Bump isort, enable Cython package resorting (#419)

With rapidsai/integration#286, the version of `isort` running on gpuCI will be bumped to 5.6.4, allowing us to enforce the sorting of packages in Cython (pyx, pxd) files. This PR intends to:

- Enable these checks in the gpuCI style script
- Enable Cython package resorting in the pre-commit hook
- Resort all the Cython files in this repo so they pass the newly enabled checks

These checks are optional, meaning that even without this being merged, gpuCI should still pass on style checks even when rapidsai/integration#286 is merged.

Authors:
  - Charles Blackmon-Luca (https://github.com/charlesbluca)

Approvers:
  - H. Thomson Comer (https://github.com/thomcom)
  - AJ Schmidt (https://github.com/ajschmidt8)

URL: #419

Author: charlesbluca

.pre-commit-config.yaml

@@ -1,16 +1,23 @@
 repos:
-      - repo: https://github.com/timothycrosley/isort
-        rev: 5.0.4
+      - repo: https://github.com/pycqa/isort
+        rev: 5.6.4
         hooks:
               - id: isort
+                args: ["--settings-path=python/cuspatial/setup.cfg"]
+                files: python/cuspatial/.*
+                exclude: __init__.py$
+                types: [text]
+                types_or: [python, cython]
       - repo: https://github.com/ambv/black
-        rev: stable
+        rev: 19.10b0
         hooks:
               - id: black
+                files: python/cuspatial/.*
       - repo: https://gitlab.com/pycqa/flake8
         rev: 3.7.7
         hooks:
               - id: flake8
+                files: python/cuspatial/.*\.py
       - repo: https://gitlab.com/pycqa/flake8
         rev: 3.7.7
         hooks:

ci/checks/style.sh

@@ -15,7 +15,7 @@ LANG=C.UTF-8
 conda activate rapids
 
 # Run isort and get results/return code
-ISORT=`isort --check-only python/**/*.py`
+ISORT=`isort --check-only python/cuspatial --settings-path=python/cuspatial/setup.cfg`
 ISORT_RETVAL=$?
 
 # Run black and get results/return code

python/cuspatial/cuspatial/_lib/cpp/coordinate_transform.pxd

@@ -1,11 +1,11 @@
 # Copyright (c) 2020, NVIDIA CORPORATION.
 
+from libcpp.memory cimport unique_ptr
+from libcpp.pair cimport pair
+
 from cudf._lib.cpp.column.column cimport column
 from cudf._lib.cpp.column.column_view cimport column_view
 
-from libcpp.pair cimport pair
-from libcpp.memory cimport unique_ptr
-
 
 cdef extern from "cuspatial/coordinate_transform.hpp" namespace "cuspatial" \
         nogil:

python/cuspatial/cuspatial/_lib/cpp/hausdorff.pxd

@@ -1,10 +1,10 @@
 # Copyright (c) 2020, NVIDIA CORPORATION.
 
+from libcpp.memory cimport unique_ptr
+
 from cudf._lib.cpp.column.column cimport column
 from cudf._lib.cpp.column.column_view cimport column_view
 
-from libcpp.memory cimport unique_ptr
-
 
 cdef extern from "cuspatial/hausdorff.hpp" namespace "cuspatial" nogil:
 

python/cuspatial/cuspatial/_lib/cpp/interpolate.pxd

@@ -1,10 +1,10 @@
 # Copyright (c) 2020, NVIDIA CORPORATION.
 
+from libcpp.memory cimport unique_ptr
+
 from cudf._lib.column cimport column, column_view
 from cudf._lib.table cimport table, table_view
 
-from libcpp.memory cimport unique_ptr
-
 
 cdef extern from "cuspatial/cubic_spline.hpp" namespace "cuspatial" nogil:
     cdef unique_ptr[table] cubicspline_coefficients \

python/cuspatial/cuspatial/_lib/cpp/point_in_polygon.pxd

@@ -1,9 +1,9 @@
 # Copyright (c) 2020, NVIDIA CORPORATION.
 
