Note
This tutorial was generated from an IPython notebook that can be downloaded here.
theano version: 1.0.4
pymc3 version: 3.7
exoplanet version: 0.2.0
The exoplanet package is mostly just glue that connects many other
ideas and software. In a situation like this, it can be easy to forget
about the important infrastructure upon which our science is built. In
order to make sure that you can easily give credit where credit is due,
we have tried to make it as painless as possible to work out which
citations are expected for a model fit using exoplanet by including a
exoplanet.citations.get_citations_for_model()
function that
introspects the current PyMC3 model and constructs a list of citations
for the functions used in that model.
For example, you might compute a quadratically limb darkened light curve
using starry
(via the
exoplanet.light_curve.StarryLightCurve
class):
import pymc3 as pm
import exoplanet as xo
with pm.Model() as model:
u = xo.distributions.QuadLimbDark("u")
orbit = xo.orbits.KeplerianOrbit(period=10.0)
light_curve = xo.StarryLightCurve(u)
transit = light_curve.get_light_curve(r=0.1, orbit=orbit, t=[0.0, 0.1])
txt, bib = xo.citations.get_citations_for_model()
The exoplanet.citations.get_citations_for_model()
function would
generate an acknowledgement that cites:
The first output from
exoplanet.citations.get_citations_for_model()
gives the
acknowledgement text:
print(txt)
This research made use of textsf{exoplanet} citep{exoplanet} and its dependencies citep{exoplanet:astropy13, exoplanet:astropy18, exoplanet:exoplanet, exoplanet:kipping13, exoplanet:luger18, exoplanet:pymc3, exoplanet:theano}.
And the second output is a string with BibTeX entries for each of the citations in the acknowledgement text:
print(bib)
@misc{exoplanet:exoplanet, author = {Dan Foreman-Mackey and Geert Barentsen and Tom Barclay}, title = {dfm/exoplanet: exoplanet v0.1.6}, month = apr, year = 2019, doi = {10.5281/zenodo.2651251}, url = {https://doi.org/10.5281/zenodo.2651251} } @article{exoplanet:pymc3, title={Probabilistic programming in Python using PyMC3}, author={Salvatier, John and Wiecki, Thomas V and Fonnesbeck, Christopher}, journal={PeerJ Computer Science}, volume={2}, pages={e55}, year={2016}, publisher={PeerJ Inc.} } @article{exoplanet:theano, title="{Theano: A {Python} framework for fast computation of mathematical expressions}", author={{Theano Development Team}}, journal={arXiv e-prints}, volume={abs/1605.02688}, year=2016, month=may, url={http://arxiv.org/abs/1605.02688} } @ARTICLE{exoplanet:kipping13, author = {{Kipping}, D.~M.}, title = "{Efficient, uninformative sampling of limb darkening coefficients for two-parameter laws}", journal = {mnras}, year = 2013, month = nov, volume = 435, pages = {2152-2160}, doi = {10.1093/mnras/stt1435}, adsurl = {http://adsabs.harvard.edu/abs/2013MNRAS.435.2152K}, adsnote = {Provided by the SAO/NASA Astrophysics Data System} } @article{exoplanet:astropy13, author = {{Astropy Collaboration} and {Robitaille}, T.~P. and {Tollerud}, E.~J. and {Greenfield}, P. and {Droettboom}, M. and {Bray}, E. and {Aldcroft}, T. and {Davis}, M. and {Ginsburg}, A. and {Price-Whelan}, A.~M. and {Kerzendorf}, W.~E. and {Conley}, A. and {Crighton}, N. and {Barbary}, K. and {Muna}, D. and {Ferguson}, H. and {Grollier}, F. and {Parikh}, M.~M. and {Nair}, P.~H. and {Unther}, H.~M. and {Deil}, C. and {Woillez}, J. and {Conseil}, S. and {Kramer}, R. and {Turner}, J.~E.~H. and {Singer}, L. and {Fox}, R. and {Weaver}, B.~A. and {Zabalza}, V. and {Edwards}, Z.~I. and {Azalee Bostroem}, K. and {Burke}, D.~J. and {Casey}, A.~R. and {Crawford}, S.~M. and {Dencheva}, N. and {Ely}, J. and {Jenness}, T. and {Labrie}, K. and {Lim}, P.~L. and {Pierfederici}, F. and {Pontzen}, A. and {Ptak}, A. and {Refsdal}, B. and {Servillat}, M. and {Streicher}, O.