Merge pull request #24 from Funartech/develop

Develop

Author: Nikolaj

.gitignore

@@ -1 +1,3 @@
 /build/*
+/.idea/*
+/doc/build/*

README.md

@@ -1,2 +1,4 @@
 # sparse_lib
-Python/Cython library to replace PySparse (temporary name)
+Python/Cython library to replace PySparse.
+
+SparseLib is a temporary name. Probably, we'll call it *CySparse*.

benchmarks/todo.txt

@@ -0,0 +1,6 @@
+Benchmarks:
+
+compare to:
+  - PySparse
+  - Scipy sparse matrices
+  - with the use of BLAS via Tokyo

clean.py

@@ -0,0 +1,36 @@
+import os
+import shutil
+
+# ad hoc script to clean repository
+directories = ['build']
+directories_to_skip = ['.git', '.idea', 'tests', 'benchmarks', 'doc']
+
+files_exts = ['.c', '.so', '.pyc']
+
+
+def scandirs(path):
+    for root, dirs, files in os.walk(path):
+        if any(root.endswith(name) for name in directories_to_skip):
+            continue
+        for currentFile in files:
+            #print "processing file: " + currentFile
+            if any(currentFile.lower().endswith(ext) for ext in files_exts):
+                os.remove(os.path.join(root, currentFile))
+
+########################################################################################################################
+# main
+########################################################################################################################
+
+current_path = os.path.curdir
+
+try:
+    for dir in directories:
+        shutil.rmtree(os.path.join(current_path, dir))
+except:
+    pass
+
+try:
+    scandirs(current_path)
+except:
+    pass
+

doc/Makefile

@@ -0,0 +1,70 @@
+# Makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line.
+SPHINXOPTS    =
+SPHINXBUILD   = sphinx-build
+PAPER         =
+
+# Internal variables.
+PAPEROPT_a4     = -D latex_paper_size=a4
+PAPEROPT_letter = -D latex_paper_size=letter
+ALLSPHINXOPTS   = -d build/doctrees $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) source
+
+.PHONY: help clean html web pickle htmlhelp latex changes linkcheck
+
+help:
+	@echo "Please use \`make <target>' where <target> is one of"
+	@echo "  html      to make standalone HTML files"
+	@echo "  pickle    to make pickle files (usable by e.g. sphinx-web)"
+	@echo "  htmlhelp  to make HTML files and a HTML help project"
+	@echo "  latex     to make LaTeX files, you can set PAPER=a4 or PAPER=letter"
+	@echo "  changes   to make an overview over all changed/added/deprecated items"
+	@echo "  linkcheck to check all external links for integrity"
+
+clean:
+	-rm -rf build/*
+
+html:
+	mkdir -p build/html build/doctrees
+	$(SPHINXBUILD) -b html $(ALLSPHINXOPTS) build/html
+	@echo
+	@echo "Build finished. The HTML pages are in build/html."
+
+pickle:
+	mkdir -p build/pickle build/doctrees
+	$(SPHINXBUILD) -b pickle $(ALLSPHINXOPTS) build/pickle
+	@echo
+	@echo "Build finished; now you can process the pickle files or run"
+	@echo "  sphinx-web build/pickle"
+	@echo "to start the sphinx-web server."
+
+web: pickle
+
+htmlhelp:
+	mkdir -p build/htmlhelp build/doctrees
+	$(SPHINXBUILD) -b htmlhelp $(ALLSPHINXOPTS) build/htmlhelp
+	@echo
+	@echo "Build finished; now you can run HTML Help Workshop with the" \
+	      ".hhp project file in build/htmlhelp."
+
+latex:
+	mkdir -p build/latex build/doctrees
+	$(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) build/latex
+	@echo
+	@echo "Build finished; the LaTeX files are in build/latex."
+	@echo "Run \`make all-pdf' or \`make all-ps' in that directory to" \
+	      "run these through (pdf)latex."
+
+changes:
+	mkdir -p build/changes build/doctrees
+	$(SPHINXBUILD) -b changes $(ALLSPHINXOPTS) build/changes
+	@echo
+	@echo "The overview file is in build/changes."
+
+linkcheck:
+	mkdir -p build/linkcheck build/doctrees
+	$(SPHINXBUILD) -b linkcheck $(ALLSPHINXOPTS) build/linkcheck
+	@echo
+	@echo "Link check complete; look for any errors in the above output " \
+	      "or in build/linkcheck/output.txt."

