[REVIEW] Python and Cython style cleanup, pre-commit hook

.gitignore

@@ -17,12 +17,12 @@ DartConfiguration.tcl
 
 ## Python build directories & artifacts
 dist/
-cudf.egg-info/
+cuspatial.egg-info/
 python/build
 python/*/build
-python/cuspatial/*/bindings/**/*.cpp
-python/cuspatial/*/bindings/**/*.h
-python/cuspatial/*/bindings/.nfs*
+python/cuspatial/*/_lib/**/*.cpp
+python/cuspatial/*/_lib/**/*.h
+python/cuspatial/*/_lib/.nfs*
 python/cuspatial/*.ipynb
 python/cuspatial/.ipynb_checkpoints
 .Python

.pre-commit-config.yaml

@@ -0,0 +1,23 @@
+repos:
+      - repo: https://github.com/timothycrosley/isort
+        rev: 4.3.21
+        hooks:
+              - id: isort
+      - repo: https://github.com/ambv/black
+        rev: stable
+        hooks:
+              - id: black
+      - repo: https://gitlab.com/pycqa/flake8
+        rev: 3.7.7
+        hooks:
+              - id: flake8
+      - repo: https://gitlab.com/pycqa/flake8
+        rev: 3.7.7
+        hooks:
+              - id: flake8
+                alias: flake8-cython
+                name: flake8-cython
+                args: ["--config=python/cuspatial/.flake8.cython"]
+                types: [cython]
+default_language_version:
+      python: python3

CHANGELOG.md

@@ -13,6 +13,7 @@
 
 - PR #31 Add Github CODEOWNERS
 - PR #39 Add cython headers to install, python / cmake packaging cleanup
+- PR #41 Python and Cython style cleanup, pre-commit hook
 
 ## Bug Fixes
 

ci/checks/style.sh

@@ -38,3 +38,32 @@ else
   echo -e "\n\n>>>> PASSED: isort style check\n\n"
 fi
 
+if [ "$BLACK_RETVAL" != "0" ]; then
+  echo -e "\n\n>>>> FAILED: black style check; begin output\n\n"
+  echo -e "$BLACK"
+  echo -e "\n\n>>>> FAILED: black style check; end output\n\n"
+else
+  echo -e "\n\n>>>> PASSED: black style check\n\n"
+fi
+
+if [ "$FLAKE_RETVAL" != "0" ]; then
+  echo -e "\n\n>>>> FAILED: flake8 style check; begin output\n\n"
+  echo -e "$FLAKE"
+  echo -e "\n\n>>>> FAILED: flake8 style check; end output\n\n"
+else
+  echo -e "\n\n>>>> PASSED: flake8 style check\n\n"
+fi
+
+if [ "$FLAKE_CYTHON_RETVAL" != "0" ]; then
+  echo -e "\n\n>>>> FAILED: flake8-cython style check; begin output\n\n"
+  echo -e "$FLAKE_CYTHON"
+  echo -e "\n\n>>>> FAILED: flake8-cython style check; end output\n\n"
+else
+  echo -e "\n\n>>>> PASSED: flake8-cython style check\n\n"
+fi
+
+RETVALS=($ISORT_RETVAL $BLACK_RETVAL $FLAKE_RETVAL $FLAKE_CYTHON_RETVAL)
+IFS=$'\n'
+RETVAL=`echo "${RETVALS[*]}" | sort -nr | head -n1`
+
+exit $RETVAL

python/cuspatial/cuspatial/__init__.py

@@ -1,20 +1,20 @@
-from .core.trajectory import (
-    derive,
-    distance_and_speed,
-    spatial_bounds,
-    subset_trajectory_id
-)
 from .core.gis import (
     directed_hausdorff_distance,
     haversine_distance,
     lonlat_to_xy_km_coordinates,
     point_in_polygon_bitmap,
     window_points,
 )
+from .core.trajectory import (
+    derive,
+    distance_and_speed,
+    spatial_bounds,
+    subset_trajectory_id,
+)
 from .io.soa import (
-    read_uint,
     read_its_timestamps,
     read_points_lonlat,
     read_points_xy_km,
-    read_polygon
+    read_polygon,
+    read_uint,
 )

