From a545ad56b83ae12cfdfec87c4cf9d1deb490b240 Mon Sep 17 00:00:00 2001
From: Andreas Kloeckner <inform@tiker.net>
Date: Wed, 6 Apr 2016 14:40:13 -0500
Subject: [PATCH] Documentation scaffolding
---
.gitignore | 2 +
doc/Makefile | 223 +++++++++++++++++++++++
doc/_static/akdoc.css | 59 ++++++
doc/_templates/layout.html | 2 +
doc/codegen.rst | 5 +
doc/conf.py | 323 +++++++++++++++++++++++++++++++++
doc/expansion.rst | 14 ++
doc/index.rst | 30 +++
doc/interactions.rst | 17 ++
doc/kernel.rst | 4 +
doc/misc.rst | 70 +++++++
doc/upload-docs.sh | 3 +
sumpy/assignment_collection.py | 9 +
sumpy/codegen.py | 11 ++
sumpy/e2e.py | 21 ++-
sumpy/e2p.py | 20 +-
sumpy/expansion/__init__.py | 4 +
sumpy/expansion/local.py | 14 +-
sumpy/expansion/multipole.py | 14 +-
sumpy/fmm.py | 3 +
sumpy/kernel.py | 46 ++++-
sumpy/p2e.py | 20 +-
sumpy/p2p.py | 20 +-
sumpy/qbx.py | 20 +-
24 files changed, 923 insertions(+), 31 deletions(-)
create mode 100644 doc/Makefile
create mode 100644 doc/_static/akdoc.css
create mode 100644 doc/_templates/layout.html
create mode 100644 doc/codegen.rst
create mode 100644 doc/conf.py
create mode 100644 doc/expansion.rst
create mode 100644 doc/index.rst
create mode 100644 doc/interactions.rst
create mode 100644 doc/kernel.rst
create mode 100644 doc/misc.rst
create mode 100755 doc/upload-docs.sh
diff --git a/.gitignore b/.gitignore
index cd88b4a2..16e8eba7 100644
--- a/.gitignore
+++ b/.gitignore
@@ -12,3 +12,5 @@ setuptools.pth
distribute*egg
distribute*tar.gz
a.out
+
+doc/_build
diff --git a/doc/Makefile b/doc/Makefile
new file mode 100644
index 00000000..cae96bdb
--- /dev/null
+++ b/doc/Makefile
@@ -0,0 +1,223 @@
+# Makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line.
+SPHINXOPTS =
+SPHINXBUILD = sphinx-build
+PAPER =
+BUILDDIR = _build
+
+# User-friendly check for sphinx-build
+ifeq ($(shell which $(SPHINXBUILD) >/dev/null 2>&1; echo $$?), 1)
+ $(error The '$(SPHINXBUILD)' command was not found. Make sure you have Sphinx installed, then set the SPHINXBUILD environment variable to point to the full path of the '$(SPHINXBUILD)' executable. Alternatively you can add the directory with the executable to your PATH. If you don\'t have Sphinx installed, grab it from http://sphinx-doc.org/)
+endif
+
+# Internal variables.
+PAPEROPT_a4 = -D latex_paper_size=a4
+PAPEROPT_letter = -D latex_paper_size=letter
+ALLSPHINXOPTS = -d $(BUILDDIR)/doctrees $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) .
+# the i18n builder cannot share the environment and doctrees with the others
+I18NSPHINXOPTS = $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) .
+
+.PHONY: help
+help:
+ @echo "Please use \`make <target>' where <target> is one of"
+ @echo " html to make standalone HTML files"
+ @echo " dirhtml to make HTML files named index.html in directories"
+ @echo " singlehtml to make a single large HTML file"
+ @echo " pickle to make pickle files"
+ @echo " json to make JSON files"
+ @echo " htmlhelp to make HTML files and a HTML help project"
+ @echo " qthelp to make HTML files and a qthelp project"
+ @echo " applehelp to make an Apple Help Book"
+ @echo " devhelp to make HTML files and a Devhelp project"
+ @echo " epub to make an epub"
+ @echo " epub3 to make an epub3"
+ @echo " latex to make LaTeX files, you can set PAPER=a4 or PAPER=letter"
+ @echo " latexpdf to make LaTeX files and run them through pdflatex"
+ @echo " latexpdfja to make LaTeX files and run them through platex/dvipdfmx"
+ @echo " text to make text files"
+ @echo " man to make manual pages"
+ @echo " texinfo to make Texinfo files"
+ @echo " info to make Texinfo files and run them through makeinfo"
+ @echo " gettext to make PO message catalogs"
+ @echo " changes to make an overview of all changed/added/deprecated items"
+ @echo " xml to make Docutils-native XML files"
+ @echo " pseudoxml to make pseudoxml-XML files for display purposes"
+ @echo " linkcheck to check all external links for integrity"
+ @echo " doctest to run all doctests embedded in the documentation (if enabled)"
+ @echo " coverage to run coverage check of the documentation (if enabled)"
+
+.PHONY: clean
+clean:
+ rm -rf $(BUILDDIR)/*
+
+.PHONY: html
+html:
+ $(SPHINXBUILD) -b html $(ALLSPHINXOPTS) $(BUILDDIR)/html
+ @echo
+ @echo "Build finished. The HTML pages are in $(BUILDDIR)/html."
