rtds

docs/.gitignore

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+_build
+xml

docs/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) .
+
+default: dirhtml
+
+.PHONY: clean
+clean:
+	rm -rf $(BUILDDIR)/* $(TUTORIALS)
+
+.PHONY: html
+html:
+	$(SPHINXBUILD) -b html $(ALLSPHINXOPTS) $(BUILDDIR)/html
+	@echo
+	@echo "Build finished. The HTML pages are in $(BUILDDIR)/html."
+
+.PHONY: dirhtml
+dirhtml:
+	$(SPHINXBUILD) -b dirhtml $(ALLSPHINXOPTS) $(BUILDDIR)/dirhtml
+	@echo
+	@echo "Build finished. The HTML pages are in $(BUILDDIR)/dirhtml."
+
+.PHONY: singlehtml
+singlehtml:
+	$(SPHINXBUILD) -b singlehtml $(ALLSPHINXOPTS) $(BUILDDIR)/singlehtml
+	@echo
+	@echo "Build finished. The HTML page is in $(BUILDDIR)/singlehtml."

docs/api/install.rst

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+.. _install:
+
+Installation
+============
+
+The core implementation of celerite is written in C++ so this will need to be
+compiled to be called from Python. The easiest way for a new user to do this
+will be by following the directions in the :ref:`using-conda` section below.
+Power users might be able to eke out a bit more performance by tuning the
+linear algebra library and installing :ref:`source`.
+
+.. _using-conda:
+
+Using conda
+-----------
+
+The easiest way to install celerite is using `conda
+<http://continuum.io/downloads>`_ (via `conda-forge
+<https://conda-forge.github.io/>`_) with the following command:
+
+.. code-block:: bash
+
+    conda install -c conda-forge celerite
+
+
+Using pip
+---------
+
+celerite can also be installed using `pip <https://pip.pypa.io>`_ after
+installing `Eigen <http://eigen.tuxfamily.org/>`_:
+
+.. code-block:: bash
+
+    pip install celerite
+
+
+.. _source:
+
+From Source
+-----------
+
+The source code for celerite can be downloaded `from GitHub
+<https://github.com/dfm/celerite>`_ by running
+
+.. code-block:: bash
+
+    git clone https://github.com/dfm/celerite.git
+
+
+.. _python-deps:
+
+Dependencies
+++++++++++++
+
+For the Python interface, you'll (obviously) need a Python installation and I
+recommend `conda <http://continuum.io/downloads>`_ if you don't already have
+your own opinions.
+
+After installing Python, the following dependencies are required to build
+celerite:
+
+1. `NumPy <http://www.numpy.org/>`_ for math and linear algebra in Python, and
+2. `pybind11 <https://pybind11.readthedocs.io>`_ for the Python–C++ interface.
+3. `autograd <https://github.com/HIPS/autograd>`_ (optional) for computing
+   gradients in celerite models.
+
+If you're using conda, you can install all of the dependencies with the
+following command:
+
+.. code-block:: bash
+
+    conda install -c conda-forge numpy pybind11 autograd
+
+Building
+++++++++
+
+After installing the dependencies, you can build the celerite module by
+running:
+
+.. code-block:: bash
+
+    python setup.py install
+
+in the root directory of the source tree.
+
+Automatic differentiation
++++++++++++++++++++++++++
+
+Gradients of celerite models are computed using automatic differentiation. By
+default, this is implemented using the ``AutoDiffScalar`` in Eigen, but it is
+possible to get faster performance by using the `stan-math library
+<https://github.com/stan-dev/math>`_. To do this, download the library from
+`the GitHub page <https://github.com/stan-dev/math>`_ and build celerite using
+the following command:
+
+.. code-block:: bash
+
+    python setup.py build_ext -I${STAN}:${STAN}/lib/boost_1.62.0:${STAN}/lib/cvodes_2.9.0/include -DUSE_STAN_MATH install
+
+where ``${STAN}`` is the directory where you downloaded the stan-math library.
+
+
+Testing
+-------
+
+To run the unit tests, install `pytest <http://doc.pytest.org/>`_ and then
+execute:
+
+.. code-block:: bash
+
+    py.test -v
+
+All of the tests should (of course) pass.
+If any of the tests don't pass and if you can't sort out why, `open an issue
+on GitHub <https://github.com/dfm/celerite/issues>`_.

