Python: Use black, flake8, isort

.flake8

@@ -0,0 +1,21 @@
+[flake8]
+max_line_length = 88
+ignore =
+    C408 # Unnecessary dict/list/tuple call - rewrite as a literal
+    E203 # whitespace before ':' - doesn't work well with black
+    E225 # missing whitespace around operator - let black worry about that
+    E262 # inline comment should start with '# '
+    E265 # block comment should start with '# '
+    E266 # too many leading '#' for block comment
+    E302 # expected 2 blank lines, found 1
+    E402 # module level import not at top of file
+    E501 # line too long - let black handle that
+    E711 # comparison to None should be
+    E712 # comparison to False/True should be
+    E741 # ambiguous variable name
+    F405 # may be undefined, or defined from star imports
+    W291 # trailing
+    W503 # line break occurred before a binary operator - let black worry about that
+    W504 # line break occurred after a binary operator - let black worry about that
+per-file-ignores =
+    __init__.py:F401

.isort.cfg

@@ -0,0 +1,3 @@
+[settings]
+known_first_party=exactextract
+profile=black

.pre-commit-config.yaml

@@ -1,4 +1,16 @@
 repos:
+    -   repo: https://github.com/psf/black
+        rev: 22.3.0
+        hooks:
+        -   id: black
+    -   repo: https://github.com/timothycrosley/isort
+        rev: 5.12.0
+        hooks:
+        -   id: isort
+    -   repo: https://github.com/pycqa/flake8
+        rev: 3.9.2
+        hooks:
+        -   id: flake8
     -   repo: https://github.com/pre-commit/mirrors-clang-format
         rev: 'v15.0.7'
         hooks:

python/setup.py

@@ -1,12 +1,11 @@
-
 # -*- coding: utf-8 -*-
+import configparser
 import os
-import sys
 import subprocess
-import configparser
+import sys
 from pathlib import Path
 
-from setuptools import setup, Extension
+from setuptools import Extension, setup
 from setuptools.command.build_ext import build_ext
 
 
@@ -18,53 +17,55 @@ def __init__(self, name):
 class CMakeBuild(build_ext):
     def run(self):
         try:
-            subprocess.check_output(['cmake', '--version'])
+            subprocess.check_output(["cmake", "--version"])
         except OSError:
             raise RuntimeError(
-                "CMake must be installed to build the following extensions: " +
-                ", ".join(e.name for e in self.extensions))
+                "CMake must be installed to build the following extensions: "
+                + ", ".join(e.name for e in self.extensions)
+            )
 
         build_directory = os.path.abspath(self.build_temp)
 
         cmake_args = [
-            '-DCMAKE_LIBRARY_OUTPUT_DIRECTORY=' + build_directory,
-            '-DPYTHON_EXECUTABLE=' + sys.executable,
-            '-DBUILD_CLI=OFF',
-            '-DBUILD_TEST=OFF',
-            '-DBUILD_DOC=OFF'
+            "-DCMAKE_LIBRARY_OUTPUT_DIRECTORY=" + build_directory,
+            "-DPYTHON_EXECUTABLE=" + sys.executable,
+            "-DBUILD_CLI=OFF",
+            "-DBUILD_TEST=OFF",
+            "-DBUILD_DOC=OFF",
         ]
 
-        cfg = 'Debug' if self.debug else 'Release'
-        build_args = ['--config', cfg]
+        cfg = "Debug" if self.debug else "Release"
+        build_args = ["--config", cfg]
 
-        cmake_args += ['-DCMAKE_BUILD_TYPE=' + cfg]
+        cmake_args += ["-DCMAKE_BUILD_TYPE=" + cfg]
 
         # Assuming Makefiles
-        build_args += ['--', '-j2']
+        build_args += ["--", "-j2"]
 
         self.build_args = build_args
 
         env = os.environ.copy()
-        env['CXXFLAGS'] = '{} -DVERSION_INFO=\\"{}\\"'.format(
-            env.get('CXXFLAGS', ''),
-            self.distribution.get_version())  # type: ignore
+        env["CXXFLAGS"] = '{} -DVERSION_INFO=\\"{}\\"'.format(
+            env.get("CXXFLAGS", ""), self.distribution.get_version()
+        )  # type: ignore
         if not os.path.exists(self.build_temp):
             os.makedirs(self.build_temp)
 
         # CMakeLists.txt is in the parent directory of this setup.py file
-        cmake_list_dir = os.path.abspath(os.path.join(os.path.dirname(__file__), os.pardir))
-        print('-' * 10, 'Running CMake prepare', '-' * 40)
-        subprocess.check_call(['cmake', cmake_list_dir] + cmake_args,
-                              cwd=self.build_temp, env=env)
+        cmake_list_dir = os.path.abspath(
+            os.path.join(os.path.dirname(__file__), os.pardir)
+        )
+        print("-" * 10, "Running CMake prepare", "-" * 40)
+        subprocess.check_call(
+            ["cmake", cmake_list_dir] + cmake_args, cwd=self.build_temp, env=env
+        )
 
