Setup ruff rules + apply them

.pre-commit-config.yaml

@@ -1,16 +1,12 @@
 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/astral-sh/ruff-pre-commit
+      rev: "v0.6.3"
+      hooks:
+          # Format the code
+          - id: ruff-format
+          # Lint the code
+          - id: ruff
+            # args: [ --fix ]
     -   repo: https://github.com/pre-commit/mirrors-clang-format
         rev: 'v15.0.7'
         hooks:

pyproject.toml

@@ -49,3 +49,88 @@ wheel.packages=["python/src/exactextract"]
 provider = "scikit_build_core.metadata.regex"
 input = "cmake/VersionSource.cmake"
 regex = "EXACTEXTRACT_VERSION_SOURCE \"(?P<value>.+)\""
+
+[tool.ruff]
+line-length = 88
+extend-exclude = ["*.ipynb", "local_ignore/*"]
+
+[tool.ruff.lint]
+select = [
+    # pyflakes
+    "F",
+    # pycodestyle
+    "E",
+    "W",
+    # pyupgrade
+    "UP",
+    # flake8-bugbear
+    "B",
+    # flake8-debugger
+    "T10",
+    # flake8-simplify
+    # "SIM",
+    # pylint
+    "PLC",
+    "PLE",
+    "PLR",
+    "PLW",
+    # misc lints
+    "PIE",
+    # implicit string concatenation
+    "ISC",
+    # type-checking imports
+    "TCH",
+    # comprehensions
+    "C4",
+    # Ruff-specific rules
+    "RUF",
+    # isort
+    "I",
+    # pydocstyle
+    #"D",
+]
+
+ignore = [
+    ### Intentionally disabled
+    # module level import not at top of file
+    "E402",
+    # do not assign a lambda expression, use a def
+    "E731",
+    # mutable-argument-default
+    "B006",
+    # unused-loop-control-variable
+    "B007",
+    # get-attr-with-constant
+    "B009",
+    # Only works with python >=3.10
+    "B905",
+    # dict literals
+    "C408",
+    # Too many arguments to function call
+    "PLR0913",
+    # Too many returns
+    "PLR0911",
+    # Too many branches
+    "PLR0912",
+    # Too many statements
+    "PLR0915",
+    # Magic number
+    "PLR2004",
+    # Consider `elif` instead of `else` then `if` to remove indentation level
+    "PLR5501",
+    # Redefined loop name
+    "PLW2901",
+    # Global statements are discouraged
+    "PLW0603",
+    # compare-to-empty-string
+    "PLC1901",
+]
+
+[tool.ruff.lint.per-file-ignores]
+"tests/*" = ["D"]
+
+[tool.ruff.lint.pydocstyle]
+convention = "google"
+
+[tool.ruff.lint.pyupgrade]
+keep-runtime-typing = true

python/doc/conf.py

@@ -1,4 +1,3 @@
-# -*- coding: utf-8 -*-
 #
 # Configuration file for the Sphinx documentation builder.
 #
@@ -74,7 +73,6 @@
 
 
 def autoapi_skip_member(app, what, name, obj, skip, options):
-
     shortname = name.split(".")[-1]
 
     # Don't emit documentation for anything named beginning with

python/src/exactextract/__init__.py

@@ -1,5 +1,5 @@
-# -*- coding: utf-8 -*-
-""" Python bindings for exactextract """
+"""Python bindings for exactextract."""
+# ruff: noqa: F401
 
 from ._exactextract import __version__
 from .exact_extract import exact_extract

python/src/exactextract/exact_extract.py

@@ -2,8 +2,9 @@
 import functools
 import os
 import warnings
+from collections.abc import Mapping
 from itertools import chain
-from typing import Mapping, Optional
+from typing import Optional
 
 from .feature import (
     FeatureSource,
@@ -40,7 +41,8 @@ def make_raster_names(root: str, nbands: int) -> list:
 
 def prep_raster_gdal(rast, name_root=None) -> list:
     try:
-        # eagerly import gdal_array to avoid possible ImportError when reading raster data
+        # eagerly import gdal_array to avoid possible ImportError when reading raster
+        # data
         from osgeo import gdal, gdal_array  # noqa: F401
 
         if isinstance(rast, (str, os.PathLike)):
@@ -93,7 +95,6 @@ def prep_raster_rasterio(rast, name_root=None) -> list:
 
 
 def prep_raster_xarray(rast, name_root=None) -> list:
-
     try:
         import rioxarray  # noqa: F401
         import xarray
@@ -240,7 +241,7 @@ def prep_ops(stats, values, weights=None, *, add_unique=False):
                 if "No weights provided" in str(e):
                     raise Exception(
                         f"No weights provided but {stat.__name__} expects 3 arguments"
-                    )
+                    ) from None
                 else:
                     raise
         elif isinstance(stat, Operation):
@@ -328,8 +329,10 @@ def warn_on_crs_mismatch(vec, ops):
         if check_rast_vec and not crs_matches(vec, op.values):
             check_rast_vec = False
             warnings.warn(
-                "Spatial reference system of input features does not exactly match raster.",
+                "Spatial reference system of input features does not exactly match "
+                "raster.",
                 RuntimeWarning,
+                stacklevel=2,
             )
 
         if (
@@ -339,8 +342,10 @@ def warn_on_crs_mismatch(vec, ops):
         ):
             check_rast_weights = False
             warnings.warn(
-                "Spatial reference system of input features does not exactly match weighting raster.",
+                "Spatial reference system of input features does not exactly match "
+                "weighting raster.",
                 RuntimeWarning,
+                stacklevel=2,
             )
 
