Merge pull request #26 from dtamayo/master

Fork sync with upstream

.gitignore

@@ -35,7 +35,6 @@ doc/doxygen/html/
 doc/ipython
 doc/search.json
 problems/
-*.txt
 *.dSYM
 Untitled*
 .vscode/*

.travis.yml

@@ -60,13 +60,19 @@ script:
     - if [[ $TESTPART == "IPYTHON1" ]]; then cd $TRAVIS_BUILD_DIR/ipython_examples/ && python ipynb2py.py Migration.ipynb; fi
     - if [[ $TESTPART == "IPYTHON1" ]]; then cd $TRAVIS_BUILD_DIR/ipython_examples/ && python ipynb2py.py Radiation_Forces_Circumplanetary_Dust.ipynb; fi
     - if [[ $TESTPART == "IPYTHON1" ]]; then cd $TRAVIS_BUILD_DIR/ipython_examples/ && python ipynb2py.py Radiation_Forces_Debris_Disk.ipynb; fi
+    - if [[ $TESTPART == "IPYTHON1" ]]; then cd $TRAVIS_BUILD_DIR/ipython_examples/ && python ipynb2py.py CentralForce.ipynb; fi 
+    - if [[ $TESTPART == "IPYTHON1" ]]; then cd $TRAVIS_BUILD_DIR/ipython_examples/ && python ipynb2py.py CustomSplittingIntegrationSchemes.ipynb; fi
+    - if [[ $TESTPART == "IPYTHON1" ]]; then cd $TRAVIS_BUILD_DIR/ipython_examples/ && python ipynb2py.py TidesConstantTimeLag.ipynb; fi
     - if [[ $TESTPART == "IPYTHON2" ]]; then cd $TRAVIS_BUILD_DIR/ipython_examples/ && python ipynb2py.py Custom_Effects.ipynb; fi
     - if [[ $TESTPART == "IPYTHON2" ]]; then cd $TRAVIS_BUILD_DIR/ipython_examples/ && python ipynb2py.py ModifyMass.ipynb; fi
     - if [[ $TESTPART == "IPYTHON2" ]]; then cd $TRAVIS_BUILD_DIR/ipython_examples/ && python ipynb2py.py GettingStartedParameters.ipynb; fi
     - if [[ $TESTPART == "IPYTHON2" ]]; then cd $TRAVIS_BUILD_DIR/ipython_examples/ && python ipynb2py.py TidesConstantTimeLag.ipynb; fi
     - if [[ $TESTPART == "IPYTHON2" ]]; then cd $TRAVIS_BUILD_DIR/ipython_examples/ && python ipynb2py.py SimulationArchive.ipynb; fi
     - if [[ $TESTPART == "IPYTHON2" ]]; then cd $TRAVIS_BUILD_DIR/ipython_examples/ && python ipynb2py.py SavingAndLoadingSimulations.ipynb; fi
     - if [[ $TESTPART == "IPYTHON2" ]]; then cd $TRAVIS_BUILD_DIR/ipython_examples/ && python ipynb2py.py TrackMinDistance.ipynb; fi
+    - if [[ $TESTPART == "IPYTHON2" ]]; then cd $TRAVIS_BUILD_DIR/ipython_examples/ && python ipynb2py.py IntegrateForce.ipynb; fi
+    - if [[ $TESTPART == "IPYTHON2" ]]; then cd $TRAVIS_BUILD_DIR/ipython_examples/ && python ipynb2py.py J2.ipynb; fi
+    - if [[ $TESTPART == "IPYTHON2" ]]; then cd $TRAVIS_BUILD_DIR/ipython_examples/ && python ipynb2py.py ParameterInterpolation.ipynb; fi
 
 after_success:
     - if [[ $TESTPART == "PYTHON" ]] && [[ ${TRAVIS_PYTHON_VERSION:0:3} == "2.7" ]]; then coveralls; fi

