Merge pull request #39 from kkraus14/update-setup.py

[REVIEW] Add cython headers to install, python / cmake packaging cleanup

CHANGELOG.md

@@ -10,7 +10,8 @@
 
 ## Improvements
 
-- #31 Add Github CODEOWNERS
+- PR #31 Add Github CODEOWNERS
+- PR #39 Add cython headers to install, python / cmake packaging cleanup
 
 ## Bug Fixes
 

cpp/CMakeLists.txt

@@ -52,9 +52,9 @@ if(CMAKE_COMPILER_IS_GNUCXX)
 
     option(CMAKE_CXX11_ABI "Enable the GLIBCXX11 ABI" ON)
     if(CMAKE_CXX11_ABI)
-        message(STATUS "CUDF: Enabling the GLIBCXX11 ABI")
+        message(STATUS "CUSPATIAL: Enabling the GLIBCXX11 ABI")
     else()
-        message(STATUS "CUDF: Disabling the GLIBCXX11 ABI")
+        message(STATUS "CUSPATIAL: Disabling the GLIBCXX11 ABI")
         set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -D_GLIBCXX_USE_CXX11_ABI=0")
         set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -D_GLIBCXX_USE_CXX11_ABI=0")
         set(CMAKE_CUDA_FLAGS "${CMAKE_CUDA_FLAGS} -Xcompiler -D_GLIBCXX_USE_CXX11_ABI=0")
@@ -101,20 +101,31 @@ include(FeatureSummary)
 include(CheckIncludeFiles)
 include(CheckLibraryExists)
 
+###################################################################################################
+# - conda environment -----------------------------------------------------------------------------
+
+if("$ENV{CONDA_BUILD}" STREQUAL "1")
+    set(CMAKE_SYSTEM_PREFIX_PATH "$ENV{BUILD_PREFIX};$ENV{PREFIX};${CMAKE_SYSTEM_PREFIX_PATH}")
+    set(CONDA_INCLUDE_DIRS "$ENV{BUILD_PREFIX}/include" "$ENV{PREFIX}/include")
+    set(CONDA_LINK_DIRS "$ENV{BUILD_PREFIX}/lib" "$ENV{PREFIX}/lib")
+    message(STATUS "Conda build detected, CMAKE_SYSTEM_PREFIX_PATH set to: ${CMAKE_SYSTEM_PREFIX_PATH}")
+elseif(DEFINED ENV{CONDA_PREFIX})
+    set(CMAKE_SYSTEM_PREFIX_PATH "$ENV{CONDA_PREFIX};${CMAKE_SYSTEM_PREFIX_PATH}")
+    set(CONDA_INCLUDE_DIRS "$ENV{CONDA_PREFIX}/include")
+    set(CONDA_LINK_DIRS "$ENV{CONDA_PREFIX}/lib")
+    message(STATUS "Conda environment detected, CMAKE_SYSTEM_PREFIX_PATH set to: ${CMAKE_SYSTEM_PREFIX_PATH}")
+endif("$ENV{CONDA_BUILD}" STREQUAL "1")
+
 ###################################################################################################
 # - RMM -------------------------------------------------------------------------------------------
 
 find_path(RMM_INCLUDE "rmm"
-          HINTS "$ENV{RMM_ROOT}/include"
-                "$ENV{CONDA_PREFIX}/include/rmm"
-                "$ENV{CONDA_PREFIX}/include")
+          HINTS "$ENV{RMM_ROOT}/include")
 
 find_library(RMM_LIBRARY "rmm"
-             HINTS "$ENV{RMM_ROOT}/lib"
-                   "$ENV{CONDA_PREFIX}/lib")
+             HINTS "$ENV{RMM_ROOT}/lib")
 
 message(STATUS "RMM: RMM_ROOT set to $ENV{RMM_ROOT}")
-message(STATUS "RMM: CONDA_PREFIX set to $ENV{CONDA_PREFIX}")
 message(STATUS "RMM: RMM_LIBRARY set to ${RMM_LIBRARY}")
 message(STATUS "RMM: RMM_INCLUDE set to ${RMM_INCLUDE}")
 
