From 625db3bc6b41691eeec325308a4db8635722fc97 Mon Sep 17 00:00:00 2001 From: Sarah Blunt Date: Fri, 1 Mar 2024 12:32:11 -0600 Subject: [PATCH 01/30] draft of JOSS paper --- paper/paper.bib | 242 ++++++++++++++++++++++++++++++++++++++++++++++++ paper/paper.md | 152 ++++++++++++++++++++++++++++++ 2 files changed, 394 insertions(+) create mode 100644 paper/paper.bib create mode 100644 paper/paper.md diff --git a/paper/paper.bib b/paper/paper.bib new file mode 100644 index 00000000..c4577696 --- /dev/null +++ b/paper/paper.bib @@ -0,0 +1,242 @@ +@ARTICLE{Blunt:2020, + author = {{Blunt}, Sarah and {Wang}, Jason J. and {Angelo}, Isabel and {Ngo}, Henry and {Cody}, Devin and {De Rosa}, Robert J. and {Graham}, James R. and {Hirsch}, Lea and {Nagpal}, Vighnesh and {Nielsen}, Eric L. and {Pearce}, Logan and {Rice}, Malena and {Tejada}, Roberto}, + title = "{orbitize!: A Comprehensive Orbit-fitting Software Package for the High-contrast Imaging Community}", + journal = {\aj}, + keywords = {Open source software, Orbit determination, 1866, 1175, Astrophysics - Earth and Planetary Astrophysics}, + year = 2020, + month = mar, + volume = {159}, + number = {3}, + eid = {89}, + pages = {89}, + doi = {10.3847/1538-3881/ab6663}, +archivePrefix = {arXiv}, + eprint = {1910.01756}, + primaryClass = {astro-ph.EP}, + adsurl = {https://ui.adsabs.harvard.edu/abs/2020AJ....159...89B}, + adsnote = {Provided by the SAO/NASA Astrophysics Data System} +} + +@ARTICLE{Bryan:2020, + author = {{Bryan}, Marta L. and {Chiang}, Eugene and {Bowler}, Brendan P. and {Morley}, Caroline V. and {Millholland}, Sarah and {Blunt}, Sarah and {Ashok}, Katelyn B. and {Nielsen}, Eric and {Ngo}, Henry and {Mawet}, Dimitri and {Knutson}, Heather A.}, + title = "{Obliquity Constraints on an Extrasolar Planetary-mass Companion}", + journal = {\aj}, + keywords = {Exoplanet systems, High resolution spectroscopy, Direct imaging, Photometry, 484, 2096, 387, 1234, Astrophysics - Earth and Planetary Astrophysics, Astrophysics - Instrumentation and Methods for Astrophysics, Astrophysics - Solar and Stellar Astrophysics}, + year = 2020, + month = apr, + volume = {159}, + number = {4}, + eid = {181}, + pages = {181}, + doi = {10.3847/1538-3881/ab76c6}, +archivePrefix = {arXiv}, + eprint = {2002.11131}, + primaryClass = {astro-ph.EP}, + adsurl = {https://ui.adsabs.harvard.edu/abs/2020AJ....159..181B}, + adsnote = {Provided by the SAO/NASA Astrophysics Data System} +} + +@ARTICLE{Ferrer-Chavez:2021, + author = {{Ferrer-Ch{\'a}vez}, Rodrigo and {Blunt}, Sarah and {Wang}, Jason J.}, + title = "{Algorithmic Speedups and Posterior Biases from Orbit Fitting of Directly Imaged Exoplanets in Cartesian Coordinates}", + journal = {Research Notes of the American Astronomical Society}, + keywords = {Exoplanets, Exoplanet astronomy, Direct imaging, Exoplanet detection methods, Bayesian statistics, Posterior distribution, Markov chain Monte Carlo, Affine invariant, 498, 486, 387, 489, 1900, 1926, 1889, 1890}, + year = 2021, + month = jul, + volume = {5}, + number = {7}, + eid = {162}, + pages = {162}, + doi = {10.3847/2515-5172/ac151d}, + adsurl = {https://ui.adsabs.harvard.edu/abs/2021RNAAS...5..162F}, + adsnote = {Provided by the SAO/NASA Astrophysics Data System} +} + + + +@article{Surti:2023, + abstract = {The exoplanet orbit-fitting software package orbitize! was initially designed to fit the orbits of directly imaged planets with relative astrometric measurements using a Markov Chain Monte Carlo (MCMC) algorithm. Since the publication of orbitize! v1.0, the ability to jointly fit radial velocities and astrometry has been incorporated. We first implemented a Basis class into orbitize! that enables users to add and fit in various orbit parameterizations. We then introduced a radial velocity-focused parameterization of the Keplerian orbital elements for the joint radial velocity and astrometry fits. We compared MCMC convergence speeds of the new radial velocity-focused basis to the original orbitize! standard basis for the system HD 190771, which has full orbital coverage in radial velocity data. We found a 16% faster convergence in time with the radial velocity-focused basis. We encourage users to consider using this basis when doing joint radial velocity and astrometry fits.}, + author = {Tirth Surti and Lea Hirsch and Tabassom Madayen and Ziyyad Ali and Eric Nielsen and Sarah Blunt and Jason Wang and Rodrigo Ferrer-Ch{\'a}vez and Bruce Macintosh}, + doi = {10.3847/2515-5172/acdc29}, + journal = {Research Notes of the AAS}, + month = {jun}, + number = {6}, + pages = {121}, + publisher = {The American Astronomical Society}, + title = {Improving MCMC Convergence for Joint Astrometry and Radial Velocity Orbit-fits Through Reparameterization}, + url = {https://dx.doi.org/10.3847/2515-5172/acdc29}, + volume = {7}, + year = {2023}, + bdsk-url-1 = {https://dx.doi.org/10.3847/2515-5172/acdc29}} + + +@ARTICLE{Covarrubias:2022, + author = {{Covarrubias}, Sofia and {Blunt}, Sarah and {Wang}, Jason J.}, + title = "{N-body Interactions will be Detectable in the HR-8799 System within 5 yr with VLTI-GRAVITY}", + journal = {Research Notes of the American Astronomical Society}, + keywords = {Astrometric exoplanet detection, Exoplanet dynamics, Exoplanet systems, 2130, 490, 484, Astrophysics - Earth and Planetary Astrophysics}, + year = 2022, + month = mar, + volume = {6}, + number = {3}, + eid = {66}, + pages = {66}, + doi = {10.3847/2515-5172/ac61d8}, +archivePrefix = {arXiv}, + eprint = {2204.03679}, + primaryClass = {astro-ph.EP}, + adsurl = {https://ui.adsabs.harvard.edu/abs/2022RNAAS...6...66C}, + adsnote = {Provided by the SAO/NASA Astrophysics Data System} +} + + + +@ARTICLE{Speagle:2020, + author = {{Speagle}, Joshua S.}, + title = "{DYNESTY: a dynamic nested sampling package for estimating Bayesian posteriors and evidences}", + journal = {\mnras}, + keywords = {methods: data analysis, methods: statistical, Astrophysics - Instrumentation and Methods for Astrophysics, Statistics - Computation}, + year = 2020, + month = apr, + volume = {493}, + number = {3}, + pages = {3132-3158}, + doi = {10.1093/mnras/staa278}, +archivePrefix = {arXiv}, + eprint = {1904.02180}, + primaryClass = {astro-ph.IM}, + adsurl = {https://ui.adsabs.harvard.edu/abs/2020MNRAS.493.3132S}, + adsnote = {Provided by the SAO/NASA Astrophysics Data System} +} + + + +@ARTICLE{Nielsen:2020, + author = {{Nielsen}, Eric L. and {De Rosa}, Robert J. and {Wang}, Jason J. and {Sahlmann}, Johannes and {Kalas}, Paul and {Duch{\^e}ne}, Gaspard and {Rameau}, Julien and {Marley}, Mark S. and {Saumon}, Didier and {Macintosh}, Bruce and {Millar-Blanchaer}, Maxwell A. and {Nguyen}, Meiji M. and {Ammons}, S. Mark and {Bailey}, Vanessa P. and {Barman}, Travis and {Bulger}, Joanna and {Chilcote}, Jeffrey and {Cotten}, Tara and {Doyon}, Rene and {Esposito}, Thomas M. and {Fitzgerald}, Michael P. and {Follette}, Katherine B. and {Gerard}, Benjamin L. and {Goodsell}, Stephen J. and {Graham}, James R. and {Greenbaum}, Alexandra Z. and {Hibon}, Pascale and {Hung}, Li-Wei and {Ingraham}, Patrick and {Konopacky}, Quinn and {Larkin}, James E. and {Maire}, J{\'e}r{\^o}me and {Marchis}, Franck and {Marois}, Christian and {Metchev}, Stanimir and {Oppenheimer}, Rebecca and {Palmer}, David and {Patience}, Jennifer and {Perrin}, Marshall and {Poyneer}, Lisa and {Pueyo}, Laurent and {Rajan}, Abhijith and {Rantakyr{\"o}}, Fredrik T. and {Ruffio}, Jean-Baptiste and {Savransky}, Dmitry and {Schneider}, Adam C. and {Sivaramakrishnan}, Anand and {Song}, Inseok and {Soummer}, Remi and {Thomas}, Sandrine and {Wallace}, J. Kent and {Ward-Duong}, Kimberly and {Wiktorowicz}, Sloane and {Wolff}, Schuyler}, + title = "{The Gemini Planet Imager Exoplanet Survey: Dynamical Mass of the Exoplanet {\ensuremath{\beta}} Pictoris b from Combined Direct Imaging and Astrometry}", + journal = {\aj}, + keywords = {Astrometry, Direct imaging, Exoplanets, Coronagraphic imaging, Orbit determination, 80, 387, 498, 313, 1175, Astrophysics - Earth and Planetary Astrophysics, Astrophysics - Solar and Stellar Astrophysics}, + year = 2020, + month = feb, + volume = {159}, + number = {2}, + eid = {71}, + pages = {71}, + doi = {10.3847/1538-3881/ab5b92}, +archivePrefix = {arXiv}, + eprint = {1911.11273}, + primaryClass = {astro-ph.EP}, + adsurl = {https://ui.adsabs.harvard.edu/abs/2020AJ....159...71N}, + adsnote = {Provided by the SAO/NASA Astrophysics Data System} +} + + + +@ARTICLE{Blunt:2023, + author = {{Blunt}, Sarah and {Balmer}, W.~O. and {Wang}, J.~J. and {Lacour}, S. and {Petrus}, S. and {Bourdarot}, G. and {Kammerer}, J. and {Pourr{\'e}}, N. and {Rickman}, E. and {Shangguan}, J. and {Winterhalder}, T. and {Abuter}, R. and {Amorim}, A. and {Asensio-Torres}, R. and {Benisty}, M. and {Berger}, J. -P. and {Beust}, H. and {Boccaletti}, A. and {Bohn}, A. and {Bonnefoy}, M. and {Bonnet}, H. and {Brandner}, W. and {Cantalloube}, F. and {Caselli}, P. and {Charnay}, B. and {Chauvin}, G. and {Chavez}, A. and {Choquet}, E. and {Christiaens}, V. and {Cl{\'e}net}, Y. and {Du Foresto}, V. Coud{\'e} and {Cridland}, A. and {Dembet}, R. and {Drescher}, A. and {Duvert}, G. and {Eckart}, A. and {Eisenhauer}, F. and {Feuchtgruber}, H. and {Garcia}, P. and {Garcia Lopez}, R. and {Gendron}, E. and {Genzel}, R. and {Gillessen}, S. and {Girard}, J.~H. and {Haubois}, X. and {Hei{\ss}el}, G. and {Henning}, Th. and {Hinkley}, S. and {Hippler}, S. and {Horrobin}, M. and {Houll{\'e}}, M. and {Hubert}, Z. and {Jocou}, L. and {Keppler}, M. and {Kervella}, P. and {Kreidberg}, L. and {Lagrange}, A. -M. and {Lapeyr{\`e}re}, V. and {Le Bouquin}, J. -B. and {L{\'e}na}, P. and {Lutz}, D. and {Maire}, A. -L. and {Mang}, F. and {Marleau}, G. -D. and {M{\'e}rand}, A. and {Molli{\`e}re}, P. and {Monnier}, J.~D. and {Mordasini}, C. and {Mouillet}, D. and {Nasedkin}, E. and {Nowak}, M. and {Ott}, T. and {Otten}, G.~P.~P.~L. and {Paladini}, C. and {Paumard}, T. and {Perraut}, K. and {Perrin}, G. and {Pfuhl}, O. and {Pueyo}, L. and {Rameau}, J. and {Rodet}, L. and {Rustamkulov}, Z. and {Shimizu}, T. and {Sing}, D. and {Stolker}, T. and {Straubmeier}, C. and {Sturm}, E. and {Tacconi}, L.~J. and {van Dishoeck}, E.~F. and {Vigan}, A. and {Vincent}, F. and {Ward-Duong}, K. and {Widmann}, F. and {Wieprecht}, E. and {Wiezorrek}, E. and {Woillez}, J. and {Yazici}, S. and {Young}, A. and {Exogravity Collaboration}}, + title = "{First VLTI/GRAVITY Observations of HIP 65426 b: Evidence for a Low or Moderate Orbital Eccentricity}", + journal = {\aj}, + keywords = {Exoplanets, Exoplanet formation, Astrometry, Optical interferometry, 498, 492, 80, 1168, Astrophysics - Earth and Planetary Astrophysics}, + year = 2023, + month = dec, + volume = {166}, + number = {6}, + eid = {257}, + pages = {257}, + doi = {10.3847/1538-3881/ad06b7}, +archivePrefix = {arXiv}, + eprint = {2310.00148}, + primaryClass = {astro-ph.EP}, + adsurl = {https://ui.adsabs.harvard.edu/abs/2023AJ....166..257B}, + adsnote = {Provided by the SAO/NASA Astrophysics Data System} +} + + + + +@ARTICLE{Bowler:2016, + author = {{Bowler}, Brendan P.}, + title = "{Imaging Extrasolar Giant Planets}", + journal = {\pasp}, + keywords = {Astrophysics - Earth and Planetary Astrophysics}, + year = 2016, + month = oct, + volume = {128}, + number = {968}, + pages = {102001}, + doi = {10.1088/1538-3873/128/968/102001}, +archivePrefix = {arXiv}, + eprint = {1605.02731}, + primaryClass = {astro-ph.EP}, + adsurl = {https://ui.adsabs.harvard.edu/abs/2016PASP..128j2001B}, + adsnote = {Provided by the SAO/NASA Astrophysics Data System} +} + +@ARTICLE{Brandt:2021, + author = {{Brandt}, Timothy D.}, + title = "{The Hipparcos-Gaia Catalog of Accelerations: Gaia EDR3 Edition}", + journal = {\apjs}, + keywords = {Astrometry, Astrometric exoplanet detection, Astrometric binary stars, 80, 2130, 79, Astrophysics - Astrophysics of Galaxies, Astrophysics - Earth and Planetary Astrophysics, Astrophysics - Instrumentation and Methods for Astrophysics, Astrophysics - Solar and Stellar Astrophysics}, + year = 2021, + month = jun, + volume = {254}, + number = {2}, + eid = {42}, + pages = {42}, + doi = {10.3847/1538-4365/abf93c}, +archivePrefix = {arXiv}, + eprint = {2105.11662}, + primaryClass = {astro-ph.GA}, + adsurl = {https://ui.adsabs.harvard.edu/abs/2021ApJS..254...42B}, + adsnote = {Provided by the SAO/NASA Astrophysics Data System} +} + +@ARTICLE{Lacour:2021, + author = {{Lacour}, S. and {Wang}, J.~J. and {Rodet}, L. and {Nowak}, M. and {Shangguan}, J. and {Beust}, H. and {Lagrange}, A. -M. and {Abuter}, R. and {Amorim}, A. and {Asensio-Torres}, R. and {Benisty}, M. and {Berger}, J. -P. and {Blunt}, S. and {Boccaletti}, A. and {Bohn}, A. and {Bolzer}, M. -L. and {Bonnefoy}, M. and {Bonnet}, H. and {Bourdarot}, G. and {Brandner}, W. and {Cantalloube}, F. and {Caselli}, P. and {Charnay}, B. and {Chauvin}, G. and {Choquet}, E. and {Christiaens}, V. and {Cl{\'e}net}, Y. and {Coud{\'e} Du Foresto}, V. and {Cridland}, A. and {Dembet}, R. and {Dexter}, J. and {de Zeeuw}, P.~T. and {Drescher}, A. and {Duvert}, G. and {Eckart}, A. and {Eisenhauer}, F. and {Gao}, F. and {Garcia}, P. and {Garcia Lopez}, R. and {Gendron}, E. and {Genzel}, R. and {Gillessen}, S. and {Girard}, J.~H. and {Haubois}, X. and {Hei{\ss}el}, G. and {Henning}, Th. and {Hinkley}, S. and {Hippler}, S. and {Horrobin}, M. and {Houll{\'e}}, M. and {Hubert}, Z. and {Jocou}, L. and {Kammerer}, J. and {Keppler}, M. and {Kervella}, P. and {Kreidberg}, L. and {Lapeyr{\`e}re}, V. and {Le Bouquin}, J. -B. and {L{\'e}na}, P. and {Lutz}, D. and {Maire}, A. -L. and {M{\'e}rand}, A. and {Molli{\`e}re}, P. and {Monnier}, J.~D. and {Mouillet}, D. and {Nasedkin}, E. and {Ott}, T. and {Otten}, G.~P.~P.~L. and {Paladini}, C. and {Paumard}, T. and {Perraut}, K. and {Perrin}, G. and {Pfuhl}, O. and {Rickman}, E. and {Pueyo}, L. and {Rameau}, J. and {Rousset}, G. and {Rustamkulov}, Z. and {Samland}, M. and {Shimizu}, T. and {Sing}, D. and {Stadler}, J. and {Stolker}, T. and {Straub}, O. and {Straubmeier}, C. and {Sturm}, E. and {Tacconi}, L.~J. and {van Dishoeck}, E.~F. and {Vigan}, A. and {Vincent}, F. and {von Fellenberg}, S.~D. and {Ward-Duong}, K. and {Widmann}, F. and {Wieprecht}, E. and {Wiezorrek}, E. and {Woillez}, J. and {Yazici}, S. and {Young}, A. and {Gravity Collaboration}}, + title = "{The mass of {\ensuremath{\beta}} Pictoris c from {\ensuremath{\beta}} Pictoris b orbital motion}", + journal = {\aap}, + keywords = {planets and satellites: detection, astrometry, instrumentation: interferometers, instrumentation: high angular resolution, Astrophysics - Earth and Planetary Astrophysics, Astrophysics - Instrumentation and Methods for Astrophysics}, + year = 2021, + month = oct, + volume = {654}, + eid = {L2}, + pages = {L2}, + doi = {10.1051/0004-6361/202141889}, +archivePrefix = {arXiv}, + eprint = {2109.10671}, + primaryClass = {astro-ph.EP}, + adsurl = {https://ui.adsabs.harvard.edu/abs/2021A&A...654L...2L}, + adsnote = {Provided by the SAO/NASA Astrophysics Data System} +} + +@ARTICLE{Bowler:2020, + author = {{Bowler}, Brendan P. and {Blunt}, Sarah C. and {Nielsen}, Eric L.}, + title = "{Population-level Eccentricity Distributions of Imaged Exoplanets and Brown Dwarf Companions: Dynamical Evidence for Distinct Formation Channels}", + journal = {\aj}, + keywords = {Exoplanet formation, Brown dwarfs, Extrasolar gaseous giant planets, 492, 185, 509, Astrophysics - Earth and Planetary Astrophysics, Astrophysics - Solar and Stellar Astrophysics}, + year = 2020, + month = feb, + volume = {159}, + number = {2}, + eid = {63}, + pages = {63}, + doi = {10.3847/1538-3881/ab5b11}, +archivePrefix = {arXiv}, + eprint = {1911.10569}, + primaryClass = {astro-ph.EP}, + adsurl = {https://ui.adsabs.harvard.edu/abs/2020AJ....159...63B}, + adsnote = {Provided by the SAO/NASA Astrophysics Data System} +} + + + +@software{orbitize, + author = {Sarah Blunt and Jason Wang and Henry Ngo and isabelangelo and Devin Cody and TirthDS and vighnesh-nagpal and jorgellop and Robert De Rosa and Sofia Covarrubias and Mireya Arora and Rodrigo Ferrer Ch{\'a}vez and Malena Rice and Lea Hirsch and Adam J. R. W. Smith and Ryan Rubenzahl and Arya Das and hgallamore and Logan Pearce and MissingBrainException and Tomas Stolker and Will Thompson}, + doi = {10.5281/zenodo.8102085}, + month = jun, + publisher = {Zenodo}, + title = {{sblunt/orbitize: tests overwrite previously existing file bugfix}}, + url = {https://doi.org/10.5281/zenodo.8102085}, + version = {2.2.2}, + year = 2023, + bdsk-url-1 = {https://doi.org/10.5281/zenodo.8102085}} diff --git a/paper/paper.md b/paper/paper.md new file mode 100644 index 00000000..a9c946f2 --- /dev/null +++ b/paper/paper.md @@ -0,0 +1,152 @@ +--- +title: 'orbitize! v3: Orbit-fitting for the High-contrast Imaging Community' +tags: + - Python + - astronomy + - orbit-fitting + - exoplanets + - high-contrast imaging +authors: + - name: Sarah Blunt + orcid: 0000-0002-3199-2888 + corresponding: true + affiliation: "1,2" + - name: Jason Wang + affiliation: + - name: Lea Hirsch + affiliation: + - name: Roberto Tejada + affiliation: + - name: Vighnesh Nagpal + affiliation: + - name: Tirth Dharmesh Surti + affiliation: + - name: Sofia Covarrubias + affiliation: + - name: Thea McKenna + affiliation: + - name: Rodrigo Ferrer Chávez + affiliation: + - name: Jorge Llop Sayson + affiliation: + - name: Mireya Arora + affiliation: + - name: Amanda Chavez + affiliation: + - name: Devin Cody + affiliation: + - name: Saanika Choudhary + affiliation: + - name: Adam Smith + affiliation: + - name: William Balmer + affiliation: + - name: Thomas Stolker + affiliation: + - name: Hannah Gallamore + affiliation: + - name: Clarissa Do Ó + affiliation: + - name: Eric Nielsen + affiliation: + - name: Robert de Rosa + affiliation: + +affiliations: + - name: Center for Interdisciplinary Exploration and Research in Astrophysics (CIERA), Northwestern University + index: 1 + - name: California Institute of Technology + index: 2 + +date: 1 March 2024 +bibliography: paper.bib + +--- + +# Summary + +`orbitize!` is a package for Bayesian modeling of the orbital parameters of resolved binary +objects from timeseries measurements. It was developed with the needs of the high-contrast +imaging community in mind, and has since also become widely used in the binary star community. +A generic `orbitize!` use case involves translating relative astrometric timeseries, combined +with auxiliary data and timeseries, into a set of derived orbital posteriors. + +This paper is published alongside the release of `orbitize!` version 3.0, which +has seen significant expansions in functionality and accessibility since the +release of version 1.0 [@Blunt:2020]. + +# Statement of need + +The orbital parameters of directly-imaged planets and binary stars can tell us about +their present-day dynamics and formation histories [@Bowler:2016], as well as about +their inherent physical characteristics (particularly mass, generally called ``dynamical +mass'' when derived from orbital constraints, e.g. [@Brandt:2021], [@Lacour:2021]). + +`orbitize!` is used widely in the imaged exoplanet and binary star communities for +translating astrometric data to information about eccentricities [@Bowler:2020], obliquities [@Bryan:2020], +dynamical masses [@Lacour:2021], and more. + +Each new released version of the `orbitize!` source code is automatically archived on Zenodo [@orbitize]. + +# Major features added since v1 + +For a detailed overview of the `orbitize!` API, core functionality (including information +about our Kepler solver), and initial verification, we refer readers to [@Blunt:2020]. +This section lists major new features that have been added to the +code since the release of version 1.0 and directs readers to more information about each. +A complete descriptive list of modifications to the code is maintained in our +[changelog](https://orbitize.readthedocs.io/en/latest/#changelog). + +Major new features since v1 include: + +1. The ability to jointly fit radial velocity (RV) timeseries, both RVs of the secondary + companion (see Section 3 of [Blunt:2023a]) and RVs of the primary + star. RVs of the primary star can either be passed into `orbitize!` directly (see the [radial velocity tutorial](https://orbitize.readthedocs.io/en/latest/tutorials/RV_MCMC_Tutorial.html)), or fit separately and passed in as prior + information (see the [non-orbitize! posteriors as priors tutorial](https://orbitize.readthedocs.io/en/latest/tutorials/Using_nonOrbitize_Posteriors_as_Priors.html).) + +2. The ability to jointly fit absolute astrometry of the primary star. `orbitize!