Merge pull request #261 from sandialabs/update_setuppy

Refactor setup.py and add test() to pycompadre

CMakeLists.txt

@@ -78,7 +78,7 @@ else() # Raw CMake Project
   SET(CMAKE_SKIP_BUILD_RPATH  FALSE)
   SET(CMAKE_BUILD_WITH_INSTALL_RPATH FALSE)
   SET(CMAKE_INSTALL_RPATH_USE_LINK_PATH TRUE)
-  SET(CMAKE_INSTALL_RPATH ${CMAKE_INSTALL_LIBDIR} ${CMAKE_INSTALL_RPATH})
+  SET(CMAKE_INSTALL_RPATH "../${CMAKE_INSTALL_LIBDIR}")
 
   # RPATH should always include the folder it is called from
   bob_option(PYTHON_CALLING_BUILD "Python setuptools calling build" OFF)
@@ -96,17 +96,17 @@ else() # Raw CMake Project
         OUTPUT_STRIP_TRAILING_WHITESPACE )
     ENDIF()
     MESSAGE(STATUS "PYTHON_EXECUTABLE: ${PYTHON_EXECUTABLE}")
-    if (APPLE)
-      SET(CMAKE_BUILD_RPATH ${CMAKE_BUILD_RPATH} "@loader_path/")
-      SET(CMAKE_INSTALL_RPATH ${CMAKE_INSTALL_RPATH} "@loader_path/")
-      if (NOT(PYTHON_CALLING_BUILD))
-        # If python is calling the build, it will provide these flags
-        SET(CMAKE_PYTHON_SHARED_LINKER_FLAGS "-undefined dynamic_lookup -nodefaultlibs")
+    # change RPATH for a flat directory structure
+    # when installing pycompadre as Python package
+    if (PYTHON_CALLING_BUILD)
+      if (APPLE)
+        SET(CMAKE_BUILD_RPATH ${CMAKE_BUILD_RPATH} "@loader_path/")
+        SET(CMAKE_INSTALL_RPATH ${CMAKE_INSTALL_RPATH} "@loader_path/")
+      else()
+        SET(CMAKE_BUILD_RPATH ${CMAKE_BUILD_RPATH} "$ORIGIN/")
+        SET(CMAKE_INSTALL_RPATH ${CMAKE_INSTALL_RPATH} "$ORIGIN/")
+        SET(CMAKE_SHARED_LINKER_FLAGS "${CMAKE_SHARED_LINKER_FLAGS} -Wl,-z,origin")
       endif()
-    else()
-      SET(CMAKE_BUILD_RPATH ${CMAKE_BUILD_RPATH} "$ORIGIN/")
-      SET(CMAKE_INSTALL_RPATH ${CMAKE_INSTALL_RPATH} "$ORIGIN/")
-      SET(CMAKE_SHARED_LINKER_FLAGS "${CMAKE_SHARED_LINKER_FLAGS} -Wl,-z,origin")
     endif()
   endif()
 
@@ -420,6 +420,7 @@ set(Compadre_KEY_BOOLS
     Compadre_USE_CUDA
     Compadre_USE_MPI
     Compadre_USE_PYTHON
+    PYTHON_CALLING_BUILD
    )
 
 set(Compadre_KEY_INTS
@@ -433,7 +434,6 @@ set(Compadre_KEY_STRINGS
     Compadre_COMMIT
     Compadre_CXX_FLAGS
     Compadre_CMAKE_ARGS
-    GMLS_Module_DEST
     Compadre_INSTALL_PREFIX
 )
 

cmake/Compadre_Version.txt

@@ -1 +1 @@
-1.4.0
+1.4.1

examples/CMakeLists.txt

@@ -1,9 +1,5 @@
 include_tribits_build()
 
-# ERROR MESSAGES IF A TEST IS NOT RUN
-SET(OPENBLAS_NUM_THREADS "1")
-
-
 ###############
 #
 #
@@ -193,6 +189,8 @@ if (Compadre_EXAMPLES)
 
