jgrss/features delayed

.flake8

@@ -0,0 +1,4 @@
+[flake8]
+extend-ignore = E203, E266, E501, W503, F403, F401, F841, C901
+max-line-length = 79
+max-complexity = 10

.pre-commit-config.yaml

@@ -16,3 +16,7 @@ repos:
         --wrap-descriptions,
         '79',
       ]
+  - repo: https://github.com/pycqa/flake8
+    rev: 6.0.0
+    hooks:
+    - id: flake8

pyproject.toml

@@ -5,3 +5,22 @@ requires = [
     'Cython>=0.29.0,<3.0.0',
     'numpy>=1.19.0'
 ]
+
+[tool.black]
+line-length = 79
+include = '\.pyi?$'
+exclude = '''
+/(
+    \.git
+  | \.hg
+  | \.mypy_cache
+  | \.tox
+  | \.venv
+  | \.vscode
+  | \.idea
+  | _build
+  | buck-out
+  | build
+  | dist
+)/
+'''

setup.cfg

@@ -59,6 +59,7 @@ docs = numpydoc
 tests = testfixtures
     jax
     jaxlib
+    pre-commit
 coreg = earthpy
     pyfftw==0.12.0
     bottleneck

src/geowombat/__init__.py

@@ -12,6 +12,7 @@
 from .core import calc_area
 from .core import subset
 from .core import clip
+from .core import clip_by_polygon
 from .core import mask
 from .core import replace
 from .core import recode
@@ -53,6 +54,7 @@
     'calc_area',
     'subset',
     'clip',
+    'clip_by_polygon',
     'mask',
     'replace',
     'recode',
@@ -81,5 +83,5 @@
     'bounds_to_coords',
     'lonlat_to_xy',
     'xy_to_lonlat',
-    '__version__'
+    '__version__',
 ]

src/geowombat/backends/rasterio_.py

@@ -36,20 +36,31 @@
     import numcodecs
 
     ZARR_INSTALLED = True
-except:
+except ImportError:
     ZARR_INSTALLED = False
 
 
 logger = logging.getLogger(__name__)
 
 
+def get_dims_from_bounds(
+    bounds: BoundingBox, res: T.Tuple[float, float]
+) -> T.Tuple[int, int]:
+    width = int((bounds.right - bounds.left) / abs(res[0]))
+    height = int((bounds.top - bounds.bottom) / abs(res[1]))
+
+    return height, width
+
+
 def get_file_info(src_obj):
     src_bounds = src_obj.bounds
     src_res = src_obj.res
     src_width = src_obj.width
     src_height = src_obj.height
 
-    FileInfo = namedtuple('FileInfo', 'src_bounds src_res src_width src_height')
+    FileInfo = namedtuple(
+        'FileInfo', 'src_bounds src_res src_width src_height'
+    )
 
     return FileInfo(
         src_bounds=src_bounds,
@@ -60,7 +71,15 @@ def get_file_info(src_obj):
 
 
 def to_gtiff(
-    filename, data, window, indexes, transform, n_workers, separate, tags, kwargs
+    filename,
+    data,
+    window,
+    indexes,
+    transform,
+    n_workers,
+    separate,
+    tags,
+    kwargs,
 ):
     """Writes data to a GeoTiff file.
 
@@ -140,7 +159,11 @@ def to_gtiff(
 
 class RasterioStore(object):
     def __init__(
-        self, filename: T.Union[str, Path], mode: str = 'w', tags: dict = None, **kwargs
+        self,
+        filename: T.Union[str, Path],
+        mode: str = 'w',
+        tags: dict = None,
+        **kwargs,
     ):
         self.filename = Path(filename)
         self.mode = mode
@@ -153,7 +176,9 @@ def __setitem__(self, key, item):
             index_range, y, x = key
             indexes = list(
                 range(
-                    index_range.start + 1, index_range.stop + 1, index_range.step or 1
+                    index_range.start + 1,
+                    index_range.stop + 1,
+                    index_range.step or 1,
                 )
             )
         else:
@@ -204,10 +229,13 @@ def close_delayed(self, store):
 
