Initial commit of eofs.

.gitignore

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+## Generic files to ignore
+*~
+*.lock
+*.DS_Store
+*.swp
+*.out
+
+## Python specific
+*.mo
+*.egg
+*.egg-info
+*.EGG
+*.EGG-INFO
+build
+dist
+*.pyc
+*.pyo
+*.tmp*
+.coverage
+MANIFEST

README.md

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+eofs - EOF analysis in Python
+=============================
+
+
+Overview
+--------
+
+eofs is a Python package for performing EOF analysis on spatial-temporal data sets, licensed under the GNU GPLv3.
+
+The package was created to simplify the process of EOF analysis in the Python environment.
+Some of the key features are listed below:
+
+* Suitable for large data sets: computationally efficient for the large data sets typical of modern climate model output.
+* Transparent handling of missing values: missing values are removed automatically when computing EOFs and re-inserted into output fields.
+* Meta-data preserving interfaces (optional): works with both the cdms2 module (from CDAT) and the Iris data analysis package to carry meta-data over from input fields to output.
+* No Fortran dependencies: written in Python using the power of NumPy, no compilers required.
+
+
+Requirements
+------------
+
+eofs only requires the NumPy package.
+In order to use the meta-data preserving interfaces one (or both) of cdms2 or iris > 1.2 is required.
+cdms2 is part of the Climate Data Analysis Tools ([CDAT](http://www2-pcmdi.llnl.gov/cdat)) or can be obtained separately in the [cdat_lite](http://proj.badc.rl.ac.uk/ndg/wiki/CdatLite) package.
+[Iris](http://scitools.org.uk/iris/) is a Python library for meteorology and climatology.
+
+
+Documentation
+-------------
+
+Documentation is available [online](http://ajdawson.github.com/eofs).
+The package docstrings are also very complete and can be used as a source of reference when working interactively.
+
+
+Frequently asked questions
+--------------------------
+
+* **Do I need CDAT/cdms2 or Iris to use eofs?**
+  No. All the computation code uses NumPy only.
+  The cdms2 module or Iris are only required for the meta-data preserving interfaces.
+
+
+Installation
+------------
+
+    sudo python setup.py install
+
+to install system-wide, or to install in your home directory:
+
+    python setup.py install --user
+
+
+History
+-------
+
+This code is the next generation of the [eof2](http://github.com/ajdawson/eof2) package. 
+It has been re-written to make it easier to add support for meta-data interfaces other than cdms2/CDAT.
+The name has been changed because the old name only makes sense in the context of CDAT.

doc/.gitignore

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+_build
+gh-pages

doc/Makefile

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+# Makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line.
+SPHINXOPTS    =
+SPHINXBUILD   = sphinx-build
+PAPER         =
+BUILDDIR      = _build
+
+# 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 clean html dirhtml singlehtml pickle json htmlhelp qthelp devhelp epub latex latexpdf text man changes linkcheck doctest gettext
+
+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 "  devhelp    to make HTML files and a Devhelp project"
+	@echo "  epub       to make an epub"
+	@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 "  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 "  linkcheck  to check all external links for integrity"
+	@echo "  doctest    to run all doctests embedded in the documentation (if enabled)"
+
+clean:
+	-rm -rf $(BUILDDIR)/* gh-pages
+
+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."
+
+singlehtml:
+	$(SPHINXBUILD) -b singlehtml $(ALLSPHINXOPTS) $(BUILDDIR)/singlehtml
+	@echo
+	@echo "Build finished. The HTML page is in $(BUILDDIR)/singlehtml."
+
+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/eof2.qhcp"
+	@echo "To view the help file:"
+	@echo "# assistant -collectionFile $(BUILDDIR)/qthelp/eof2.qhc"
+
+devhelp:
+	$(SPHINXBUILD) -b devhelp $(ALLSPHINXOPTS) $(BUILDDIR)/devhelp
+	@echo
+	@echo "Build finished."
+	@echo "To view the help file:"
+	@echo "# mkdir -p $$HOME/.local/share/devhelp/eof2"
+	@echo "# ln -s $(BUILDDIR)/devhelp $$HOME/.local/share/devhelp/eof2"
+	@echo "# devhelp"
+
+epub:
+	$(SPHINXBUILD) -b epub $(ALLSPHINXOPTS) $(BUILDDIR)/epub
+	@echo
+	@echo "Build finished. The epub file is in $(BUILDDIR)/epub."
+
+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)."
+
+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."
+
+text:
+	$(SPHINXBUILD) -b text $(ALLSPHINXOPTS) $(BUILDDIR)/text
+	@echo
+	@echo "Build finished. The text files are in $(BUILDDIR)/text."
+
+man:
+	$(SPHINXBUILD) -b man $(ALLSPHINXOPTS) $(BUILDDIR)/man
+	@echo
+	@echo "Build finished. The manual pages are in $(BUILDDIR)/man."
+
+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)."
+
+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."
+
+gettext:
+	$(SPHINXBUILD) -b gettext $(I18NSPHINXOPTS) $(BUILDDIR)/locale
+	@echo
+	@echo "Build finished. The message catalogs are in $(BUILDDIR)/locale."
+
+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."
+
+gh-pages: clean html
+	python gh-pages.py
+