+
+.PHONY: dirhtml
+dirhtml:
+ $(SPHINXBUILD) -b dirhtml $(ALLSPHINXOPTS) $(BUILDDIR)/dirhtml
+ @echo
+ @echo "Build finished. The HTML pages are in $(BUILDDIR)/dirhtml."
+
+.PHONY: singlehtml
+singlehtml:
+ $(SPHINXBUILD) -b singlehtml $(ALLSPHINXOPTS) $(BUILDDIR)/singlehtml
+ @echo
+ @echo "Build finished. The HTML page is in $(BUILDDIR)/singlehtml."
+
+.PHONY: pickle
+pickle:
+ $(SPHINXBUILD) -b pickle $(ALLSPHINXOPTS) $(BUILDDIR)/pickle
+ @echo
+ @echo "Build finished; now you can process the pickle files."
+
+.PHONY: json
+json:
+ $(SPHINXBUILD) -b json $(ALLSPHINXOPTS) $(BUILDDIR)/json
+ @echo
+ @echo "Build finished; now you can process the JSON files."
+
+.PHONY: htmlhelp
+htmlhelp:
+ $(SPHINXBUILD) -b htmlhelp $(ALLSPHINXOPTS) $(BUILDDIR)/htmlhelp
+ @echo
+ @echo "Build finished; now you can run HTML Help Workshop with the" \
+ ".hhp project file in $(BUILDDIR)/htmlhelp."
+
+.PHONY: qthelp
+qthelp:
+ $(SPHINXBUILD) -b qthelp $(ALLSPHINXOPTS) $(BUILDDIR)/qthelp
+ @echo
+ @echo "Build finished; now you can run "qcollectiongenerator" with the" \
+ ".qhcp project file in $(BUILDDIR)/qthelp, like this:"
+ @echo "# qcollectiongenerator $(BUILDDIR)/qthelp/sumpy.qhcp"
+ @echo "To view the help file:"
+ @echo "# assistant -collectionFile $(BUILDDIR)/qthelp/sumpy.qhc"
+
+.PHONY: applehelp
+applehelp:
+ $(SPHINXBUILD) -b applehelp $(ALLSPHINXOPTS) $(BUILDDIR)/applehelp
+ @echo
+ @echo "Build finished. The help book is in $(BUILDDIR)/applehelp."
+ @echo "N.B. You won't be able to view it unless you put it in" \
+ "~/Library/Documentation/Help or install it in your application" \
+ "bundle."
+
+.PHONY: devhelp
+devhelp:
+ $(SPHINXBUILD) -b devhelp $(ALLSPHINXOPTS) $(BUILDDIR)/devhelp
+ @echo
+ @echo "Build finished."
+ @echo "To view the help file:"
+ @echo "# mkdir -p $$HOME/.local/share/devhelp/sumpy"
+ @echo "# ln -s $(BUILDDIR)/devhelp $$HOME/.local/share/devhelp/sumpy"
+ @echo "# devhelp"
+
+.PHONY: epub
+epub:
+ $(SPHINXBUILD) -b epub $(ALLSPHINXOPTS) $(BUILDDIR)/epub
+ @echo
+ @echo "Build finished. The epub file is in $(BUILDDIR)/epub."
+
+.PHONY: epub3
+epub3:
+ $(SPHINXBUILD) -b epub3 $(ALLSPHINXOPTS) $(BUILDDIR)/epub3
+ @echo
+ @echo "Build finished. The epub3 file is in $(BUILDDIR)/epub3."
+
+.PHONY: latex
+latex:
+ $(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex
+ @echo
+ @echo "Build finished; the LaTeX files are in $(BUILDDIR)/latex."
+ @echo "Run \`make' in that directory to run these through (pdf)latex" \
+ "(use \`make latexpdf' here to do that automatically)."
+
+.PHONY: latexpdf
+latexpdf:
+ $(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex
+ @echo "Running LaTeX files through pdflatex..."
+ $(MAKE) -C $(BUILDDIR)/latex all-pdf
+ @echo "pdflatex finished; the PDF files are in $(BUILDDIR)/latex."
+
+.PHONY: latexpdfja
+latexpdfja:
+ $(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex
+ @echo "Running LaTeX files through platex and dvipdfmx..."
+ $(MAKE) -C $(BUILDDIR)/latex all-pdf-ja
+ @echo "pdflatex finished; the PDF files are in $(BUILDDIR)/latex."
+
+.PHONY: text
+text:
+ $(SPHINXBUILD) -b text $(ALLSPHINXOPTS) $(BUILDDIR)/text
+ @echo
+ @echo "Build finished. The text files are in $(BUILDDIR)/text."
+
+.PHONY: man
+man:
+ $(SPHINXBUILD) -b man $(ALLSPHINXOPTS) $(BUILDDIR)/man
+ @echo
+ @echo "Build finished. The manual pages are in $(BUILDDIR)/man."
+
+.PHONY: texinfo
+texinfo:
+ $(SPHINXBUILD) -b texinfo $(ALLSPHINXOPTS) $(BUILDDIR)/texinfo
+ @echo
+ @echo "Build finished. The Texinfo files are in $(BUILDDIR)/texinfo."
+ @echo "Run \`make' in that directory to run these through makeinfo" \
+ "(use \`make info' here to do that automatically)."
+
+.PHONY: info
+info:
+ $(SPHINXBUILD) -b texinfo $(ALLSPHINXOPTS) $(BUILDDIR)/texinfo
+ @echo "Running Texinfo files through makeinfo..."
+ make -C $(BUILDDIR)/texinfo info
+ @echo "makeinfo finished; the Info files are in $(BUILDDIR)/texinfo."
+
+.PHONY: gettext
+gettext:
+ $(SPHINXBUILD) -b gettext $(I18NSPHINXOPTS) $(BUILDDIR)/locale
+ @echo
+ @echo "Build finished. The message catalogs are in $(BUILDDIR)/locale."
+
+.PHONY: changes
+changes:
+ $(SPHINXBUILD) -b changes $(ALLSPHINXOPTS) $(BUILDDIR)/changes
+ @echo
+ @echo "The overview file is in $(BUILDDIR)/changes."
+
+.PHONY: linkcheck
+linkcheck:
+ $(SPHINXBUILD) -b linkcheck $(ALLSPHINXOPTS) $(BUILDDIR)/linkcheck
+ @echo
+ @echo "Link check complete; look for any errors in the above output " \
+ "or in $(BUILDDIR)/linkcheck/output.txt."
+
+.PHONY: doctest
+doctest:
+ $(SPHINXBUILD) -b doctest $(ALLSPHINXOPTS) $(BUILDDIR)/doctest
+ @echo "Testing of doctests in the sources finished, look at the " \
+ "results in $(BUILDDIR)/doctest/output.txt."
+
+.PHONY: coverage
+coverage:
+ $(SPHINXBUILD) -b coverage $(ALLSPHINXOPTS) $(BUILDDIR)/coverage
+ @echo "Testing of coverage in the sources finished, look at the " \
+ "results in $(BUILDDIR)/coverage/python.txt."
+
+.PHONY: xml
+xml:
+ $(SPHINXBUILD) -b xml $(ALLSPHINXOPTS) $(BUILDDIR)/xml
+ @echo
+ @echo "Build finished. The XML files are in $(BUILDDIR)/xml."
+
+.PHONY: pseudoxml
+pseudoxml:
+ $(SPHINXBUILD) -b pseudoxml $(ALLSPHINXOPTS) $(BUILDDIR)/pseudoxml
+ @echo
+ @echo "Build finished. The pseudo-XML files are in $(BUILDDIR)/pseudoxml."
diff --git a/doc/_static/akdoc.css b/doc/_static/akdoc.css
new file mode 100644
index 00000000..d8b61e3f
--- /dev/null
+++ b/doc/_static/akdoc.css
@@ -0,0 +1,59 @@
+pre {
+ line-height: 110%;
+}
+
+.footer {
+ background-color: #eee;
+}
+
+body > div.container {
+ margin-top:10px;
+}
+
+dd {
+ margin-left: 40px;
+}
+
+tt.descname {
+ font-size: 100%;
+}
+
+code {
+ color: rgb(51,51,51);
+}
+
+h1 {
+ padding-bottom:7px;
+ border-bottom: 1px solid #ccc;
+}
+
+h2 {
+ padding-bottom:5px;
+ border-bottom: 1px solid #ccc;
+}
+
+h3 {
+ padding-bottom:5px;
+ border-bottom: 1px solid #ccc;
+}
+
+.rubric {
+ font-size: 120%;
+ padding-bottom:1px;
+ border-bottom: 1px solid #ccc;
+}
+
+.headerlink {
+ padding-left: 1ex;
+ padding-right: 1ex;
+}
+
+a.headerlink:hover {
+ text-decoration: none;
+}
+
+blockquote p {
+ font-size: 100%;
+ font-weight: normal;
+ line-height: normal;
+};
diff --git a/doc/_templates/layout.html b/doc/_templates/layout.html
new file mode 100644
index 00000000..400e7ec1
--- /dev/null
+++ b/doc/_templates/layout.html
@@ -0,0 +1,2 @@
+{% extends "!layout.html" %}
+{% set bootswatch_css_custom = ['_static/akdoc.css']%}
diff --git a/doc/codegen.rst b/doc/codegen.rst
new file mode 100644
index 00000000..66fc5b2d
--- /dev/null
+++ b/doc/codegen.rst
@@ -0,0 +1,5 @@
+Code Generation
+===============
+
+.. automodule:: sumpy.codegen
+.. automodule:: sumpy.assignment_collection
diff --git a/doc/conf.py b/doc/conf.py
new file mode 100644
index 00000000..df0cefcc
--- /dev/null
+++ b/doc/conf.py
@@ -0,0 +1,323 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+#
+# sumpy documentation build configuration file, created by
+# sphinx-quickstart on Wed Apr 6 14:00:41 2016.