@@ -126,21 +137,17 @@ endif (RMM_INCLUDE AND RMM_LIBRARY)
 # - CUDF -------------------------------------------------------------------------------------------
 
 find_path(CUDF_INCLUDE "cudf"
-          "$ENV{CUDF_HOME}/cpp/include"
-          "$ENV{CONDA_PREFIX}/include/cudf"
-          "$ENV{CONDA_PREFIX}/include")
+          HINTS "$ENV{CUDF_ROOT}/cpp/include")
 
 find_library(CUDF_LIBRARY "cudf"
-             "$ENV{CUDF_HOME}/cpp/build"
-             "$ENV{CONDA_PREFIX}/lib")
-
-SET(CUDF_SRC_INCLUDE "$ENV{CUDF_HOME}/cpp/src")    
+             HINTS "$ENV{CUDF_ROOT}/lib")
+
+SET(CUDF_SRC_INCLUDE "$ENV{CUDF_HOME}/cpp/src")
 SET(CUB_INCLUDE "$ENV{CUDF_HOME}/cpp/thirdparty/cub")
 SET(JITIFY_INCLUDE "$ENV{CUDF_HOME}/cpp/thirdparty/jitify")
 SET(CUDF_TEST_INCLUDE "$ENV{CUDF_HOME}/cpp/")
 
 message(STATUS "CUDF: CUDF_HOME set to $ENV{CUDF_HOME}")
-message(STATUS "CUDF: CONDA_PREFIX set to $ENV{CONDA_PREFIX}")
 message(STATUS "CUDF: CUDF_LIBRARY set to ${CUDF_LIBRARY}")
 message(STATUS "CUDF: CUDF_INCLUDE set to ${CUDF_INCLUDE}")
 message(STATUS "CUDF SRC: CUDF_SRC_INCLUDE set to ${CUDF_SRC_INCLUDE}")
@@ -157,21 +164,16 @@ endif (CUDF_INCLUDE AND CUDF_LIBRARY)
 # - NVStrings -------------------------------------------------------------------------------------
 
 find_path(NVSTRINGS_INCLUDE "nvstrings"
-          HINTS "$ENV{NVSTRINGS_ROOT}/include"
-                "$ENV{CONDA_PREFIX}/include/nvstrings"
-                "$ENV{CONDA_PREFIX}/include")
+          HINTS "$ENV{NVSTRINGS_ROOT}/include")
 
 find_library(NVSTRINGS_LIBRARY "NVStrings"
-             HINTS "$ENV{NVSTRINGS_ROOT}/lib"
-                   "$ENV{CONDA_PREFIX}/lib")
+             HINTS "$ENV{NVSTRINGS_ROOT}/lib")
 
 find_library(NVCATEGORY_LIBRARY "NVCategory"
-             HINTS "$ENV{NVSTRINGS_ROOT}/lib"
-                   "$ENV{CONDA_PREFIX}/lib")
+             HINTS "$ENV{NVSTRINGS_ROOT}/lib")
 
 find_library(NVTEXT_LIBRARY "NVText"
-             HINTS "$ENV{NVSTRINGS_ROOT}/lib"
-                   "$ENV{CONDA_PREFIX}/lib")
+             HINTS "$ENV{NVSTRINGS_ROOT}/lib")
 
 message(STATUS "NVSTRINGS: NVSTRINGS_INCLUDE set to ${NVSTRINGS_INCLUDE}")
 message(STATUS "NVSTRINGS: NVSTRINGS_LIBRARY set to ${NVSTRINGS_LIBRARY}")
@@ -213,9 +215,9 @@ endif(BUILD_TESTS)
 # - add google benchmark --------------------------------------------------------------------------
 
 if(BUILD_BENCHMARKS)
-  
+
   include(ConfigureGoogleBenchmark)
-  
+
   if(GBENCH_FOUND)
     message(STATUS "Google C++ Benchmarking Framework (Google Benchmark) found in ${GBENCH_ROOT}")
     include_directories(${GBENCH_INCLUDE_DIR})
@@ -236,13 +238,13 @@ endif(CMAKE_CUDA_TOOLKIT_INCLUDE_DIRECTORIES)
 include_directories("${CMAKE_BINARY_DIR}/include"
                     "${CMAKE_SOURCE_DIR}/include"
                     "${CMAKE_SOURCE_DIR}/src"
-       		    "${CMAKE_SOURCE_DIR}/thirdparty/cub"             
+       		        "${CMAKE_SOURCE_DIR}/thirdparty/cub"
                     "${RMM_INCLUDE}"
                     "${CUDF_SRC_INCLUDE}"
                     "${CUDF_INCLUDE}"
                     "${CUB_INCLUDE}"
                     "${JITIFY_INCLUDE}")
-		
+
 