     def write(self, data: xr.DataArray, compute: bool = False) -> Delayed:
         if isinstance(data.data, da.Array):
-            return da.store(da.squeeze(data.data), self, lock=True, compute=compute)
+            return da.store(
+                da.squeeze(data.data), self, lock=True, compute=compute
+            )
         else:
             self.dst.write(
-                data.squeeze().data, indexes=list(range(1, data.data.shape[0] + 1))
+                data.squeeze().data,
+                indexes=list(range(1, data.data.shape[0] + 1)),
             )
 
     def close(self):
@@ -294,7 +322,9 @@ def __setitem__(self, key, item):
             index_range, y, x = key
             indexes = list(
                 range(
-                    index_range.start + 1, index_range.stop + 1, index_range.step or 1
+                    index_range.start + 1,
+                    index_range.stop + 1,
+                    index_range.step or 1,
                 )
             )
 
@@ -307,12 +337,14 @@ def __setitem__(self, key, item):
 
             if self.out_block_type.lower() == 'zarr':
 
-                group_name = '{BASE}_y{Y:09d}_x{X:09d}_h{H:09d}_w{W:09d}'.format(
-                    BASE=self.f_base,
-                    Y=y.start,
-                    X=x.start,
-                    H=y.stop - y.start,
-                    W=x.stop - x.start,
+                group_name = (
+                    '{BASE}_y{Y:09d}_x{X:09d}_h{H:09d}_w{W:09d}'.format(
+                        BASE=self.f_base,
+                        Y=y.start,
+                        X=x.start,
+                        H=y.stop - y.start,
+                        W=x.stop - x.start,
+                    )
                 )
 
                 group = self.root.create_group(group_name)
@@ -322,7 +354,10 @@ def __setitem__(self, key, item):
                     item,
                     compressor=self.compressor,
                     dtype=item.dtype.name,
-                    chunks=(self.kwargs['blockysize'], self.kwargs['blockxsize']),
+                    chunks=(
+                        self.kwargs['blockysize'],
+                        self.kwargs['blockxsize'],
+                    ),
                 )
 
                 group.attrs['row_off'] = y.start
@@ -405,7 +440,9 @@ def __setitem__(self, key, item):
             self.separate and self.out_block_type.lower() == 'gtiff'
         ):
 
-            with rio.open(out_filename, mode=io_mode, sharing=False, **kwargs) as dst_:
+            with rio.open(
+                out_filename, mode=io_mode, sharing=False, **kwargs
+            ) as dst_:
 
                 dst_.write(item, window=w, indexes=indexes)
 
@@ -605,7 +642,13 @@ def window_to_bounds(filenames, w):
     return left, bottom, right, top
 
 
-def align_bounds(minx, miny, maxx, maxy, res):
+def align_bounds(
+    minx: float,
+    miny: float,
+    maxx: float,
+    maxy: float,
+    res: T.Tuple[float, float],
+) -> T.Tuple[Affine, int, int]:
     """Aligns bounds to resolution.
 
     Args:
@@ -620,9 +663,8 @@ def align_bounds(minx, miny, maxx, maxy, res):
     """
     xres, yres = res
 
-    new_height = (maxy - miny) / yres
-    new_width = (maxx - minx) / xres
-
+    new_height = int(np.floor((maxy - miny) / yres))
+    new_width = int(np.floor((maxx - minx) / xres))
     new_transform = Affine(xres, 0.0, minx, 0.0, -yres, maxy)
 
     return aligned_target(new_transform, new_width, new_height, res)
@@ -666,7 +708,12 @@ def get_file_bounds(
                 dst_res = src_info.src_res
 
             # Transform the extent to the reference CRS
-            bounds_left, bounds_bottom, bounds_right, bounds_top = transform_bounds(
+            (
+                bounds_left,
+                bounds_bottom,
+                bounds_right,
+                bounds_top,
+            ) = transform_bounds(
                 src_crs,
                 dst_crs,
                 src_info.src_bounds.left,
@@ -785,7 +832,11 @@ def warp_images(
         # Get the union bounds of all images.
         #   *Target-aligned-pixels are returned.
         warp_kwargs['bounds'] = get_file_bounds(
-            filenames, bounds_by=bounds_by, crs=crs, res=res, return_bounds=True
+            filenames,
+            bounds_by=bounds_by,
+            crs=crs,
+            res=res,
+            return_bounds=True,
         )
 