     # WORKING_DIRECTORY ${EXECUTABLE_OUTPUT_PATH} )
     if (Compadre_USE_PYTHON)
+      FILE(COPY "${CMAKE_CURRENT_SOURCE_DIR}/../pycompadre/examples/test_pycompadre.py" DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/../pycompadre/examples")
+      FILE(COPY "${CMAKE_CURRENT_SOURCE_DIR}/../pycompadre/examples/test_pycompadre_manifold.py" DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/../pycompadre/examples")
       CONFIGURE_FILE("${CMAKE_CURRENT_SOURCE_DIR}/Python_3D_Convergence.py.in" "${CMAKE_CURRENT_BINARY_DIR}/Python_3D_Convergence.py" @ONLY)
       ADD_TEST(NAME GMLS_Python_Convergence_Test_3d_Point_Reconstruction COMMAND "${PYTHON_EXECUTABLE}" "${CMAKE_CURRENT_BINARY_DIR}/Python_3D_Convergence.py" "--kokkos-threads=4")
       SET_TESTS_PROPERTIES(GMLS_Python_Convergence_Test_3d_Point_Reconstruction PROPERTIES LABELS "IntegrationTest;integration;python;kokkos" TIMEOUT 10)
@@ -201,6 +199,10 @@ if (Compadre_EXAMPLES)
         ADD_TEST(NAME GMLS_Matlab_Python_Interface_1d_Point_Reconstruction COMMAND "matlab" "-nodisplay" "-nojvm" "-nosplash" "-nodesktop" "-r \"try, run('${SWIG_PREFIX}/Matlab_1D_Using_Python_Interface.m'), catch, exit(1), end, exit(0);\"")
         SET_TESTS_PROPERTIES(GMLS_Matlab_Python_Interface_1d_Point_Reconstruction PROPERTIES LABELS "IntegrationTest;integration;python;kokkos;matlab" TIMEOUT 10)
       endif()
+
+      ADD_TEST(NAME PyCOMPADRE_Tests COMMAND "${PYTHON_EXECUTABLE}" "-c" "import sys;sys.path.insert(0,'${PYTHON_LIBRARY_PREFIX}');import pycompadre;pycompadre.test();")
+      SET_TESTS_PROPERTIES(PyCOMPADRE_Tests PROPERTIES LABELS "pycompadre" TIMEOUT 10)
+
     endif()
 
   endif (Compadre_TESTS)

examples/Python_3D_Convergence.py.in

@@ -2,7 +2,7 @@ import sys
 
 # installation folder
 gmls_python_installation_path = "@PYTHON_LIBRARY_PREFIX@"
-sys.path.append(gmls_python_installation_path)
+sys.path.insert(0,gmls_python_installation_path)
 
 import pycompadre
 

pycompadre/examples/test_pycompadre.py

@@ -3,8 +3,9 @@
 import math
 import random
 import pycompadre
+import sys
 
-kokkos_obj=pycompadre.KokkosParser()
+kokkos_obj=pycompadre.KokkosParser(sys.argv)
 
 # function used to generate sample data
 def exact(coord,order,dimension):

pycompadre/examples/test_pycompadre_manifold.py

@@ -1,9 +1,10 @@
 from unittest import TestCase
 import pycompadre
 import numpy as np
+import sys
 
 # initialize Kokkos
-kp = pycompadre.KokkosParser()
+kp = pycompadre.KokkosParser(sys.argv)
 
 # get GMLS approximate at all x_pred, as well as reconstruction about attempt_center_about_coord
 def approximate(input_dimensions, porder, wpower, wtype, epsilon_multiplier, attempt_center_about_coord):

pycompadre/pycompadre.cpp

@@ -807,6 +807,48 @@ Implementation details at:
 
     m.def("Wab", &GMLS::Wab, py::arg("r"), py::arg("h"), py::arg("weighting type"), py::arg("p"), py::arg("n"), "Evaluate weighting kernel.");
 
+    m.def("test", [] {
+            py::module_ nose;
+            try {
+                nose = py::module_::import("nose");
+            } catch (...) {
+                std::cerr << "test() requires nose module." << std::endl;
+            }
+
+            py::module_ pathlib;
+            try {
+                pathlib = py::module::import("pathlib");
+            } catch (...) {
+                std::cerr << "test() requires pathlib module." << std::endl;
+            }
+
+            std::string examples_path;
+            try {
+                py::object this_pycompadre = py::module::import("pycompadre");
+                auto location = this_pycompadre.attr("__file__").cast<std::string>();
+                py::object path = pathlib.attr("Path")(location);
+#ifdef PYTHON_CALLING_BUILD
+                examples_path = py::str(path.attr("parent")).cast<std::string>() + "/examples";
+#else
+                examples_path = py::str(path.attr("parent")).cast<std::string>() + "/pycompadre/examples";
+#endif
+            } catch (...) {
+                std::cerr << "Error getting examples path from pycompadre module." << std::endl;
+            }
+
+            bool result = false;
+            try {
+                printf("Running examples in: %s\n", examples_path.c_str());
+                std::vector<std::string> argv = {"--where", examples_path, "-v"};
+                using namespace pybind11::literals;
+                result = nose.attr("run")("argv"_a=argv).cast<bool>();
+            } catch (...) {
+                std::cerr << "Error running nosetests." << std::endl;
+            }
+            return result;
+        }
+    );
+
 #ifdef COMPADRE_VERSION_MAJOR
     m.attr("__version__") = std::to_string(COMPADRE_VERSION_MAJOR) + "." + std::to_string(COMPADRE_VERSION_MINOR) + "." + std::to_string(COMPADRE_VERSION_PATCH);
 #else