 ###################################################################################################
 # - library paths ---------------------------------------------------------------------------------
@@ -264,7 +266,7 @@ add_library(cuspatial SHARED
             src/io/soa/timestamp_soa_reader.cu
             src/query/spatial_window_points.cu
             src/spatial/point_in_polygon.cu
-            src/spatial/haversine.cu	
+            src/spatial/haversine.cu
             src/spatial/hausdorff.cu
             src/spatial/lonlat_to_coordinate.cu
             src/trajectory/trajectory_spatial_bound.cu

cpp/tests/CMakeLists.txt

@@ -1,6 +1,6 @@
 cmake_minimum_required(VERSION 3.12 FATAL_ERROR)
 
-project(CUDF_TESTS LANGUAGES C CXX CUDA)
+project(CUSPATIAL_TESTS LANGUAGES C CXX CUDA)
 
 if(NOT CMAKE_CUDA_COMPILER)
   message(SEND_ERROR "CMake cannot locate a CUDA compiler")
@@ -9,17 +9,16 @@ endif()
 ###################################################################################################
 # - common test utils -----------------------------------------------------------------------------
 
-add_library(cudftestutil STATIC
-            "${CUDF_TEST_INCLUDE}/tests/utilities/cudf_test_utils.cu"
-            "${CUDF_TEST_INCLUDE}/tests/utilities/valid_vectors.cpp"
-            "${CUDF_TEST_INCLUDE}/tests/utilities/nvcategory_utils.cu")
+find_library(CUDFTESTUTIL_LIBRARY "libcudftestutil.a"
+             HINTS "$ENV{CUDF_ROOT}/lib")
 
-target_link_libraries(cudftestutil cudf cuspatial rmm cudart cuda nvrtc NVCategory  NVStrings)
-                     
+message(STATUS "CUDFTESTUTIL: CUDFTESTUTIL_LIBRARY set to ${CUDFTESTUTIL_LIBRARY}")
+message(STATUS "CUDFTESTUTIL: CUDF_TEST_INCLUDE set to ${CUDF_TEST_INCLUDE}")
 
-if(USE_NVTX)
-    target_link_libraries(cudftestutil ${NVTX_LIBRARY})
-endif(USE_NVTX)
+add_library(cudftestutil STATIC IMPORTED ${CUDFTESTUTIL_LIBRARY})
+if (CUDF_TEST_INCLUDE AND CUDFTESTUTIL_LIBRARY)
+    set_target_properties(cudftestutil PROPERTIES IMPORTED_LOCATION ${CUDFTESTUTIL_LIBRARY})
+endif (CUDF_TEST_INCLUDE AND CUDFTESTUTIL_LIBRARY)
 
 ###################################################################################################
 # - compiler function -----------------------------------------------------------------------------
@@ -28,7 +27,7 @@ function(ConfigureTest CMAKE_TEST_NAME CMAKE_TEST_SRC)
     add_executable(${CMAKE_TEST_NAME}
                    ${CMAKE_TEST_SRC})
     set_target_properties(${CMAKE_TEST_NAME} PROPERTIES POSITION_INDEPENDENT_CODE ON)
-    target_link_libraries(${CMAKE_TEST_NAME} gmock gtest gmock_main gtest_main pthread cudf
+    target_link_libraries(${CMAKE_TEST_NAME} gmock gtest gmock_main gtest_main pthread cuspatial cudf
                           cudftestutil rmm cudart cuda "${ARROW_LIB}" ${ZLIB_LIBRARIES} NVCategory
                           NVStrings nvrtc)
     if(USE_NVTX)
@@ -39,14 +38,14 @@ function(ConfigureTest CMAKE_TEST_NAME CMAKE_TEST_SRC)
     add_test(NAME ${CMAKE_TEST_NAME} COMMAND ${CMAKE_TEST_NAME})
 endfunction(ConfigureTest)
 
-option(CMAKE_ENABLE_BENCHMARKS "Enable building cuDF benchmarks" OFF)
+option(CMAKE_ENABLE_BENCHMARKS "Enable building cuSpatial benchmarks" OFF)
 
 function(ConfigureBench CMAKE_BENCH_NAME CMAKE_BENCH_SRC)
     if(CMAKE_ENABLE_BENCHMARKS)
         add_executable(${CMAKE_BENCH_NAME}
                     ${CMAKE_BENCH_SRC})
         set_target_properties(${CMAKE_BENCH_NAME} PROPERTIES POSITION_INDEPENDENT_CODE ON)
-        target_link_libraries(${CMAKE_BENCH_NAME} cudf cudftestutil)
+        target_link_libraries(${CMAKE_BENCH_NAME} cuspatial cudf cudftestutil)
         set_target_properties(${CMAKE_BENCH_NAME} PROPERTIES
                                 RUNTIME_OUTPUT_DIRECTORY "${CMAKE_BINARY_DIR}/bench")
         add_test(NAME ${CMAKE_BENCH_NAME} COMMAND ${CMAKE_BENCH_NAME})
@@ -80,7 +79,7 @@ include_directories("${CMAKE_BINARY_DIR}/include"
 