-from cudf._lib.column cimport column, column_view
-
 from libcpp.memory cimport unique_ptr
 
+from cudf._lib.column cimport column, column_view
+
 
 cdef extern from "cuspatial/point_in_polygon.hpp" namespace "cuspatial" nogil:
     cdef unique_ptr[column] point_in_polygon(

python/cuspatial/cuspatial/_lib/cpp/polygon_bounding_box.pxd

@@ -1,10 +1,10 @@
 # Copyright (c) 2020, NVIDIA CORPORATION.
 
+from libcpp.memory cimport unique_ptr
+
 from cudf._lib.cpp.column.column_view cimport column_view
 from cudf._lib.cpp.table.table cimport table
 
-from libcpp.memory cimport unique_ptr
-
 
 cdef extern from "cuspatial/polygon_bounding_box.hpp" \
         namespace "cuspatial" nogil:

python/cuspatial/cuspatial/_lib/cpp/polyline_bounding_box.pxd

@@ -1,10 +1,10 @@
 # Copyright (c) 2020, NVIDIA CORPORATION.
 
+from libcpp.memory cimport unique_ptr
+
 from cudf._lib.cpp.column.column_view cimport column_view
 from cudf._lib.cpp.table.table cimport table
 
-from libcpp.memory cimport unique_ptr
-
 
 cdef extern from "cuspatial/polyline_bounding_box.hpp" \
         namespace "cuspatial" nogil:

python/cuspatial/cuspatial/_lib/cpp/quadtree.pxd

@@ -1,15 +1,14 @@
 # Copyright (c) 2020, NVIDIA CORPORATION.
 
+from libc.stdint cimport int8_t
+from libcpp.memory cimport unique_ptr
+from libcpp.pair cimport pair
+
 from cudf._lib.cpp.column.column cimport column
 from cudf._lib.cpp.column.column_view cimport column_view
 from cudf._lib.cpp.table.table cimport table
 from cudf._lib.cpp.types cimport size_type
 
-from libc.stdint cimport int8_t
-
-from libcpp.pair cimport pair
-from libcpp.memory cimport unique_ptr
-
 
 cdef extern from "cuspatial/point_quadtree.hpp" namespace "cuspatial" nogil:
     cdef pair[unique_ptr[column], unique_ptr[table]] quadtree_on_points(

python/cuspatial/cuspatial/_lib/cpp/shapefile_reader.pxd

@@ -1,11 +1,11 @@
 # Copyright (c) 2020, NVIDIA CORPORATION.
 
-from cudf._lib.cpp.column.column cimport column
-
 from libcpp.memory cimport unique_ptr
 from libcpp.string cimport string
 from libcpp.vector cimport vector
 
+from cudf._lib.cpp.column.column cimport column
+
 
 cdef extern from "cuspatial/shapefile_reader.hpp" namespace "cuspatial" nogil:
     cdef vector[unique_ptr[column]] \

python/cuspatial/cuspatial/_lib/cpp/spatial.pxd

@@ -1,9 +1,9 @@
 # Copyright (c) 2019-2020, NVIDIA CORPORATION.
 
-from cudf._lib.column cimport column, column_view
-
 from libcpp.memory cimport unique_ptr
 
+from cudf._lib.column cimport column, column_view
+
 
 cdef extern from "cuspatial/haversine.hpp" namespace "cuspatial" nogil:
     cdef unique_ptr[column] haversine_distance(

python/cuspatial/cuspatial/_lib/cpp/spatial_join.pxd

@@ -1,12 +1,11 @@
 # Copyright (c) 2020, NVIDIA CORPORATION.
 
-from cudf._lib.column cimport column_view
-from cudf._lib.table cimport table, table_view
-
 from libc.stdint cimport int8_t
-
 from libcpp.memory cimport unique_ptr
 
+from cudf._lib.column cimport column_view
+from cudf._lib.table cimport table, table_view
+
 
 cdef extern from "cuspatial/spatial_join.hpp" namespace "cuspatial" nogil:
 

python/cuspatial/cuspatial/_lib/cpp/spatial_window.pxd

@@ -1,10 +1,10 @@
 # Copyright (c) 2020, NVIDIA CORPORATION.
 