}, title = "{Astropy: A community Python package for astronomy}", journal = {aap}, year = 2013, month = oct, volume = 558, pages = {A33}, doi = {10.1051/0004-6361/201322068}, adsurl = {http://adsabs.harvard.edu/abs/2013A%26A...558A..33A}, adsnote = {Provided by the SAO/NASA Astrophysics Data System} } @article{exoplanet:astropy18, author = {{Astropy Collaboration} and {Price-Whelan}, A.~M. and {Sip{H o}cz}, B.~M. and {G{"u}nther}, H.~M. and {Lim}, P.~L. and {Crawford}, S.~M. and {Conseil}, S. and {Shupe}, D.~L. and {Craig}, M.~W. and {Dencheva}, N. and {Ginsburg}, A. and {VanderPlas}, J.~T. and {Bradley}, L.~D. and {P{'e}rez-Su{'a}rez}, D. and {de Val-Borro}, M. and {Aldcroft}, T.~L. and {Cruz}, K.~L. and {Robitaille}, T.~P. and {Tollerud}, E.~J. and {Ardelean}, C. and {Babej}, T. and {Bach}, Y.~P. and {Bachetti}, M. and {Bakanov}, A.~V. and {Bamford}, S.~P. and {Barentsen}, G. and {Barmby}, P. and {Baumbach}, A. and {Berry}, K.~L. and {Biscani}, F. and {Boquien}, M. and {Bostroem}, K.~A. and {Bouma}, L.~G. and {Brammer}, G.~B. and {Bray}, E.~M. and {Breytenbach}, H. and {Buddelmeijer}, H. and {Burke}, D.~J. and {Calderone}, G. and {Cano Rodr{'{i}}guez}, J.~L. and {Cara}, M. and {Cardoso}, J.~V.~M. and {Cheedella}, S. and {Copin}, Y. and {Corrales}, L. and {Crichton}, D. and {D'Avella}, D. and {Deil}, C. and {Depagne}, {'E}. and {Dietrich}, J.~P. and {Donath}, A. and {Droettboom}, M. and {Earl}, N. and {Erben}, T. and {Fabbro}, S. and {Ferreira}, L.~A. and {Finethy}, T. and {Fox}, R.~T. and {Garrison}, L.~H. and {Gibbons}, S.~L.~J. and {Goldstein}, D.~A. and {Gommers}, R. and {Greco}, J.~P. and {Greenfield}, P. and {Groener}, A.~M. and {Grollier}, F. and {Hagen}, A. and {Hirst}, P. and {Homeier}, D. and {Horton}, A.~J. and {Hosseinzadeh}, G. and {Hu}, L. and {Hunkeler}, J.~S. and {Ivezi{'c}}, {v Z}. and {Jain}, A. and {Jenness}, T. and {Kanarek}, G. and {Kendrew}, S. and {Kern}, N.~S. and {Kerzendorf}, W.~E. and {Khvalko}, A. and {King}, J. and {Kirkby}, D. and {Kulkarni}, A.~M. and {Kumar}, A. and {Lee}, A. and {Lenz}, D. and {Littlefair}, S.~P. and {Ma}, Z. and {Macleod}, D.~M. and {Mastropietro}, M. and {McCully}, C. and {Montagnac}, S. and {Morris}, B.~M. and {Mueller}, M. and {Mumford}, S.~J. and {Muna}, D. and {Murphy}, N.~A. and {Nelson}, S. and {Nguyen}, G.~H. and {Ninan}, J.~P. and {N{"o}the}, M. and {Ogaz}, S. and {Oh}, S. and {Parejko}, J.~K. and {Parley}, N. and {Pascual}, S. and {Patil}, R. and {Patil}, A.~A. and {Plunkett}, A.~L. and {Prochaska}, J.~X. and {Rastogi}, T. and {Reddy Janga}, V. and {Sabater}, J. and {Sakurikar}, P. and {Seifert}, M. and {Sherbert}, L.~E. and {Sherwood-Taylor}, H. and {Shih}, A.~Y. and {Sick}, J. and {Silbiger}, M.~T. and {Singanamalla}, S. and {Singer}, L.~P. and {Sladen}, P.~H. and {Sooley}, K.~A. and {Sornarajah}, S. and {Streicher}, O. and {Teuben}, P. and {Thomas}, S.~W. and {Tremblay}, G.~R. and {Turner}, J.~E.~H. and {Terr{'o}n}, V. and {van Kerkwijk}, M.~H. and {de la Vega}, A. and {Watkins}, L.~L. and {Weaver}, B.~A. and {Whitmore}, J.~B. and {Woillez}, J. and {Zabalza}, V. and {Astropy Contributors}}, title = "{The Astropy Project: Building an Open-science Project and Status of the v2.0 Core Package}", journal = {aj}, year = 2018, month = sep, volume = 156, pages = {123}, doi = {10.3847/1538-3881/aabc4f}, adsurl = {http://adsabs.harvard.edu/abs/2018AJ....156..123A}, adsnote = {Provided by the SAO/NASA Astrophysics Data System} } @article{exoplanet:luger18, author = {{Luger}, R. and {Agol}, E. and {Foreman-Mackey}, D. and {Fleming}, D.~P. and {Lustig-Yaeger}, J. and {Deitrick}, R.}, title = "{starry: Analytic Occultation Light Curves}", journal = {aj}, year = 2019, month = feb, volume = 157, pages = {64}, doi = {10.3847/1538-3881/aae8e5}, adsurl = {http://adsabs.harvard.edu/abs/2019AJ....157...64L}, adsnote = {Provided by the SAO/NASA Astrophysics Data System} }