+#
+# This file is execfile()d with the current directory set to its
+# containing dir.
+#
+# Note that not all possible configuration values are present in this
+# autogenerated file.
+#
+# All configuration values have a default; values that are commented out
+# serve to show the default.
+
+import sys
+import os
+
+# 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
+# documentation root, use os.path.abspath to make it absolute, like shown here.
+#sys.path.insert(0, os.path.abspath('.'))
+
+# -- General configuration ------------------------------------------------
+
+# If your documentation needs a minimal Sphinx version, state it here.
+#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
+# ones.
+extensions = [
+ 'sphinx.ext.autodoc',
+ 'sphinx.ext.doctest',
+ 'sphinx.ext.intersphinx',
+ 'sphinx.ext.coverage',
+ 'sphinx.ext.mathjax',
+ 'sphinx.ext.viewcode',
+ ]
+
+# Add any paths that contain templates here, relative to this directory.
+templates_path = ['_templates']
+
+# The suffix(es) of source filenames.
+# You can specify multiple suffix as a list of string:
+# source_suffix = ['.rst', '.md']
+source_suffix = '.rst'
+
+# The encoding of source files.
+#source_encoding = 'utf-8-sig'
+
+# The master toctree document.
+master_doc = 'index'
+
+# General information about the project.
+project = 'sumpy'
+copyright = '2016, Andreas Kloeckner'
+author = 'Andreas Kloeckner'
+
+# 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.
+version = '2016.1'
+# The full version, including alpha/beta/rc tags.
+release = '2016.1'
+
+# The language for content autogenerated by Sphinx. Refer to documentation
+# for a list of supported languages.
+#
+# This is also used if you do content translation via gettext catalogs.
+# Usually you set "language" from the command line for these cases.
+language = None
+
+# There are two options for replacing |today|: either, you set today to some
+# non-false value, then it is used:
+#today = ''
+# Else, today_fmt is used as the format for a strftime call.
+#today_fmt = '%B %d, %Y'
+
+# List of patterns, relative to source directory, that match files and
+# directories to ignore when looking for source files.
+# This patterns also effect to html_static_path and html_extra_path
+exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store']
+
+# The reST default role (used for this markup: `text`) to use for all
+# documents.
+#default_role = None
+
+# If true, '()' will be appended to :func: etc. cross-reference text.
+#add_function_parentheses = True
+
+# If true, the current module name will be prepended to all description
+# unit titles (such as .. function::).
+#add_module_names = True
+
+# If true, sectionauthor and moduleauthor directives will be shown in the
+# output. They are ignored by default.
+#show_authors = False
+
+# The name of the Pygments (syntax highlighting) style to use.
+pygments_style = 'sphinx'
+
+# A list of ignored prefixes for module index sorting.
+#modindex_common_prefix = []
+
+# If true, keep warnings as "system message" paragraphs in the built documents.
+#keep_warnings = False
+
+# If true, `todo` and `todoList` produce output, else they produce nothing.
+todo_include_todos = False
+
+
+# -- Options for HTML output ----------------------------------------------
+
+try:
+ import sphinx_bootstrap_theme
+except:
+ from warnings import warn
+ warn("I would like to use the sphinx bootstrap theme, but can't find it.\n"
+ "'pip install sphinx_bootstrap_theme' to fix.")
+else:
+ # Activate the theme.
+ html_theme = 'bootstrap'
+ html_theme_path = sphinx_bootstrap_theme.get_html_theme_path()
+
+ # 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
+ # documentation.
+ html_theme_options = {
+ "navbar_fixed_top": "true",
+ "navbar_site_name": "Contents",
+ 'bootstrap_version': '3',
+ 'source_link_position': 'footer',
+ }
+
+# 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
+# documentation.
+#html_theme_options = {}
+
+# Add any paths that contain custom themes here, relative to this directory.
+#html_theme_path = []
+
+# The name for this set of Sphinx documents.
+# "<project> v<release> documentation" by default.
+#html_title = 'sumpy v2016.1'
+
+# A shorter title for the navigation bar. Default is the same as html_title.
+#html_short_title = None
+
+# The name of an image file (relative to this directory) to place at the top
+# of the sidebar.
+#html_logo = None
+
+# The name of an image file (relative to this directory) to use as a favicon of
+# the docs. This file should be a Windows icon file (.ico) being 16x16 or 32x32
+# pixels large.
+#html_favicon = None
+
+# 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']
+
+# Add any extra paths that contain custom files (such as robots.txt or
+# .htaccess) here, relative to this directory. These files are copied
+# directly to the root of the documentation.
+#html_extra_path = []
+
+# If not None, a 'Last updated on:' timestamp is inserted at every page
+# bottom, using the given strftime format.