+from libcpp.memory cimport unique_ptr
+
 from cudf._lib.column cimport column, column_view
 from cudf._lib.table cimport table, table_view
 
-from libcpp.memory cimport unique_ptr
-
 
 cdef extern from "cuspatial/spatial_window.hpp" namespace "cuspatial" nogil:
     cdef unique_ptr[table] points_in_spatial_window \

python/cuspatial/cuspatial/_lib/cpp/trajectory.pxd

@@ -1,13 +1,13 @@
 # Copyright (c) 2020, NVIDIA CORPORATION.
 
+from libcpp.memory cimport unique_ptr
+from libcpp.pair cimport pair
+
 from cudf._lib.cpp.column.column cimport column
 from cudf._lib.cpp.column.column_view cimport column_view
 from cudf._lib.cpp.table.table cimport table
 from cudf._lib.cpp.types cimport size_type
 
-from libcpp.pair cimport pair
-from libcpp.memory cimport unique_ptr
-
 
 cdef extern from "cuspatial/trajectory.hpp" namespace "cuspatial" nogil:
 

python/cuspatial/cuspatial/_lib/hausdorff.pyx

@@ -1,12 +1,13 @@
 # Copyright (c) 2019, NVIDIA CORPORATION.
 
-from cudf._lib.column cimport column, column_view, Column
+from libcpp.memory cimport unique_ptr
+from libcpp.utility cimport move
 
-from cuspatial._lib.cpp.hausdorff \
-    cimport directed_hausdorff_distance as directed_cpp_hausdorff_distance
+from cudf._lib.column cimport Column, column, column_view
 
-from libcpp.utility cimport move
-from libcpp.memory cimport unique_ptr
+from cuspatial._lib.cpp.hausdorff cimport (
+    directed_hausdorff_distance as directed_cpp_hausdorff_distance,
+)
 
 
 def directed_hausdorff_distance(

python/cuspatial/cuspatial/_lib/interpolate.pyx

@@ -1,15 +1,16 @@
 # Copyright (c) 2019-2020, NVIDIA CORPORATION.
 
-from cudf._lib.table cimport table, Table
-from cudf._lib.column cimport column, Column
+from libcpp.memory cimport unique_ptr
+from libcpp.utility cimport move
+
+from cudf._lib.column cimport Column, column
+from cudf._lib.table cimport Table, table
 
 from cuspatial._lib.cpp.interpolate cimport (
-    cubicspline_interpolate as cpp_cubicspline_interpolate,
     cubicspline_coefficients as cpp_cubicspline_coefficients,
+    cubicspline_interpolate as cpp_cubicspline_interpolate,
 )
 
-from libcpp.utility cimport move
-from libcpp.memory cimport unique_ptr
 
 cpdef cubicspline_coefficients(
     Column t,

python/cuspatial/cuspatial/_lib/point_in_polygon.pyx

@@ -1,14 +1,14 @@
 # Copyright (c) 2020, NVIDIA CORPORATION.
 
-from cudf._lib.column cimport column, column_view, Column
+from libcpp.memory cimport unique_ptr
+from libcpp.utility cimport move
+
+from cudf._lib.column cimport Column, column, column_view
 
 from cuspatial._lib.cpp.point_in_polygon cimport (
     point_in_polygon as cpp_point_in_polygon,
 )
 
-from libcpp.utility cimport move
-from libcpp.memory cimport unique_ptr
-
 
 def point_in_polygon(
     Column test_points_x,

python/cuspatial/cuspatial/_lib/polygon_bounding_boxes.pyx

@@ -1,19 +1,20 @@
 # Copyright (c) 2020, NVIDIA CORPORATION.
 
+from libcpp.memory cimport unique_ptr
+from libcpp.pair cimport pair
+from libcpp.utility cimport move
+
+from cudf._lib.column cimport Column
 from cudf._lib.cpp.column.column cimport column
 from cudf._lib.cpp.column.column_view cimport column_view
 from cudf._lib.cpp.table.table cimport table
 from cudf._lib.cpp.types cimport size_type
-from cudf._lib.column cimport Column
 from cudf._lib.table cimport Table
 
 from cuspatial._lib.cpp.polygon_bounding_box cimport (
     polygon_bounding_boxes as cpp_polygon_bounding_boxes,
 )
 
-from libcpp.memory cimport unique_ptr
-from libcpp.pair cimport pair
-from libcpp.utility cimport move
 
 cpdef polygon_bounding_boxes(Column poly_offsets,
                              Column ring_offsets,

python/cuspatial/cuspatial/_lib/polyline_bounding_boxes.pyx

@@ -1,19 +1,20 @@
 # Copyright (c) 2020, NVIDIA CORPORATION.
 
