Add docs, bump version.

AUTHORS

@@ -0,0 +1,16 @@
+.. -*- rst -*-
+
+Authors & Acknowledgments
+=========================
+
+This software was written and packaged by Lev Givon, currently at the
+Bionet Group [1]_ at Columbia University. 
+
+Special thanks are due to Yiyin Zhou and Rob Turetsky (also at the
+Bionet Group) for invaluable feedback, improvements, and code
+contributions. Thanks are also due to Ying Wei (Daniel) Fan (at Emory
+University) for kindly permitting the reuse of the CUBLAS wrapper code
+in his PARRET [2]_ software in this package.
+
+.. [1] http://bionet.ee.columbia.edu/
+.. [2] http://www.mathcs.emory.edu/~yfan/PARRET

CHANGES

@@ -3,8 +3,12 @@
 Change Log
 ==========
 
+Release 0.011 - (September 21, 2010)
+------------------------------------
+* Add documentation.
+* Update copyright information.
+
 Release 0.01 - (September 17, 2010)
 -----------------------------------
-
 * First public release.
 

INSTALL

@@ -3,20 +3,34 @@
 Installation Instructions
 =========================
 
+Obtaining the Latest Software
+-----------------------------
+
+The latest version of ``scikits.cuda`` can be downloaded from the
+`Bionet Code Repository <http://bionet.ee.columbia.edu/code/>`_.
+
 Prerequisites
 -------------
 
-This package requires that the following software packages be
+``scikits.cuda`` requires that the following software packages be
 installed:
 
 * `Python <http://www.python.org>`_ 2.5 or later.
-* `setuptools <http://peak.telecommunity.com/DevCenter/setuptools>_ 0.6c10 or later.
-* `Numpy <http://numpy.scipy.org>`_ 1.2.0 or later.
-* `Scipy <http://www.scipy.org>`_ 0.7.0 or later.
+* `setuptools <http://peak.telecommunity.com/DevCenter/setuptools>`_ 0.6c10 or later.
+* `NumPy <http://numpy.scipy.org>`_ 1.2.0 or later.
+* `SciPy <http://www.scipy.org>`_ 0.7.0 or later.
 * `PyCUDA <http://mathema.tician.de/software/pycuda>`_ 0.94rc or later.
 * `NIVIDIA CUDA Toolkit <http://www.nvidia.com/object/cuda_home_new.html>`_ 3.0 or later
 
-This software has been tested on Linux.
+To build the documentation, the following packages are also required:
+
+* `Docutils <http://docutils.sourceforge.net>`_ 0.5 or later.
+* `Sphinx <http://sphinx.pocoo.org>`_ 1.0.1 or later
+* `Jinja2 <http://jinja.pocoo.org>`_ 2.2 or later
+* `Pygments <http://pygments.org>`_ 0.8 or later
+
+The software has been tested on Linux; it should also work on other
+platforms supported by the above packages.
 
 Building and Installation
 -------------------------
@@ -31,5 +45,8 @@ demonstrating how to use different parts of the toolbox is located in
 the ``demos/`` subdirectory. Many of the high-level functions also
 contain doctests that describe their usage.
 
+To rebuild the documentation, run::
 
+   make
 
+from within the ``doc/`` subdirectory and follow the directions.

LICENSE

@@ -3,7 +3,7 @@
 License
 =======
 
-Copyright (c) 2009-2010, Trustees of Columbia University.
+Copyright (c) 2009-2010, Lev Givon.
 All rights reserved.
 
 Redistribution and use in source and binary forms, with or without
@@ -16,7 +16,7 @@ met:
   copyright notice, this list of conditions and the following
   disclaimer in the documentation and/or other materials provided
   with the distribution.
-* Neither the name of Columbia University nor the names of its
+* Neither the name of Lev Givon nor the names of any
   contributors may be used to endorse or promote products derived
   from this software without specific prior written permission.
 

