Merge pull request #256 from ASFHyP3/develop

Release v0.8.2

.github/workflows/static-analysis.yml

@@ -3,10 +3,12 @@ name: Static analysis
 on: push
 
 jobs:
+  # Docs: https://github.com/ASFHyP3/actions
   call-secrets-analysis-workflow:
-    # Docs: https://github.com/ASFHyP3/actions
     uses: ASFHyP3/actions/.github/workflows/[email protected]
 
   call-ruff-workflow:
-    # Docs: https://github.com/ASFHyP3/actions
     uses: ASFHyP3/actions/.github/workflows/[email protected]
+
+  call-mypy-workflow:
+    uses: ASFHyP3/actions/.github/workflows/[email protected]

CHANGELOG.md

@@ -6,6 +6,11 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 and this project adheres to [PEP 440](https://www.python.org/dev/peps/pep-0440/) 
 and uses [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## [0.8.2]
+
+### Added
+- Add `mypy` to [`static-analysis`](.github/workflows/static-analysis.yml)
+
 ## [0.8.1]
 
 ### Fixed

environment.yml

@@ -10,6 +10,7 @@ dependencies:
   # - arcpy  # windows only
   - python-build
   - ruff
+  - mypy
   - setuptools>=61
   - setuptools_scm>=6.2
   - pytest

pyproject.toml

@@ -54,6 +54,7 @@ flood_map = "asf_tools.hydrosar.flood_map:hyp3"
 develop = [
     "gdal-utils",
     "ruff",
+    "mypy",
     "pytest",
     "pytest-cov",
     "pytest-console-scripts",
@@ -103,3 +104,12 @@ convention = "google"
 [tool.ruff.lint.isort]
 case-sensitive = true
 lines-after-imports = 2
+
+[tool.mypy]
+python_version = "3.10"
+warn_redundant_casts = true
+warn_unused_ignores = true
+warn_unreachable = true
+strict_equality = true
+check_untyped_defs = true
+explicit_package_bases = true

src/asf_tools/composite.py

@@ -151,7 +151,7 @@ def reproject_to_target(raster_info: dict, target_epsg_code: int, target_resolut
     return target_raster_info
 
 
-def make_composite(out_name: str, rasters: list[str], resolution: float = None):
+def make_composite(out_name: str, rasters: list[str], resolution: float | None = None):
     """Creates a local-resolution-weighted composite from Sentinel-1 RTC products
 
     Args:
@@ -201,8 +201,8 @@ def make_composite(out_name: str, rasters: list[str], resolution: float = None):
         for raster, info in raster_info.items():
             log.info(f'Processing raster {raster}')
             log.debug(
-                f"Raster upper left: {info['cornerCoordinates']['upperLeft']}; "
-                f"lower right: {info['cornerCoordinates']['lowerRight']}"
+                f'Raster upper left: {info["cornerCoordinates"]["upperLeft"]}; '
+                f'lower right: {info["cornerCoordinates"]["lowerRight"]}'
             )
 
             values = read_as_array(raster)
@@ -261,7 +261,7 @@ def main():
         '-r',
         '--resolution',
         type=float,
-        help='Desired output resolution in meters ' '(default is the max resolution of all the input files)',
+        help='Desired output resolution in meters (default is the max resolution of all the input files)',
     )
     parser.add_argument('-v', '--verbose', action='store_true', help='Turn on verbose logging')
     args = parser.parse_args()

src/asf_tools/hydrosar/flood_map.py

@@ -31,14 +31,14 @@
 log = logging.getLogger(__name__)
 
 
-def get_pw_threshold(water_array: np.array) -> float:
+def get_pw_threshold(water_array: np.ndarray) -> float:
     hist, bin_edges = np.histogram(water_array, density=True, bins=100)
     reverse_cdf = np.cumsum(np.flipud(hist)) * (bin_edges[1] - bin_edges[0])
     ths_orig = np.flipud(bin_edges)[np.searchsorted(np.array(reverse_cdf), 0.95)]
     return round(ths_orig) + 1
 
 
-def get_waterbody(input_info: dict, threshold: float | None = None) -> np.array:
+def get_waterbody(input_info: dict, threshold: float | None = None) -> np.ndarray:
     epsg = get_epsg_code(input_info)
 
     west, south, east, north = get_coordinates(input_info)
@@ -67,9 +67,9 @@ def get_waterbody(input_info: dict, threshold: float | None = None) -> np.array:
 
 
 def iterative(
-    hand: np.array,
-    extent: np.array,
-    water_levels: np.array = np.arange(15),
+    hand: np.ndarray,
+    extent: np.ndarray,
+    water_levels: np.ndarray = np.arange(15),
     minimization_metric: str = 'ts',
 ):
     def get_confusion_matrix(w):
@@ -344,7 +344,7 @@ def optional_float(value: str) -> float | None:
 def _get_cli(interface: Literal['hyp3', 'main']) -> argparse.ArgumentParser:
     parser = argparse.ArgumentParser(description=__doc__, formatter_class=argparse.ArgumentDefaultsHelpFormatter)
 