python/cuspatial/cuspatial/_lib/soa_readers.pxd

@@ -8,10 +8,26 @@ from cudf._lib.cudf cimport *
 from libcpp.pair cimport pair
 
 cdef extern from "soa_readers.hpp" namespace "cuspatial" nogil:
-    cdef gdf_column read_uint32_soa(const char *pnt_fn) except +
-    cdef gdf_column read_timestamp_soa(const char *ts_fn) except +
-    cdef pair[gdf_column, gdf_column] read_lonlat_points_soa(const char *pnt_fn) except +
-    cdef pair[gdf_column, gdf_column] read_xy_points_soa(const char *pnt_fn) except +
-    cdef void read_polygon_soa(const char *ply_fn, gdf_column* ply_fpos,
-                               gdf_column* ply_rpos, gdf_column* ply_x,
-                               gdf_column* ply_y) except +
+    cdef gdf_column read_uint32_soa(
+        const char *pnt_fn
+    ) except +
+
+    cdef gdf_column read_timestamp_soa(
+        const char *ts_fn
+    ) except +
+
+    cdef pair[gdf_column, gdf_column] read_lonlat_points_soa(
+        const char *pnt_fn
+    ) except +
+
+    cdef pair[gdf_column, gdf_column] read_xy_points_soa(
+        const char *pnt_fn
+    ) except +
+
+    cdef void read_polygon_soa(
+        const char *ply_fn,
+        gdf_column* ply_fpos,
+        gdf_column* ply_rpos,
+        gdf_column* ply_x,
+        gdf_column* ply_y
+    ) except +

python/cuspatial/cuspatial/_lib/soa_readers.pyx

@@ -1,78 +1,104 @@
+# Copyright (c) 2019, NVIDIA CORPORATION.
+
+# cython: profile=False
+# distutils: language = c++
+# cython: embedsignature = True
+# cython: language_level = 3
+
+
 from cudf.core.column import Column
 from cudf._lib.cudf import *
 from libc.stdlib cimport calloc, malloc, free
 from libcpp.pair cimport pair
 
 cpdef cpp_read_uint_soa(soa_file_name):
-    # print("in cpp_read_id_soa, reading ",soa_file_name)
     cdef bytes py_bytes = soa_file_name.encode()
     cdef char* c_string = py_bytes
     cdef gdf_column c_id
+
     with nogil:
-        c_id = read_uint32_soa(c_string)
+        c_id = read_uint32_soa(
+            c_string
+        )
+
     id_data, id_mask = gdf_column_to_column_mem(&c_id)
-    id=Column.from_mem_views(id_data,id_mask)
+    id = Column.from_mem_views(id_data, id_mask)
 
     return id
 
 cpdef cpp_read_ts_soa(soa_file_name):
-    # print("in cpp_read_ts_soa, reading ",soa_file_name)
     cdef bytes py_bytes = soa_file_name.encode()
     cdef char* c_string = py_bytes
     cdef gdf_column c_ts
+
     with nogil:
-        c_ts = read_timestamp_soa(c_string)
+        c_ts = read_timestamp_soa(
+            c_string
+        )
+
     ts_data, ts_mask = gdf_column_to_column_mem(&c_ts)
-    ts=Column.from_mem_views(ts_data,ts_mask)
+    ts = Column.from_mem_views(ts_data, ts_mask)
 
     return ts
 
 cpdef cpp_read_pnt_lonlat_soa(soa_file_name):
-    # print("in cpp_read_pnt_lonlat_soa, reading ",soa_file_name)
     cdef bytes py_bytes = soa_file_name.encode()
     cdef char* c_string = py_bytes
     cdef pair[gdf_column, gdf_column] columns
+
     with nogil:
-        columns = read_lonlat_points_soa(c_string)
+        columns = read_lonlat_points_soa(
+            c_string
+        )
+
     lon_data, lon_mask = gdf_column_to_column_mem(&columns.first)
-    lon=Column.from_mem_views(lon_data,lon_mask)
+    lon = Column.from_mem_views(lon_data, lon_mask)
     lat_data, lat_mask = gdf_column_to_column_mem(&columns.second)
-    lat=Column.from_mem_views(lat_data,lat_mask)
+    lat = Column.from_mem_views(lat_data, lat_mask)
 
-    return lon,lat
+    return lon, lat
 
 cpdef cpp_read_pnt_xy_soa(soa_file_name):
-    # print("in cpp_read_pnt_xy_soa, reading ",soa_file_name)
     cdef bytes py_bytes = soa_file_name.encode()
     cdef char* c_string = py_bytes
     cdef pair[gdf_column, gdf_column] columns
+
     with nogil:
-        columns = read_xy_points_soa(c_string)
+        columns = read_xy_points_soa(
+            c_string
+        )
+
     x_data, x_mask = gdf_column_to_column_mem(&columns.first)
-    x=Column.from_mem_views(x_data,x_mask)
+    x = Column.from_mem_views(x_data, x_mask)
     y_data, y_mask = gdf_column_to_column_mem(&columns.second)
-    y=Column.from_mem_views(y_data,y_mask)
+    y = Column.from_mem_views(y_data, y_mask)
 
-    return x,y
+    return x, y
 
 cpdef cpp_read_polygon_soa(soa_file_name):
-    # print("in cpp_read_polygon_soa, reading ",soa_file_name)
     cdef bytes py_bytes = soa_file_name.encode()
     cdef char* c_string = py_bytes
-    cdef gdf_column* c_ply_fpos=<gdf_column*>malloc(sizeof(gdf_column))
-    cdef gdf_column* c_ply_rpos=<gdf_column*>malloc(sizeof(gdf_column))
-    cdef gdf_column* c_ply_x=<gdf_column*>malloc(sizeof(gdf_column))
-    cdef gdf_column* c_ply_y=<gdf_column*>malloc(sizeof(gdf_column))
+    cdef gdf_column* c_ply_fpos = <gdf_column*>malloc(sizeof(gdf_column))
+    cdef gdf_column* c_ply_rpos = <gdf_column*>malloc(sizeof(gdf_column))
+    cdef gdf_column* c_ply_x = <gdf_column*>malloc(sizeof(gdf_column))
+    cdef gdf_column* c_ply_y = <gdf_column*>malloc(sizeof(gdf_column))
+
     with nogil:
-        read_polygon_soa(c_string,c_ply_fpos, c_ply_rpos, c_ply_x, c_ply_y)
+        read_polygon_soa(
+            c_string,
+            c_ply_fpos,
+            c_ply_rpos,
+            c_ply_x,
+            c_ply_y
+        )
+
     f_data, f_mask = gdf_column_to_column_mem(c_ply_fpos)
-    f_pos=Column.from_mem_views(f_data,f_mask)
+    f_pos = Column.from_mem_views(f_data, f_mask)
     r_data, r_mask = gdf_column_to_column_mem(c_ply_rpos)
-    r_pos=Column.from_mem_views(r_data,r_mask)
+    r_pos = Column.from_mem_views(r_data, r_mask)
     x_data, x_mask = gdf_column_to_column_mem(c_ply_x)
-    x=Column.from_mem_views(x_data,x_mask)
+    x = Column.from_mem_views(x_data, x_mask)
     y_data, y_mask = gdf_column_to_column_mem(c_ply_y)
-    y=Column.from_mem_views(y_data,y_mask)
-
-    return f_pos,r_pos,x,y
+    y = Column.from_mem_views(y_data, y_mask)
 
+    return f_pos, r_pos, x, y

python/cuspatial/cuspatial/_lib/spatial.pxd

@@ -9,33 +9,44 @@ from cudf._lib.cudf cimport *
 from libcpp.pair cimport pair
 
 cdef extern from "point_in_polygon.hpp" namespace "cuspatial" nogil:
- cdef gdf_column point_in_polygon_bitmap(const gdf_column& pnt_x,
-                                         const gdf_column& pnt_y,
-                                         const gdf_column& ply_fpos,
-                                         const gdf_column& ply_rpos,
-                                         const gdf_column& ply_x,
-                                         const gdf_column& ply_y) except +
+    cdef gdf_column point_in_polygon_bitmap(
+        const gdf_column& pnt_x,
+        const gdf_column& pnt_y,
+        const gdf_column& ply_fpos,
+        const gdf_column& ply_rpos,
+        const gdf_column& ply_x,
+        const gdf_column& ply_y
+    ) except +
 
-cdef extern from "coordinate_transform.hpp" namespace "cuspatial" nogil: 
- cdef pair[gdf_column, gdf_column] lonlat_to_coord(const gdf_scalar cam_x,
-                                                   const gdf_scalar cam_y,
-                                                   const gdf_column  & in_x,
-                                                   const gdf_column  & in_y) except +
+cdef extern from "coordinate_transform.hpp" namespace "cuspatial" nogil:
+    cdef pair[gdf_column, gdf_column] lonlat_to_coord(
+        const gdf_scalar& cam_x,
+        const gdf_scalar& cam_y,
+        const gdf_column& in_x,
+        const gdf_column& in_y
+    ) except +
 
-cdef extern from "haversine.hpp" namespace "cuspatial" nogil:  
- gdf_column haversine_distance(const gdf_column& x1, const gdf_column& y1,
-                               const gdf_column& x2, const gdf_column& y2) except +
+cdef extern from "haversine.hpp" namespace "cuspatial" nogil:
+    gdf_column haversine_distance(
+        const gdf_column& x1,
+        const gdf_column& y1,
+        const gdf_column& x2,
+        const gdf_column& y2
+    ) except +
 
-cdef extern from "hausdorff.hpp" namespace "cuspatial" nogil:  
- gdf_column& directed_hausdorff_distance(const gdf_column& coor_x,
-                                         const gdf_column& coor_y,
-                                         const gdf_column& cnt)except +
+cdef extern from "hausdorff.hpp" namespace "cuspatial" nogil:
+    gdf_column& directed_hausdorff_distance(
+        const gdf_column& coor_x,
+        const gdf_column& coor_y,
+        const gdf_column& cnt
+    ) except +
 
 cdef extern from "query.hpp" namespace "cuspatial" nogil:
- cdef pair[gdf_column, gdf_column] spatial_window_points(
+    cdef pair[gdf_column, gdf_column] spatial_window_points(
         const gdf_scalar& left,
         const gdf_scalar& bottom,
         const gdf_scalar& right,
         const gdf_scalar& top,
         const gdf_column& x,
-        const gdf_column& y) except +
+        const gdf_column& y
+    ) except +