setup.py

@@ -80,18 +80,32 @@
 import sys
 import platform
 import subprocess
-import distutils
+from pkg_resources import parse_version
 
-from setuptools import setup, Extension
+from setuptools import setup, Extension, Command
 from setuptools.command.build_ext import build_ext
-from distutils.version import LooseVersion
 from setuptools.command.install import install
 
 class CMakeExtension(Extension):
     def __init__(self, name, sourcedir=''):
         Extension.__init__(self, name, sources=[])
         self.sourcedir = os.path.abspath(sourcedir)
 
+# Overload Command for SetupTest to prevent build_ext being called again
+class SetupTest(Command):
+    '''
+    Tests the installed pycompadre module
+    '''
+    user_options=list()
+    def initialize_options(self): pass
+    def finalize_options(self): pass
+    def run(self):
+        try:
+            import pycompadre
+        except:
+            print('Install pycompadre before running test')
+        pycompadre.test()
+
 class CMakeBuild(build_ext):
     def run(self):
         try:
@@ -101,7 +115,7 @@ def run(self):
                                ", ".join(e.name for e in self.extensions))
 
         if platform.system() == "Windows":
-            cmake_version = LooseVersion(re.search(r'version\s*([\d.]+)', out.decode()).group(1))
+            cmake_version = parse_version(re.search(r'version\s*([\d.]+)', out.decode()).group(1))
             if cmake_version < '3.1.0':
                 raise RuntimeError("CMake >= 3.1.0 is required on Windows")
 
@@ -115,48 +129,88 @@ def build_extension(self, ext):
         if not extdir.endswith(os.path.sep):
             extdir += os.path.sep
 
-        # Parse string for kokkos architecture
-
         cmake_config = os.getenv("CMAKE_CONFIG_FILE")
         if cmake_config:
-            print("Custom cmake args file set to: %s"%(cmake_config,))
+            if os.path.exists(cmake_config):
+                print("Custom cmake args file set to: %s"%(cmake_config,))
+            else:
+                assert False, "CMAKE_CONFIG_FILE specified, but does not exist." 
         else:
-            cmake_config = ""
-            print("Custom cmake args file not set.")
-
-        #cmake_file_string = ""
-        #try:
-        #    if cmake_file != None:
-        #        cmake_file_string = str(cmake_file)
-        #        print("Custom cmake args file set to: %s"%(cmake_file_string,))
-        #    else:
-        #        print("Custom cmake args file not set.")
-        #except:
-        #    print("Custom cmake args file not set.")
+            # look for cmake_opts.txt and use it if found
+            if os.path.exists(ext.sourcedir+"/cmake_opts.txt"):
+                cmake_config = ext.sourcedir+"/cmake_opts.txt"
+                print("CMAKE_CONFIG_FILE not set, but cmake_opts.txt FOUND, so using: %s"%(cmake_config,))
+            else:
+                cmake_config = ""
+                print("Custom cmake args file not set.")
 
         # Configure CMake
-        #config = 'Debug' if self.debug else 'Release'
         cmake_args = ['-DCMAKE_LIBRARY_OUTPUT_DIRECTORY=' + extdir,
-                      '-DCMAKE_CXX_FLAGS= -O3 ',
                       '-DPYTHON_EXECUTABLE=' + sys.executable,
-                      '-DGMLS_Module_DEST=' + extdir,
                       '-DCMAKE_INSTALL_PREFIX=' + extdir,
-                      '-DCMAKE_OSX_DEPLOYMENT_TARGET=10.9',
                       '-DCompadre_USE_PYTHON:BOOL=ON',
-                      '-DCompadre_USE_MATLAB:BOOL=ON',
-                      '-DCompadre_EXAMPLES:BOOL=OFF',
                       '-DPYTHON_CALLING_BUILD:BOOL=ON',]
 
         cmake_file_list = list()
-        #if (cmake_file_string != ""):
         if (cmake_config != ""):
-            #cmake_arg_list = [line.rstrip('\n') for line in open(cmake_file_string)]
             cmake_arg_list = [line.rstrip('\n') for line in open(cmake_config)]
             for arg in cmake_arg_list:
                 cmake_args.append('-D'+arg)
             print('Custom CMake Args: ', cmake_arg_list)
 