 
@@ -396,22 +401,25 @@ def exact_extract(
                    a cost of higher memory usage.
        max_cells_in_memory: Indicates the maximum number of raster cells that should be
                             loaded into memory at a given time.
-       grid_compat_tol: require value and weight grids to align within ``grid_compat_tol`` times the smaller of the two grid resolutions
+       grid_compat_tol: require value and weight grids to align within
+            ``grid_compat_tol`` times the smaller of the two grid resolutions
        output: An :py:class:`OutputWriter` or one of the following strings:
 
-                 - "geojson" (the default): return a list of GeoJSON-like features
-                 - "pandas": return a ``pandas.DataFrame`` or ``geopandas.GeoDataFrame``,
-                             depending on the value of ``include_geom``
-                 - "gdal": write results to disk using GDAL/OGR as they are written. This
-                           option (with ``strategy="feature-sequential"``) avoids the need
-                           to maintain results for all features in memory at a single time,
-                           which may be significant for operations with large result sizes
-                           such as ``cell_id``, ``values``, etc.
-       output_options: an optional dictionary of options passed to the :py:class:`writer.JSONWriter`, :py:class:`writer.PandasWriter`, or :py:class:`writer.GDALWriter`.
-       progress: if `True`, a progress bar will be displayed. Alternatively, a
-                 function may be provided that will be called with the completion fraction
-                 and a status message.
-    """
+                - "geojson" (the default): return a list of GeoJSON-like features
+                - "pandas": return a ``pandas.DataFrame`` or ``geopandas.GeoDataFrame``,
+                            depending on the value of ``include_geom``
+                - "gdal": write results to disk using GDAL/OGR as they are written. This
+                          option (with ``strategy="feature-sequential"``) avoids the
+                          need to maintain results for all features in memory at a
+                          single time, which may be significant for operations with
+                          large result sizes such as ``cell_id``, ``values``, etc.
+       output_options: an optional dictionary of options passed to the
+            :py:class:`writer.JSONWriter`, :py:class:`writer.PandasWriter`, or
+            :py:class:`writer.GDALWriter`.
+       progress: if `True`, a progress bar will be displayed. Alternatively, a function
+            may be provided that will be called with the completion fraction and a
+            status message.
+    """  # noqa: E501
     rast = prep_raster(rast)
     weights = prep_raster(weights, name_root="weight")
     vec = prep_vec(vec)

python/src/exactextract/feature.py

@@ -13,8 +13,7 @@
 
 
 class FeatureSource(_FeatureSource):
-    """
-    Source from which polygon features can be read.
+    """Source from which polygon features can be read.
 
     Several implementations are included in exactextract:
 
@@ -25,24 +24,26 @@ class FeatureSource(_FeatureSource):
     """
 
     def __init__(self):
+        """Constructor."""
         super().__init__()
 
 
 class GDALFeatureSource(FeatureSource):
-    """
-    A FeatureSource using the GDAL/OGR Python interface to provide features.
-    """
+    """A FeatureSource using the GDAL/OGR Python interface to provide features."""
 
     def __init__(self, src):
-        """
+        """Constructor.
+
         Args:
-            src: one of the following
-                 - string or Path to a file/datasource that can be opened with GDAL/OGR
-                 - a ``gdal.Dataset``
-                 - an ``ogr.DataSource``
-                 - an ``ogr.Layer``
-                 If the file has more than one layer, e.g., a GeoPackage, an
-                 ``ogr.Layer`` must be provided directly.
+            src: one of the following:
+
+                - string or Path to a file/datasource that can be opened with GDAL/OGR
+                - a ``gdal.Dataset``
+                - an ``ogr.DataSource``
+                - an ``ogr.Layer``
+                If the file has more than one layer, e.g., a GeoPackage, an
+                ``ogr.Layer`` must be provided directly.
+
         """
         super().__init__()
 
@@ -59,7 +60,8 @@ def __init__(self, src):
             self.ds = src  # keep a reference to ds
             if nlayers > 1:
                 raise Exception(
-                    "Can only process a single layer; call directly with ogr.Layer object."
+                    "Can only process a single layer; call directly with ogr.Layer "
+                    "object."
                 )
 
             self.src = src.GetLayer(0)
@@ -124,9 +126,7 @@ def fields(self):
 
 
 class JSONFeatureSource(FeatureSource):
-    """
-    A FeatureSource providing GeoJSON-like features.
-    """
+    """A FeatureSource providing GeoJSON-like features."""
 
     def __init__(self, src, *, srs_wkt=None):
         super().__init__()
@@ -197,9 +197,7 @@ def fields(self):
 
 
 class GeoPandasFeatureSource(FeatureSource):
-    """
-    A FeatureSource using GeoPandas GeoDataFrame to provide features.
-    """
+    """A FeatureSource using GeoPandas GeoDataFrame to provide features."""
 
     def __init__(self, src):
         super().__init__()