326")),
+        (["--output-crs", "epsg:4326"], _get_called_dict(output_crs="epsg:4326"),),
         (["-r", "-10", "10"], _get_called_dict(resolution=(-10, 10))),
         (["--resolution", "-10", "10"], _get_called_dict(resolution=(-10, 10))),
         (["-a", "-10", "10"], _get_called_dict(align=(-10, 10))),