` can fit + the Hipparcos-Gaia catalog of accelerations [@Brandt:2021] (see the [HGCA tutorial](https://github.com/sblunt/orbitize/blob/v3/docs/tutorials/HGCA_tutorial.ipynb)), as well as Hipparcos intermediate astrometric data and Gaia + astrometry, following [@Nielsen:2020] (see the [Hipparcos IAD tutorial](https://orbitize.readthedocs.io/en/latest/tutorials/Hipparcos_IAD.html)). It can also handle arbitrary absolute astrometry (Sarah to add tutorial link). + +3. In addition to the MCMC and OFTI posterior computation algorithms documented in [@Blunt:2020], + `orbitize!` version 3 also implements a nested sampling backend, via `dynesty` [@Speagle:2020] + (see the [`dynesty` tutorial](https://github.com/sblunt/orbitize/blob/dynesty/docs/tutorials/dynesty_tutorial.ipynb).) + +4. `orbitize!` version 3 implements two prescriptions for handling multi-planet effects. + Keplerian epicyclic motion of the primary star due to multiple orbiting bodies, + following [@Lacour:2021], is discussed in the [multi-planet tutorial](https://orbitize.readthedocs.io/en/latest/tutorials/Multiplanet_Tutorial.html), and N-body interactions are discussed in [@Covarrubias:2022]. + +5. The ability to fit in different orbital bases [@Surti:2023], [@Ferrer-Chavez:2021] (see the + [changing basis](https://orbitize.readthedocs.io/en/latest/tutorials/Changing_bases_tutorial.html) tutorial). + +# Verification and Documentation + +`orbitize!` implements a full stack of automated testing and documentation building +practices. We use GitHub Actions to automatically run a suite of unit tests, maintained in orbitize/tests, +each time code is committed to the public repository or a pull request is opened. The jupyter notebook +tutorials, maintained in orbitize/docs/tutorials, are also automatically run when a +pull request to the `main` branch is opened. Documentation is built using `sphinx`, and hosted +on readthedocs.org at [orbitize.info](https://orbitize.readthedocs.io/en/latest/). We also +maintain a set of longer-running tests in orbitize/tests/end-to-end-tests that show real +scientific use cases of the code. These tests are not automatically run. + +`orbitize!` is documented through API docstrings describing individual functions, which are accessible on [our readthedocs page](https://orbitize.readthedocs.io/en/latest/api.html), a set of [jupyter notebook tutorials](https://orbitize.readthedocs.io/en/latest/tutorials.html) walking the user through a particular application, a set of [frequently asked questions](https://orbitize.readthedocs.io/en/latest/faq.html), +and an in-progress [``manual,''](https://orbitize.readthedocs.io/en/orbitize-manual/manual.html) describing orbit-fitting with `orbitize!` from first principles. + +# Comparison to Similar Packages + +Since the release of `orbitize!` version 1, other open-source packages have been released that have +similar goals to `orbitize!`, notably `orvara` and `octofitter`. This is a wonderful and welcome development! + +Best practices for orbit-fitting, particularly using radial velocities, for which treatment of stellar +activity is an active area of research, and absolute astrometry with Gaia and Hipparcos, for which +correlated error treatment is an active area of research, evolve quickly. The philosophy of `orbitize!` +is to, as much as possible, implement multiple approaches to a problem, evidenced by our multiple +implementations of radial velocity joint fitting and absolute astrometry joint fitting (described above). +For detailed information about our particular implementations, we direct the reader to our documentation. + +# Acknowledgements + +Our team gratefully acknowledges support from NASA and the Heising-Simons Foundation. + +# References \ No newline at end of file From 49b790c238f668f883c8fe92eafa66825d289168 Mon Sep 17 00:00:00 2001 From: Sarah Blunt Date: Fri, 1 Mar 2024 13:57:59 -0600 Subject: [PATCH 02/30] Create joss-compile action --- .github/workflows/joss-compile | 23 +++++++++++++++++++++++ 1 file changed, 23 insertions(+) create mode 100644 .github/workflows/joss-compile diff --git a/.github/workflows/joss-compile b/.github/workflows/joss-compile new file mode 100644 index 00000000..eecf0d13 --- /dev/null +++ b/.github/workflows/joss-compile @@ -0,0 +1,23 @@ +on: [push] + +jobs: + paper: + runs-on: ubuntu-latest + name: Paper Draft + steps: + - name: Checkout + uses: actions/checkout@v4 + - name: Build draft PDF + uses: openjournals/openjournals-draft-action@master + with: + journal: joss + # This should be the path to the paper within your repo. + paper-path: paper/paper.md + - name: Upload + uses: actions/upload-artifact@v1 + with: + name: paper + # This is the output path where Pandoc will write the compiled + # PDF. Note, this should be the same directory as the input + # paper.md + path: paper/paper.pdf From b44c6ad85dfb451dff28155b60e3c46509d4be91 Mon Sep 17 00:00:00 2001 From: Sarah Blunt Date: Fri, 1 Mar 2024 14:13:18 -0600 Subject: [PATCH 03/30] Rename joss-compile to joss-compile.yml --- .github/workflows/{joss-compile => joss-compile.yml} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename .github/workflows/{joss-compile => joss-compile.yml} (100%) diff --git a/.github/workflows/joss-compile b/.github/workflows/joss-compile.yml similarity index 100% rename from .github/workflows/joss-compile rename to .github/workflows/joss-compile.yml From 6a2d9d7f3a9f56769b89db2ec2ae8f835e9ba432 Mon Sep 17 00:00:00 2001 From: Sarah Blunt Date: Thu, 14 Mar 2024 14:34:41 -0700 Subject: [PATCH 04/30] implement jason's comments --- paper/paper.md | 23 +++++++++++++++++------ 1 file changed, 17 insertions(+), 6 deletions(-) diff --git a/paper/paper.md b/paper/paper.md index a9c946f2..ae186d8d 100644 --- a/paper/paper.md +++ b/paper/paper.md @@ -12,7 +12,8 @@ authors: corresponding: true affiliation: "1,2" - name: Jason Wang - affiliation: + orcid: 0000-0003-0774-6502 + affiliation: "1" - name: Lea Hirsch affiliation: - name: Roberto Tejada @@ -68,8 +69,8 @@ bibliography: paper.bib `orbitize!` is a package for Bayesian modeling of the orbital parameters of resolved binary objects from timeseries measurements. It was developed with the needs of the high-contrast imaging community in mind, and has since also become widely used in the binary star community. -A generic `orbitize!` use case involves translating relative astrometric timeseries, combined -with auxiliary data and timeseries, into a set of derived orbital posteriors. +A generic `orbitize!` use case involves translating relative astrometric timeseries, optionally +combined with radial velocity or astrometric timeseries, into a set of derived orbital posteriors. This paper is published alongside the release of `orbitize!` version 3.0, which has seen significant expansions in functionality and accessibility since the @@ -114,7 +115,9 @@ Major new features since v1 include: 4. `orbitize!` version 3 implements two prescriptions for handling multi-planet effects. Keplerian epicyclic motion of the primary star due to multiple orbiting bodies, - following [@Lacour:2021], is discussed in the [multi-planet tutorial](https://orbitize.readthedocs.io/en/latest/tutorials/Multiplanet_Tutorial.html), and N-body interactions are discussed in [@Covarrubias:2022]. + following [@Lacour:2021], is discussed in the [multi-planet tutorial](https://orbitize.readthedocs.io/en/latest/tutorials/Multiplanet_Tutorial.html), and N-body interactions are discussed in [@Covarrubias:2022]. The Keplerian epicyclic motion + prescription only accounts for star-planet interactions, treating the motion of the star as a sum of Keplerians, + while the N-body prescription models this effect as well as planet-planet interactions. 5. The ability to fit in different orbital bases [@Surti:2023], [@Ferrer-Chavez:2021] (see the [changing basis](https://orbitize.readthedocs.io/en/latest/tutorials/Changing_bases_tutorial.html) tutorial). @@ -136,7 +139,14 @@ and an in-progress [``manual,''](https://orbitize.readthedocs.io/en/orbitize-man # Comparison to Similar Packages Since the release of `orbitize!` version 1, other open-source packages have been released that have -similar goals to `orbitize!`, notably `orvara` and `octofitter`. This is a wonderful and welcome development! +similar goals to `orbitize!`, notably `orvara` and `octofitter`. This is a wonderful development, as +each package has benefitted from open sharing of knowledge. `orbitize!`, `orvara`, and `octofitter` can +do many similar things, but each has unique features and strengths; as an example, `octofitter` is +extraordinarily fast, and enables joint astrometry extraction and orbit modeling, while `orbitize!` has unique +abilities to fit arbitrary absolute astrometry (i.e. not from Hipparcos or Gaia) and model data using an N-body backend. +`orvara` analytically marginalizes over parallax assuming a prior informed by Gaia, a significant speed advantage, while +`orbitize!` allows different parallax priors to be used. We recommend users of each package compare the implementations +of the particular features they wish to use. Best practices for orbit-fitting, particularly using radial velocities, for which treatment of stellar activity is an active area of research, and absolute astrometry with Gaia and Hipparcos, for which @@ -147,6 +157,7 @@ For detailed information about our particular implementations, we direct the rea # Acknowledgements -Our team gratefully acknowledges support from NASA and the Heising-Simons Foundation. +Our team gratefully acknowledges support the Heising-Simons Foundation. S.B. and J.J.W. are supported +by NASA Grant 80NSSC23K0280. # References \ No newline at end of file From f63f0b2c22da748fd0c72d2550b8a62f57a13b05 Mon Sep 17 00:00:00 2001 From: Sarah Blunt Date: Thu, 14 Mar 2024 14:40:42 -0700 Subject: [PATCH 05/30] implement tomas' comments --- paper/paper.md | 17 ++++++++++------- 1 file changed, 10 insertions(+), 7 deletions(-) diff --git a/paper/paper.md b/paper/paper.md index ae186d8d..ef92f263 100644 --- a/paper/paper.md +++ b/paper/paper.md @@ -42,8 +42,9 @@ authors: affiliation: - name: William Balmer affiliation: - - name: Thomas Stolker - affiliation: + - name: Tomas Stolker + orcid: 0000-0002-5823-3072 + affiliation: "3" - name: Hannah Gallamore affiliation: - name: Clarissa Do Ó @@ -58,6 +59,8 @@ affiliations: index: 1 - name: California Institute of Technology index: 2 + - name: Leiden Observatory, Leiden University, Niels Bohrweg 2, 2333 CA Leiden, The Netherlands + index: 3 date: 1 March 2024 bibliography: paper.bib @@ -83,7 +86,7 @@ their present-day dynamics and formation histories [@Bowler:2016], as well as ab their inherent physical characteristics (particularly mass, generally called ``dynamical mass'' when derived from orbital constraints, e.g. [@Brandt:2021], [@Lacour:2021]). -`orbitize!