-        cfg = 'Debug' if self.debug else 'Release'
+        # turn off examples and tests unless specified in a file
+        tests_in_cmake_args = False
+        for arg in cmake_args:
+            if 'Compadre_TESTS' in arg:
+                tests_in_cmake_args = True
+                break
+        if not tests_in_cmake_args:
+            cmake_args += ['-DCompadre_TESTS:BOOL=OFF']
+        examples_in_cmake_args = False
+        for arg in cmake_args:
+            if 'Compadre_EXAMPLES' in arg:
+                examples_in_cmake_args = True
+                break
+        if not examples_in_cmake_args:
+            cmake_args += ['-DCompadre_EXAMPLES:BOOL=OFF']
+
+        # add level 3 optimization if not specified in a file
+        flag_in_cmake_args = False
+        for arg in cmake_args:
+            if 'CMAKE_CXX_FLAGS' in arg:
+                flag_in_cmake_args = True
+                break
+        if not flag_in_cmake_args:
+            cmake_args += ['-DCMAKE_CXX_FLAGS= -O3 -g ']
+
+        # add level 3 optimization if not specified in a file
+        build_type_in_cmake_args = False
+        for arg in cmake_args:
+            if 'CMAKE_BUILD_TYPE' in arg:
+                build_type_in_cmake_args = True
+                break
+
+        # allow 'python setup.py build_ext --debug install' to have precedence over CMAKE_BUILD_TYPE
+        if self.debug and not build_type_in_cmake_args:
+            cfg = 'Debug'
+            cmake_args += ['-DCMAKE_BUILD_TYPE=Debug']
+        elif not self.debug and not build_type_in_cmake_args:
+            cfg = 'None'
+            cmake_args += ['-DCMAKE_BUILD_TYPE=None']
+        elif not self.debug: # was specified in file only
+            for arg in cmake_args[:]:
+                if 'CMAKE_BUILD_TYPE' in arg:
+                    # break down and copy to cfg
+                    cfg = arg.split('=')[1]
+                    break
+        else: # was specified in file and --debug in command
+            # delete specified from cmake_args 
+            for arg in cmake_args[:]:
+                if 'CMAKE_BUILD_TYPE' in arg:
+                    cmake_args.remove(arg)
+            cmake_args += ['-DCMAKE_BUILD_TYPE=Debug']
+            cfg = 'Debug'
+
         build_args = ['--config', cfg]
 
         if platform.system() == "Windows":
@@ -165,15 +219,16 @@ def build_extension(self, ext):
                 cmake_args += ['-A', 'x64']
             build_args += ['--', '/m']
         else:
-            cmake_args += ['-DCMAKE_BUILD_TYPE=' + cfg]
             build_args += ['--', '-j2']
 
         env = os.environ.copy()
         env['CXXFLAGS'] = '{} -DVERSION_INFO=\\"{}\\"'.format(env.get('CXXFLAGS', ''),
                                                               self.distribution.get_version())
         if not os.path.exists(self.build_temp):
             os.makedirs(self.build_temp)
+        print("CMake Args:", cmake_args)
         subprocess.check_call(['cmake', ext.sourcedir] + cmake_args, cwd=self.build_temp, env=env)
+        print("Build Args:", build_args)
         subprocess.check_call(['cmake', '--build', '.'] + build_args, cwd=self.build_temp)
 
 with open("README.md", "r") as fh:
@@ -200,9 +255,10 @@ def build_extension(self, ext):
     ext_modules=[CMakeExtension('pycompadre'),],
     cmdclass={
         'build_ext': CMakeBuild,
+        'test': SetupTest,
     },
-    tests_require=['nose','numpy'],
-    test_suite='nose.collector',
+    data_files=[('examples', ['pycompadre/examples/test_pycompadre.py',
+                              'pycompadre/examples/test_pycompadre_manifold.py']),],
     include_package_data=True,
     zip_safe=False,
 )