Merge pull request #77 from inducer/dofarray-not-ndarray-subclass

Stop subclassing DOFArray from numpy.ndarray

doc/conf.py

@@ -12,8 +12,8 @@
 # All configuration values have a default; values that are commented out
 # serve to show the default.
 
-import sys
-import os
+import sys  # noqa: F401
+import os  # noqa: F401
 
 # If extensions (or modules to document with autodoc) are in another directory,
 # add these directories to sys.path here. If the directory is relative to the
@@ -23,42 +23,45 @@
 # -- General configuration ------------------------------------------------
 
 # If your documentation needs a minimal Sphinx version, state it here.
-#needs_sphinx = '1.0'
+#needs_sphinx = "1.0"
 
 # Add any Sphinx extension module names here, as strings. They can be
-# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
+# extensions coming with Sphinx (named "sphinx.ext.*") or your custom
 # ones.
 extensions = [
-    'sphinx.ext.autodoc',
-    'sphinx.ext.doctest',
-    'sphinx.ext.intersphinx',
-    'sphinx.ext.mathjax',
-    'sphinx.ext.graphviz',
+    "sphinx.ext.autodoc",
+    "sphinx.ext.doctest",
+    "sphinx.ext.intersphinx",
+    "sphinx.ext.mathjax",
+    "sphinx.ext.graphviz",
 ]
 
 # Add any paths that contain templates here, relative to this directory.
-templates_path = ['_templates']
+templates_path = ["_templates"]
 
 # The suffix of source filenames.
-source_suffix = '.rst'
+source_suffix = ".rst"
 
 # The encoding of source files.
-#source_encoding = 'utf-8-sig'
+#source_encoding = "utf-8-sig"
 
 # The master toctree document.
-master_doc = 'index'
+master_doc = "index"
 
 # General information about the project.
-project = u'meshmode'
-copyright = u'2014, Andreas Klöckner'
+project = u"meshmode"
+copyright = u"2014, Andreas Klöckner"
 
 # The version info for the project you're documenting, acts as replacement for
 # |version| and |release|, also used in various other places throughout the
 # built documents.
 #
 # The short X.Y version.
 ver_dic = {}
-exec(compile(open("../meshmode/version.py").read(), "../meshmode/version.py", 'exec'), ver_dic)
+exec(
+        compile(
+            open("../meshmode/version.py").read(), "../meshmode/version.py", "exec"),
+        ver_dic)
 version = ".".join(str(x) for x in ver_dic["VERSION"])
 # The full version, including alpha/beta/rc tags.
 release = ver_dic["VERSION_TEXT"]
@@ -75,7 +78,7 @@
 
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.
-exclude_patterns = ['_build']
+exclude_patterns = ["_build"]
 
 # The reST default role (used for this markup: `text`) to use for all
 # documents.
@@ -93,7 +96,7 @@
 #show_authors = False
 
 # The name of the Pygments (syntax highlighting) style to use.
-pygments_style = 'sphinx'
+pygments_style = "sphinx"
 
 # A list of ignored prefixes for module index sorting.
 #modindex_common_prefix = []
@@ -114,11 +117,11 @@
         }
 
 html_sidebars = {
-    '**': [
-        'about.html',
-        'navigation.html',
-        'relations.html',
-        'searchbox.html',
+    "**": [
+        "about.html",
+        "navigation.html",
+        "relations.html",
+        "searchbox.html",
     ]
 }
 
@@ -194,28 +197,28 @@
 #html_file_suffix = None
 
 # Output file base name for HTML help builder.
-htmlhelp_basename = 'meshmodedoc'
+htmlhelp_basename = "meshmodedoc"
 
 
 # -- Options for LaTeX output ---------------------------------------------
 
 latex_elements = {
-# The paper size ('letterpaper' or 'a4paper').
-#'papersize': 'letterpaper',
+    # The paper size ("letterpaper" or "a4paper").
+    #"papersize": "letterpaper",
 
-# The font size ('10pt', '11pt' or '12pt').
-#'pointsize': '10pt',
+    # The font size ("10pt", "11pt" or "12pt").
+    #"pointsize": "10pt",
 
-# Additional stuff for the LaTeX preamble.
-#'preamble': '',
+    # Additional stuff for the LaTeX preamble.
+    #"preamble": '',
 }
 
 # Grouping the document tree into LaTeX files. List of tuples
 # (source start file, target name, title,
 #  author, documentclass [howto, manual, or own class]).
 latex_documents = [
-  ('index', 'meshmode.tex', u'meshmode Documentation',
-   u'Andreas Klöckner', 'manual'),
+        ("index", "meshmode.tex", u"meshmode Documentation",
+            u"Andreas Klöckner", "manual"),
 ]
 
 # The name of an image file (relative to this directory) to place at the top of
@@ -244,8 +247,8 @@
 # One entry per manual page. List of tuples
 # (source start file, name, description, authors, manual section).
 man_pages = [
-    ('index', 'meshmode', u'meshmode Documentation',
-     [u'Andreas Klöckner'], 1)
+    ("index", "meshmode", u"meshmode Documentation",
+     [u"Andreas Klöckner"], 1)
 ]
 