-        print('-' * 10, 'Building extensions', '-' * 40)
-        cmake_cmd = ['cmake', '--build', '.'] + self.build_args
-        subprocess.check_call(cmake_cmd,
-                              cwd=self.build_temp)
+        print("-" * 10, "Building extensions", "-" * 40)
+        cmake_cmd = ["cmake", "--build", "."] + self.build_args
+        subprocess.check_call(cmake_cmd, cwd=self.build_temp)
 
-        make_cmd = ['make']
-        subprocess.check_call(make_cmd,
-                              cwd=self.build_temp)
+        make_cmd = ["make"]
+        subprocess.check_call(make_cmd, cwd=self.build_temp)
 
         # Move from build temp to final position
         for ext in self.extensions:
@@ -81,42 +82,48 @@ def move_output(self, ext):
 
 def find_version():
     version_script = os.path.abspath(
-            os.path.join(os.path.dirname(__file__), os.pardir, 'cmake', 'VersionSource.cmake'))
-    version = subprocess.run(['cmake', '-P', version_script],
-        capture_output=True,
-        text=True).stderr.split(':')[1].strip()
+        os.path.join(
+            os.path.dirname(__file__), os.pardir, "cmake", "VersionSource.cmake"
+        )
+    )
+    version = (
+        subprocess.run(["cmake", "-P", version_script], capture_output=True, text=True)
+        .stderr.split(":")[1]
+        .strip()
+    )
     print(f"Version: {version}")
     return version
 
+
 # The information here can also be placed in setup.cfg - better separation of
 # logic and declaration, and simpler if you include description/version in a file.
 
 # For now, just parse from config file
 config = configparser.ConfigParser()
-config.read('project.ini')
-
-project = config['base']['project']
-copyright = config['base']['copyright']
-author = config['base']['author']
-url = config['base']['url']
-title = config['base']['title']
-description = config['base']['description']
-tag = config['base']['tag']
+config.read("project.ini")
+
+project = config["base"]["project"]
+copyright = config["base"]["copyright"]
+author = config["base"]["author"]
+url = config["base"]["url"]
+title = config["base"]["title"]
+description = config["base"]["description"]
+tag = config["base"]["tag"]
 version = find_version()
 
 setup(
     name=project,
     version=version,
     author=author,
     url=url,
-    author_email='',
+    author_email="",
     description=description,
-    packages=['exactextract'],
-    package_dir={'exactextract': 'src/exactextract'},
+    packages=["exactextract"],
+    package_dir={"exactextract": "src/exactextract"},
     ext_modules=[CMakeExtension("_exactextract")],
     cmdclass={"build_ext": CMakeBuild},
     zip_safe=False,
     extras_require={"test": ["pytest>=6.0"]},
     python_requires=">=3.7",
-    install_requires=["pybind11>=2.2"]
+    install_requires=["pybind11>=2.2"],
 )

python/src/exactextract/__init__.py

@@ -8,16 +8,16 @@
 from .feature_source import (
     FeatureSource,
     GDALFeatureSource,
-    JSONFeatureSource,
     GeoPandasFeatureSource,
+    JSONFeatureSource,
 )
 from .operation import Operation
 from .processor import FeatureSequentialProcessor, RasterSequentialProcessor
 from .raster_source import (
-    RasterSource,
     GDALRasterSource,
     NumPyRasterSource,
     RasterioRasterSource,
+    RasterSource,
     XArrayRasterSource,
 )
-from .writer import Writer, JSONWriter, GDALWriter
+from .writer import GDALWriter, JSONWriter, Writer

python/src/exactextract/exact_extract.py

@@ -3,12 +3,17 @@
 from .feature_source import (
     FeatureSource,
     GDALFeatureSource,
-    JSONFeatureSource,
     GeoPandasFeatureSource,
+    JSONFeatureSource,
 )
-from .raster_source import RasterSource, GDALRasterSource, RasterioRasterSource, XArrayRasterSource
 from .operation import Operation
 from .processor import FeatureSequentialProcessor, RasterSequentialProcessor
+from .raster_source import (
+    GDALRasterSource,
+    RasterioRasterSource,
+    RasterSource,
+    XArrayRasterSource,
+)
 from .writer import JSONWriter
 