` is used widely in the imaged exoplanet and binary star communities for +`orbitize!` is used widely in the exoplanet imaging and binary star communities for translating astrometric data to information about eccentricities [@Bowler:2020], obliquities [@Bryan:2020], dynamical masses [@Lacour:2021], and more. @@ -127,14 +130,14 @@ Major new features since v1 include: `orbitize!` implements a full stack of automated testing and documentation building practices. We use GitHub Actions to automatically run a suite of unit tests, maintained in orbitize/tests, each time code is committed to the public repository or a pull request is opened. The jupyter notebook -tutorials, maintained in orbitize/docs/tutorials, are also automatically run when a +tutorials, maintained in [orbitize/docs/tutorials](https://github.com/sblunt/orbitize/tree/main/docs/tutorials), are also automatically run when a pull request to the `main` branch is opened. Documentation is built using `sphinx`, and hosted on readthedocs.org at [orbitize.info](https://orbitize.readthedocs.io/en/latest/). We also -maintain a set of longer-running tests in orbitize/tests/end-to-end-tests that show real +maintain a set of longer-running tests in [orbitize/tests/end-to-end-tests](https://github.com/sblunt/orbitize/tree/main/tests/end-to-end-tests) that show real scientific use cases of the code. These tests are not automatically run. `orbitize!` is documented through API docstrings describing individual functions, which are accessible on [our readthedocs page](https://orbitize.readthedocs.io/en/latest/api.html), a set of [jupyter notebook tutorials](https://orbitize.readthedocs.io/en/latest/tutorials.html) walking the user through a particular application, a set of [frequently asked questions](https://orbitize.readthedocs.io/en/latest/faq.html), -and an in-progress [``manual,''](https://orbitize.readthedocs.io/en/orbitize-manual/manual.html) describing orbit-fitting with `orbitize!` from first principles. +and an in-progress ["manual"](https://orbitize.readthedocs.io/en/orbitize-manual/manual.html) describing orbit-fitting with `orbitize!` from first principles. # Comparison to Similar Packages @@ -153,7 +156,7 @@ activity is an active area of research, and absolute astrometry with Gaia and Hi correlated error treatment is an active area of research, evolve quickly. The philosophy of `orbitize!` is to, as much as possible, implement multiple approaches to a problem, evidenced by our multiple implementations of radial velocity joint fitting and absolute astrometry joint fitting (described above). -For detailed information about our particular implementations, we direct the reader to our documentation. +For detailed information about our particular implementations, we direct the reader to our [documentation](https://orbitize.readthedocs.io/en/latest/). # Acknowledgements From c4421157a58141584a6cd9f46dd2d683f15dc7c2 Mon Sep 17 00:00:00 2001 From: Sarah Blunt Date: Thu, 14 Mar 2024 14:43:01 -0700 Subject: [PATCH 06/30] typo fix --- paper/paper.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/paper/paper.md b/paper/paper.md index ef92f263..16bfa37c 100644 --- a/paper/paper.md +++ b/paper/paper.md @@ -83,8 +83,8 @@ release of version 1.0 [@Blunt:2020]. The orbital parameters of directly-imaged planets and binary stars can tell us about their present-day dynamics and formation histories [@Bowler:2016], as well as about -their inherent physical characteristics (particularly mass, generally called ``dynamical -mass'' when derived from orbital constraints, e.g. [@Brandt:2021], [@Lacour:2021]). +their inherent physical characteristics (particularly mass, generally called "dynamical +mass" when derived from orbital constraints, e.g. [@Brandt:2021], [@Lacour:2021]). `orbitize!` is used widely in the exoplanet imaging and binary star communities for translating astrometric data to information about eccentricities [@Bowler:2020], obliquities [@Bryan:2020], From d2e46f6ccc4dc5be98f04d5272c846f208f1793c Mon Sep 17 00:00:00 2001 From: Sarah Blunt Date: Thu, 14 Mar 2024 14:49:35 -0700 Subject: [PATCH 07/30] add thea & devin affils --- paper/paper.md | 28 ++++++++++++++++++++++------ 1 file changed, 22 insertions(+), 6 deletions(-) diff --git a/paper/paper.md b/paper/paper.md index 16bfa37c..01fac3e5 100644 --- a/paper/paper.md +++ b/paper/paper.md @@ -21,21 +21,24 @@ authors: - name: Vighnesh Nagpal affiliation: - name: Tirth Dharmesh Surti - affiliation: + affiliation: "5" - name: Sofia Covarrubias affiliation: - name: Thea McKenna - affiliation: + orcid: 0009-0008-0290-2143 + affiliation: "1,6,7,8" - name: Rodrigo Ferrer Chávez affiliation: - - name: Jorge Llop Sayson - affiliation: + - name: Jorge Llop-Sayson + orcid: 0000-0002-3414-784X + affiliation: "4" - name: Mireya Arora affiliation: - name: Amanda Chavez affiliation: - name: Devin Cody - affiliation: + orcid: 0000-0002-7713-5937 + affiliation: "9" - name: Saanika Choudhary affiliation: - name: Adam Smith @@ -59,8 +62,21 @@ affiliations: index: 1 - name: California Institute of Technology index: 2 - - name: Leiden Observatory, Leiden University, Niels Bohrweg 2, 2333 CA Leiden, The Netherlands + - name: Leiden Observatory, Leiden University index: 3 + - name: Jet Propulsion Laboratory, California Institute of Technology + index: 4 + - name: Department of Physics/Kavli Institute for Particle Astrophysics and Cosmology, Stanford University + index: 5 + - name: Southeastern Universities Research Association + index: 6 + - name: Astronomy Department, Cornell University + index: 7 + - name: NASA Goddard Space Flight Center, Code 698 + index: 8 + - name: Google, Inc. + index: 9 + date: 1 March 2024 bibliography: paper.bib From 4b7c5aae3250e021c9b2a553438d5938eb1c3737 Mon Sep 17 00:00:00 2001 From: Sarah Blunt Date: Thu, 14 Mar 2024 14:57:46 -0700 Subject: [PATCH 08/30] address clarissa's comments --- paper/paper.bib | 19 +++++++++++++++++++ paper/paper.md | 10 +++++++--- 2 files changed, 26 insertions(+), 3 deletions(-) diff --git a/paper/paper.bib b/paper/paper.bib index c4577696..2de9b0f2 100644 --- a/paper/paper.bib +++ b/paper/paper.bib @@ -17,6 +17,25 @@ @ARTICLE{Blunt:2020 adsnote = {Provided by the SAO/NASA Astrophysics Data System} } +@ARTICLE{ONeil:2019, + author = {{O'Neil}, K. Kosmo and {Martinez}, G.~D. and {Hees}, A. and {Ghez}, A.~M. and {Do}, T. and {Witzel}, G. and {Konopacky}, Q. and {Becklin}, E.~E. and {Chu}, D.~S. and {Lu}, J.~R. and {Matthews}, K. and {Sakai}, S.}, + title = "{Improving Orbit Estimates for Incomplete Orbits with a New Approach to Priors: with Applications from Black Holes to Planets}", + journal = {\aj}, + keywords = {Galaxy: center, Galaxy: fundamental parameters, methods: statistical, planets and satellites: fundamental parameters, Astrophysics - Earth and Planetary Astrophysics, Astrophysics - Astrophysics of Galaxies}, + year = 2019, + month = jul, + volume = {158}, + number = {1}, + eid = {4}, + pages = {4}, + doi = {10.3847/1538-3881/ab1d66}, +archivePrefix = {arXiv}, + eprint = {1809.05490}, + primaryClass = {astro-ph.EP}, + adsurl = {https://ui.adsabs.harvard.edu/abs/2019AJ....158....4O}, + adsnote = {Provided by the SAO/NASA Astrophysics Data System} +} + @ARTICLE{Bryan:2020, author = {{Bryan}, Marta L. and {Chiang}, Eugene and {Bowler}, Brendan P. and {Morley}, Caroline V. and {Millholland}, Sarah and {Blunt}, Sarah and {Ashok}, Katelyn B. and {Nielsen}, Eric and {Ngo}, Henry and {Mawet}, Dimitri and {Knutson}, Heather A.}, title = "{Obliquity Constraints on an Extrasolar Planetary-mass Companion}", diff --git a/paper/paper.md b/paper/paper.md index 01fac3e5..60a2caf7 100644 --- a/paper/paper.md +++ b/paper/paper.md @@ -50,8 +50,9 @@ authors: affiliation: "3" - name: Hannah Gallamore affiliation: - - name: Clarissa Do Ó - affiliation: + - name: Clarissa R. Do Ó + orcid: 0000-0001-5173-2947 + affiliation: "10" - name: Eric Nielsen affiliation: - name: Robert de Rosa @@ -76,6 +77,8 @@ affiliations: index: 8 - name: Google, Inc. index: 9 + - name: Department of Astronomy & Astrophysics, University of California San Diego + index: 10 date: 1 March 2024 @@ -139,7 +142,8 @@ Major new features since v1 include: while the N-body prescription models this effect as well as planet-planet interactions. 5. The ability to fit in different orbital bases [@Surti:2023], [@Ferrer-Chavez:2021] (see the - [changing basis](https://orbitize.readthedocs.io/en/latest/tutorials/Changing_bases_tutorial.html) tutorial). + [changing basis](https://orbitize.readthedocs.io/en/latest/tutorials/Changing_bases_tutorial.html) tutorial), as well + as the ability to apply the observation-based priors derived in [@ONeil:2019] (see the [observation-based priors tutorial](https://github.com/sblunt/orbitize/blob/main/docs/tutorials/ONeil-ObsPriors.ipynb)). # Verification and Documentation From 009cf4fe3ef54b60cc2ac16efdcb9abf55f231f8 Mon Sep 17 00:00:00 2001 From: Sarah Blunt Date: Thu, 14 Mar 2024 14:59:44 -0700 Subject: [PATCH 09/30] add jason's middle name --- paper/paper.