-    available_estimators = ['iterative', 'logstat', 'nmad', 'numpy']
+    available_estimators: list[str | None] = ['iterative', 'logstat', 'nmad', 'numpy']
     estimator_help = 'Flood depth estimation approach.'
     if interface == 'hyp3':
         parser.add_argument('--bucket')
@@ -384,7 +384,7 @@ def _get_cli(interface: Literal['hyp3', 'main']) -> argparse.ArgumentParser:
         '--known-water-threshold',
         type=optional_float,
         default=None,
-        help='Threshold for extracting known water area in percent.' ' If `None`, threshold will be calculated.',
+        help='Threshold for extracting known water area in percent. If `None`, threshold will be calculated.',
     )
     parser.add_argument(
         '--minimization-metric',
@@ -421,7 +421,7 @@ def _get_cli(interface: Literal['hyp3', 'main']) -> argparse.ArgumentParser:
             type=int,
             nargs=2,
             default=[0, 15],
-            help='Minimum and maximum bound on the flood depths calculated using the iterative ' 'estimator.',
+            help='Minimum and maximum bound on the flood depths calculated using the iterative estimator.',
         )
     else:
         raise NotImplementedError(f'Unknown interface: {interface}')

src/asf_tools/hydrosar/hand/calculate.py

@@ -203,7 +203,7 @@ def make_copernicus_hand(
 
 
 def none_or_int(value: str):
-    if value.lower == 'none':
+    if value.lower() == 'none':
         return None
     return int(value)
 
@@ -226,8 +226,7 @@ def main():
         '--acc-threshold',
         type=none_or_int,
         default=100,
-        help='Accumulation threshold for determining the drainage mask. '
-        'If `None`, the mean accumulation value is used',
+        help='Accumulation threshold for determining the drainage mask. If `None`, the mean accumulation value is used',
     )
 
     parser.add_argument('-v', '--verbose', action='store_true', help='Turn on verbose logging')

src/asf_tools/hydrosar/threshold.py

@@ -95,7 +95,7 @@ def expectation_maximization_threshold(tile: np.ndarray, number_of_classes: int
     class_means = class_means + minimum - 1
     s = image_copy.shape
     posterior = np.zeros((s[0], s[1], number_of_classes))
-    posterior_lookup = dict()
+    posterior_lookup: dict = dict()
     for i in range(0, s[0]):
         for j in range(0, s[1]):
             pixel_val = image_copy2[i, j]

src/asf_tools/hydrosar/water_map.py

@@ -53,8 +53,8 @@ def select_hand_tiles(
 
     tile_indexes = np.arange(tiles.shape[0])
 
-    tiles = np.ma.masked_greater_equal(tiles, hand_threshold)
-    percent_valid_pixels = np.sum(~tiles.mask, axis=(1, 2)) / (tiles.shape[1] * tiles.shape[2])
+    masked_tiles = np.ma.masked_greater_equal(tiles, hand_threshold)
+    percent_valid_pixels = np.sum(~masked_tiles.mask, axis=(1, 2)) / (masked_tiles.shape[1] * masked_tiles.shape[2])
 
     return tile_indexes[percent_valid_pixels > hand_fraction]
 
@@ -100,10 +100,10 @@ def calculate_slope_magnitude(array: np.ndarray, pixel_size) -> np.ndarray:
 def determine_membership_limits(
     array: np.ndarray, mask_percentile: float = 90.0, std_range: float = 3.0
 ) -> tuple[float, float]:
-    array = np.ma.masked_values(array, 0.0)
-    array = np.ma.masked_greater(array, np.nanpercentile(array.filled(np.nan), mask_percentile))
-    lower_limit = np.ma.median(array)
-    upper_limit = lower_limit + std_range * array.std() + 5.0
+    masked_array = np.ma.masked_values(array, 0.0)
+    masked_array = np.ma.masked_greater(masked_array, np.nanpercentile(masked_array.filled(np.nan), mask_percentile))
+    lower_limit = np.ma.median(masked_array)
+    upper_limit = lower_limit + std_range * masked_array.std() + 5.0
     return lower_limit, upper_limit
 
 

src/asf_tools/raster.py

@@ -59,16 +59,16 @@ def read_as_masked_array(raster: str | Path, band: int = 1) -> np.ma.MaskedArray
     """
     log.debug(f'Reading raster values from {raster}')
     ds = gdal.Open(str(raster))
-    band = ds.GetRasterBand(band)
-    data = np.ma.masked_invalid(band.ReadAsArray())
-    nodata = band.GetNoDataValue()
+    raster_band = ds.GetRasterBand(band)
+    data = np.ma.masked_invalid(raster_band.ReadAsArray())
+    nodata = raster_band.GetNoDataValue()
     if nodata is not None:
         return np.ma.masked_values(data, nodata)
     del ds  # How to close w/ gdal
     return data
 