 
@@ -63,7 +68,7 @@ def prep_raster(rast, band=None, name_root=None, names=None):
         pass
 
     try:
-        import rioxarray
+        import rioxarray  # noqa: F401
         import xarray
 
         if isinstance(rast, xarray.core.dataarray.DataArray):
@@ -73,9 +78,9 @@ def prep_raster(rast, band=None, name_root=None, names=None):
                 if not names:
                     names = [f"{name_root}_{i+1}" for i in range(rast.rio.count)]
                 return [
-                        XArrayRasterSource(rast, i+1, name=names[i])
-                            for i in range(rast.rio.count)
-                            ]
+                    XArrayRasterSource(rast, i + 1, name=names[i])
+                    for i in range(rast.rio.count)
+                ]
 
     except ImportError:
         pass

python/src/exactextract/feature.py

@@ -25,7 +25,7 @@ def __init__(self, f=None):
         Feature.__init__(self)
         if f is None:
             self.feature = {}
-        elif hasattr(f, '__geo_interface__'):
+        elif hasattr(f, "__geo_interface__"):
             self.feature = f.__geo_interface__
         else:
             self.feature = f

python/src/exactextract/feature_source.py

@@ -1,7 +1,7 @@
-from _exactextract import FeatureSource
-
 import os
 
+from _exactextract import FeatureSource
+
 from .feature import GDALFeature, JSONFeature
 
 

python/src/exactextract/processor.py

@@ -1,12 +1,10 @@
 #!/usr/bin/env python3
 # -*- coding: utf-8 -*-
 
-from typing import List, Union
+from typing import List
 
-from _exactextract import (
-    FeatureSequentialProcessor as _FeatureSequentialProcessor,
-    RasterSequentialProcessor as _RasterSequentialProcessor,
-)
+from _exactextract import FeatureSequentialProcessor as _FeatureSequentialProcessor
+from _exactextract import RasterSequentialProcessor as _RasterSequentialProcessor
 
 from .feature_source import FeatureSource
 from .operation import Operation

python/src/exactextract/raster_source.py

@@ -1,10 +1,9 @@
 #!/usr/bin/env python3
 # -*- coding: utf-8 -*-
 
-import numpy as np
 import os
-import pathlib
 
+import numpy as np
 from _exactextract import RasterSource
 
 
@@ -134,7 +133,7 @@ def __init__(self, ds, band_idx=1, *, name=None):
         super().__init__()
 
         if isinstance(ds, (str, os.PathLike)):
-            import rioxarray
+            import rioxarray  # noqa: F401
             import xarray
 
             ds = xarray.open_dataarray(ds)
@@ -143,15 +142,14 @@ def __init__(self, ds, band_idx=1, *, name=None):
         if self.ds.rio.crs is None:
             # Set a default CRS to prevent clip_box from
             # complaining that we don't have one
-            self.ds.rio.set_crs('EPSG:4326', inplace=True)
+            self.ds.rio.set_crs("EPSG:4326", inplace=True)
         self.band_idx = band_idx
         self.band_dim = self._band_dim(self.ds)
         self.bounds = self.ds.rio.bounds()
-        
+
         if name:
             self.set_name(name)
 
-
     @staticmethod
     def _band_dim(ds):
         dims = list(ds.dims)
@@ -165,19 +163,15 @@ def _band_dim(ds):
         else:
             raise Exception("Cannot handle >1 non-spatial dimension")
 
-
     def res(self):
         return tuple(abs(x) for x in self.ds.rio.resolution())
 
-
     def extent(self):
         return self.bounds
 
-
     def nodata_value(self):
         return self.ds.rio.nodata
 
-
     def read_window(self, x0, y0, nx, ny):
         lats = self.ds[self.ds.rio.y_dim]
         flipped = bool(len(lats) > 1 and lats[1] > lats[0])
@@ -188,8 +182,8 @@ def read_window(self, x0, y0, nx, ny):
         selection = {}
         if self.band_dim is not None:
             selection[self.band_dim] = self.ds[self.band_dim][self.band_idx - 1]
-        selection[self.ds.rio.x_dim] = self.ds[self.ds.rio.x_dim][x0 : x0+nx]
-        selection[self.ds.rio.y_dim] = self.ds[self.ds.rio.y_dim][y0 : y0+ny]
+        selection[self.ds.rio.x_dim] = self.ds[self.ds.rio.x_dim][x0 : x0 + nx]
+        selection[self.ds.rio.y_dim] = self.ds[self.ds.rio.y_dim][y0 : y0 + ny]
 
         ret = self.ds.sel(**selection).to_numpy()
 

python/src/exactextract/writer.py

@@ -1,11 +1,9 @@
 #!/usr/bin/env python3
 # -*- coding: utf-8 -*-
 
-import pathlib
-from typing import Union, Dict, List
-
 from _exactextract import Writer
-from .feature import JSONFeature, GDALFeature
+
+from .feature import GDALFeature, JSONFeature
 
 
 class JSONWriter(Writer):

python/tests/conftest.py

@@ -1,6 +1,6 @@
 import pytest
 
-from exactextract import NumPyRasterSource, JSONFeature
+from exactextract import NumPyRasterSource
 
 
 @pytest.fixture()