 link_directories("${CMAKE_CUDA_IMPLICIT_LINK_DIRECTORIES}" # CMAKE_CUDA_IMPLICIT_LINK_DIRECTORIES is an undocumented/unsupported variable containing the link directories for nvcc
                  "${CMAKE_BINARY_DIR}/lib"
-                  "${GTEST_LIBRARY_DIR}"
+                 "${GTEST_LIBRARY_DIR}"
                  "${RMM_LIBRARY}"
                  "${CUDF_LIBRARY}"
                  "${CUSPATIAL_LIBRARY}"

pyproject.toml

@@ -0,0 +1,19 @@
+[tool.black]
+line-length = 79
+target-version = ["py36"]
+include = '\.py?$'
+exclude = '''
+/(
+    thirdparty |
+    \.eggs |
+    \.git |
+    \.hg |
+    \.mypy_cache |
+    \.tox |
+    \.venv |
+    _build |
+    buck-out |
+    build |
+    dist
+)/
+'''

python/cuspatial/.flake8.cython

@@ -0,0 +1,29 @@
+#
+# Copyright (c) 2018-2019, NVIDIA CORPORATION.
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+#
+
+[flake8]
+filename = *.pyx, *.pxd
+exclude = *.egg, build, docs, .git
+ignore = E999, E225, E226, E227, W503, W504, E211
+
+# Rules ignored:
+# E999: invalid syntax (works for Python, not Cython)
+# E211: whitespace before '(' (used in multi-line imports)
+# E225: Missing whitespace around operators (breaks cython casting syntax like <int>)
+# E226: Missing whitespace around arithmetic operators (breaks cython pointer syntax like int*)
+# E227: Missing whitespace around bitwise or shift operator (Can also break casting syntax)
+# W503: line break before binary operator (breaks lines that start with a pointer)
+# W504: line break after binary operator (breaks lines that end with a pointer)

python/cuspatial/setup.cfg

@@ -20,19 +20,13 @@ ignore =
     # whitespace before :
     E203
 
-known_third_party= 
-    cython,
-    msgpack,
-    numba,
-    numpy,
-    packaging,
-    pandas,
-    pyarrow,
-    pytest,
-    setuptools,
-    six,
-    toolz,
-    versioneer
+[isort]
+line_length=79
+multi_line_output=3
+include_trailing_comma=True
+force_grid_wrap=0
+combine_as_imports=True
+order_by_type=True
 known_dask=
     dask
     distributed
@@ -46,6 +40,9 @@ known_rapids=
     cugraph
     cudf
     dask_cudf
+known_first_party=
+    cuspatial
+default_section=THIRDPARTY
 sections=FUTURE,STDLIB,THIRDPARTY,DASK,RAPIDS,FIRSTPARTY,LOCALFOLDER
 skip=
     thirdparty
@@ -59,3 +56,4 @@ skip=
     buck-out
     build
     dist
+    __init__.py

python/cuspatial/setup.py

@@ -19,14 +19,13 @@
         sources=cython_files,
         include_dirs=[
             "../../cpp/include/cuspatial",
-            os.environ['CONDA_PREFIX']+"/include/cudf",
             os.path.dirname(sysconfig.get_path("include")),
-            np.get_include()
+            np.get_include(),
         ],
         library_dirs=[get_python_lib()],
-        libraries=["cudf","cuspatial"],
+        libraries=["cudf", "cuspatial"],
         language="c++",
-        extra_compile_args=["-std=c++14"]
+        extra_compile_args=["-std=c++14"],
     )
 ]
 
@@ -50,6 +49,7 @@
     setup_requires=["cython"],
     ext_modules=cythonize(extensions),
     packages=find_packages(include=["cuspatial", "cuspatial.*"]),
+    package_data={"cuspatial._lib": ["*.pxd"]},
     cmdclass=versioneer.get_cmdclass(),
     install_requires=install_requires,
     zip_safe=False,

setup.cfg

@@ -0,0 +1,7 @@
+[flake8]
+exclude = img,thirdparty,__init__.py,build
+ignore =
+    # line break before binary operator
+    W503
+    # whitespace before :
+    E203