Merged in prabhuramachandran/pysph/fix-bugs (pull request #172)

Fix a bunch of issues

docs/source/installation.rst

@@ -35,7 +35,7 @@ Core dependencies
 The core dependencies are:
 
   - NumPy_
-  - Cython_ (version 0.19 and above)
+  - Cython_ (version 0.20 and above)
   - Mako_
   - nose_ for running the unit tests.
 
@@ -184,7 +184,7 @@ On OS X, your best bet is to install `Enthought Canopy`_ or Anaconda_ or some
 other Python distribution.  Ensure that you have gcc or clang installed by
 installing XCode.  See `this
 <http://stackoverflow.com/questions/12228382/after-install-xcode-where-is-clang>`_
-if you installed XCode but can't find clang or gcc.  
+if you installed XCode but can't find clang or gcc.
 
 ^^^^^^^^^^^^^
 OpenMP on OSX

pysph/__init__.py

@@ -1,5 +1,5 @@
 # See PEP 440 for more on suitable version numbers.
-__version__ = '1.0a1.dev'
+__version__ = '1.0a1.dev0'
 
 
 # Conditional Imports for Parallel stuff

pysph/sph/equation.py

@@ -53,7 +53,12 @@ class Context(dict):
         >>> c.keys()
         ['a', 'x', 'b']
     """
-    __getattr__ = dict.__getitem__
+    def __getattr__(self, key):
+        try:
+            return self.__getitem__(key)
+        except KeyError:
+            raise AttributeError('Context has no attribute %s'%key)
+
     def __setattr__(self, key, value):
         self[key] = value
 

pysph/tools/interpolator.py

@@ -77,24 +77,29 @@ class Interpolator(object):
     """
 
     def __init__(self, particle_arrays, num_points=125000, kernel=None,
-                 x=None, y=None, z=None):
+                 x=None, y=None, z=None, domain_manager=None):
         """
-        Parameters
-        ----------
-
-        particle_arrays: A list of particle arrays.
-        num_points: the number of points to interpolate on to.
-        kernel: the kernel to use for interpolation.
-
-        x: ndarray: the x-coordinate of points on which to interpolate.
-        y: ndarray: the y-coordinate of points on which to interpolate.
-        z: ndarray: the z-coordinate of points on which to interpolate.
-
-
         The x, y, z coordinates need not be specified, and if they are not,
         the bounds of the interpolated domain is automatically computed and
         `num_points` number of points are used in this domain uniformly placed.
 
+        Parameters
+        ----------
+
+        particle_arrays: list
+            A list of particle arrays.
+        num_points: int
+            the number of points to interpolate on to.
+        kernel: Kernel
+            the kernel to use for interpolation.
+        x: ndarray
+            the x-coordinate of points on which to interpolate.
+        y: ndarray
+            the y-coordinate of points on which to interpolate.
+        z: ndarray
+            the z-coordinate of points on which to interpolate.
+        domain_manager: DomainManager
+            An optional Domain manager for periodic domains.
         """
         self._set_particle_arrays(particle_arrays)
         bounds = get_bounding_box(self.particle_arrays)
@@ -109,6 +114,7 @@ def __init__(self, particle_arrays, num_points=125000, kernel=None,
         self.pa = None
         self.nnps = None
         self.func_eval = None
+        self.domain_manager = domain_manager
         if x is None and y is None and z is None:
             self.set_domain(bounds, shape)
         else:
@@ -118,16 +124,20 @@ def __init__(self, particle_arrays, num_points=125000, kernel=None,
     def set_interpolation_points(self, x=None, y=None, z=None):
         """Set the points on which we must interpolate the arrays.
 
-        Parameters
-        -----------
-
-        x: ndarray: the x-coordinate of points on which to interpolate.
-        y: ndarray: the y-coordinate of points on which to interpolate.
-        z: ndarray: the z-coordinate of points on which to interpolate.
-
         If any of x, y, z is not passed it is assumed to be 0.0 and shaped
         like the other non-None arrays.
 
+
+        Parameters
+        ----------
+
+        x: ndarray
+            the x-coordinate of points on which to interpolate.
+        y: ndarray
+            the y-coordinate of points on which to interpolate.
+        z: ndarray
+            the z-coordinate of points on which to interpolate.
+
         """
         tmp = None
         for tmp in (x, y, z):
@@ -153,26 +163,34 @@ def _get_array(_t):
     def set_domain(self, bounds, shape):
         """Set the domain to interpolate into.
 
-        Parameters:
-        -----------
+        Parameters
+        ----------
 
-        bounds: (xmin, xmax, ymin, ymax, zmin, zmax)
-        shape: (nx, ny, nz)
+        bounds: tuple
+            (xmin, xmax, ymin, ymax, zmin, zmax)
+        shape: tuple
+            (nx, ny, nz)
         """
         self.bounds = np.asarray(bounds)
         self.shape = np.asarray(shape)
         x, y, z = self._create_default_points(self.bounds, self.shape)
         self.set_interpolation_points(x, y, z)
 
     def interpolate(self, prop, gradient=False):
-        """
+        """Interpolate given property.
+
+        Parameters
+        ----------
 
-        :prop: The name of the property to interpolate.
+        prop: str
+            The name of the property to interpolate.
 