 
-def read_as_array(raster: str, band: int = 1) -> np.array:
+def read_as_array(raster: str, band: int = 1) -> np.ndarray:
     """Reads data from a raster image into memory
 
     Args:

src/asf_tools/tile.py

@@ -4,7 +4,7 @@
 def tile_array(
     array: np.ndarray | np.ma.MaskedArray,
     tile_shape: tuple[int, int] = (200, 200),
-    pad_value: float = None,
+    pad_value: float | None = None,
 ) -> np.ndarray | np.ma.MaskedArray:
     """Tile a 2D numpy array
 
@@ -49,6 +49,7 @@ def tile_array(
         raise ValueError(f'Cannot evenly tile a {array.shape} array into ({tile_rows},{tile_columns}) tiles')
 
     if rpad or cpad:
+        assert pad_value is not None
         padded_array = np.pad(array, ((0, rpad), (0, cpad)), constant_values=pad_value)
         if isinstance(array, np.ma.MaskedArray):
             mask = np.pad(array.mask, ((0, rpad), (0, cpad)), constant_values=True)
@@ -127,6 +128,7 @@ def untile_array(
             ] = tiled_array[ii * untiled_columns + jj, :, :]
 
     if isinstance(tiled_array, np.ma.MaskedArray):
+        assert len(untiled.shape) == 2
         untiled_mask = untile_array(tiled_array.mask, untiled.shape)
         untiled = np.ma.MaskedArray(untiled, mask=untiled_mask)
 

src/asf_tools/vector.py

@@ -17,6 +17,7 @@ def get_property_values_for_intersecting_features(geometry: ogr.Geometry, featur
     for feature in features:
         if feature.GetGeometryRef().Intersects(geometry):
             return True
+    return False
 
 
 def intersecting_feature_properties(geometry: ogr.Geometry, features: Iterator, feature_property: str) -> list[str]:

src/asf_tools/watermasking/generate_osm_tiles.py

@@ -102,7 +102,7 @@ def extract_water(water_file, lat, lon, tile_width_deg, tile_height_deg, interio
     tile_geojson = tile + '.geojson'
 
     # Extract tile from the main pbf, then convert it to a tif.
-    bbox = f'--bbox {lon},{lat},{lon+tile_width_deg},{lat+tile_height_deg}'
+    bbox = f'--bbox {lon},{lat},{lon + tile_width_deg},{lat + tile_height_deg}'
     extract_command = f'osmium extract -s smart -S tags=natural=water {bbox} {water_file} -o {tile_pbf}'.split(' ')
     export_command = f'osmium export --geometry-types=polygon {tile_pbf} -o {tile_geojson}'.split(' ')
     subprocess.run(extract_command)

tests/hydrosar/conftest.py

@@ -8,7 +8,7 @@
 def raster_tiles():
     tiles_file = Path(__file__).parent / 'data' / 'em_tiles.npz'
     tile_data = np.load(tiles_file)
-    tiles = np.ma.MaskedArray(tile_data['tiles'], mask=tile_data['mask'])
+    tiles: np.ma.MaskedArray = np.ma.MaskedArray(tile_data['tiles'], mask=tile_data['mask'])
     return np.log10(tiles) + 30
 
 

tests/test_raster.py

@@ -48,7 +48,7 @@ def test_convert_scale():
 
 
 def test_convert_scale_masked_arrays():
-    masked_array = np.ma.MaskedArray([-1, 0, 1, 4, 9], mask=[False, False, False, False, False])
+    masked_array: np.ma.MaskedArray = np.ma.MaskedArray([-1, 0, 1, 4, 9], mask=[False, False, False, False, False])
     c = raster.convert_scale(masked_array, 'power', 'db')
     assert np.allclose(c.mask, [True, True, False, False, False])
     assert np.allclose(

tests/test_tile.py

@@ -46,7 +46,7 @@ def test_tile_masked_array():
         ]
     )
 
-    ma = np.ma.MaskedArray(a, mask=m)
+    ma: np.ma.MaskedArray = np.ma.MaskedArray(a, mask=m)
     tiled = tile.tile_array(ma, tile_shape=(2, 2))
 
     assert tiled.shape == (4, 2, 2)
@@ -119,7 +119,7 @@ def test_untile_masked_array():
         ]
     )
 
-    ma = np.ma.MaskedArray(a, mask=m)
+    ma: np.ma.MaskedArray = np.ma.MaskedArray(a, mask=m)
     untiled = tile.untile_array(tile.tile_array(ma.copy(), tile_shape=(2, 2)), array_shape=a.shape)
 
     assert np.all(ma == untiled)