Merge 00b5d0d into 381fef8

docs/installation.rst

@@ -115,7 +115,7 @@ from source also requires `Microsoft Visual C++ Compiler for Python 2.7
 
 .. _Anaconda: http://docs.continuum.io/anaconda/
 .. _pip: https://pip.pypa.io/en/latest/
-.. _OpenMP: http://openmp.org
+.. _OpenMP: http://openmp.org/
 .. _GNU GCC: https://gcc.gnu.org/
 .. _Homebrew: http://brew.sh/
 .. _MacPorts: https://www.macports.org/

pandana/network.py

@@ -92,16 +92,16 @@ def __init__(self, node_x, node_y, edge_from, edge_to, edge_weights,
                            self._node_indexes(edges_df["to"])], axis=1)
 
         self.net = cyaccess(self.node_idx.values,
-                            nodes_df.astype('double').as_matrix(),
-                            edges.as_matrix(),
+                            nodes_df.astype('double').values,
+                            edges.values,
                             edges_df[edge_weights.columns].transpose()
                                                           .astype('double')
-                                                          .as_matrix(),
+                                                          .values,
                             twoway)
 
         self._twoway = twoway
 
-        self.kdtree = KDTree(nodes_df.as_matrix())
+        self.kdtree = KDTree(nodes_df.values)
 
     @classmethod
     def from_hdf5(cls, filename):
@@ -381,7 +381,7 @@ def get_node_ids(self, x_col, y_col, mapping_distance=None):
         """
         xys = pd.DataFrame({'x': x_col, 'y': y_col})
 
-        distances, indexes = self.kdtree.query(xys.as_matrix())
+        distances, indexes = self.kdtree.query(xys.values)
         indexes = np.transpose(indexes)[0]
         distances = np.transpose(distances)[0]
 

setup.py

@@ -12,6 +12,10 @@
 from setuptools.command.build_ext import build_ext
 
 
+###############################################
+## Invoking tests
+###############################################
+
 class PyTest(TestCommand):
     user_options = [('pytest-args=', 'a', "Arguments to pass to py.test")]
 
@@ -46,53 +50,62 @@ def run(self):
         build_ext.run(self)
 
 
-include_dirs = [
-    '.'
-]
+###############################################
+## Building the C++ extension
+###############################################
 
-packages = find_packages(exclude=["*.tests", "*.tests.*", "tests.*", "tests"])
+extra_compile_args = ['-w', '-std=c++11', '-O3']
+extra_link_args = []
+
+# Mac compilation: flags are for the llvm compilers included with recent
+# versions of Xcode Command Line Tools, or newer versions installed separately
+
+if sys.platform.startswith('darwin'):  # Mac
+
+    # This environment variable sets the earliest OS version that the compiled
+    # code will be compatible with. In certain contexts the default is too old
+    # to allow using libc++; supporting OS X 10.9 and later seems safe
+    os.environ['MACOSX_DEPLOYMENT_TARGET'] = '10.9'
+
+    extra_compile_args += ['-D NO_TR1_MEMORY', '-stdlib=libc++']
+    extra_link_args += ['-stdlib=libc++']
+
+    if os.environ.get('USEOPENMP'):
+        extra_compile_args += ['-fopenmp']
 
-source_files = [
-    'src/accessibility.cpp',
-    'src/graphalg.cpp',
-    "src/cyaccess.pyx",
-    'src/contraction_hierarchies/src/libch.cpp'
-]
-
-extra_compile_args = [
-    '-w',
-    '-std=c++0x',
-    '-O3',
-    '-fpic',
-    '-g',
-]
-extra_link_args = None
-
-# separate compiler options for Windows
-if sys.platform.startswith('win'):
+# Window compilation: flags are for Visual C++
+
+elif sys.platform.startswith('win'):  # Windows
     extra_compile_args = ['/w', '/openmp']
-# Use OpenMP if directed or not on a Mac
-elif os.environ.get('USEOPENMP') or not sys.platform.startswith('darwin'):
+
+# Linux compilation: flags are for gcc 4.8 and later
+
+else:  # Linux
     extra_compile_args += ['-fopenmp']
-    extra_link_args = [
-        '-lgomp'
-    ]
-
-# recent versions of the OS X SDK don't have the tr1 namespace
-# and we need to flag that during compilation.
-# here we need to check what version of OS X is being targeted
-# for the installation.
-# this is potentially different than the version of OS X on the system.
-if platform.system() == 'Darwin':
-    mac_ver = sysconfig.get_config_var('MACOSX_DEPLOYMENT_TARGET')
-    if mac_ver:
-        mac_ver = [int(x) for x in mac_ver.split('.')]
-        if mac_ver >= [10, 7]:
-            extra_compile_args += ['-D NO_TR1_MEMORY']
-            extra_compile_args += ['-stdlib=libc++']
+    extra_link_args += ['-lgomp']
+
+
+cyaccess = Extension(
+        name='pandana.cyaccess',
+        sources=[
+            'src/accessibility.cpp',
+            'src/graphalg.cpp',
+            'src/cyaccess.pyx',
+            'src/contraction_hierarchies/src/libch.cpp'],
+        language='c++',
+        include_dirs=['.'],
+        extra_compile_args=extra_compile_args,
+        extra_link_args=extra_link_args)
+
+
+###############################################
+## Standard setup
+###############################################
 
 version = '0.4.1'
 