+# The empty string is equivalent to '%b %d, %Y'.
+#html_last_updated_fmt = None
+
+# If true, SmartyPants will be used to convert quotes and dashes to
+# typographically correct entities.
+#html_use_smartypants = True
+
+# Custom sidebar templates, maps document names to template names.
+#html_sidebars = {}
+
+# Additional templates that should be rendered to pages, maps page names to
+# template names.
+#html_additional_pages = {}
+
+# If false, no module index is generated.
+#html_domain_indices = True
+
+# If false, no index is generated.
+#html_use_index = True
+
+# If true, the index is split into individual pages for each letter.
+#html_split_index = False
+
+# If true, links to the reST sources are added to the pages.
+#html_show_sourcelink = True
+
+# If true, "Created using Sphinx" is shown in the HTML footer. Default is True.
+#html_show_sphinx = True
+
+# If true, "(C) Copyright ..." is shown in the HTML footer. Default is True.
+#html_show_copyright = True
+
+# If true, an OpenSearch description file will be output, and all pages will
+# contain a <link> tag referring to it. The value of this option must be the
+# base URL from which the finished HTML is served.
+#html_use_opensearch = ''
+
+# This is the file name suffix for HTML files (e.g. ".xhtml").
+#html_file_suffix = None
+
+# Language to be used for generating the HTML full-text search index.
+# Sphinx supports the following languages:
+# 'da', 'de', 'en', 'es', 'fi', 'fr', 'h', 'it', 'ja'
+# 'nl', 'no', 'pt', 'ro', 'r', 'sv', 'tr', 'zh'
+#html_search_language = 'en'
+
+# A dictionary with options for the search language support, empty by default.
+# 'ja' uses this config value.
+# 'zh' user can custom change `jieba` dictionary path.
+#html_search_options = {'type': 'default'}
+
+# The name of a javascript file (relative to the configuration directory) that
+# implements a search results scorer. If empty, the default will be used.
+#html_search_scorer = 'scorer.js'
+
+# Output file base name for HTML help builder.
+htmlhelp_basename = 'sumpydoc'
+
+# -- Options for LaTeX output ---------------------------------------------
+
+latex_elements = {
+# The paper size ('letterpaper' or 'a4paper').
+#'papersize': 'letterpaper',
+
+# The font size ('10pt', '11pt' or '12pt').
+#'pointsize': '10pt',
+
+# Additional stuff for the LaTeX preamble.
+#'preamble': '',
+
+# Latex figure (float) alignment
+#'figure_align': 'htbp',
+}
+
+# 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 = [
+ (master_doc, 'sumpy.tex', 'sumpy Documentation',
+ 'Andreas Kloeckner', 'manual'),
+]
+
+# The name of an image file (relative to this directory) to place at the top of
+# the title page.
+#latex_logo = None
+
+# For "manual" documents, if this is true, then toplevel headings are parts,
+# not chapters.
+#latex_use_parts = False
+
+# If true, show page references after internal links.
+#latex_show_pagerefs = False
+
+# If true, show URL addresses after external links.
+#latex_show_urls = False
+
+# Documents to append as an appendix to all manuals.
+#latex_appendices = []
+
+# If false, no module index is generated.
+#latex_domain_indices = True
+
+
+# -- Options for manual page output ---------------------------------------
+
+# One entry per manual page. List of tuples
+# (source start file, name, description, authors, manual section).
+man_pages = [
+ (master_doc, 'sumpy', 'sumpy Documentation',
+ [author], 1)
+]
+
+# If true, show URL addresses after external links.
+#man_show_urls = False
+
+
+# -- Options for Texinfo output -------------------------------------------
+
+# Grouping the document tree into Texinfo files. List of tuples
+# (source start file, target name, title, author,
+# dir menu entry, description, category)
+texinfo_documents = [
+ (master_doc, 'sumpy', 'sumpy Documentation',
+ author, 'sumpy', 'One line description of project.',
+ 'Miscellaneous'),
+]
+
+# Documents to append as an appendix to all manuals.
+#texinfo_appendices = []
+
+# If false, no module index is generated.
+#texinfo_domain_indices = True
+
+# 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 = {
+ 'http://docs.python.org/': None,
+ 'http://docs.scipy.org/doc/numpy/': None,
+ 'http://documen.tician.de/modepy/': None,
+ 'http://documen.tician.de/pyopencl/': None,
+ 'http://documen.tician.de/pymbolic/': None,
+ 'http://documen.tician.de/loopy/': None,
+ 'http://documen.tician.de/pytential/': None,
+ 'http://documen.tician.de/boxtree/': None,
+ }
diff --git a/doc/expansion.rst b/doc/expansion.rst
new file mode 100644
index 00000000..4dc38171
--- /dev/null
+++ b/doc/expansion.rst
@@ -0,0 +1,14 @@
+Expansions
+==========
+
+.. automodule:: sumpy.expansion
+
+Local Expansions
+----------------
+
+.. automodule:: sumpy.expansion.local
+
+Multipole Expansions
+--------------------
+
+.. automodule:: sumpy.expansion.multipole
diff --git a/doc/index.rst b/doc/index.rst
new file mode 100644
index 00000000..8a97711e
--- /dev/null
+++ b/doc/index.rst
@@ -0,0 +1,30 @@
+Welcome to sumpy's documentation!