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/paper/paper.md b/paper/paper.md index 60a2caf7..2c400df1 100644 --- a/paper/paper.md +++ b/paper/paper.md @@ -11,7 +11,7 @@ authors: orcid: 0000-0002-3199-2888 corresponding: true affiliation: "1,2" - - name: Jason Wang + - name: Jason Jinfei Wang orcid: 0000-0003-0774-6502 affiliation: "1" - name: Lea Hirsch From 5cd8d51c5fc3f960a60604d27738a9d943ddf219 Mon Sep 17 00:00:00 2001 From: Sarah Blunt Date: Thu, 14 Mar 2024 15:02:21 -0700 Subject: [PATCH 10/30] cite octofitter & orvara --- paper/paper.bib | 42 ++++++++++++++++++++++++++++++++++++++++++ paper/paper.md | 3 +-- 2 files changed, 43 insertions(+), 2 deletions(-) diff --git a/paper/paper.bib b/paper/paper.bib index 2de9b0f2..8d5b981b 100644 --- a/paper/paper.bib +++ b/paper/paper.bib @@ -17,6 +17,48 @@ @ARTICLE{Blunt:2020 adsnote = {Provided by the SAO/NASA Astrophysics Data System} } +@ARTICLE{Thompson:2023, + author = {{Thompson}, William and {Lawrence}, Jensen and {Blakely}, Dori and {Marois}, Christian and {Wang}, Jason and {Giordano}, Mos{\'e} and {Brandt}, Timothy and {Johnstone}, Doug and {Ruffio}, Jean-Baptiste and {Ammons}, S. Mark and {Crotts}, Katie A. and {Do {\'O}}, Clarissa R. and {Gonzales}, Eileen C. and {Rice}, Malena}, + title = "{Octofitter: Fast, Flexible, and Accurate Orbit Modeling to Detect Exoplanets}", + journal = {\aj}, + keywords = {Exoplanet detection methods, Bayesian statistics, Direct imaging, 489, 1900, 387, Astrophysics - Earth and Planetary Astrophysics, Astrophysics - Instrumentation and Methods for Astrophysics}, + year = 2023, + month = oct, + volume = {166}, + number = {4}, + eid = {164}, + pages = {164}, + doi = {10.3847/1538-3881/acf5cc}, +archivePrefix = {arXiv}, + eprint = {2402.01971}, + primaryClass = {astro-ph.EP}, + adsurl = {https://ui.adsabs.harvard.edu/abs/2023AJ....166..164T}, + adsnote = {Provided by the SAO/NASA Astrophysics Data System} +} + + + +@ARTICLE{Brandt:2021, + author = {{Brandt}, Timothy D. and {Dupuy}, Trent J. and {Li}, Yiting and {Brandt}, G. Mirek and {Zeng}, Yunlin and {Michalik}, Daniel and {Bardalez Gagliuffi}, Daniella C. and {Raposo-Pulido}, Virginia}, + title = "{orvara: An Efficient Code to Fit Orbits Using Radial Velocity, Absolute, and/or Relative Astrometry}", + journal = {\aj}, + keywords = {Orbit determination, Keplerian orbit, Astronomy software, Exoplanet astronomy, Astrometric exoplanet detection, Radial velocity, 1175, 884, 1855, 486, 2130, 1332, Astrophysics - Instrumentation and Methods for Astrophysics, Astrophysics - Earth and Planetary Astrophysics, Astrophysics - Solar and Stellar Astrophysics}, + year = 2021, + month = nov, + volume = {162}, + number = {5}, + eid = {186}, + pages = {186}, + doi = {10.3847/1538-3881/ac042e}, +archivePrefix = {arXiv}, + eprint = {2105.11671}, + primaryClass = {astro-ph.IM}, + adsurl = {https://ui.adsabs.harvard.edu/abs/2021AJ....162..186B}, + adsnote = {Provided by the SAO/NASA Astrophysics Data System} +} + + + @ARTICLE{ONeil:2019, author = {{O'Neil}, K. Kosmo and {Martinez}, G.~D. and {Hees}, A. and {Ghez}, A.~M. and {Do}, T. and {Witzel}, G. and {Konopacky}, Q. and {Becklin}, E.~E. and {Chu}, D.~S. and {Lu}, J.~R. and {Matthews}, K. and {Sakai}, S.}, title = "{Improving Orbit Estimates for Incomplete Orbits with a New Approach to Priors: with Applications from Black Holes to Planets}", diff --git a/paper/paper.md b/paper/paper.md index 2c400df1..4a8e8b5e 100644 --- a/paper/paper.md +++ b/paper/paper.md @@ -162,8 +162,7 @@ and an in-progress ["manual"](https://orbitize.readthedocs.io/en/orbitize-manual # Comparison to Similar Packages Since the release of `orbitize!` version 1, other open-source packages have been released that have -similar goals to `orbitize!`, notably `orvara` and `octofitter`. This is a wonderful development, as -each package has benefitted from open sharing of knowledge. `orbitize!`, `orvara`, and `octofitter` can +similar goals to `orbitize!`, notably `orvara` [@Brandt:2021] and `octofitter` [@Thompson:2023]. This is a wonderful development, since all packages benefit from open sharing of knowledge! `orbitize!`, `orvara`, and `octofitter` can do many similar things, but each has unique features and strengths; as an example, `octofitter` is extraordinarily fast, and enables joint astrometry extraction and orbit modeling, while `orbitize!` has unique abilities to fit arbitrary absolute astrometry (i.e. not from Hipparcos or Gaia) and model data using an N-body backend. From e10fa1de3fb8caabf3a2160f78742898a8eeda37 Mon Sep 17 00:00:00 2001 From: Sarah Blunt Date: Thu, 14 Mar 2024 15:09:55 -0700 Subject: [PATCH 11/30] add everyone's affilitions --- paper/paper.md | 46 ++++++++++++++++++++++++++++++---------------- 1 file changed, 30 insertions(+), 16 deletions(-) diff --git a/paper/paper.md b/paper/paper.md index 4a8e8b5e..4aefe61c 100644 --- a/paper/paper.md +++ b/paper/paper.md @@ -15,48 +15,48 @@ authors: orcid: 0000-0003-0774-6502 affiliation: "1" - name: Lea Hirsch - affiliation: + affiliation: "11" - name: Roberto Tejada - affiliation: + affiliation: "12" - name: Vighnesh Nagpal - affiliation: + affiliation: "13" - name: Tirth Dharmesh Surti affiliation: "5" - name: Sofia Covarrubias - affiliation: + affiliation: "2" - name: Thea McKenna orcid: 0009-0008-0290-2143 affiliation: "1,6,7,8" - name: Rodrigo Ferrer Chávez - affiliation: + affiliation: "1" - name: Jorge Llop-Sayson orcid: 0000-0002-3414-784X affiliation: "4" - name: Mireya Arora - affiliation: + affiliation: "14" - name: Amanda Chavez - affiliation: + affiliation: "1" - name: Devin Cody orcid: 0000-0002-7713-5937 affiliation: "9" - name: Saanika Choudhary - affiliation: + affiliation: "1" - name: Adam Smith - affiliation: + affiliation: "15" - name: William Balmer - affiliation: + affiliation: "16" - name: Tomas Stolker orcid: 0000-0002-5823-3072 affiliation: "3" - name: Hannah Gallamore - affiliation: + affiliation: "15" - name: Clarissa R. Do Ó orcid: 0000-0001-5173-2947 affiliation: "10" - name: Eric Nielsen - affiliation: + affiliation: "15" - name: Robert de Rosa - affiliation: + affiliation: "17" affiliations: - name: Center for Interdisciplinary Exploration and Research in Astrophysics (CIERA), Northwestern University @@ -79,9 +79,23 @@ affiliations: index: 9 - name: Department of Astronomy & Astrophysics, University of California San Diego index: 10 - - -date: 1 March 2024 + - name: Department of Chemical & Physical Sciences, University of Toronto Mississauga + index: 11 + - name: Department of Astrophysical Sciences, Princeton University + index: 12 + - name: University of California, Berkeley + index: 13 + - name: University of Michigan + index: 14 + - name: New Mexico State University + index: 15 + - name: Johns Hopkins University + index: 16 + - name: European Southern Observatory + index: 17 + + +date: 14 March 2024 bibliography: paper.bib --- From dbf3023a8b0ee510a78062ed41f7e02cacfb0ff4 Mon Sep 17 00:00:00 2001 From: Sarah Blunt Date: Thu, 14 Mar 2024 15:44:27 -0700 Subject: [PATCH 12/30] add sofia's orcid --- paper/paper.md | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/paper/paper.md b/paper/paper.md index 4aefe61c..e6bc0d11 100644 --- a/paper/paper.md +++ b/paper/paper.md @@ -23,6 +23,7 @@ authors: - name: Tirth Dharmesh Surti affiliation: "5" - name: Sofia Covarrubias + orcid: 0000-0003-1858-561X affiliation: "2" - name: Thea McKenna orcid: 0009-0008-0290-2143 @@ -196,4 +197,4 @@ For detailed information about our particular implementations, we direct the rea Our team gratefully acknowledges support the Heising-Simons Foundation. S.B. and J.J.W. are supported by NASA Grant 80NSSC23K0280. -# References \ No newline at end of file +# References From 9fa935cd8ab6f1d0d112b53345d541809ec29420 Mon Sep 17 00:00:00 2001 From: Sarah Blunt Date: Wed, 27 Mar 2024 15:18:42 -0700 Subject: [PATCH 13/30] add rob's orcid --- paper/paper.md | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/paper/paper.md b/paper/paper.md index e6bc0d11..ee48f641 100644 --- a/paper/paper.md +++ b/paper/paper.md @@ -56,7 +56,8 @@ authors: affiliation: "10" - name: Eric Nielsen affiliation: "15" - - name: Robert de Rosa + - name: Robert J. De Rosa + orcid: 0000-0002-4918-0247 affiliation: "17" affiliations: From 0b8f27b2fadd0a5491897a39047c248984944a42 Mon Sep 17 00:00:00 2001 From: Sarah Blunt Date: Wed, 29 May 2024 18:35:56 -0700 Subject: [PATCH 14/30] add note about installing from git and a little snark --- docs/installation.rst | 13 +++++++++++++ 1 file changed, 13 insertions(+) diff --git a/docs/installation.rst b/docs/installation.rst index cb69ee3b..869dc218 100644 --- a/docs/installation.rst +++ b/docs/installation.rst @@ -3,6 +3,19 @@ Installation ============ +Important Temporary Note +++++++++++++++++++++++++ +Sarah has been locked out of her pypi.org account (???) which means that you can't pip install +the latest version of `orbitize`. If you want to install version 3, you can install the +version of the code on github using: + +.. code-block:: bash + + $ pip install git+https://github.com/sblunt/orbitize.git + +If you're reading this, please upvote Sarah's request to reinstate her pypi.org account: https://github.com/pypi/support/issues/3898 + + For Users +++++++++ From 01453853bd87429a288032e5c2d85e107b3558e5 Mon Sep 17 00:00:00 2001 From: Sarah Blunt Date: Mon, 12 Aug 2024 11:47:03 -0700 Subject: [PATCH 15/30] fix for Result File From Resumed MCMC Fails to Save #370 --- orbitize/results.py | 8 +++----- 1 file changed, 3 insertions(+), 5 deletions(-) diff --git a/orbitize/results.py b/orbitize/results.py index ba502574..cecacaff 100644 --- a/orbitize/results.py +++ b/orbitize/results.py @@ -197,7 +197,7 @@ def load_results(self, filename, append=False): iad_data = hf.get("IAD_datafile") if iad_data is not None: - tmpfile = 'thisisprettyhackysorrylmao' + tmpfile = 'tmpfile_OkToDeleteAfterFitFinishes' with open(tmpfile, 'w+') as f: try: for l in np.array(iad_data): @@ -218,8 +218,6 @@ def load_results(self, filename, append=False): renormalize_errors, ) - os.system('rm {}'.format(tmpfile)) - # load Gaia data try: gaia_num = int(hf.attrs['gaia_num']) @@ -232,14 +230,14 @@ def load_results(self, filename, append=False): gaiagost_data = hf.get("Gaia_GOST") if gaiagost_data is not None: - tmpfile = 'thisisprettyhackysorrylmao' + tmpfile = 'tmpfile_OkToDeleteAfterFitFinishes' tmptbl = table.Table(np.array(gaiagost_data)) tmptbl.write(tmpfile, format="ascii", overwrite=True) gaia = orbitize.gaia.HGCALogProb(int(hip_num), hipparcos_IAD, tmpfile) hipparcos_IAD = None # HGCA handles hipparocs, so don't want to pass Hipparcos also into the system - os.system('rm {}'.format(tmpfile)) + else: hipparcos_IAD = None gaia = None From 717eed837d2d50763a0433096aa463191e7258e5 Mon Sep 17 00:00:00 2001 From: Sarah Blunt Date: Mon, 12 Aug 2024 11:51:07 -0700 Subject: [PATCH 16/30] extend hipparcos unit test to cover situation in #370 --- tests/test_hipparcos.py | 3 +++ 1 file changed, 3 insertions(+) diff --git a/tests/test_hipparcos.py b/tests/test_hipparcos.py index cb39df40..ebe1012d 100644 --- a/tests/test_hipparcos.py +++ b/tests/test_hipparcos.py @@ -258,6 +258,9 @@ def test_save_load_2021(): myResults = results.Results() myResults.load_results(filename) + filename = "tmp3.hdf5" + myResults.results.saveresults(filename) + os.system("rm tmp*.hdf5") From f87b66fc0ccf6e3e15d103ceba2139dbbe694cf3 Mon Sep 17 00:00:00 2001 From: Sarah Blunt Date: Mon, 12 Aug 2024 12:49:13 -0700 Subject: [PATCH 17/30] typo in unit test fixed --- tests/test_hipparcos.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tests/test_hipparcos.py b/tests/test_hipparcos.py index ebe1012d..f6693e51 100644 --- a/tests/test_hipparcos.py +++ b/tests/test_hipparcos.py @@ -259,7 +259,7 @@ def test_save_load_2021(): myResults.load_results(filename) filename = "tmp3.hdf5" - myResults.results.saveresults(filename) + myResults.saveresults(filename) os.system("rm tmp*.hdf5") From 63383fb037ce41f45278555bfe78926a7d6e4329 Mon Sep 17 00:00:00 2001 From: Sarah Blunt Date: Tue, 13 Aug 2024 16:32:05 -0700 Subject: [PATCH 18/30] fixed another typo (and ran test on my machine this time to make sure) --- tests/test_hipparcos.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/tests/test_hipparcos.py b/tests/test_hipparcos.py index f6693e51..08299835 100644 --- a/tests/test_hipparcos.py +++ b/tests/test_hipparcos.py @@ -259,9 +259,9 @@ def test_save_load_2021(): myResults.load_results(filename) filename = "tmp3.hdf5" - myResults.saveresults(filename) + myResults.save_results(filename) - os.system("rm tmp*.hdf5") + os.system("rm tmp*") if __name__ == "__main__": From 207a032d350eb7553c93ef58176ef5f46f42c8c8 Mon Sep 17 00:00:00 2001 From: Sarah Blunt Date: Mon, 19 Aug 2024 10:53:04 -0700 Subject: [PATCH 19/30] remove temporary install instructions now that I have access to pypi again *bless* --- docs/installation.rst | 13 ------------- 1 file changed, 13 deletions(-) diff --git a/docs/installation.rst b/docs/installation.rst index 869dc218..cb69ee3b 100644 --- a/docs/installation.rst +++ b/docs/installation.rst @@ -3,19 +3,6 @@ Installation ============ -Important Temporary Note -++++++++++++++++++++++++ -Sarah has been locked out of her pypi.org account (???) which means that you can't pip install -the latest version of `orbitize`. If you want to install version 3, you can install the -version of the code on github using: - -.. code-block:: bash - - $ pip install git+https://github.com/sblunt/orbitize.git - -If you're reading this, please upvote Sarah's request to reinstate her pypi.org account: https://github.com/pypi/support/issues/3898 - - For Users +++++++++ From ab6fcba9a5705f47a2f9eb44358a8152cd67d4d1 Mon Sep 17 00:00:00 2001 From: Sarah Blunt Date: Mon, 19 Aug 2024 10:55:10 -0700 Subject: [PATCH 20/30] update changelog for 3.0.1 --- docs/index.rst | 4 ++++ orbitize/__init__.py | 2 +- 2 files changed, 5 insertions(+), 1 deletion(-) diff --git a/docs/index.rst b/docs/index.rst index a6ae3821..327fb51f 100644 --- a/docs/index.rst +++ b/docs/index.rst @@ -55,6 +55,10 @@ User Guide: Changelog: ++++++++++ +**3.0.1 (2024-8-19)** + +- bugfix for issue #370 involving saving and loading hipparcos.py objects (@sblunt) + **3.0.0 (2024-4-15)** - implementation of Hipparcos-Gaia catalog of accelerations fitting! (@semaphoreP) diff --git a/orbitize/__init__.py b/orbitize/__init__.py index 4f31da90..1bebb014 100644 --- a/orbitize/__init__.py +++ b/orbitize/__init__.py @@ -1,6 +1,6 @@ import os -__version__ = "3.0.0" +__version__ = "3.0.1" # set Python env variable to keep track of example data dir orbitize_dir = os.path.dirname(__file__) From 402b78c18eda56f773e3ca8d33cc73009de0aec2 Mon Sep 17 00:00:00 2001 From: Sarah Blunt Date: Mon, 19 Aug 2024 11:41:28 -0700 Subject: [PATCH 21/30] separate out requirements & orbitize install commands in install instructions --- docs/installation.rst | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/docs/installation.rst b/docs/installation.rst index cb69ee3b..e7ab5c92 100644 --- a/docs/installation.rst +++ b/docs/installation.rst @@ -87,7 +87,8 @@ of the repo: .. code-block:: bash - $ pip install -r requirements.txt -e . + $ pip install -r requirements.txt + $ pip install -e . --upgrade Issues? +++++++ From 96ad737e44bd3d75dbd9e3f7f8bc113ab49513f1 Mon Sep 17 00:00:00 2001 From: Sarah Blunt Date: Wed, 21 Aug 2024 11:35:20 -0700 Subject: [PATCH 22/30] fixing some formatting bugs in joss paper --- paper/paper.bib | 21 ++++++++++++--------- paper/paper.md | 24 ++++++++++++------------ 2 files changed, 24 insertions(+), 21 deletions(-) diff --git a/paper/paper.bib b/paper/paper.bib index 8d5b981b..55f393e1 100644 --- a/paper/paper.bib +++ b/paper/paper.bib @@ -193,7 +193,7 @@ @ARTICLE{Nielsen:2020 -@ARTICLE{Blunt:2023, +@ARTICLE{Blunt:2023a, author = {{Blunt}, Sarah and {Balmer}, W.~O. and {Wang}, J.~J. and {Lacour}, S. and {Petrus}, S. and {Bourdarot}, G. and {Kammerer}, J. and {Pourr{\'e}}, N. and {Rickman}, E. and {Shangguan}, J. and {Winterhalder}, T. and {Abuter}, R. and {Amorim}, A. and {Asensio-Torres}, R. and {Benisty}, M. and {Berger}, J. -P. and {Beust}, H. and {Boccaletti}, A. and {Bohn}, A. and {Bonnefoy}, M. and {Bonnet}, H. and {Brandner}, W. and {Cantalloube}, F. and {Caselli}, P. and {Charnay}, B. and {Chauvin}, G. and {Chavez}, A. and {Choquet}, E. and {Christiaens}, V. and {Cl{\'e}net}, Y. and {Du Foresto}, V. Coud{\'e} and {Cridland}, A. and {Dembet}, R. and {Drescher}, A. and {Duvert}, G. and {Eckart}, A. and {Eisenhauer}, F. and {Feuchtgruber}, H. and {Garcia}, P. and {Garcia Lopez}, R. and {Gendron}, E. and {Genzel}, R. and {Gillessen}, S. and {Girard}, J.~H. and {Haubois}, X. and {Hei{\ss}el}, G. and {Henning}, Th. and {Hinkley}, S. and {Hippler}, S. and {Horrobin}, M. and {Houll{\'e}}, M. and {Hubert}, Z. and {Jocou}, L. and {Keppler}, M. and {Kervella}, P. and {Kreidberg}, L. and {Lagrange}, A. -M. and {Lapeyr{\`e}re}, V. and {Le Bouquin}, J. -B. and {L{\'e}na}, P. and {Lutz}, D. and {Maire}, A. -L. and {Mang}, F. and {Marleau}, G. -D. and {M{\'e}rand}, A. and {Molli{\`e}re}, P. and {Monnier}, J.~D. and {Mordasini}, C. and {Mouillet}, D. and {Nasedkin}, E. and {Nowak}, M. and {Ott}, T. and {Otten}, G.~P.~P.~L. and {Paladini}, C. and {Paumard}, T. and {Perraut}, K. and {Perrin}, G. and {Pfuhl}, O. and {Pueyo}, L. and {Rameau}, J. and {Rodet}, L. and {Rustamkulov}, Z. and {Shimizu}, T. and {Sing}, D. and {Stolker}, T. and {Straubmeier}, C. and {Sturm}, E. and {Tacconi}, L.~J. and {van Dishoeck}, E.~F. and {Vigan}, A. and {Vincent}, F. and {Ward-Duong}, K. and {Widmann}, F. and {Wieprecht}, E. and {Wiezorrek}, E. and {Woillez}, J. and {Yazici}, S. and {Young}, A. and {Exogravity Collaboration}}, title = "{First VLTI/GRAVITY Observations of HIP 65426 b: Evidence for a Low or Moderate Orbital Eccentricity}", journal = {\aj}, @@ -291,13 +291,16 @@ @ARTICLE{Bowler:2020 + @software{orbitize, - author = {Sarah Blunt and Jason Wang and Henry Ngo and isabelangelo and Devin Cody and TirthDS and vighnesh-nagpal and jorgellop and Robert De Rosa and Sofia Covarrubias and Mireya Arora and Rodrigo Ferrer Ch{\'a}vez and Malena Rice and Lea Hirsch and Adam J. R. W. Smith and Ryan Rubenzahl and Arya Das and hgallamore and Logan Pearce and MissingBrainException and Tomas Stolker and Will Thompson}, - doi = {10.5281/zenodo.8102085}, - month = jun, + author = {Sarah Blunt and Jason Wang and Henry Ngo and isabelangelo and Devin Cody and TirthDS and vighneshnagpal and Sofia Covarrubias and thea-mckenna and jorgellop and Robert De Rosa and Mireya Arora and Rodrigo Ferrer-Ch{\'a}vez and Malena Rice and William O Balmer and Lea Hirsch and Adam J. R. W. Smith and Dino Chih-Chun Hsu and Michael Poon and Ryan Rubenzahl and Arya Das and Clarissa Rizzo Credidio Do O and hgallamore and Logan Pearce and MissingBrainException and Saanikachoudhary and Tomas Stolker and William Thompson and wcroberson}, + date-modified = {2024-08-21 11:28:42 -0700}, + doi = {10.5281/zenodo.1475226}, + month = aug, publisher = {Zenodo}, - title = {{sblunt/orbitize: tests overwrite previously existing file bugfix}}, - url = {https://doi.org/10.5281/zenodo.8102085}, - version = {2.2.2}, - year = 2023, - bdsk-url-1 = {https://doi.org/10.5281/zenodo.8102085}} + title = {{sblunt/orbitize: Hotfix for hipparcos saving/loading bug}}, + url = {https://doi.org/10.5281/zenodo.1475226}, + version = {v3.0.1}, + year = 2024, + bdsk-url-1 = {https://doi.org/10.5281/zenodo.1475226}} + diff --git a/paper/paper.md b/paper/paper.md index ee48f641..b4304927 100644 --- a/paper/paper.md +++ b/paper/paper.md @@ -119,7 +119,7 @@ release of version 1.0 [@Blunt:2020]. The orbital parameters of directly-imaged planets and binary stars can tell us about their present-day dynamics and formation histories [@Bowler:2016], as well as about their inherent physical characteristics (particularly mass, generally called "dynamical -mass" when derived from orbital constraints, e.g. [@Brandt:2021], [@Lacour:2021]). +mass" when derived from orbital constraints, e.g. @Brandt:2021, @Lacour:2021). `orbitize!` is used widely in the exoplanet imaging and binary star communities for translating astrometric data to information about eccentricities [@Bowler:2020], obliquities [@Bryan:2020], @@ -130,7 +130,7 @@ Each new released version of the `orbitize!` source code is automatically archiv # Major features added since v1 For a detailed overview of the `orbitize!` API, core functionality (including information -about our Kepler solver), and initial verification, we refer readers to [@Blunt:2020]. +about our Kepler solver), and initial verification, we refer readers to @Blunt:2020. This section lists major new features that have been added to the code since the release of version 1.0 and directs readers to more information about each. A complete descriptive list of modifications to the code is maintained in our @@ -139,32 +139,32 @@ A complete descriptive list of modifications to the code is maintained in our Major new features since v1 include: 1. The ability to jointly fit radial velocity (RV) timeseries, both RVs of the secondary - companion (see Section 3 of [Blunt:2023a]) and RVs of the primary + companion (see Section 3 of @Blunt:2023a) and RVs of the primary star. RVs of the primary star can either be passed into `orbitize!` directly (see the [radial velocity tutorial](https://orbitize.readthedocs.io/en/latest/tutorials/RV_MCMC_Tutorial.html)), or fit separately and passed in as prior information (see the [non-orbitize! posteriors as priors tutorial](https://orbitize.readthedocs.io/en/latest/tutorials/Using_nonOrbitize_Posteriors_as_Priors.html).) 2. The ability to jointly fit absolute astrometry of the primary star. `orbitize!` can fit - the Hipparcos-Gaia catalog of accelerations [@Brandt:2021] (see the [HGCA tutorial](https://github.com/sblunt/orbitize/blob/v3/docs/tutorials/HGCA_tutorial.ipynb)), as well as Hipparcos intermediate astrometric data and Gaia - astrometry, following [@Nielsen:2020] (see the [Hipparcos IAD tutorial](https://orbitize.readthedocs.io/en/latest/tutorials/Hipparcos_IAD.html)). It can also handle arbitrary absolute astrometry (Sarah to add tutorial link). + the Hipparcos-Gaia catalog of accelerations (@Brandt:2021; see the [HGCA tutorial](https://github.com/sblunt/orbitize/blob/v3/docs/tutorials/HGCA_tutorial.ipynb)), as well as Hipparcos intermediate astrometric data and Gaia + astrometry, following @Nielsen:2020 (see the [Hipparcos IAD tutorial](https://orbitize.readthedocs.io/en/latest/tutorials/Hipparcos_IAD.html)). It can also handle arbitrary absolute astrometry (see the [Fitting Arbitrary Astrometry tutorial](https://orbitize.readthedocs.io/en/latest/tutorials/abs_astrometry.html)). -3. In addition to the MCMC and OFTI posterior computation algorithms documented in [@Blunt:2020], - `orbitize!` version 3 also implements a nested sampling backend, via `dynesty` [@Speagle:2020] - (see the [`dynesty` tutorial](https://github.com/sblunt/orbitize/blob/dynesty/docs/tutorials/dynesty_tutorial.ipynb).) +3. In addition to the MCMC and OFTI posterior computation algorithms documented in @Blunt:2020, + `orbitize!` version 3 also implements a nested sampling backend, via `dynesty` + (@Speagle:2020; see the [`dynesty` tutorial](https://github.com/sblunt/orbitize/blob/dynesty/docs/tutorials/dynesty_tutorial.ipynb).) 4. `orbitize!` version 3 implements two prescriptions for handling multi-planet effects. Keplerian epicyclic motion of the primary star due to multiple orbiting bodies, - following [@Lacour:2021], is discussed in the [multi-planet tutorial](https://orbitize.readthedocs.io/en/latest/tutorials/Multiplanet_Tutorial.html), and N-body interactions are discussed in [@Covarrubias:2022]. The Keplerian epicyclic motion + following @Lacour:2021, is discussed in the [multi-planet tutorial](https://orbitize.readthedocs.io/en/latest/tutorials/Multiplanet_Tutorial.html), and N-body interactions are discussed in @Covarrubias:2022. The Keplerian epicyclic motion prescription only accounts for star-planet interactions, treating the motion of the star as a sum of Keplerians, while the N-body prescription models this effect as well as planet-planet interactions. -5. The ability to fit in different orbital bases [@Surti:2023], [@Ferrer-Chavez:2021] (see the +5. The ability to fit in different orbital bases (@Ferrer-Chavez:2021, @Surti:2023; see the [changing basis](https://orbitize.readthedocs.io/en/latest/tutorials/Changing_bases_tutorial.html) tutorial), as well - as the ability to apply the observation-based priors derived in [@ONeil:2019] (see the [observation-based priors tutorial](https://github.com/sblunt/orbitize/blob/main/docs/tutorials/ONeil-ObsPriors.ipynb)). + as the ability to apply the observation-based priors derived in @ONeil:2019 (see the [observation-based priors tutorial](https://github.com/sblunt/orbitize/blob/main/docs/tutorials/ONeil-ObsPriors.ipynb)). # Verification and Documentation `orbitize!` implements a full stack of automated testing and documentation building -practices. We use GitHub Actions to automatically run a suite of unit tests, maintained in orbitize/tests, +practices. We use GitHub Actions to automatically run a suite of unit tests, maintained in [orbitize/tests]((https://github.com/sblunt/orbitize/tree/main/tests)), each time code is committed to the public repository or a pull request is opened. The jupyter notebook tutorials, maintained in [orbitize/docs/tutorials](https://github.com/sblunt/orbitize/tree/main/docs/tutorials), are also automatically run when a pull request to the `main` branch is opened. Documentation is built using `sphinx`, and hosted From d1636c10c803302882595c03641c48785d1631fc Mon Sep 17 00:00:00 2001 From: Sarah Blunt Date: Wed, 21 Aug 2024 11:41:44 -0700 Subject: [PATCH 23/30] two more typo fixes --- paper/paper.md | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/paper/paper.md b/paper/paper.md index b4304927..50f58c4a 100644 --- a/paper/paper.md +++ b/paper/paper.md @@ -148,8 +148,7 @@ Major new features since v1 include: astrometry, following @Nielsen:2020 (see the [Hipparcos IAD tutorial](https://orbitize.readthedocs.io/en/latest/tutorials/Hipparcos_IAD.html)). It can also handle arbitrary absolute astrometry (see the [Fitting Arbitrary Astrometry tutorial](https://orbitize.readthedocs.io/en/latest/tutorials/abs_astrometry.html)). 3. In addition to the MCMC and OFTI posterior computation algorithms documented in @Blunt:2020, - `orbitize!` version 3 also implements a nested sampling backend, via `dynesty` - (@Speagle:2020; see the [`dynesty` tutorial](https://github.com/sblunt/orbitize/blob/dynesty/docs/tutorials/dynesty_tutorial.ipynb).) + `orbitize!` version 3 also implements a nested sampling backend, via `dynesty` (@Speagle:2020; see the [`dynesty` tutorial](https://github.com/sblunt/orbitize/blob/dynesty/docs/tutorials/dynesty_tutorial.ipynb).) 4. `orbitize!` version 3 implements two prescriptions for handling multi-planet effects. Keplerian epicyclic motion of the primary star due to multiple orbiting bodies, @@ -164,7 +163,7 @@ Major new features since v1 include: # Verification and Documentation `orbitize!` implements a full stack of automated testing and documentation building -practices. We use GitHub Actions to automatically run a suite of unit tests, maintained in [orbitize/tests]((https://github.com/sblunt/orbitize/tree/main/tests)), +practices. We use GitHub Actions to automatically run a suite of unit tests, maintained in [orbitize/tests](https://github.com/sblunt/orbitize/tree/main/tests), each time code is committed to the public repository or a pull request is opened. The jupyter notebook tutorials, maintained in [orbitize/docs/tutorials](https://github.com/sblunt/orbitize/tree/main/docs/tutorials), are also automatically run when a pull request to the `main` branch is opened. Documentation is built using `sphinx`, and hosted From b42ac6d1e44089ebf74bb6ea7eb701c7ffed2289 Mon Sep 17 00:00:00 2001 From: Sarah Blunt Date: Wed, 21 Aug 2024 11:55:07 -0700 Subject: [PATCH 24/30] add vighnesh orcid --- paper/paper.md | 1 + 1 file changed, 1 insertion(+) diff --git a/paper/paper.md b/paper/paper.md index 50f58c4a..2952a2ee 100644 --- a/paper/paper.md +++ b/paper/paper.md @@ -19,6 +19,7 @@ authors: - name: Roberto Tejada affiliation: "12" - name: Vighnesh Nagpal + orcid: 0000-0001-5909-4433 affiliation: "13" - name: Tirth Dharmesh Surti affiliation: "5" From 7772ba7032b2386ce84598a2f8df5900c3a3db15 Mon Sep 17 00:00:00 2001 From: Sarah Blunt Date: Mon, 26 Aug 2024 17:01:01 -0700 Subject: [PATCH 25/30] address copy-edits --- paper/paper.bib | 26 +++++++++---------- paper/paper.md | 67 +++++++++++++++++++++++-------------------------- 2 files changed, 45 insertions(+), 48 deletions(-) diff --git a/paper/paper.bib b/paper/paper.bib index 55f393e1..e311971e 100644 --- a/paper/paper.bib +++ b/paper/paper.bib @@ -1,7 +1,7 @@ @ARTICLE{Blunt:2020, author = {{Blunt}, Sarah and {Wang}, Jason J. and {Angelo}, Isabel and {Ngo}, Henry and {Cody}, Devin and {De Rosa}, Robert J. and {Graham}, James R. and {Hirsch}, Lea and {Nagpal}, Vighnesh and {Nielsen}, Eric L. and {Pearce}, Logan and {Rice}, Malena and {Tejada}, Roberto}, title = "{orbitize!: A Comprehensive Orbit-fitting Software Package for the High-contrast Imaging Community}", - journal = {\aj}, + journal = {The Astronomical Journal}, keywords = {Open source software, Orbit determination, 1866, 1175, Astrophysics - Earth and Planetary Astrophysics}, year = 2020, month = mar, @@ -20,7 +20,7 @@ @ARTICLE{Blunt:2020 @ARTICLE{Thompson:2023, author = {{Thompson}, William and {Lawrence}, Jensen and {Blakely}, Dori and {Marois}, Christian and {Wang}, Jason and {Giordano}, Mos{\'e} and {Brandt}, Timothy and {Johnstone}, Doug and {Ruffio}, Jean-Baptiste and {Ammons}, S. Mark and {Crotts}, Katie A. and {Do {\'O}}, Clarissa R. and {Gonzales}, Eileen C. and {Rice}, Malena}, title = "{Octofitter: Fast, Flexible, and Accurate Orbit Modeling to Detect Exoplanets}", - journal = {\aj}, + journal = {The Astronomical Journal}, keywords = {Exoplanet detection methods, Bayesian statistics, Direct imaging, 489, 1900, 387, Astrophysics - Earth and Planetary Astrophysics, Astrophysics - Instrumentation and Methods for Astrophysics}, year = 2023, month = oct, @@ -41,7 +41,7 @@ @ARTICLE{Thompson:2023 @ARTICLE{Brandt:2021, author = {{Brandt}, Timothy D. and {Dupuy}, Trent J. and {Li}, Yiting and {Brandt}, G. Mirek and {Zeng}, Yunlin and {Michalik}, Daniel and {Bardalez Gagliuffi}, Daniella C. and {Raposo-Pulido}, Virginia}, title = "{orvara: An Efficient Code to Fit Orbits Using Radial Velocity, Absolute, and/or Relative Astrometry}", - journal = {\aj}, + journal = {The Astronomical Journal}, keywords = {Orbit determination, Keplerian orbit, Astronomy software, Exoplanet astronomy, Astrometric exoplanet detection, Radial velocity, 1175, 884, 1855, 486, 2130, 1332, Astrophysics - Instrumentation and Methods for Astrophysics, Astrophysics - Earth and Planetary Astrophysics, Astrophysics - Solar and Stellar Astrophysics}, year = 2021, month = nov, @@ -62,7 +62,7 @@ @ARTICLE{Brandt:2021 @ARTICLE{ONeil:2019, author = {{O'Neil}, K. Kosmo and {Martinez}, G.~D. and {Hees}, A. and {Ghez}, A.~M. and {Do}, T. and {Witzel}, G. and {Konopacky}, Q. and {Becklin}, E.~E. and {Chu}, D.~S. and {Lu}, J.