README.rst

@@ -1,4 +1,4 @@
-.. image:: http://img.shields.io/badge/REBOUNDx-v3.0.5-green.svg?style=flat
+.. image:: http://img.shields.io/badge/REBOUNDx-v3.1.0-green.svg?style=flat
     :target: http://reboundx.readthedocs.org
 .. image:: https://badge.fury.io/py/reboundx.svg
     :target: https://badge.fury.io/py/reboundx
@@ -15,27 +15,35 @@
 .. image:: https://img.shields.io/badge/launch-binder-ff69b4.svg?style=flat
     :target: http://mybinder.org/repo/dtamayo/reboundx
 
-New Version and Paper!
-======================
-
-We've made some big improvements to REBOUNDx to make it more robust and easily extendable, so definitely upgrade to this new version (3.0) if you haven't already.
-We've also improved the binary format to better interface with the REBOUND SimulationArchive for the sharing and analysis of machine independent results.
-
-Definitely also check out our paper where we give an overview of the library, analyze the effects of dissipative forces on symplectic integrators, and give some recommendations:`Tamayo, Rein, Shi and Hernandez 2019 <http://arxiv.org/abs/1908.05634>`_
-
 Welcome to REBOUNDx (eXtras)
 ============================
 
 REBOUNDx allows you to easily incorporate additional physics into your REBOUND simulations.
-All the computationally expensive parts of the code are written in C, so that the code will run much faster than if you define your own custom `additional_forces` functions in Python.
+The main code is written in C, and we provide a convenient Python wrapper.
+For an overview of the technical details and some practical recommendations, see `Tamayo, Rein, Shi and Hernandez 2019 <http://arxiv.org/abs/1908.05634>`_.
+The paper publication lines up with REBOUNDx version 3.0.0.
+
+Documentation
+=============
 
-For a list of supported effects, installation instructions, tutorials/examples and documentation, please see http://reboundx.readthedocs.io.
+For a list of supported effects, and descriptions of the parameters that need to be set for each effect, see the documentation at `http://reboundx.readthedocs.io <http://reboundx.readthedocs.io>`_.
+You can also find installation instructions and a quickstart guide there.
 
-.. image:: https://github.com/dtamayo/dtamayo.github.io/blob/master/pix/reboundx.png
+Attribution
+===========
+
+We have tried to structure the documentation in a way that makes it easy to credit the various people who have contributed to any given effect.
+Please see the Attribution section at `http://reboundx.readthedocs.io <http://reboundx.readthedocs.io>`_ for direct links to ADS.
 
 Changelog
 =========
 
+Version 3.1.0
+-------------
+
+* Added interpolator object for interpolating parameters
+* Many improvements to the documentation
+
 Version 3.0.5
 -------------
 

doc/add_effect.rst

@@ -124,7 +124,6 @@ Now we just modify the ``problem.c`` file in our new ``stark_force`` folder, e.g
 
 In the terminal in the ``stark_force`` folder then just ``make clean``, ``make``  and then run it with  ``./rebound``. 
 In the visualization press 'w' to see the orbits. You should see a mess with the orbit getting more and less eccentric.
-(See Sec. 2.4 of `OpenGL Keyboard Commands <http://rebound.readthedocs.org/en/latest/c_quickstart.html>`_ for a list of the visualization keyboard commands).
 If you get an error about OpenGL or GLUT, just google `install openGL glut libraries <your OS here>` for instructions, or open your ``Makefile`` and set OPENGL=0 to turn it off.
 
 Python Example

doc/c_quickstart.rst

@@ -1,7 +1,7 @@
 .. _c_quickstart:
 
-Quickstart Guide (C)
-====================
+Quickstart (C)
+==============
 
 Installation
 ------------
@@ -63,7 +63,7 @@ Once you're done setting up all the effects you want, just run the REBOUND simul
     reb_integrate(sim, tmax);
 
 Probably the quickest way to get up and running is to modify an existing example for your effect.
-You can find links to the appropriate examples here: :ref:`effects`, along with implementation descriptions and citations.
+You can find links to the appropriate examples here: :ref:`effects`, along with implementation descriptions.
 You can find the example files in the ``reboundx/examples`` folder.
 