 # If true, show URL addresses after external links.
@@ -258,9 +261,9 @@
 # (source start file, target name, title, author,
 #  dir menu entry, description, category)
 texinfo_documents = [
-  ('index', 'meshmode', u'meshmode Documentation',
-   u'Andreas Klöckner', 'meshmode', 'One line description of project.',
-   'Miscellaneous'),
+        ("index", "meshmode", u"meshmode Documentation",
+            u"Andreas Klöckner", "meshmode", "One line description of project.",
+            "Miscellaneous"),
 ]
 
 # Documents to append as an appendix to all manuals.
@@ -269,24 +272,25 @@
 # If false, no module index is generated.
 #texinfo_domain_indices = True
 
-# How to display URL addresses: 'footnote', 'no', or 'inline'.
-#texinfo_show_urls = 'footnote'
+# How to display URL addresses: "footnote", "no", or "inline".
+#texinfo_show_urls = "footnote"
 
 # If true, do not generate a @detailmenu in the "Top" node's menu.
 #texinfo_no_detailmenu = False
 
 intersphinx_mapping = {
-    'https://docs.python.org/': None,
-    'https://docs.scipy.org/doc/numpy/': None,
-    'https://documen.tician.de/pyopencl': None,
-    'https://documen.tician.de/meshpy': None,
-    'https://documen.tician.de/modepy': None,
-    'https://documen.tician.de/loopy': None,
-    'https://documen.tician.de/gmsh_interop': None,
-    'https://firedrakeproject.org/': None,
-    'https://tisaac.gitlab.io/recursivenodes/': None,
-    'https://fenics.readthedocs.io/projects/fiat/en/latest/': None,
-    'https://finat.github.io/FInAT/': None,
+    "https://docs.python.org/3/": None,
+    "https://numpy.org/doc/stable/": None,
+    "https://documen.tician.de/pytools": None,
+    "https://documen.tician.de/pyopencl": None,
+    "https://documen.tician.de/meshpy": None,
+    "https://documen.tician.de/modepy": None,
+    "https://documen.tician.de/loopy": None,
+    "https://documen.tician.de/gmsh_interop": None,
+    "https://firedrakeproject.org/": None,
+    "https://tisaac.gitlab.io/recursivenodes/": None,
+    "https://fenics.readthedocs.io/projects/fiat/en/latest/": None,
+    "https://finat.github.io/FInAT/": None,
 }
 
 autoclass_content = "class"

examples/simple-dg.py

@@ -30,7 +30,7 @@
         flat_obj_array, make_obj_array,
         obj_array_vectorize)
 from meshmode.mesh import BTAG_ALL, BTAG_NONE  # noqa
-from meshmode.dof_array import DOFArray, freeze, thaw
+from meshmode.dof_array import freeze, thaw
 from meshmode.array_context import PyOpenCLArrayContext, make_loopy_program
 
 
@@ -146,9 +146,7 @@ def get_connection(self, src, tgt):
             raise ValueError(f"locations '{src}'->'{tgt}' not understood")
 
     def interp(self, src, tgt, vec):
-        if (isinstance(vec, np.ndarray)
-                and vec.dtype.char == "O"
-                and not isinstance(vec, DOFArray)):
+        if isinstance(vec, np.ndarray):
             return obj_array_vectorize(
                     lambda el: self.interp(src, tgt, el), vec)
 
@@ -237,9 +235,7 @@ def get_inverse_mass_matrix(self, grp, dtype):
         return actx.freeze(actx.from_numpy(matrix))
 
     def inverse_mass(self, vec):
-        if (isinstance(vec, np.ndarray)
-                and vec.dtype.char == "O"
-                and not isinstance(vec, DOFArray)):
+        if isinstance(vec, np.ndarray):
             return obj_array_vectorize(
                     lambda el: self.inverse_mass(el), vec)
 
@@ -291,11 +287,8 @@ def get_local_face_mass_matrix(self, afgrp, volgrp, dtype):
         return actx.freeze(actx.from_numpy(matrix))
 
     def face_mass(self, vec):
-        if (isinstance(vec, np.ndarray)
-                and vec.dtype.char == "O"
-                and not isinstance(vec, DOFArray)):
-            return obj_array_vectorize(
-                    lambda el: self.face_mass(el), vec)
+        if isinstance(vec, np.ndarray):
+            return obj_array_vectorize(lambda el: self.face_mass(el), vec)
 
         @memoize_in(self, "face_mass_knl")
         def knl():

meshmode/array_context.py

@@ -25,7 +25,6 @@
 import loopy as lp
 from loopy.version import MOST_RECENT_LANGUAGE_VERSION
 from pytools import memoize_method
-from pytools.obj_array import obj_array_vectorized_n_args
 
 __doc__ = """
 .. autofunction:: make_loopy_program
@@ -58,7 +57,7 @@ def __init__(self, array_context):
         self._array_context = array_context
 
     def __getattr__(self, name):
-        def f(*args):
+        def loopy_implemented_elwise_func(*args):
             actx = self._array_context
             # FIXME: Maybe involve loopy type inference?
             result = actx.empty(args[0].shape, args[0].dtype)
@@ -68,14 +67,15 @@ def f(*args):
                     **{"inp%d" % i: arg for i, arg in enumerate(args)})
             return result
 