-        :gradient: bool: Evaluate gradient and not function.
+        gradient: bool
+            Evaluate gradient and not function.
 
-        :return: A numpy array suitably shaped with the property
-        interpolated.
+        Returns
+        -------
+        A numpy array suitably shaped with the property interpolated.
         """
         for array in self.particle_arrays:
             data = array.get(prop, only_real_particles=False)
@@ -202,6 +220,7 @@ def _create_nnps(self, arrays):
         # create the neighbor locator object
         self.nnps = NNPS(dim=self.kernel.dim, particles=arrays,
                          radius_scale=self.kernel.radius_scale,
+                         domain=self.domain_manager,
                          cache=True)
         self.nnps.update()
         self.func_eval.set_nnps(self.nnps)

pyzoltan/core/carray.pxd

@@ -1,9 +1,8 @@
-# This file (carray.pxd) has been generated automatically on
-# Sat May 16 00:36:51 2015
+# This file (carray.pxd) has been generated automatically.
 # DO NOT modify this file
 # To make changes modify the source templates (carray.pxd.mako) and regenerate
 """
-Implementation of arrays of different types in Cython.
+Implementation of resizeable arrays of different types in Cython.
 
 Declaration File.
 
@@ -201,4 +200,3 @@ cdef class DoubleArray(BaseArray):
     cpdef reset(self)
     cpdef long index(self, double value)
 
-

pyzoltan/core/carray.pxd.mako

@@ -1,19 +1,16 @@
 <%
-import datetime
-now = datetime.datetime.now()
 type_info = [
     ('int', 'IntArray', 'NPY_INT'),
     ('unsigned int', 'UIntArray', 'NPY_UINT'),
     ('long', 'LongArray', 'NPY_LONG'),
     ('float', 'FloatArray', 'NPY_FLOAT'),
     ('double', 'DoubleArray', 'NPY_DOUBLE'),
 ]
-%># This file (carray.pxd) has been generated automatically on
-# ${now.strftime('%c')}
+%># This file (carray.pxd) has been generated automatically.
 # DO NOT modify this file
 # To make changes modify the source templates (carray.pxd.mako) and regenerate
 """
-Implementation of arrays of different types in Cython.
+Implementation of resizeable arrays of different types in Cython.
 
 Declaration File.
 
@@ -93,4 +90,3 @@ cdef class ${CLASSNAME}(BaseArray):
     cpdef long index(self, ${ARRAY_TYPE} value)
 
 % endfor
-

pyzoltan/core/carray.pyx

@@ -1,7 +1,6 @@
-# This file (carray.pxd) has been generated automatically on
-# Sat May 16 01:28:08 2015
+# This file (carray.pxd) has been generated automatically.
 # DO NOT modify this file
-# To make changes modify the source templates (carray_pxd.src) and regenerate
+# To make changes modify the source templates (carray.pxd.mako) and regenerate
 """
 Implementation of resizeable arrays of different types in Cython.
 
@@ -2300,4 +2299,3 @@ cdef class DoubleArray(BaseArray):
         self.minimum = min_val
         self.maximum = max_val
 
-

pyzoltan/core/carray.pyx.mako

@@ -1,19 +1,14 @@
 <%
-import datetime
-now = datetime.datetime.now()
 type_info = [
     ('int', 'IntArray', 'NPY_INT'),
     ('unsigned int', 'UIntArray', 'NPY_UINT'),
     ('long', 'LongArray', 'NPY_LONG'),
     ('float', 'FloatArray', 'NPY_FLOAT'),
     ('double', 'DoubleArray', 'NPY_DOUBLE'),
 ]
-%># This file (carray.pxd) has been generated automatically on
-# ${now.strftime('%c')}
-## The section below is the header section which is copied unmodified into
-## the generated file
+%># This file (carray.pxd) has been generated automatically.
 # DO NOT modify this file
-# To make changes modify the source templates (carray_pxd.src) and regenerate
+# To make changes modify the source templates (carray.pxd.mako) and regenerate
 """
 Implementation of resizeable arrays of different types in Cython.
 