doc/source/conf.py

@@ -0,0 +1,216 @@
+# -*- coding: utf-8 -*-
+#
+# Pysparse documentation build configuration file, created by
+# sphinx-quickstart on Sat Nov  8 00:17:09 2008.
+#
+# This file is execfile()d with the current directory set to its containing dir.
+#
+# The contents of this file are pickled, so don't put values in the namespace
+# that aren't pickleable (module imports are okay, they're removed automatically).
+#
+# All configuration values have a default; values that are commented out
+# serve to show the default.
+
+import sys, os
+
+# If your extensions are in another directory, add it here. If the directory
+# is relative to the documentation root, use os.path.abspath to make it
+# absolute, like shown here.
+#sys.path.append(os.path.abspath('../../../Lib'))
+sys.path.append('sphinxext')
+
+# Import support for ipython console session syntax highlighting (lives
+# in the sphinxext directory defined above)
+import ipython_console_highlighting
+import mathjax
+
+import sphinx_bootstrap_theme
+
+# General configuration
+# ---------------------
+
+# 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']
+extensions += ['sphinx.ext.todo']
+extensions += ['sphinx.ext.inheritance_diagram']
+extensions += ['ipython_console_highlighting']
+extensions += ['mathjax']
+mathjax_path = 'https://c328740.ssl.cf1.rackcdn.com/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'
+
+graphviz_output_format = 'svg'
+inheritance_node_attrs = dict(shape='box', fontsize=12,
+                              color='gray70', style='rounded')
+inheritance_graph_attrs = dict(rankdir="TB", size='""', bgcolor="transparent")
+
+# Add any paths that contain templates here, relative to this directory.
+templates_path = ['.templates']
+
+# The suffix of source filenames.
+source_suffix = '.rst'
+
+# The encoding of source files.
+#source_encoding = 'utf-8'
+
+# The master toctree document.
+master_doc = 'contents'
+
+# General information about the project.
+project = u'SparseLib'
+copyright = u'2015, Dominique Orban and Nikolaj van Omme'
+
+# 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 = '0.0'
+# The full version, including alpha/beta/rc tags.
+release = '0.0.1'
+
+# The language for content autogenerated by Sphinx. Refer to documentation
+# for a list of supported languages.
+#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 documents that shouldn't be included in the build.
+#unused_docs = []
+
+# List of directories, relative to source directory, that shouldn't be searched
+# for source files.
+exclude_trees = []
+
+# 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'
+
+# TODO list
+todo_include_todos = False
+
+
+# Options for HTML output
+# -----------------------
+
+# The style sheet to use for HTML and HTML Help pages. A file of that name
+# must exist either in Sphinx' static/ path, or in one of the custom paths
+# given in html_static_path.
+html_theme = "bootstrap"
+html_theme_path = sphinx_bootstrap_theme.get_html_theme_path()
+html_theme_options = {
+  'source_link_position': "footer",
+  # Bootswatch (http://bootswatch.com/) theme.
+  'bootswatch_theme': "spacelab",
+}
+
+# The name for this set of Sphinx documents.  If None, it defaults to
+# "<project> v<release> documentation".
+#html_title = None
+
+# 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 = 'spmatrix-logo.png'
+
+# The name of an image file (within the static path) to use as 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']
+
+# If not '', a 'Last updated on:' timestamp is inserted at every page bottom,
+# using the given strftime format.
+#html_last_updated_fmt = '%b %d, %Y'
+
+# If true, SmartyPants will be used to convert quotes and dashes to
+# typographically correct entities.
+#html_use_smartypants = True
+
+html_index = 'index.html'
+
+# Custom sidebar templates, maps document names to template names.
+#html_sidebars = {'index' : 'indexsidebar.html'}
+
+# Additional templates that should be rendered to pages, maps page names to
+# template names.
+#html_additional_pages = {'index' : 'index.html'}
+
+# If false, no module index is generated.
+#html_use_modindex = 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, the reST sources are included in the HTML build as _sources/<name>.
+#html_copy_source = 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 = ''
+
+# If nonempty, this is the file name suffix for HTML files (e.g. ".xhtml").
+#html_file_suffix = ''
+
+# Output file base name for HTML help builder.
+htmlhelp_basename = 'CySparseDoc'
+
+
+# Options for LaTeX output
+# ------------------------
+
+# The paper size ('letter' or 'a4').
+#latex_paper_size = 'letter'
+
+# The font size ('10pt', '11pt' or '12pt').
+#latex_font_size = '10pt'
+
+# Grouping the document tree into LaTeX files. List of tuples
+# (source start file, target name, title, author, document class [howto/manual]).
+latex_documents = [
+  ('contents', 'Pysparse.tex', ur'Pysparse Documentation',
+   ur'Roman Geus, Daniel Wheeler and Dominique Orban', 'manual'),
+]
+
+# The name of an image file (relative to this directory) to place at the top of
+# the title page.
+latex_logo = 'spmatrix-logo.png'
+
+# For "manual" documents, if this is true, then toplevel headings are parts,
+# not chapters.
+#latex_use_parts = False
+
+# Additional stuff for the LaTeX preamble.
+latex_preamble = '\usepackage{amsfonts,amsmath}'
+
+# Documents to append as an appendix to all manuals.
+#latex_appendices = []
+
+# If false, no module index is generated.
+#latex_use_modindex = True

doc/source/contents.rst

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+
+=======================
+CySparse documentation
+=======================
+
+:Release: |version|
+:Date: |today|
+
+.. module:: sparse_lib
+
+.. toctree::
+   :maxdepth: 2
+
+   introduction
+   installation
+   sparse_matrix_formats
+   sparse_mat_hierarchy
+   ll_mat
+   cysparse_cython_users
+   
+..   #Sparse Matrix Formats <formats>
+   #Low-Level Sparse Matrix Types <spmatrix>
+   #Preconditioners <precon>
+   #Iterative Solvers <itsolvers>
+   #Direct Solvers <fact>
+   #Eigenvalue Solver <jdsym>
+   #Higher-Level Sparse Matrix Classes <pysparsematrix>
+   #Other Sparse Matrix Packages <other>
+   #License <license>
+
+Some pages of this documentation display equations via the `jsMath
+<http://www.math.union.edu/~dpvc/jsMath/welcome.html>`_ package. They should
+look reasonably good with most setups but the best rendering is obtained by
+installing the TeX fonts. Please refer to
+`http://www.math.union.edu/~dpvc/jsMath/users/welcome.html
+<http://www.math.union.edu/~dpvc/jsMath/users/welcome.html>`_.
+
+
+Indices and Tables
+==================
+
+* :ref:`genindex`
+* :ref:`modindex`
+* :ref:`search`

doc/source/cysparse_cython_users.rst

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+..  cysparse_for_cython_users:
+
+=========================================================
+:program:`CySparse` for :program:`Cython` users
+=========================================================
+
+I efficiency is a major concern to you, we strongly encourage you to use :program:`Cython` to 
+compile your own Python extension. 
+
+Accessing matrix elements
+==========================