     return [warp(fn, **warp_kwargs) for fn in filenames]
@@ -859,7 +910,12 @@ def warp(
         # Check if the data need to be subset
         if (bounds is None) or (tuple(bounds) == tuple(src_info.src_bounds)):
             if crs:
-                left_coord, bottom_coord, right_coord, top_coord = transform_bounds(
+                (
+                    left_coord,
+                    bottom_coord,
+                    right_coord,
+                    top_coord,
+                ) = transform_bounds(
                     src_crs,
                     dst_crs,
                     src_info.src_bounds.left,
@@ -905,7 +961,10 @@ def warp(
 
             elif isinstance(bounds, (list, np.ndarray, tuple)):
                 dst_bounds = BoundingBox(
-                    left=bounds[0], bottom=bounds[1], right=bounds[2], top=bounds[3]
+                    left=bounds[0],
+                    bottom=bounds[1],
+                    right=bounds[2],
+                    top=bounds[3],
                 )
 
             else:
@@ -915,8 +974,7 @@ def warp(
                 )
                 raise TypeError
 
-        dst_width = int((dst_bounds.right - dst_bounds.left) / dst_res[0])
-        dst_height = int((dst_bounds.top - dst_bounds.bottom) / dst_res[1])
+        dst_height, dst_width = get_dims_from_bounds(dst_bounds, dst_res)
 
         # Do not warp if all the key metadata match the reference information
         if (
@@ -940,7 +998,12 @@ def warp(
                 src_info.src_bounds.top,
             )
             dst_transform = Affine(
-                dst_res[0], 0.0, dst_bounds.left, 0.0, -dst_res[1], dst_bounds.top
+                dst_res[0],
+                0.0,
+                dst_bounds.left,
+                0.0,
+                -dst_res[1],
+                dst_bounds.top,
             )
 
             if tac:
@@ -992,7 +1055,9 @@ def reproject_array(
     num_threads: int,
 ) -> np.ndarray:
     """Reprojects a DataArray and translates to a numpy ndarray."""
-    dst_array = np.zeros((data.gw.nbands, dst_height, dst_width), dtype=data.dtype)
+    dst_array = np.zeros(
+        (data.gw.nbands, dst_height, dst_width), dtype=data.dtype
+    )
     dst_array, dst_transform = reproject(
         data.gw.compute(num_workers=num_threads),
         dst_array,
@@ -1109,20 +1174,32 @@ def transform_crs(
         if isinstance(dst_width, int) and isinstance(dst_height, int):
             xs = (
                 dst_transform
-                * (np.arange(0, dst_width) + 0.5, np.arange(0, dst_width) + 0.5)
+                * (
+                    np.arange(0, dst_width) + 0.5,
+                    np.arange(0, dst_width) + 0.5,
+                )
             )[0]
             ys = (
                 dst_transform
-                * (np.arange(0, dst_height) + 0.5, np.arange(0, dst_height) + 0.5)
+                * (
+                    np.arange(0, dst_height) + 0.5,
+                    np.arange(0, dst_height) + 0.5,
+                )
             )[1]
         else:
             xs = (
                 dst_transform
-                * (np.arange(0, dst_width_) + 0.5, np.arange(0, dst_width_) + 0.5)
+                * (
+                    np.arange(0, dst_width_) + 0.5,
+                    np.arange(0, dst_width_) + 0.5,
+                )
             )[0]
             ys = (
                 dst_transform
-                * (np.arange(0, dst_height_) + 0.5, np.arange(0, dst_height_) + 0.5)
+                * (
+                    np.arange(0, dst_height_) + 0.5,
+                    np.arange(0, dst_height_) + 0.5,
+                )
             )[1]
 
         XYCoords = namedtuple('XYCoords', 'xs ys')
@@ -1162,10 +1239,17 @@ def transform_crs(
 
     # Ensure the final transform is set based on adjusted bounds
     dst_transform = Affine(
-        abs(dst_res[0]), 0.0, dst_bounds.left, 0.0, -abs(dst_res[1]), dst_bounds.top
+        abs(dst_res[0]),
+        0.0,
+        dst_bounds.left,
+        0.0,
+        -abs(dst_res[1]),
+        dst_bounds.top,
     )
 
-    proj_func = dask.delayed(reproject_array) if delayed_array else reproject_array
+    proj_func = (
+        dask.delayed(reproject_array) if delayed_array else reproject_array
+    )
     transformed_array = proj_func(
         data_src,
         dst_height,