+from libcpp.memory cimport unique_ptr
+from libcpp.pair cimport pair
+from libcpp.utility cimport move
+
+from cudf._lib.column cimport Column
 from cudf._lib.cpp.column.column cimport column
 from cudf._lib.cpp.column.column_view cimport column_view
 from cudf._lib.cpp.table.table cimport table
 from cudf._lib.cpp.types cimport size_type
-from cudf._lib.column cimport Column
 from cudf._lib.table cimport Table
 
 from cuspatial._lib.cpp.polyline_bounding_box cimport (
     polyline_bounding_boxes as cpp_polyline_bounding_boxes,
 )
 
-from libcpp.memory cimport unique_ptr
-from libcpp.pair cimport pair
-from libcpp.utility cimport move
 
 cpdef polyline_bounding_boxes(Column poly_offsets,
                               Column x, Column y,

python/cuspatial/cuspatial/_lib/quadtree.pyx

@@ -1,21 +1,21 @@
 # Copyright (c) 2020, NVIDIA CORPORATION.
 
+from libc.stdint cimport int8_t
+from libcpp.memory cimport unique_ptr
+from libcpp.pair cimport pair
+from libcpp.utility cimport move
+
+from cudf._lib.column cimport Column
 from cudf._lib.cpp.column.column cimport column
 from cudf._lib.cpp.column.column_view cimport column_view
 from cudf._lib.cpp.table.table cimport table
 from cudf._lib.cpp.types cimport size_type
-from cudf._lib.column cimport Column
 from cudf._lib.table cimport Table
 
 from cuspatial._lib.cpp.quadtree cimport (
     quadtree_on_points as cpp_quadtree_on_points,
 )
 
-from libc.stdint cimport int8_t
-
-from libcpp.memory cimport unique_ptr
-from libcpp.pair cimport pair
-from libcpp.utility cimport move
 
 cpdef quadtree_on_points(Column x, Column y,
                          double x_min, double x_max,

python/cuspatial/cuspatial/_lib/shapefile_reader.pyx

@@ -1,16 +1,16 @@
 # Copyright (c) 2019-2020, NVIDIA CORPORATION.
 
+from libcpp.memory cimport unique_ptr
+from libcpp.string cimport string
+from libcpp.utility cimport move
+from libcpp.vector cimport vector
+
 from cudf._lib.column cimport Column, column
 
 from cuspatial._lib.cpp.shapefile_reader cimport (
     read_polygon_shapefile as cpp_read_polygon_shapefile,
 )
 
-from libcpp.memory cimport unique_ptr
-from libcpp.string cimport string
-from libcpp.utility cimport move
-from libcpp.vector cimport vector
-
 
 cpdef read_polygon_shapefile(object filepath):
     cdef string c_string = str(filepath).encode()

python/cuspatial/cuspatial/_lib/spatial.pyx

@@ -1,20 +1,22 @@
 # Copyright (c) 2019, NVIDIA CORPORATION.
 
 from cudf import Series
+
+from libcpp.memory cimport unique_ptr
+from libcpp.pair cimport pair
+from libcpp.utility cimport move
+
 from cudf._lib.column cimport Column
 from cudf._lib.cpp.column.column cimport column
 from cudf._lib.cpp.column.column_view cimport column_view
+
 from cuspatial._lib.cpp.coordinate_transform cimport (
-    lonlat_to_cartesian as cpp_lonlat_to_cartesian
+    lonlat_to_cartesian as cpp_lonlat_to_cartesian,
 )
-
 from cuspatial._lib.cpp.spatial cimport (
-    haversine_distance as cpp_haversine_distance
+    haversine_distance as cpp_haversine_distance,
 )
 
-from libcpp.memory cimport unique_ptr
-from libcpp.pair cimport pair
-from libcpp.utility cimport move
 
 cpdef haversine_distance(Column x1, Column y1, Column x2, Column y2):
     cdef column_view c_x1 = x1.view()