+packages = find_packages(exclude=["*.tests", "*.tests.*", "tests.*", "tests"])
+
 # read long description from README
 with open('README.rst', 'r') as f:
     long_description = f.read()
@@ -107,14 +120,7 @@ def run(self):
                  'dataframes of network queries, quickly'),
     long_description=long_description,
     url='https://udst.github.io/pandana/',
-    ext_modules=[Extension(
-            'pandana.cyaccess',
-            source_files,
-            language="c++",
-            include_dirs=include_dirs,
-            extra_compile_args=extra_compile_args,
-            extra_link_args=extra_link_args,
-        )],
+    ext_modules=[cyaccess],
     install_requires=[
         'matplotlib>=1.3.1',
         'numpy>=1.8.0',
@@ -125,7 +131,10 @@ def run(self):
         'cython>=0.25.2',
         'scikit-learn>=0.18.1'
     ],
-    tests_require=['pytest'],
+    tests_require=[
+        'pycodestyle',
+        'pytest'
+    ],
     cmdclass={
         'test': PyTest,
         'lint': Lint,

src/contraction_hierarchies/src/DataStructures/Percent.h

@@ -54,8 +54,8 @@ class Percent
             _nextThreshold += _intervalPercent;
             printPercent( currentValue / (double)_maxValue * 100 );
         }
-        // if (currentValue + 1 == _maxValue)
-            // std::cout << " 100%" << std::endl;
+        if (currentValue + 1 == _maxValue)
+            std::cout << " 100%" << std::endl;
     }
 
     void printIncrement()
@@ -77,12 +77,12 @@ class Percent
         while (percent >= _lastPercent+_step) {
             _lastPercent+=_step;
             if (_lastPercent % 10 == 0) {
-                // std::cout << " " << _lastPercent << "% ";
+                std::cout << " " << _lastPercent << "% ";
             }
             else {
-                // std::cout << ".";
+                std::cout << ".";
             }
-            // std::cout.flush();
+            std::cout.flush();
         }
     }
 };

src/contraction_hierarchies/src/libch.cpp

@@ -202,6 +202,10 @@ inline ostream& operator<< (ostream& os, const Edge& e) {
                 }
             }
         }
+
+        FILE_LOG(logINFO) << "Range graph removed " << edges.size() - edge 
+                          << " edges of " << edges.size() << "\n";
+
         //INFO("Range graph removed " << edges.size() - edge << " edges of " << edges.size());
         assert(edge <= edges.size());
         edges.resize( edge );

src/contraction_hierarchies/src/libch.h

@@ -34,6 +34,8 @@ or see http://www.gnu.org/licenses/agpl.txt.
 #include "DataStructures/StaticGraph.h"
 #include "POIIndex/POIIndex.h"
 
+#define FILE_LOG(logINFO) (std::cout)
+
 struct _HeapData {
     NodeID parent;
     _HeapData( NodeID p ) : parent(p) { }

src/graphalg.cpp

@@ -9,6 +9,10 @@ Graphalg::Graphalg(
     this->numnodes = numnodes;
 
     int num = omp_get_max_threads();
+
+    FILE_LOG(logINFO) << "Generating contraction hierarchies with "
+                      << num << " threads.\n";
+
     ch = CH::ContractionHierarchies(num);
 
     vector<CH::Node> nv;
@@ -20,6 +24,9 @@ Graphalg::Graphalg(
         nv.push_back(n);
     }
 
+    FILE_LOG(logINFO) << "Setting CH node vector of size "
+                      << nv.size() << "\n";
+
     ch.SetNodeVector(nv);
 
     vector<CH::Edge> ev;
@@ -30,6 +37,9 @@ Graphalg::Graphalg(
         ev.push_back(e);
     }
 
+    FILE_LOG(logINFO) << "Setting CH edge vector of size "
+                      << ev.size() << "\n";
+
     ch.SetEdgeVector(ev);
     ch.RunPreprocessing();
 }

src/shared.h

@@ -8,4 +8,5 @@
 #endif
 #ifdef _OPENMP
 #include <omp.h>
-#endif
+#endif
+#define FILE_LOG(logINFO) (std::cout)