+=================================
+
+Example
+-------
+
+See :download:`example/curve-pot.py <../examples/curve-pot.py>`
+for a usage example.
+
+Contents
+--------
+
+.. toctree::
+ :maxdepth: 2
+
+ kernel
+ expansion
+ interactions
+ codegen
+ misc
+
+
+
+Indices and tables
+==================
+
+* :ref:`genindex`
+* :ref:`modindex`
+* :ref:`search`
+
diff --git a/doc/interactions.rst b/doc/interactions.rst
new file mode 100644
index 00000000..47e4e032
--- /dev/null
+++ b/doc/interactions.rst
@@ -0,0 +1,17 @@
+Interaction routines
+====================
+
+.. automodule:: sumpy.p2p
+.. automodule:: sumpy.qbx
+
+Translation routines
+====================
+
+.. automodule:: sumpy.p2e
+.. automodule:: sumpy.e2e
+.. automodule:: sumpy.e2p
+
+Integration with :mod:`boxtree`
+===============================
+
+.. automodule:: sumpy.fmm
diff --git a/doc/kernel.rst b/doc/kernel.rst
new file mode 100644
index 00000000..c421ba3b
--- /dev/null
+++ b/doc/kernel.rst
@@ -0,0 +1,4 @@
+Kernels
+=======
+
+.. automodule:: sumpy.kernel
diff --git a/doc/misc.rst b/doc/misc.rst
new file mode 100644
index 00000000..d0f54155
--- /dev/null
+++ b/doc/misc.rst
@@ -0,0 +1,70 @@
+Installation
+============
+
+This command should install :mod:`sumpy`::
+
+ pip install sumpy
+
+You may need to run this with :command:`sudo`.
+If you don't already have `pip <https://pypi.python.org/pypi/pip>`_,
+run this beforehand::
+
+ curl -O https://raw.github.com/pypa/pip/master/contrib/get-pip.py
+ python get-pip.py
+
+For a more manual installation, download the source, unpack it,
+and say::
+
+ python setup.py install
+
+In addition, you need to have :mod:`numpy` installed.
+
+User-visible Changes
+====================
+
+Version 2016.1
+--------------
+.. note::
+
+ This version is currently under development. You can get snapshots from
+ sumpy's `git repository <https://github.com/inducer/sumpy>`_
+
+* Initial release.
+
+.. _license:
+
+License
+=======
+
+:mod:`sumpy` is licensed to you under the MIT/X Consortium license:
+
+Copyright (c) 2012-16 Andreas Klöckner
+
+Permission is hereby granted, free of charge, to any person
+obtaining a copy of this software and associated documentation
+files (the "Software"), to deal in the Software without
+restriction, including without limitation the rights to use,
+copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the
+Software is furnished to do so, subject to the following
+conditions:
+
+The above copyright notice and this permission notice shall be
+included in all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
+OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
+OTHER DEALINGS IN THE SOFTWARE.
+
+Frequently Asked Questions
+==========================
+
+The FAQ is maintained collaboratively on the
+`Wiki FAQ page <http://wiki.tiker.net/Sumpy/FrequentlyAskedQuestions>`_.
+
+
diff --git a/doc/upload-docs.sh b/doc/upload-docs.sh
new file mode 100755
index 00000000..fbe47d73
--- /dev/null
+++ b/doc/upload-docs.sh
@@ -0,0 +1,3 @@
+#! /bin/sh
+
+rsync --progress --verbose --archive --delete _build/html/* doc-upload:doc/sumpy
diff --git a/sumpy/assignment_collection.py b/sumpy/assignment_collection.py
index 2f203303..761b051c 100644
--- a/sumpy/assignment_collection.py
+++ b/sumpy/assignment_collection.py
@@ -31,6 +31,15 @@ import sympy as sp
import logging
logger = logging.getLogger(__name__)
+__doc__ = """
+
+Manipulating batches of assignments
+-----------------------------------
+
+.. autoclass:: SymbolicAssignmentCollection
+
+"""
+
def _generate_unique_possibilities(prefix):
yield prefix
diff --git a/sumpy/codegen.py b/sumpy/codegen.py
index 30bac80a..6ee517f8 100644
--- a/sumpy/codegen.py
+++ b/sumpy/codegen.py
@@ -44,6 +44,17 @@ import logging
logger = logging.getLogger(__name__)
+__doc__ = """
+
+Conversion of :mod:`sympy` expressions to :mod:`loopy`
+------------------------------------------------------
+
+.. autoclass:: SympyToPymbolicMapper
+.. autofunction:: to_loopy_insns
+
+"""
+
+
# {{{ sympy -> pymbolic mapper
class SympyToPymbolicMapper(SympyToPymbolicMapperBase):
diff --git a/sumpy/e2e.py b/sumpy/e2e.py
index e17024c0..1d7e3bb5 100644
--- a/sumpy/e2e.py
+++ b/sumpy/e2e.py
@@ -1,7 +1,4 @@
-from __future__ import division
-from __future__ import absolute_import
-import six
-from six.moves import range
+from __future__ import division, absolute_import
__copyright__ = "Copyright (C) 2013 Andreas Kloeckner"
@@ -25,6 +22,9 @@ OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
THE SOFTWARE.
