Merge release v1.0.1 from 'develop'

LICENSE.txt

@@ -1,4 +1,4 @@
-Copyright (c) 2012-2014, The Regents of the University of California
+Copyright (c) 2012-2015, Justin Kitzes and Mark Wilber
 All rights reserved.
 
 Redistribution and use in source and binary forms, with or without

README.rst

@@ -3,6 +3,6 @@ Macroeco: Ecological pattern analysis in Python
 
 Macroeco is a Python package that provides a comprehensive set of functions for analyzing empirical patterns in ecological data, predicting patterns from theory, and comparing empirical results to theory. Many major macroecological patterns can be analyzed using this package, including the species abundance distribution, the species and endemics area relationships, several measures of beta diversity, and many others.
 
-Extensive documentation for macroeco, including detailed installation instructions, tutorials, and a reference guide, is available at http://macroeco.org. The most recent stable version of the macroeco package can be installed from PyPI (``pip install macroeco``). For users who do not program in Python, a standalone application called Macroeco Desktop, which provides most of the functionality of macroeco through a simple interface that requires no programming, is also available.
+Extensive documentation for macroeco, including detailed installation instructions, tutorials, and a reference guide, is available at http://macroeco.org. The most recent stable version of the macroeco package can be installed from PyPI (``pip install macroeco``). For users who do not program in Python, a standalone application called Macroeco Desktop, which provides most of the functionality of macroeco through a simple interface that requires no programming, is also available.  To download this standalone application, click on the **releases** tab at the top of the repository home page (or `this link <https://github.com/jkitzes/macroeco/releases>`_) and download the file ``MacroecoDesktop_Mac_Standalone.zip`` from the most current version.
 
 The current version of macroeco is developed and maintained by Justin Kitzes (UC Berkeley) and Mark Wilber (UC Santa Barbara). Other contributors include Chloe Lewis and Ethan White. The development of macroeco has been supported by the National Science Foundation, the Gordon and Betty Moore Foundation, and the Berkeley Institute for Data Science.

doc/_ext/juliadoc/.gitignore

@@ -0,0 +1,35 @@
+*.py[cod]
+
+# C extensions
+*.so
+
+# Packages
+*.egg
+*.egg-info
+dist
+build
+eggs
+parts
+bin
+var
+sdist
+develop-eggs
+.installed.cfg
+lib
+lib64
+
+# Installer logs
+pip-log.txt
+
+# Unit test / coverage reports
+.coverage
+.tox
+nosetests.xml
+
+# Translations
+*.mo
+
+# Mr Developer
+.mr.developer.cfg
+.project
+.pydevproject

doc/_ext/juliadoc/README.md

@@ -0,0 +1,52 @@
+JuliaDoc
+========
+JuliaDoc is a Python package providing Sphinx extensions and a theme for the Julia language documentation at https://julia.readthedocs.org/. It can also be used by Julia packages to create documentation that is visually unified with the language documentation.
+
+Usage with ReadTheDocs
+----------------------
+In the ReadTheDocs admin page for your package's documentation:
+
+1. Turn on the "Use virtualenv" option.
+
+1. Under "Requirements file", enter `doc/requirements.txt`.
+
+1. Add [this `requirements.txt` file](https://gist.github.com/pao/5658342/raw/requirements.txt) to your package repository's `doc` folder. This will tell ReadTheDocs where to find the JuliaDoc theme and extensions.
+
+1. In your `doc.conf.py` file, do at least the following:
+
+```Python
+import juliadoc
+
+extensions = ['juliadoc.julia', 'juliadoc.jlhelp']
+html_theme_path = [juliadoc.get_theme_dir()]
+html_sidebars = juliadoc.default_sidebars()
+```
+
+License
+-------
+The MIT License (MIT)
+
+Copyright (c) 2013 Jeff Bezanson, Stefan Karpinski, Viral Shah, Alan Edelman, et al.
+
+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.
+
+
+Acknowledgements
+----------------
+The packaging is directly inspired by the [Caktus theme for Sphinx](https://github.com/caktus/caktus-sphinx-theme/).

doc/_ext/juliadoc/juliadoc/__init__.py

@@ -0,0 +1,21 @@
+import os
+
+def get_theme_dir():
+    """
+    Returns path to directory containing this package's theme.
+    
+    This is designed to be used when setting the ``html_theme_path``
+    option within Sphinx's ``conf.py`` file.
+    """
+    return os.path.abspath(os.path.join(os.path.dirname(__file__), "theme"))
+
+def default_sidebars():
+    """
+    Returns a dictionary mapping for the templates used to render the
+    sidebar on the index page and sub-pages.
+    """
+    return {
+        '**': ['localtoc.html', 'relations.html', 'searchbox.html'],
+        'index': ['searchbox.html'],
+        'search': [],
+    }