-        return obj_array_vectorized_n_args(f)
+        from meshmode.dof_array import obj_or_dof_array_vectorized_n_args
+        return obj_or_dof_array_vectorized_n_args(loopy_implemented_elwise_func)
 
-    @obj_array_vectorized_n_args
     def conjugate(self, x):
         # NOTE: conjugate distribute over object arrays, but it looks for a
         # `conjugate` ufunc, while some implementations only have the shorter
         # `conj` (e.g. cl.array.Array), so this should work for everybody
-        return x.conj()
+        from meshmode.dof_array import obj_or_dof_array_vectorize
+        return obj_or_dof_array_vectorize(lambda obj: obj.conj(), x)
 
     conj = conjugate
 
@@ -225,20 +225,21 @@ def thaw(self, array):
 # {{{ PyOpenCLArrayContext
 
 class _PyOpenCLFakeNumpyNamespace(_BaseFakeNumpyNamespace):
-    @obj_array_vectorized_n_args
     def maximum(self, x, y):
         import pyopencl.array as cl_array
-        return cl_array.maximum(x, y)
+        from meshmode.dof_array import obj_or_dof_array_vectorize_n_args
+        return obj_or_dof_array_vectorize_n_args(cl_array.maximum, x, y)
 
-    @obj_array_vectorized_n_args
     def minimum(self, x, y):
         import pyopencl.array as cl_array
-        return cl_array.minimum(x, y)
+        from meshmode.dof_array import obj_or_dof_array_vectorize_n_args
+        return obj_or_dof_array_vectorize_n_args(cl_array.minimum, x, y)
 
-    @obj_array_vectorized_n_args
     def where(self, criterion, then, else_):
         import pyopencl.array as cl_array
-        return cl_array.if_positive(criterion != 0, then, else_)
+        from meshmode.dof_array import obj_or_dof_array_vectorize_n_args
+        return obj_or_dof_array_vectorize_n_args(
+                cl_array.if_positive, criterion != 0, then, else_)
 
 
 class PyOpenCLArrayContext(ArrayContext):

meshmode/discretization/__init__.py

@@ -237,9 +237,9 @@ def _new_array(self, actx, creation_func, dtype=None):
         else:
             dtype = np.dtype(dtype)
 
-        return _DOFArray.from_list(actx, [
+        return _DOFArray(actx, tuple(
             creation_func(shape=(grp.nelements, grp.nunit_dofs), dtype=dtype)
-            for grp in self.groups])
+            for grp in self.groups))
 
     def empty(self, actx: ArrayContext, dtype=None):
         """Return an empty :class:`~meshmode.dof_array.DOFArray`.
@@ -297,11 +297,11 @@ def get_mat(grp):
 
             return mat
 
-        return _DOFArray.from_list(actx, [
+        return _DOFArray(actx, tuple(
                 actx.call_loopy(
                     prg(), diff_mat=actx.from_numpy(get_mat(grp)), vec=vec[grp.index]
                     )["result"]
-                for grp in self.groups])
+                for grp in self.groups))
 
     @memoize_method
     def quad_weights(self):
@@ -316,14 +316,14 @@ def prg():
                 "result[iel,idof] = weights[idof]",
                 name="quad_weights")
 
-        return _DOFArray.from_list(None, [
+        return _DOFArray(None, tuple(
                 actx.freeze(
                     actx.call_loopy(
                         prg(),
                         weights=actx.from_numpy(grp.weights),
                         nelements=grp.nelements,
                         )["result"])
-                for grp in self.groups])
+                for grp in self.groups))
 
     @memoize_method
     def nodes(self):
@@ -348,15 +348,15 @@ def prg():
                 name="nodes")
 
         return make_obj_array([
-            _DOFArray.from_list(None, [
+            _DOFArray(None, tuple(
                 actx.freeze(
                     actx.call_loopy(
                         prg(),
                         resampling_mat=actx.from_numpy(
                             grp.from_mesh_interp_matrix()),
                         nodes=actx.from_numpy(grp.mesh_el_group.nodes[iaxis])
                         )["result"])
-                for grp in self.groups])
+                for grp in self.groups))
             for iaxis in range(self.ambient_dim)])
 
 # vim: fdm=marker

meshmode/discretization/visualization.py

@@ -22,7 +22,7 @@
 
 import numpy as np
 from pytools import memoize_method, Record
-from meshmode.dof_array import DOFArray, flatten, thaw
+from meshmode.dof_array import flatten, thaw
 
 
 __doc__ = """
@@ -73,9 +73,7 @@ def separate_by_real_and_imag(names_and_fields, real_only):
 
 
 def resample_to_numpy(conn, vec):
-    if (isinstance(vec, np.ndarray)
-            and vec.dtype.char == "O"
-            and not isinstance(vec, DOFArray)):
+    if isinstance(vec, np.ndarray):
         from pytools.obj_array import obj_array_vectorize
         return obj_array_vectorize(lambda x: resample_to_numpy(conn, x), vec)