"""
+import six
+from six.moves import range
+
import numpy as np
import loopy as lp
import sympy as sp
@@ -34,6 +34,19 @@ import logging
logger = logging.getLogger(__name__)
+__doc__ = """
+
+Expansion-to-expansion
+----------------------
+
+.. autoclass:: E2EBase
+.. autoclass:: E2EFromCSR
+.. autoclass:: E2EFromParent
+.. autoclass:: E2EFromChildren
+
+"""
+
+
# {{{ translation base class
class E2EBase(KernelCacheWrapper):
diff --git a/sumpy/e2p.py b/sumpy/e2p.py
index 9b1a1dd6..4735fcc0 100644
--- a/sumpy/e2p.py
+++ b/sumpy/e2p.py
@@ -1,7 +1,4 @@
-from __future__ import division
-from __future__ import absolute_import
-import six
-from six.moves import range
+from __future__ import division, absolute_import
__copyright__ = "Copyright (C) 2013 Andreas Kloeckner"
@@ -25,12 +22,27 @@ OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
THE SOFTWARE.
"""
+import six
+from six.moves import range
+
import numpy as np
import loopy as lp
import sympy as sp
from sumpy.tools import KernelCacheWrapper
+__doc__ = """
+
+Expansion-to-particle
+---------------------
+
+.. autoclass:: E2PBase
+.. autoclass:: E2PFromCSR
+.. autoclass:: E2PFromSingleBox
+
+"""
+
+
# {{{ E2P base class
class E2PBase(KernelCacheWrapper):
diff --git a/sumpy/expansion/__init__.py b/sumpy/expansion/__init__.py
index 7e4848f2..b67fae02 100644
--- a/sumpy/expansion/__init__.py
+++ b/sumpy/expansion/__init__.py
@@ -25,6 +25,10 @@ THE SOFTWARE.
from pytools import memoize_method
+__doc__ = """
+.. autoclass:: ExpansionBase
+"""
+
# {{{ base class
diff --git a/sumpy/expansion/local.py b/sumpy/expansion/local.py
index f70cbe41..92cae781 100644
--- a/sumpy/expansion/local.py
+++ b/sumpy/expansion/local.py
@@ -1,7 +1,5 @@
-from __future__ import division
-from __future__ import absolute_import
-from six.moves import range
-from six.moves import zip
+from __future__ import division, absolute_import
+from six.moves import range, zip
__copyright__ = "Copyright (C) 2012 Andreas Kloeckner"
@@ -36,6 +34,14 @@ class LocalExpansionBase(ExpansionBase):
import logging
logger = logging.getLogger(__name__)
+__doc__ = """
+
+.. autoclass:: VolumeTaylorLocalExpansion
+.. autoclass:: H2DLocalExpansion
+.. autoclass:: LineTaylorLocalExpansion
+
+"""
+
# {{{ line taylor
diff --git a/sumpy/expansion/multipole.py b/sumpy/expansion/multipole.py
index 19deba91..4d659401 100644
--- a/sumpy/expansion/multipole.py
+++ b/sumpy/expansion/multipole.py
@@ -1,7 +1,4 @@
-from __future__ import division
-from __future__ import absolute_import
-from six.moves import range
-from six.moves import zip
+from __future__ import division, absolute_import
__copyright__ = "Copyright (C) 2012 Andreas Kloeckner"
@@ -25,6 +22,7 @@ OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
THE SOFTWARE.
"""
+from six.moves import range, zip
import sympy as sp # noqa
from sumpy.expansion import ExpansionBase, VolumeTaylorExpansionBase
@@ -33,6 +31,14 @@ import logging
logger = logging.getLogger(__name__)
+__doc__ = """
+
+.. autoclass:: VolumeTaylorMultipoleExpansion
+.. autoclass:: H2DMultipoleExpansion
+
+"""
+
+
class MultipoleExpansionBase(ExpansionBase):
pass
diff --git a/sumpy/fmm.py b/sumpy/fmm.py
index 8a3b2042..51ab40a2 100644
--- a/sumpy/fmm.py
+++ b/sumpy/fmm.py
@@ -25,6 +25,9 @@ THE SOFTWARE.