doc/_templates/layout.html

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+{% extends "!layout.html" %}

doc/_themes/sphinx13/layout.html

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+{#
+    sphinxdoc/layout.html
+    ~~~~~~~~~~~~~~~~~~~~~
+
+    Sphinx layout template for the sphinxdoc theme.
+
+    :copyright: Copyright 2007-2013 by the Sphinx team, see AUTHORS.
+    :license: BSD, see LICENSE for details.
+#}
+{%- extends "basic/layout.html" %}
+
+
+{# put the sidebar before the body #}
+{% block sidebar1 %}{{ sidebar() }}{% endblock %}
+{% block sidebar2 %}{% endblock %}
+
+
+{% block extrahead %}
+    <link href='http://fonts.googleapis.com/css?family=Open+Sans:300,400,700'
+          rel='stylesheet' type='text/css' />
+    {{ super() }}
+    {%- if not embedded %}
+        <style type="text/css">
+            table.right { float: right; margin-left: 20px; }
+            table.right td { border: 1px solid #ccc; }
+        </style>
+        <script type="text/javascript">
+            // intelligent scrolling of the sidebar content
+            $(window).scroll(function() {
+                var sb = $('.sphinxsidebarwrapper');
+                var win = $(window);
+                var sbh = sb.height();
+                var offset = $('.sphinxsidebar').position()['top'];
+                var wintop = win.scrollTop();
+                var winbot = wintop + win.innerHeight();
+                var curtop = sb.position()['top'];
+                var curbot = curtop + sbh;
+                // does sidebar fit in window?
+                if (sbh < win.innerHeight()) {
+                    // yes: easy case -- always keep at the top
+                    sb.css('top', $u.min([$u.max([0, wintop - offset - 10]),
+                                         $(document).height() - sbh - 200]));
+                } else {
+                    // no: only scroll if top/bottom edge of sidebar is at
+                    // top/bottom edge of window
+                    if (curtop > wintop && curbot > winbot) {
+                        sb.css('top', $u.max([wintop - offset - 10, 0]));
+                    } else if (curtop < wintop && curbot < winbot) {
+                        sb.css('top', $u.min([winbot - sbh - offset - 20,
+                                             $(document).height() - sbh - 200]));
+                    }
+                }
+            });
+        </script>
+    {%- endif %}
+{% endblock %}
+
+
+{# put links to the home page and search in the relbar #}
+{% block rootrellink %}
+    <li><a href="{{ pathto('index') }}">home</a>|&nbsp;</li>
+    <li><a href="{{ pathto('search') }}">search</a>|&nbsp;</li>
+{% endblock %}
+
+
+{# put a header image on each page #}
+{% block header %}
+<div class="pageheader">
+  <div>
+    <a href="{{ pathto('index') }}">
+      <img src="{{ pathto('_static/eofsheader.png', 1) }}" alt="SPHINX" />
+    </a>
+  </div>
+</div>
+{% endblock %}
+
+
+{# show the full table of contents in the sidebar #}
+{% block sidebartoc %}
+    <h3>{{ _('Table of Contents') }}</h3>
+    {{ toctree() }}
+{% endblock %}