@@ -682,4 +677,3 @@ cdef class ${CLASSNAME}(BaseArray):
         self.maximum = max_val
 
 % endfor
-

requirements.txt

@@ -1,5 +1,5 @@
 numpy
 setuptools
-Cython>=0.19
+Cython>=0.20
 mako
 nose

setup.py

@@ -7,11 +7,11 @@
 from setuptools import find_packages, setup
 from Cython.Distutils import build_ext, Extension
 
-Have_MPI = True
+HAVE_MPI = True
 try:
     import mpi4py
 except ImportError:
-    Have_MPI = False
+    HAVE_MPI = False
 
 USE_ZOLTAN=True
 
@@ -23,10 +23,6 @@
     extra_compile_args = []
 
 
-mpi_inc_dirs = []
-mpi_compile_args = []
-mpi_link_args = []
-
 def get_deps(*args):
     """Given a list of basenames, this checks if a .pyx or .pxd exists
     and returns the list.
@@ -114,24 +110,47 @@ def get_zoltan_directory(varname):
     return d
 
 
-openmp_compile_args, openmp_link_args, openmp_env = get_openmp_flags()
-
-if Have_MPI:
-    mpic = 'mpic++'
-    if compiler == 'intel':
-        link_args = check_output([mpic, '-cc=icc', '-link_info']).strip()
-        link_args = link_args[3:]
-        compile_args = check_output(
-            [mpic, '-cc=icc', '-compile_info']
-        ).strip()
-        compile_args = compile_args[3:]
+def get_mpi_flags():
+    """Returns mpi_inc_dirs, mpi_compile_args, mpi_link_args.
+    """
+    global HAVE_MPI
+    mpi_inc_dirs = []
+    mpi_compile_args = []
+    mpi_link_args = []
+    if not HAVE_MPI:
+        return mpi_inc_dirs, mpi_compile_args, mpi_link_args
+    try:
+        mpic = 'mpic++'
+        if compiler == 'intel':
+            link_args = check_output([mpic, '-cc=icc', '-link_info']).strip()
+            link_args = link_args[3:]
+            compile_args = check_output(
+                [mpic, '-cc=icc', '-compile_info']
+            ).strip()
+            compile_args = compile_args[3:]
+        else:
+            link_args = check_output([mpic, '--showme:link']).strip()
+            compile_args = check_output([mpic, '--showme:compile']).strip()
+    except:
+        print '-'*80
+        print "Unable to run mpic++ correctly, skipping parallel build"
+        print '-'*80
+        HAVE_MPI = False
     else:
-        link_args = check_output([mpic, '--showme:link']).strip()
-        compile_args = check_output([mpic, '--showme:compile']).strip()
-    mpi_link_args.extend(link_args.split())
-    mpi_compile_args.extend(compile_args.split())
-    mpi_inc_dirs.append(mpi4py.get_include())
+        mpi_link_args.extend(link_args.split())
+        mpi_compile_args.extend(compile_args.split())
+        mpi_inc_dirs.append(mpi4py.get_include())
+
+    return mpi_inc_dirs, mpi_compile_args, mpi_link_args
+
 
+def get_zoltan_args():
+    """Returns zoltan_include_dirs, zoltan_library_dirs
+    """
+    global HAVE_MPI
+    zoltan_include_dirs, zoltan_library_dirs = [], []
+    if not HAVE_MPI:
+        return zoltan_include_dirs, zoltan_library_dirs
     # First try with the environment variable 'ZOLTAN'
     zoltan_base = get_zoltan_directory('ZOLTAN')
     inc = lib = ''
@@ -148,10 +167,9 @@ def get_zoltan_directory(varname):
 
     if (not USE_ZOLTAN):
         print("*"*80)
-        print("Zoltan Environment variable" \
-              "not set, not using ZOLTAN!")
+        print("Zoltan Environment variable not set, not using ZOLTAN!")
         print("*"*80)
-        Have_MPI = False
+        HAVE_MPI = False
     else:
         print('-'*70)
         print("Using Zoltan from:\n%s\n%s"%(inc, lib))
@@ -163,6 +181,14 @@ def get_zoltan_directory(varname):
         zoltan_cython_include = [ os.path.abspath('./pyzoltan/czoltan') ]
         zoltan_include_dirs += zoltan_cython_include
 
+    return zoltan_include_dirs, zoltan_library_dirs
+
+
+openmp_compile_args, openmp_link_args, openmp_env = get_openmp_flags()
+mpi_inc_dirs, mpi_compile_args, mpi_link_args = get_mpi_flags()
+zoltan_include_dirs, zoltan_library_dirs = get_zoltan_args()
+
+
 include_dirs = [numpy.get_include()]
 
 cmdclass = {'build_ext': build_ext}
@@ -227,7 +253,7 @@ def get_zoltan_directory(varname):
 for ext in ext_modules:
     ext.include_dirs = include_dirs
 
-if Have_MPI:
+if HAVE_MPI:
     zoltan_modules = [
         Extension(
             name="pyzoltan.core.zoltan",
@@ -338,7 +364,7 @@ def get_zoltan_directory(varname):
       ext_modules = ext_modules,
       include_package_data = True,
       cmdclass=cmdclass,
-      install_requires = ['numpy', 'mako', 'Cython>=0.19'],
+      install_requires = ['numpy', 'mako', 'Cython>=0.20'],
       extras_require = extras_require,
       zip_safe = False,
       entry_points = """