docs/conf.py

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+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+
+import os
+import glob
+import subprocess
+
+import sphinx_nameko_theme
+
+import exoplanet  # NOQA
+
+# Convert the tutorials
+for fn in glob.glob("_static/notebooks/*.ipynb"):
+    name = os.path.splitext(os.path.split(fn)[1])[0]
+    print("Building {0}...".format(name))
+    subprocess.check_call(
+        "jupyter nbconvert --template tutorials/tutorial_rst --to rst "
+        + fn + " --output-dir tutorials", shell=True)
+
+extensions = [
+    "sphinx.ext.autodoc",
+    "sphinx.ext.intersphinx",
+    "sphinx.ext.napoleon",
+    "sphinx.ext.mathjax",
+]
+intersphinx_mapping = {
+    'python': ('https://docs.python.org/3/', None),
+    'numpy': ('https://docs.scipy.org/doc/numpy/', None),
+    'scipy': ('https://docs.scipy.org/doc/scipy/reference/', None),
+    'astropy': ('http://docs.astropy.org/en/stable/', None),
+}
+
+templates_path = ["_templates"]
+source_suffix = ".rst"
+master_doc = "index"
+
+# General information about the project.
+project = "exoplanet"
+author = "Dan Foreman-Mackey"
+copyright = "2018, " + author
+
+version = exoplanet.__version__
+release = exoplanet.__version__
+
+exclude_patterns = ["_build"]
+pygments_style = "sphinx"
+
+# Readthedocs.
+# on_rtd = os.environ.get("READTHEDOCS", None) == "True"
+html_theme_path = [sphinx_nameko_theme.get_html_theme_path()]
+html_theme = "nameko"
+
+html_context = dict(
+    display_github=True,
+    github_user="dfm",
+    github_repo="exoplanet",
+    github_version="master",
+    conf_py_path="/docs/",
+)
+html_static_path = ["_static"]
+html_show_sourcelink = False

docs/environment.yml

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+name: exoplanet
+
+channels:
+  - conda-forge
+
+dependencies:
+  - python=3.5
+  - pandoc
+  - numpy
+  - scipy
+  - astropy
+  - setuptools
+  - pymc3
+  - jupyter
+  - pip:
+      - sphinx-nameko-theme

docs/index.rst

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+exoplanet
+=========
+
+*exoplanet* is being actively developed in `a public repository on GitHub
+<https://github.com/dfm/exoplanet>`_ so if you have any trouble, `open an issue
+<https://github.com/dfm/exoplanet/issues>`_ there.
+
+.. raw:: html
+
+    <p>
+    <a href="https://travis-ci.org/dfm/exoplanet"><img src="https://img.shields.io/travis/dfm/exoplanet/master.svg?style=flat"/></a>
+    <br>
+    <a href="https://rodluger.github.io/starry"><img src="https://img.shields.io/badge/powered_by-starry-EB5368.svg?style=flat"/></a>
+    <a href="https://celerite.readthedocs.io"><img src="https://img.shields.io/badge/powered_by-celerite-EB5368.svg?style=flat"/></a>
+    <a href="https://docs.pymc.io"><img src="https://img.shields.io/badge/powered_by-PyMC3-EB5368.svg?style=flat"/></a>
+    <a href="http://www.astropy.org"><img src="https://img.shields.io/badge/powered_by-AstroPy-EB5368.svg?style=flat"/></a>
+    </p>
+
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Tutorials
+
+   tutorials/quickstart
+   tutorials/intro-to-pymc3
+
+
+.. toctree::
+   :maxdepth: 2
+   :caption: API Documentation
+
+    api/install
+
+
+License & Attribution
+---------------------
+
+Copyright 2018, Daniel Foreman-Mackey.
+
+The source code is made available under the terms of the MIT license.
+
+If you make use of this code, please cite the following paper:
+
+.. code-block:: tex
+
+    tbd
+
+
+Changelog
+---------
+
+.. include:: ../HISTORY.rst

docs/tutorials/tutorial_rst.tpl

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+{%- extends 'display_priority.tpl' -%}
+
+{% block header %}
+.. module:: celerite
+
+.. 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 %}