MANIFEST.in

@@ -1,3 +1,4 @@
-include CHANGES INSTALL LICENSE README
+include AUTHORS CHANGES INSTALL LICENSE README
 recursive-include demos *.py
+recursive-include doc *
 exclude MANIFEST.in

README

@@ -1,6 +1,6 @@
 .. -*- rst -*-
 
-CUDA Scikit
+CUDA SciKit
 ===========
 
 Package Description
@@ -21,12 +21,8 @@ Authors & Acknowledgments
 
 This software was written and packaged by Lev Givon, currently at the
 Bionet Group [6]_ at Columbia University. 
-
-Special thanks are due to Yiyin Zhou and Rob Turetsky (also at the
-Bionet Group) for invaluable feedback, improvements, and code
-contributions. Thanks are also due to Ying Wei (Daniel) Fan (at Emory
-University) for kindly permitting the reuse of the CUBLAS wrapper code
-in his PARRET [7]_ software in this package.
+See the included AUTHORS file for more information and
+acknowledgments.
 
 License
 -------
@@ -48,4 +44,3 @@ Please direct all questions and comments pertaining to this software to
 .. [4] http://mathema.tician.de/software/pycuda/
 .. [5] http://numpy.scipy.org/
 .. [6] http://bionet.ee.columbia.edu/
-.. [7] http://www.mathcs.emory.edu/~yfan/PARRET

doc/Makefile

@@ -0,0 +1,90 @@
+# Makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line.
+SPHINXOPTS    =
+SPHINXBUILD   = sphinx-build
+PAPER         =
+BUILDDIR      = build
+SRCDIR        = source
+
+# Internal variables.
+PAPEROPT_a4     = -D latex_paper_size=a4
+PAPEROPT_letter = -D latex_paper_size=letter
+ALLSPHINXOPTS   = -d $(BUILDDIR)/doctrees $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) source
+
+.PHONY: help clean html dirhtml pickle json htmlhelp qthelp latex changes linkcheck doctest
+
+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 "  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 "  latex     to make LaTeX files, you can set PAPER=a4 or PAPER=letter"
+	@echo "  changes   to make an overview of all changed/added/deprecated items"
+	@echo "  linkcheck to check all external links for integrity"
+	@echo "  doctest   to run all doctests embedded in the documentation (if enabled)"
+
+clean:
+	-rm -rf $(BUILDDIR)/ $(SRCDIR)/generated/
+
+html:
+	$(SPHINXBUILD) -b html $(ALLSPHINXOPTS) $(BUILDDIR)/html
+	@echo
+	@echo "Build finished. The HTML pages are in $(BUILDDIR)/html."
+
+dirhtml:
+	$(SPHINXBUILD) -b dirhtml $(ALLSPHINXOPTS) $(BUILDDIR)/dirhtml
+	@echo
+	@echo "Build finished. The HTML pages are in $(BUILDDIR)/dirhtml."
+
+pickle:
+	$(SPHINXBUILD) -b pickle $(ALLSPHINXOPTS) $(BUILDDIR)/pickle
+	@echo
+	@echo "Build finished; now you can process the pickle files."
+
+json:
+	$(SPHINXBUILD) -b json $(ALLSPHINXOPTS) $(BUILDDIR)/json
+	@echo
+	@echo "Build finished; now you can process the JSON files."
+
+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."
+
+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/TED.qhcp"
+	@echo "To view the help file:"
+	@echo "# assistant -collectionFile $(BUILDDIR)/qthelp/TED.qhc"
+
+latex:
+	$(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex
+	@echo
+	@echo "Build finished; the LaTeX files are in $(BUILDDIR)/latex."
+	@echo "Run \`make all-pdf' or \`make all-ps' in that directory to" \
+	      "run these through (pdf)latex."
+
+changes:
+	$(SPHINXBUILD) -b changes $(ALLSPHINXOPTS) $(BUILDDIR)/changes
+	@echo
+	@echo "The overview file is in $(BUILDDIR)/changes."
+
+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."
+
+doctest:
+	$(SPHINXBUILD) -b doctest $(ALLSPHINXOPTS) $(BUILDDIR)/doctest
+	@echo "Testing of doctests in the sources finished, look at the " \
+	      "results in $(BUILDDIR)/doctest/output.txt."