starting to switch to ipynb tutorials

LICENSE

@@ -1,6 +1,6 @@
 The MIT License (MIT)
 
-Copyright (c) 2010-2016 Daniel Foreman-Mackey & contributors.
+Copyright (c) 2010-2017 Daniel Foreman-Mackey & contributors.
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

README.rst

@@ -52,7 +52,7 @@ The BibTeX entry for the paper is::
 License
 -------
 
-Copyright 2010-2016 Dan Foreman-Mackey and contributors.
+Copyright 2010-2017 Dan Foreman-Mackey and contributors.
 
 emcee is free software made available under the MIT License. For details see
 the LICENSE file.

docs/Makefile

@@ -16,6 +16,12 @@ I18NSPHINXOPTS  = $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) .
 
 .PHONY: help clean html dirhtml singlehtml pickle json htmlhelp qthelp devhelp epub latex latexpdf text man changes linkcheck doctest gettext
 
+default: dirhtml
+TUTORIALS = tutorials/quickstart.rst
+
+tutorials/%.rst: _static/notebooks/%.ipynb tutorials/tutorial_rst.tpl
+	jupyter nbconvert --template tutorials/tutorial_rst --to rst $< --output-dir tutorials
+
 help:
 	@echo "Please use \`make <target>' where <target> is one of"
 	@echo "  html       to make standalone HTML files"
@@ -46,7 +52,7 @@ html:
 	@echo
 	@echo "Build finished. The HTML pages are in $(BUILDDIR)/html."
 
-dirhtml:
+dirhtml: $(TUTORIALS)
 	$(SPHINXBUILD) -b dirhtml $(ALLSPHINXOPTS) $(BUILDDIR)/dirhtml
 	@echo
 	@echo "Build finished. The HTML pages are in $(BUILDDIR)/dirhtml."

docs/_static/notebooks/quickstart.ipynb

@@ -0,0 +1,136 @@
+{
+ "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": 1,
+   "metadata": {
+    "collapsed": true
+   },
+   "outputs": [],
+   "source": [
+    "%matplotlib inline\n",
+    "%config InlineBackend.figure_format = \"retina\"\n",
+    "\n",
+    "from __future__ import print_function\n",
+    "\n",
+    "from matplotlib import rcParams\n",
+    "rcParams[\"savefig.dpi\"] = 100\n",
+    "rcParams[\"figure.dpi\"] = 100\n",
+    "rcParams[\"font.size\"] = 20"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "# Quickstart \n",
+    "\n",
+    "This notebook was made with the following version of emcee:"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 2,
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "'3.0.0.dev0'"
+      ]
+     },
+     "execution_count": 2,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "import emcee\n",
+    "emcee.__version__"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "The easiest way to get started with using emcee is to use it for a project. To get you started, here’s an annotated, fully-functional example that demonstrates a standard usage pattern.\n",
+    "\n",
+    "## How to sample a multi-dimensional Gaussian\n",
+    "\n",
+    "We’re going to demonstrate how you might draw samples from the multivariate Gaussian density given by:\n",
+    "\n",
+    "$$\n",
+    "p(\\vec{x}) \\propto \\exp \\left [ - \\frac{1}{2} (\\vec{x} -\n",
+    "    \\vec{\\mu})^\\mathrm{T} \\, \\Sigma ^{-1} \\, (\\vec{x} - \\vec{\\mu})\n",
+    "    \\right ]\n",
+    "$$\n",
+    "\n",
+    "where $\\vec{\\mu}$ is an $N$-dimensional vector position of the mean of the density and $\\Sigma$ is the square N-by-N covariance matrix.\n",
+    "\n",
+    "The first thing that we need to do is import the necessary modules:"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 4,
+   "metadata": {
+    "collapsed": true
+   },
+   "outputs": [],
+   "source": [
+    "import numpy as np\n",
+    "import emcee"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "Then, we’ll code up a Python function that returns the density $p(\\vec{x})$ for specific values of $\\vec{x}$, $\\vec{\\mu}$ and $\\Sigma^{-1}$. In fact, emcee actually requires the logarithm of $p$. We’ll call it `log_prob`:"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 5,
+   "metadata": {
+    "collapsed": true
+   },
+   "outputs": [],
+   "source": [
+    "def log_prob(x, mu, icov):\n",
+    "    diff = x - mu\n",
+    "    return -0.5*np.dot(diff,np.dot(icov,diff))"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {
+    "collapsed": true
+   },
+   "outputs": [],
+   "source": []
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.6.1"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 2
+}

docs/_themes/dfm/layout.html

@@ -19,11 +19,6 @@
     <div class="footer">
       &copy; Copyright {{ copyright }}.
     </div>
-    <a href="https://github.com/dfm/emcee" class="github">
-        <img style="position: absolute; top: 0; right: 0; border: 0;"
-            src="http://s3.amazonaws.com/github/ribbons/forkme_right_darkblue_121621.png"
-            alt="Fork me on GitHub"  class="github"/>
-    </a>
 
     <script type="text/javascript">
         var _gaq = _gaq || [];

docs/_themes/dfm/static/flasky.css_t

@@ -198,7 +198,8 @@ div.body p, div.body dd, div.body li {
 }
 
 div.highlight {
-    background-color: white;
+    background: #eee;
+    padding-left: 10px;
 }
 
 dt:target, .highlight {
@@ -343,7 +344,7 @@ ul, ol {
 }
 
 pre {
-    background: #eee;
+    /*background: #eee;*/
     padding: 7px 30px;
     margin: 15px -30px;
     line-height: 1.3em;

docs/conf.py

@@ -44,7 +44,7 @@
 
 # General information about the project.
 project = u'emcee'
-copyright = u'2012–2013, Dan Foreman-Mackey & contributors'
+copyright = u'2012-2017, Dan Foreman-Mackey & contributors'
 
