Merge pull request #119 from California-Planet-Search/next-release

Version 1.1.0

.travis.yml

@@ -1,20 +1,37 @@
 language: python
+sudo: False
+
+cache:
+   directories:
+     - $HOME/download
+     - $HOME/miniconda2
+     - $HOME/miniconda3
 
 python:
   - "2.7"
-  - "3.4"
-
+  - "3.6"
+
+before_install:
+    - export py="$(echo $TRAVIS_PYTHON_VERSION | head -c 1)"
+    - wget http://repo.continuum.io/miniconda/Miniconda${py}-latest-Linux-x86_64.sh -O miniconda.sh
+    - chmod +x miniconda.sh
+    - bash miniconda.sh -b -u -p $HOME/miniconda
+    - export PATH=/home/travis/miniconda/bin:$PATH
+    - conda update --yes conda
+    - sudo rm -rf /dev/shm
+    - sudo ln -s /run/shm /dev/shm
+
 install:
-    - pip install -r requirements.txt    # installs dependencies listed in requirements.txt
-    - pip install coveralls nbformat nbconvert jupyter_client ipykernel  # install packages for testing
-    - pip install . --upgrade		 # installs radvel from current git branch
-    - python setup.py build_ext -i       # build C extension
+    - conda install --yes python=$TRAVIS_PYTHON_VERSION pip numpy scipy matplotlib cython pandas
+    - pip install nose coveralls nbformat nbconvert jupyter_client ipykernel
+    - pip install . --upgrade
+    - python setup.py build_ext -i
 
 # configure a headless display using xvbf to test plot generation
 before_script:
     - "export DISPLAY=:99.0"
     - "sh -e /etc/init.d/xvfb start"
-    - sleep 3 # give xvfb some time to start
+    - sleep 2 # give xvfb some time to start
 
 # run tests in Travis-CI virtual env
 script:
@@ -28,5 +45,3 @@ notifications:
     on_failure: always  # send a slack notification when build fails.
                         # Travis-CI runs a build every time something 
                         # in this repo changes or a pull request is made.
-
-

MANIFEST.in

@@ -1,3 +1,4 @@
 global-include src/*.pyx
 global-include src/*.c
 include requirements.txt
+include example_data/*

README.md

@@ -7,10 +7,12 @@ General Toolkit for Modeling Radial Velocities.
 [![Coverage Status](https://coveralls.io/repos/github/California-Planet-Search/radvel/badge.svg?branch=master)](https://coveralls.io/github/California-Planet-Search/radvel?branch=master)
 [![Documentation Status](https://readthedocs.org/projects/radvel/badge/?version=latest)](http://radvel.readthedocs.io/en/latest/?badge=latest)
 [![PyPI version](https://badge.fury.io/py/radvel.svg)](https://badge.fury.io/py/radvel)
+[![Requirements Status](https://requires.io/github/California-Planet-Search/radvel/requirements.svg?branch=next-release)](https://requires.io/github/California-Planet-Search/radvel/requirements/?branch=next-release)
+
 
 ## Attribution
 
-Written by BJ Fulton, Erik Petigura, and Sarah Blunt. Fulton et al. (in prep.)
+Written by BJ Fulton, Erik Petigura, Sarah Blunt, and Evan Sinukoff. Fulton et al. (submitted to PASP)
 
 Please cite the following DOI if you wish to make use of this software in any publication.
 
@@ -47,15 +49,11 @@ RadVel is
    - Kepler's equation solved in C (slower Python solver also included)
    - MCMC is multi-threaded
 
-## Future Improvements
-
-- Gaussian Process (GP) functionality
-
 ## Tutorials 
 
 Follow examples in
 
-- `radvel/tests/SyntheticData.ipynb`
-- `radvel/tests/K2-24_Fitting+MCMC.ipynb`
-- `radvel/tests/164922_Fitting+MCMC.ipynb`
-
+- `radvel/docs/tutorials/SyntheticData.ipynb`
+- `radvel/docs/tutorials/K2-24_Fitting+MCMC.ipynb`
+- `radvel/docs/tutorials/164922_Fitting+MCMC.ipynb`
+- `radvel/docs/tutorials/GaussianProcess-tutorial.ipynb`

docs/api.rst

@@ -9,6 +9,7 @@ API
    model
    orbit
    basis
+   gp
    likelihood
    posterior
    prior

docs/conf.py

@@ -24,7 +24,6 @@
 
 import radvel
 
-
 # If extensions (or modules to document with autodoc) are in another directory,
 # add these directories to sys.path here. If the directory is relative to the
 # documentation root, use os.path.abspath to make it absolute, like shown here.
@@ -44,6 +43,7 @@
     'sphinx.ext.mathjax',
     'sphinx.ext.napoleon',
     'sphinx.ext.viewcode',
+    'nbsphinx'
 ]
 
 # Add any paths that contain templates here, relative to this directory.
@@ -62,8 +62,8 @@
 
 # General information about the project.
 project = u'radvel'
-copyright = u'2015, BJ Fulton and Erik Petigura'
-author = u'BJ Fulton, Erik Petigura, and Sarah Blunt'
+copyright = u'2015, BJ Fulton, Erik Petigura, Sarah Blunt, and Evan Sinukoff'
+author = u'BJ Fulton, Erik Petigura, Sarah Blunt, and Evan Sinukoff'
 
 # The version info for the project you're documenting, acts as replacement for
 # |version| and |release|, also used in various other places throughout the
@@ -142,7 +142,7 @@
 
 # The name of an image file (relative to this directory) to place at the top
 # of the sidebar.
-html_logo = "plots/radvel_logo_small_alpha.png"
+html_logo = "plots/radvel_logo_alpha_retina.png"
 
 # The name of an image file (within the static path) to use as favicon of the
 # docs.  This file should be a Windows icon file (.ico) being 16x16 or 32x32
@@ -238,7 +238,7 @@
 #  author, documentclass [howto, manual, or own class]).
 latex_documents = [
   (master_doc, 'radvel.tex', u'radvel Documentation',
-   u'BJ Fulton, Erik Petigura, and Sarah Blunt', 'manual'),
+   u'BJ Fulton, Erik Petigura, Sarah Blunt, and Evan Sinukoff', 'manual'),
 ]
 
 # The name of an image file (relative to this directory) to place at the top of

docs/gp.rst

@@ -0,0 +1,8 @@
+.. _gp:
+
+Kernels for GPs
+=====================
+.. module:: radvel
+
+.. automodule:: radvel.gp
+   :members: