style: enable and fix many flake8 issues

benchmarks/scalar_field.py

@@ -23,15 +23,19 @@
 import os
 import time
 import warnings
-import pyopencl as cl
-import pyopencl.clrandom
+
 import numpy as np
+
 import loopy as lp
 import pymbolic as pmbl
 import pymbolic.primitives as primitives
-from pymbolic.functions import sin, cos, exp, tan, log  # noqa: F401
+import pyopencl as cl
+import pyopencl.clrandom
+from pymbolic.functions import cos, exp, log, sin, tan  # noqa: F401
+
 from volumential.tools import ScalarFieldExpressionEvaluation
 
+
 # {{{ math functions
 
 # cf.
@@ -66,7 +70,7 @@ def math_func_mangler(target, name, arg_dtypes):
 
         fname = name.name
         if not (isinstance(name.aggregate, pmbl.primitives.Variable)
-                and name.aggregate.name == 'math'):
+                and name.aggregate.name == "math"):
             raise RuntimeError("unexpected aggregate '%s'" %
                     str(name.aggregate))
 
@@ -80,7 +84,7 @@ def math_func_mangler(target, name, arg_dtypes):
                         arg_dtype)
 
             return lp.CallMangleInfo(
-                   target_name="%s_%s" % (tpname, fname),
+                   target_name=f"{tpname}_{fname}",
                    result_dtypes=(arg_dtype,),
                    arg_dtypes=(arg_dtype,))
 
@@ -139,7 +143,7 @@ def get_evaluator(dim, expression, variables=None):
 # needed for using loopy.statistics
 knl = lp.add_and_infer_dtypes(
         knl,
-        dict(x0=np.float64, x1=np.float64, x2=np.float64))
+        {"x0": np.float64, "x1": np.float64, "x2": np.float64})
 knl = lp.set_options(knl, ignore_boostable_into=True)
 
 # {{{ wall time
@@ -178,13 +182,13 @@ def get_evaluator(dim, expression, variables=None):
 op_map = lp.get_op_map(knl, subgroup_size=ncpus, count_redundant_work=True,
         count_within_subscripts=True)
 
-params = dict(n_targets=pts.shape[1])
-print('Operation counts:')
+params = {"n_targets": pts.shape[1]}
+print("Operation counts:")
 total_ops = 0
 for op in op_map.keys():
     sub_count = op_map[op].eval_with_dict(params)
     total_ops += sub_count
-    print('\t', op.name, op_map[op], sub_count)
+    print("\t", op.name, op_map[op], sub_count)
 print("Total:", total_ops)
 
 # TODO: weight each operation by running micro-benchmarks

benchmarks/table_build.py

@@ -20,12 +20,15 @@
 THE SOFTWARE.
 """
 
+import logging
 import time
+
 import pyopencl as cl
+
 from volumential.table_manager import NearFieldInteractionTableManager
 
-import logging
-logging.basicConfig(format='%(name)s:%(levelname)s: %(message)s')
+
+logging.basicConfig(format="%(name)s:%(levelname)s: %(message)s")
 
 
 def bench_table_build(queue):
@@ -68,5 +71,5 @@ def main():
     bench_table_build(queue)
 
 
-if __name__ == '__main__':
+if __name__ == "__main__":
     main()

doc/source/conf.py

@@ -1,5 +1,4 @@
 #!/usr/bin/env python3
-# -*- coding: utf-8 -*-
 #
 # Volumential documentation build configuration file, created by
 # sphinx-quickstart on Mon Oct 23 10:27:37 2017.
@@ -20,9 +19,11 @@
 import os
 import sys
 from datetime import datetime
+
 import volumential.version as __version__
 
-sys.path.insert(0, os.path.abspath('..'))
+
+sys.path.insert(0, os.path.abspath(".."))
 
 
 # -- General configuration ------------------------------------------------
@@ -35,35 +36,38 @@
 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
 # ones.
 extensions = [
-        'sphinx.ext.autodoc',
-        'sphinx.ext.todo',
-        'sphinx.ext.autosummary',
-        'sphinx.ext.coverage',
-        'sphinx.ext.mathjax',
-        'sphinx.ext.ifconfig',
-        'sphinx.ext.viewcode',
-        'sphinx.ext.intersphinx',
-        'sphinx.ext.githubpages']
+        "sphinx.ext.autodoc",
+        "sphinx.ext.todo",
+        "sphinx.ext.autosummary",
+        "sphinx.ext.coverage",
+        "sphinx.ext.mathjax",
+        "sphinx.ext.ifconfig",
+        "sphinx.ext.viewcode",
+        "sphinx.ext.intersphinx",
+        "sphinx.ext.githubpages"]
 
 # Add any paths that contain templates here, relative to this directory.
-templates_path = ['_templates']
+templates_path = ["_templates"]
 
 # Set the mathjax CDN
-mathjax_path = "https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"
+mathjax_path = (
+    "https://cdnjs.cloudflare.com/ajax/libs/"
+    "mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"
+)
 
 # The suffix(es) of source filenames.
 # You can specify multiple suffix as a list of string:
 #
 # source_suffix = ['.rst', '.md']
-source_suffix = '.rst'
+source_suffix = ".rst"
 
 # The master toctree document.
-master_doc = 'index'
+master_doc = "index"
 
 # General information about the project.
-project = 'Volumential'
-copyright = '%s, Xiaoyu Wei' % str(datetime.today().year)
-author = 'Xiaoyu Wei'
+project = "Volumential"
+copyright = "%s, Xiaoyu Wei" % str(datetime.today().year)
+author = "Xiaoyu Wei"
 
 # The version info for the project you're documenting, acts as replacement for
 # |version| and |release|, also used in various other places throughout the
@@ -88,7 +92,7 @@
 exclude_patterns = []
 
 # The name of the Pygments (syntax highlighting) style to use.
-pygments_style = 'sphinx'
+pygments_style = "sphinx"
 
 # If true, `todo` and `todoList` produce output, else they produce nothing.
 todo_include_todos = True
@@ -99,7 +103,7 @@
 # The theme to use for HTML and HTML Help pages.  See the documentation for
 # a list of builtin themes.
 #
-html_theme = 'sphinx_rtd_theme'
+html_theme = "sphinx_rtd_theme"
 
 # Theme options are theme-specific and customize the look and feel of a theme
 # further.  For a list of options available for each theme, see the
@@ -110,25 +114,25 @@
 # Add any paths that contain custom static files (such as style sheets) here,
 # relative to this directory. They are copied after the builtin static files,
 # so a file named "default.css" will overwrite the builtin "default.css".
-html_static_path = ['_static']
+html_static_path = ["_static"]
 
 # Custom sidebar templates, must be a dictionary that maps document names
 # to template names.
 #
 # This is required for the alabaster theme
 # refs: http://alabaster.readthedocs.io/en/latest/installation.html#sidebars
 html_sidebars = {
-    '**': [
-        'relations.html',  # needs 'show_related': True theme option to display
-        'searchbox.html',
+    "**": [
+        "relations.html",  # needs 'show_related': True theme option to display
+        "searchbox.html",
     ]
 }
 
 
 # -- Options for HTMLHelp output ------------------------------------------
 
 # Output file base name for HTML help builder.
-htmlhelp_basename = 'Volumentialdoc'
+htmlhelp_basename = "Volumentialdoc"
 
 # -- Options for LaTeX output ---------------------------------------------
 
@@ -154,8 +158,8 @@
 # (source start file, target name, title,
 #  author, documentclass [howto, manual, or own class]).
 latex_documents = [
-    (master_doc, 'Volumential.tex', 'Volumential Documentation',
-     'Xiaoyu Wei', 'manual'),
+    (master_doc, "Volumential.tex", "Volumential Documentation",
+     "Xiaoyu Wei", "manual"),
 ]
 
 
@@ -164,7 +168,7 @@
 # One entry per manual page. List of tuples
 # (source start file, name, description, authors, manual section).
 man_pages = [
-    (master_doc, 'volumential', 'Volumential Documentation',
+    (master_doc, "volumential", "Volumential Documentation",
      [author], 1)
 ]
 
@@ -175,7 +179,7 @@
 # (source start file, target name, title, author,
 #  dir menu entry, description, category)
 texinfo_documents = [
-    (master_doc, 'Volumential', 'Volumential Documentation',
-     author, 'Volumential', 'One line description of project.',
-     'Miscellaneous'),
+    (master_doc, "Volumential", "Volumential Documentation",
+     author, "Volumential", "One line description of project.",
+     "Miscellaneous"),
 ]

examples/laplace2d.py

@@ -1,7 +1,6 @@
 """ This example evaluates the volume potential over
     [-1,1]^2 with the Laplace kernel.
 """
-from __future__ import absolute_import, division, print_function
 
 __copyright__ = "Copyright (C) 2017 - 2018 Xiaoyu Wei"
 
@@ -27,6 +26,7 @@
 
 import logging
 
+
 logger = logging.getLogger(__name__)
 
 if 1:
@@ -36,12 +36,14 @@
     # clean
     logging.basicConfig(level=logging.CRITICAL)
 
+from functools import partial
+
 import numpy as np
-import pyopencl as cl
-from volumential.tools import ScalarFieldExpressionEvaluation as Eval
 
 import pymbolic as pmbl
-from functools import partial
+import pyopencl as cl
+
+from volumential.tools import ScalarFieldExpressionEvaluation as Eval
 
 
 def main():
@@ -205,17 +207,18 @@ def main():
 
     # {{{ build near field potential table
 
-    from volumential.table_manager import NearFieldInteractionTableManager
     import os
 
+    from volumential.table_manager import NearFieldInteractionTableManager
+
     if download_table and (not os.path.isfile(table_filename)):
         import json
-        with open("table_urls.json", 'r') as fp:
+        with open("table_urls.json") as fp:
             urls = json.load(fp)
 
-        print("Downloading table from %s" % urls['Laplace2D'])
+        print("Downloading table from %s" % urls["Laplace2D"])
         import subprocess
-        subprocess.call(["wget", "-q", urls['Laplace2D'], table_filename])
+        subprocess.call(["wget", "-q", urls["Laplace2D"], table_filename])
 
     tm = NearFieldInteractionTableManager(
         table_filename, root_extent=root_table_source_extent,
@@ -280,9 +283,7 @@ def main():
     exclude_self = True
 
     from volumential.expansion_wrangler_fpnd import (
-            FPNDExpansionWranglerCodeContainer,
-            FPNDExpansionWrangler
-            )
+        FPNDExpansionWrangler, FPNDExpansionWranglerCodeContainer)
 
     wcc = FPNDExpansionWranglerCodeContainer(
         ctx,
@@ -317,9 +318,9 @@ def main():
 
     # {{{ conduct fmm computation
 
-    from volumential.volume_fmm import drive_volume_fmm
-
     import time
+
+    from volumential.volume_fmm import drive_volume_fmm
     queue.finish()
 
     t0 = time.time()
@@ -386,8 +387,8 @@ def main():
         from mpl_toolkits.mplot3d import Axes3D
 
         plt3d = plt.figure()
-        ax = Axes3D(plt3d)  # noqa
-        surf = ax.plot_surface(oxx, oyy, opot.reshape(oxx.shape))  # noqa
+        ax = Axes3D(plt3d)
+        surf = ax.plot_surface(oxx, oyy, opot.reshape(oxx.shape))  # noqa: F841
         # ax.scatter(x, y, src.get())
         # ax.set_zlim(-0.25, 0.25)
 
@@ -472,7 +473,7 @@ def main():
     # }}} End postprocess and plot
 
 
-if __name__ == '__main__':
+if __name__ == "__main__":
     main()