 # The version info for the project you're documenting, acts as replacement for
 # |version| and |release|, also used in various other places throughout the

docs/index.rst

@@ -52,7 +52,7 @@ User Guide
    :maxdepth: 2
 
    user/install
-   user/quickstart
+   tutorials/quickstart
    user/line
    user/advanced
    user/pt

docs/tutorials/quickstart.rst

@@ -0,0 +1,67 @@
+
+.. module:: george
+
+**Note:** This tutorial was generated from an IPython notebook that can be
+downloaded `here <../../_static/notebooks/quickstart.ipynb>`_.
+
+.. _quickstart:
+
+
+Quickstart
+==========
+
+This notebook was made with the following version of emcee:
+
+.. code:: python
+
+    import emcee
+    emcee.__version__
+
+
+
+
+.. parsed-literal::
+
+    '3.0.0.dev0'
+
+
+
+The easiest way to get started with using emcee is to use it for a
+project. To get you started, here’s an annotated, fully-functional
+example that demonstrates a standard usage pattern.
+
+How to sample a multi-dimensional Gaussian
+------------------------------------------
+
+We’re going to demonstrate how you might draw samples from the
+multivariate Gaussian density given by:
+
+.. math::
+
+
+   p(\vec{x}) \propto \exp \left [ - \frac{1}{2} (\vec{x} -
+       \vec{\mu})^\mathrm{T} \, \Sigma ^{-1} \, (\vec{x} - \vec{\mu})
+       \right ]
+
+where :math:`\vec{\mu}` is an :math:`N`-dimensional vector position of
+the mean of the density and :math:`\Sigma` is the square N-by-N
+covariance matrix.
+
+The first thing that we need to do is import the necessary modules:
+
+.. code:: python
+
+    import numpy as np
+    import emcee
+
+Then, we’ll code up a Python function that returns the density
+:math:`p(\vec{x})` for specific values of :math:`\vec{x}`,
+:math:`\vec{\mu}` and :math:`\Sigma^{-1}`. In fact, emcee actually
+requires the logarithm of :math:`p`. We’ll call it ``log_prob``:
+
+.. code:: python
+
+    def log_prob(x, mu, icov):
+        diff = x - mu
+        return -0.5*np.dot(diff,np.dot(icov,diff))
+

docs/tutorials/tutorial_rst.tpl

@@ -0,0 +1,94 @@
+{%- extends 'display_priority.tpl' -%}
+
+{% block header %}
+.. module:: george
+
+**Note:** This tutorial was generated from an IPython notebook that can be
+downloaded `here <../../_static/notebooks/{{ resources.metadata.name }}.ipynb>`_.
+
+.. _{{resources.metadata.name}}:
+{% endblock %}
+
+{% block in_prompt %}
+{% endblock in_prompt %}
+
+{% block output_prompt %}
+{% endblock output_prompt %}
+
+{% block input %}
+{%- if cell.source.strip() and not cell.source.startswith("%") -%}
+.. code:: python
+
+{{ cell.source | indent}}
+{% endif -%}
+{% endblock input %}
+
+{% block error %}
+::
+
+{{ super() }}
+{% endblock error %}
+
+{% block traceback_line %}
+{{ line | indent | strip_ansi }}
+{% endblock traceback_line %}
+
+{% block execute_result %}
+{% block data_priority scoped %}
+{{ super() }}
+{% endblock %}
+{% endblock execute_result %}
+
+{% block stream %}
+.. parsed-literal::
+
+{{ output.text | indent }}
+{% endblock stream %}
+
+{% block data_svg %}
+.. image:: {{ output.metadata.filenames['image/svg+xml'] | urlencode }}
+{% endblock data_svg %}
+
+{% block data_png %}
+.. image:: {{ output.metadata.filenames['image/png'] | urlencode }}
+{% endblock data_png %}
+
+{% block data_jpg %}
+.. image:: {{ output.metadata.filenames['image/jpeg'] | urlencode }}
+{% endblock data_jpg %}
+
+{% block data_latex %}
+.. math::
+
+{{ output.data['text/latex'] | strip_dollars | indent }}
+{% endblock data_latex %}
+
+{% block data_text scoped %}
+.. parsed-literal::
+
+{{ output.data['text/plain'] | indent }}
+{% endblock data_text %}
+
+{% block data_html scoped %}
+.. raw:: html
+
+{{ output.data['text/html'] | indent }}
+{% endblock data_html %}
+
+{% block markdowncell scoped %}
+{{ cell.source | markdown2rst }}
+{% endblock markdowncell %}
+
+{%- block rawcell scoped -%}
+{%- if cell.metadata.get('raw_mimetype', '').lower() in resources.get('raw_mimetypes', ['']) %}
+{{cell.source}}
+{% endif -%}
+{%- endblock rawcell -%}
+
+{% block headingcell scoped %}
+{{ ("#" * cell.level + cell.source) | replace('\n', ' ') | markdown2rst }}
+{% endblock headingcell %}
+
+{% block unknowncell scoped %}
+unknown type  {{cell.type}}
+{% endblock unknowncell %}

setup.py

@@ -26,7 +26,8 @@
     packages=["emcee", "emcee.moves"],
     url="http://emcee.readthedocs.io",
     license="MIT",
-    description="Ensemble MCMC sampling toolkit",
+    description=("The Python ensemble sampling toolkit for affine-invariant "
+                 "MCMC"),
     long_description=open("README.rst").read(),
     package_data={"": ["LICENSE", "AUTHORS.rst"]},
     include_package_data=True,