 Even if you are using the C version, you might also take a look at the python example links at :ref:`effects`, as the iPython notebooks nicely incorporate text and may therefore have a bit longer discussions about the physical details for each effect.

doc/conf.py

@@ -19,6 +19,7 @@
 import subprocess
 import glob
 import re
+from datetime import datetime
 
 # Doxygen trigger
 read_the_docs_build = os.environ.get('READTHEDOCS', None) == 'True'
@@ -174,8 +175,9 @@ def cleanline(line):
     'sphinx.ext.todo',
     'sphinx.ext.coverage',
     'sphinx.ext.mathjax',
-    'breathe'
+    'breathe',
 ]
+releases_github_path = "dtamayo/reboundx"
 breathe_projects = { "libreboundx": "doxygen/xml/" }
 breathe_default_project = "libreboundx"
 
@@ -193,19 +195,20 @@ def cleanline(line):
 # The master toctree document.
 master_doc = 'index'
 
-# General information about the project.
-project = 'REBOUNDx'
-copyright = '2015, Dan Tamayo, Hanno Rein'
-author = 'Dan Tamayo, Hanno Rein'
-
 # The version info for the project you're documenting, acts as replacement for
 # |version| and |release|, also used in various other places throughout the
 # built documents.
 #
 # The short X.Y version.
-version = '3.0'
+version = '3.1'
 # The full version, including alpha/beta/rc tags.
-release = '3.0.5'
+release = '3.1.0'
+
+# General information about the project.
+project = u"REBOUNDx ({0})".format(release)
+year = datetime.now().year
+author = 'Dan Tamayo, Hanno Rein'
+copyright = u"{0} {1}".format(year, author)
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.
@@ -261,7 +264,11 @@ def cleanline(line):
 # Theme options are theme-specific and customize the look and feel of a theme
 # further.  For a list of options available for each theme, see the
 # documentation.
-#html_theme_options = {}
+html_theme_options = {
+    "description": "A library for additional effects in REBOUND N-body integrations",
+    "github_user": "dtamayo",
+    "github_repo": "reboundx",
+}
 
 # Add any paths that contain custom themes here, relative to this directory.
 #html_theme_path = []
@@ -303,7 +310,7 @@ def cleanline(line):
 # Custom sidebar templates, maps document names to template names.
 #html_sidebars = {}
 html_sidebars = {
-                '**': ['globaltoc.html',]
+                '**': ['about.html', 'navigation.html', 'relations.html', 'searchbox.html']
                 }
 
 # Additional templates that should be rendered to pages, maps page names to

doc/effect_headers.txt

@@ -1,7 +1,7 @@
 .. _effects:
 
-REBx Effects & Parameters
-=========================
+Implemented Effects
+===================
 
 Below are descriptions for each of the effects included in REBOUNDx.
 Different implementations for the same effect are grouped together.
@@ -41,6 +41,18 @@ $$$$$$$$$$$$
 Gravity Fields
 ^^^^^^^^^^^^^^^^^^
 
+$$$$$$$$$$$$$$$$$$$$
+Integration Steppers
+^^^^^^^^^^^^^^^^^^^^
+
+These are wrapper functions to taking steps with several of REBOUND's integrators in order to build custom splitting schemes.
+
+$$$$$$$$$$$$$$$$$$$$$$$
+Parameter Interpolation
+^^^^^^^^^^^^^^^^^^^^^^^
+
+This isn't an effect that's loaded like the others, but an object that facilitates machine-independent interpolation of parameters that can be shared by both the C and Python versions. See the examples below for how to use them.
+
 $$$$$$$$$$$$
 Miscellaneous Utilities
 ^^^^^^^^^^^^^^^^^^^^^^^