"""
__doc__ = """Integrates :mod:`boxtree` with :mod:`sumpy`.
+
+.. autoclass:: SumpyExpansionWranglerCodeContainer
+.. autoclass:: SumpyExpansionWrangler
"""
diff --git a/sumpy/kernel.py b/sumpy/kernel.py
index b29e6237..26e4dc2a 100644
--- a/sumpy/kernel.py
+++ b/sumpy/kernel.py
@@ -33,6 +33,48 @@ from sumpy.symbolic import pymbolic_real_norm_2
from pymbolic.primitives import make_sym_vector
from pymbolic import var
+__doc__ = """
+
+Kernel interface
+----------------
+
+.. autoclass:: Kernel
+.. autoclass:: KernelArgument
+
+Symbolic kernels
+----------------
+
+.. autoclass:: ExpressionKernel
+
+PDE kernels
+-----------
+
+.. autoclass:: LaplaceKernel
+.. autoclass:: HelmholtzKernel
+
+Derivatives
+-----------
+
+These objects *wrap* other kernels and take derivatives
+of them in the process.
+
+.. autoclass:: DerivativeBase
+.. autoclass:: AxisTargetDerivative
+.. autoclass:: DirectionalTargetDerivative
+.. autoclass:: DirectionalSourceDerivative
+
+Transforming kernels
+--------------------
+
+.. autoclass:: KernelMapper
+.. autoclass:: KernelCombineMapper
+.. autoclass:: KernelIdentityMapper
+.. autoclass:: AxisTargetDerivativeRemover
+.. autoclass:: TargetDerivativeRemover
+.. autoclass:: DerivativeCounter
+.. autoclass:: KernelDimensionSetter
+"""
+
class KernelArgument(object):
"""
@@ -160,13 +202,13 @@ class Kernel(object):
raise NotImplementedError
def get_args(self):
- """Return list of :cls:`KernelArgument` instances describing
+ """Return list of :class:`KernelArgument` instances describing
extra arguments used by the kernel.
"""
return []
def get_source_args(self):
- """Return list of :cls:`KernelArgument` instances describing
+ """Return list of :class:`KernelArgument` instances describing
extra arguments used by kernel in picking up contributions
from point sources.
"""
diff --git a/sumpy/p2e.py b/sumpy/p2e.py
index 087f142f..7b4d948a 100644
--- a/sumpy/p2e.py
+++ b/sumpy/p2e.py
@@ -1,7 +1,4 @@
-from __future__ import division
-from __future__ import absolute_import
-import six
-from six.moves import range
+from __future__ import division, absolute_import
__copyright__ = "Copyright (C) 2013 Andreas Kloeckner"
@@ -25,6 +22,9 @@ OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
THE SOFTWARE.
"""
+import six
+from six.moves import range
+
import numpy as np
import loopy as lp
from sumpy.tools import KernelCacheWrapper
@@ -33,6 +33,18 @@ import logging
logger = logging.getLogger(__name__)
+__doc__ = """
+
+Particle-to-expansion
+---------------------
+
+.. autoclass:: P2EBase
+.. autoclass:: P2EFromSingleBox
+.. autoclass:: P2EFromCSR
+
+"""
+
+
# {{{ P2E base class
class P2EBase(KernelCacheWrapper):
diff --git a/sumpy/p2p.py b/sumpy/p2p.py
index 57823498..6541cf94 100644
--- a/sumpy/p2p.py
+++ b/sumpy/p2p.py
@@ -1,7 +1,4 @@
-from __future__ import division
-from __future__ import absolute_import
-import six
-from six.moves import range
+from __future__ import division, absolute_import
__copyright__ = "Copyright (C) 2012 Andreas Kloeckner"
@@ -25,12 +22,27 @@ OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
THE SOFTWARE.
"""
+import six
+from six.moves import range
+
import numpy as np
import loopy as lp
from sumpy.tools import KernelComputation, KernelCacheWrapper
+__doc__ = """
+
+Particle-to-particle
+--------------------
+
+.. autoclass:: P2PBase
+.. autoclass:: P2P
+.. autoclass:: P2PFromCSR
+
+"""
+
+
# LATER:
# - Optimization for source == target (postpone)
diff --git a/sumpy/qbx.py b/sumpy/qbx.py
index 3e5a8ff3..90304db1 100644
--- a/sumpy/qbx.py
+++ b/sumpy/qbx.py
@@ -1,8 +1,4 @@
-from __future__ import division
-from __future__ import absolute_import
-import six
-from six.moves import range
-from six.moves import zip
+from __future__ import division, absolute_import
__copyright__ = "Copyright (C) 2012 Andreas Kloeckner"
@@ -27,6 +23,8 @@ THE SOFTWARE.
"""
+import six
+from six.moves import range, zip
import numpy as np
import loopy as lp
import sympy as sp
@@ -39,6 +37,18 @@ import logging
logger = logging.getLogger(__name__)
+__doc__ = """
+
+QBX for Layer Potentials
+------------------------
+
+.. autoclass:: LayerPotentialBase
+.. autoclass:: LayerPotential
+.. autoclass:: LayerPotentialMatrixGenerator
+
+"""
+
+
def stringify_expn_index(i):
if isinstance(i, tuple):
return "_".join(stringify_expn_index(i_i) for i_i in i)
--
GitLab