~R. and {Matthews}, K. and {Sakai}, S.}, title = "{Improving Orbit Estimates for Incomplete Orbits with a New Approach to Priors: with Applications from Black Holes to Planets}", - journal = {\aj}, + journal = {The Astronomical Journal}, keywords = {Galaxy: center, Galaxy: fundamental parameters, methods: statistical, planets and satellites: fundamental parameters, Astrophysics - Earth and Planetary Astrophysics, Astrophysics - Astrophysics of Galaxies}, year = 2019, month = jul, @@ -81,7 +81,7 @@ @ARTICLE{ONeil:2019 @ARTICLE{Bryan:2020, author = {{Bryan}, Marta L. and {Chiang}, Eugene and {Bowler}, Brendan P. and {Morley}, Caroline V. and {Millholland}, Sarah and {Blunt}, Sarah and {Ashok}, Katelyn B. and {Nielsen}, Eric and {Ngo}, Henry and {Mawet}, Dimitri and {Knutson}, Heather A.}, title = "{Obliquity Constraints on an Extrasolar Planetary-mass Companion}", - journal = {\aj}, + journal = {The Astronomical Journal}, keywords = {Exoplanet systems, High resolution spectroscopy, Direct imaging, Photometry, 484, 2096, 387, 1234, Astrophysics - Earth and Planetary Astrophysics, Astrophysics - Instrumentation and Methods for Astrophysics, Astrophysics - Solar and Stellar Astrophysics}, year = 2020, month = apr, @@ -119,7 +119,7 @@ @article{Surti:2023 abstract = {The exoplanet orbit-fitting software package orbitize! was initially designed to fit the orbits of directly imaged planets with relative astrometric measurements using a Markov Chain Monte Carlo (MCMC) algorithm. Since the publication of orbitize! v1.0, the ability to jointly fit radial velocities and astrometry has been incorporated. We first implemented a Basis class into orbitize! that enables users to add and fit in various orbit parameterizations. We then introduced a radial velocity-focused parameterization of the Keplerian orbital elements for the joint radial velocity and astrometry fits. We compared MCMC convergence speeds of the new radial velocity-focused basis to the original orbitize! standard basis for the system HD 190771, which has full orbital coverage in radial velocity data. We found a 16% faster convergence in time with the radial velocity-focused basis. We encourage users to consider using this basis when doing joint radial velocity and astrometry fits.}, author = {Tirth Surti and Lea Hirsch and Tabassom Madayen and Ziyyad Ali and Eric Nielsen and Sarah Blunt and Jason Wang and Rodrigo Ferrer-Ch{\'a}vez and Bruce Macintosh}, doi = {10.3847/2515-5172/acdc29}, - journal = {Research Notes of the AAS}, + journal = {Research Notes of the American Astronomical Society}, month = {jun}, number = {6}, pages = {121}, @@ -155,7 +155,7 @@ @ARTICLE{Covarrubias:2022 @ARTICLE{Speagle:2020, author = {{Speagle}, Joshua S.}, title = "{DYNESTY: a dynamic nested sampling package for estimating Bayesian posteriors and evidences}", - journal = {\mnras}, + journal = {Monthly Notices of the Royal Astronomical Society}, keywords = {methods: data analysis, methods: statistical, Astrophysics - Instrumentation and Methods for Astrophysics, Statistics - Computation}, year = 2020, month = apr, @@ -175,7 +175,7 @@ @ARTICLE{Speagle:2020 @ARTICLE{Nielsen:2020, author = {{Nielsen}, Eric L. and {De Rosa}, Robert J. and {Wang}, Jason J. and {Sahlmann}, Johannes and {Kalas}, Paul and {Duch{\^e}ne}, Gaspard and {Rameau}, Julien and {Marley}, Mark S. and {Saumon}, Didier and {Macintosh}, Bruce and {Millar-Blanchaer}, Maxwell A. and {Nguyen}, Meiji M. and {Ammons}, S. Mark and {Bailey}, Vanessa P. and {Barman}, Travis and {Bulger}, Joanna and {Chilcote}, Jeffrey and {Cotten}, Tara and {Doyon}, Rene and {Esposito}, Thomas M. and {Fitzgerald}, Michael P. and {Follette}, Katherine B. and {Gerard}, Benjamin L. and {Goodsell}, Stephen J. and {Graham}, James R. and {Greenbaum}, Alexandra Z. and {Hibon}, Pascale and {Hung}, Li-Wei and {Ingraham}, Patrick and {Konopacky}, Quinn and {Larkin}, James E. and {Maire}, J{\'e}r{\^o}me and {Marchis}, Franck and {Marois}, Christian and {Metchev}, Stanimir and {Oppenheimer}, Rebecca and {Palmer}, David and {Patience}, Jennifer and {Perrin}, Marshall and {Poyneer}, Lisa and {Pueyo}, Laurent and {Rajan}, Abhijith and {Rantakyr{\"o}}, Fredrik T. and {Ruffio}, Jean-Baptiste and {Savransky}, Dmitry and {Schneider}, Adam C. and {Sivaramakrishnan}, Anand and {Song}, Inseok and {Soummer}, Remi and {Thomas}, Sandrine and {Wallace}, J. Kent and {Ward-Duong}, Kimberly and {Wiktorowicz}, Sloane and {Wolff}, Schuyler}, title = "{The Gemini Planet Imager Exoplanet Survey: Dynamical Mass of the Exoplanet {\ensuremath{\beta}} Pictoris b from Combined Direct Imaging and Astrometry}", - journal = {\aj}, + journal = {The Astronomical Journal}, keywords = {Astrometry, Direct imaging, Exoplanets, Coronagraphic imaging, Orbit determination, 80, 387, 498, 313, 1175, Astrophysics - Earth and Planetary Astrophysics, Astrophysics - Solar and Stellar Astrophysics}, year = 2020, month = feb, @@ -196,7 +196,7 @@ @ARTICLE{Nielsen:2020 @ARTICLE{Blunt:2023a, author = {{Blunt}, Sarah and {Balmer}, W.~O. and {Wang}, J.~J. and {Lacour}, S. and {Petrus}, S. and {Bourdarot}, G. and {Kammerer}, J. and {Pourr{\'e}}, N. and {Rickman}, E. and {Shangguan}, J. and {Winterhalder}, T. and {Abuter}, R. and {Amorim}, A. and {Asensio-Torres}, R. and {Benisty}, M. and {Berger}, J. -P. and {Beust}, H. and {Boccaletti}, A. and {Bohn}, A. and {Bonnefoy}, M. and {Bonnet}, H. and {Brandner}, W. and {Cantalloube}, F. and {Caselli}, P. and {Charnay}, B. and {Chauvin}, G. and {Chavez}, A. and {Choquet}, E. and {Christiaens}, V. and {Cl{\'e}net}, Y. and {Du Foresto}, V. Coud{\'e} and {Cridland}, A. and {Dembet}, R. and {Drescher}, A. and {Duvert}, G. and {Eckart}, A. and {Eisenhauer}, F. and {Feuchtgruber}, H. and {Garcia}, P. and {Garcia Lopez}, R. and {Gendron}, E. and {Genzel}, R. and {Gillessen}, S. and {Girard}, J.~H. and {Haubois}, X. and {Hei{\ss}el}, G. and {Henning}, Th. and {Hinkley}, S. and {Hippler}, S. and {Horrobin}, M. and {Houll{\'e}}, M. and {Hubert}, Z. and {Jocou}, L. and {Keppler}, M. and {Kervella}, P. and {Kreidberg}, L. and {Lagrange}, A. -M. and {Lapeyr{\`e}re}, V. and {Le Bouquin}, J. -B. and {L{\'e}na}, P. and {Lutz}, D. and {Maire}, A. -L. and {Mang}, F. and {Marleau}, G. -D. and {M{\'e}rand}, A. and {Molli{\`e}re}, P. and {Monnier}, J.~D. and {Mordasini}, C. and {Mouillet}, D. and {Nasedkin}, E. and {Nowak}, M. and {Ott}, T. and {Otten}, G.~P.~P.~L. and {Paladini}, C. and {Paumard}, T. and {Perraut}, K. and {Perrin}, G. and {Pfuhl}, O. and {Pueyo}, L. and {Rameau}, J. and {Rodet}, L. and {Rustamkulov}, Z. and {Shimizu}, T. and {Sing}, D. and {Stolker}, T. and {Straubmeier}, C. and {Sturm}, E. and {Tacconi}, L.~J. and {van Dishoeck}, E.~F. and {Vigan}, A. and {Vincent}, F. and {Ward-Duong}, K. and {Widmann}, F. and {Wieprecht}, E. and {Wiezorrek}, E. and {Woillez}, J. and {Yazici}, S. and {Young}, A. and {Exogravity Collaboration}}, title = "{First VLTI/GRAVITY Observations of HIP 65426 b: Evidence for a Low or Moderate Orbital Eccentricity}", - journal = {\aj}, + journal = {The Astronomical Journal}, keywords = {Exoplanets, Exoplanet formation, Astrometry, Optical interferometry, 498, 492, 80, 1168, Astrophysics - Earth and Planetary Astrophysics}, year = 2023, month = dec, @@ -218,7 +218,7 @@ @ARTICLE{Blunt:2023a @ARTICLE{Bowler:2016, author = {{Bowler}, Brendan P.}, title = "{Imaging Extrasolar Giant Planets}", - journal = {\pasp}, + journal = {Publications of the Astronomical Society of the Pacific}, keywords = {Astrophysics - Earth and Planetary Astrophysics}, year = 2016, month = oct, @@ -236,7 +236,7 @@ @ARTICLE{Bowler:2016 @ARTICLE{Brandt:2021, author = {{Brandt}, Timothy D.}, title = "{The Hipparcos-Gaia Catalog of Accelerations: Gaia EDR3 Edition}", - journal = {\apjs}, + journal = {The Astrophysical Journal Supplement Series}, keywords = {Astrometry, Astrometric exoplanet detection, Astrometric binary stars, 80, 2130, 79, Astrophysics - Astrophysics of Galaxies, Astrophysics - Earth and Planetary Astrophysics, Astrophysics - Instrumentation and Methods for Astrophysics, Astrophysics - Solar and Stellar Astrophysics}, year = 2021, month = jun, @@ -255,7 +255,7 @@ @ARTICLE{Brandt:2021 @ARTICLE{Lacour:2021, author = {{Lacour}, S. and {Wang}, J.~J. and {Rodet}, L. and {Nowak}, M. and {Shangguan}, J. and {Beust}, H. and {Lagrange}, A. -M. and {Abuter}, R. and {Amorim}, A. and {Asensio-Torres}, R. and {Benisty}, M. and {Berger}, J. -P. and {Blunt}, S. and {Boccaletti}, A. and {Bohn}, A. and {Bolzer}, M. -L. and {Bonnefoy}, M. and {Bonnet}, H. and {Bourdarot}, G. and {Brandner}, W. and {Cantalloube}, F. and {Caselli}, P. and {Charnay}, B. and {Chauvin}, G. and {Choquet}, E. and {Christiaens}, V. and {Cl{\'e}net}, Y. and {Coud{\'e} Du Foresto}, V. and {Cridland}, A. and {Dembet}, R. and {Dexter}, J. and {de Zeeuw}, P.~T. and {Drescher}, A. and {Duvert}, G. and {Eckart}, A. and {Eisenhauer}, F. and {Gao}, F. and {Garcia}, P. and {Garcia Lopez}, R. and {Gendron}, E. and {Genzel}, R. and {Gillessen}, S. and {Girard}, J.~H. and {Haubois}, X. and {Hei{\ss}el}, G. and {Henning}, Th. and {Hinkley}, S. and {Hippler}, S. and {Horrobin}, M. and {Houll{\'e}}, M. and {Hubert}, Z. and {Jocou}, L. and {Kammerer}, J. and {Keppler}, M. and {Kervella}, P. and {Kreidberg}, L. and {Lapeyr{\`e}re}, V. and {Le Bouquin}, J. -B. and {L{\'e}na}, P. and {Lutz}, D. and {Maire}, A. -L. and {M{\'e}rand}, A. and {Molli{\`e}re}, P. and {Monnier}, J.~D. and {Mouillet}, D. and {Nasedkin}, E. and {Ott}, T. and {Otten}, G.~P.~P.~L. and {Paladini}, C. and {Paumard}, T. and {Perraut}, K. and {Perrin}, G. and {Pfuhl}, O. and {Rickman}, E. and {Pueyo}, L. and {Rameau}, J. and {Rousset}, G. and {Rustamkulov}, Z. and {Samland}, M. and {Shimizu}, T. and {Sing}, D. and {Stadler}, J. and {Stolker}, T. and {Straub}, O. and {Straubmeier}, C. and {Sturm}, E. and {Tacconi}, L.~J. and {van Dishoeck}, E.~F. and {Vigan}, A. and {Vincent}, F. and {von Fellenberg}, S.~D. and {Ward-Duong}, K. and {Widmann}, F. and {Wieprecht}, E. and {Wiezorrek}, E. and {Woillez}, J. and {Yazici}, S. and {Young}, A. and {Gravity Collaboration}}, title = "{The mass of {\ensuremath{\beta}} Pictoris c from {\ensuremath{\beta}} Pictoris b orbital motion}", - journal = {\aap}, + journal = {Astronomy \& Astrophysics}, keywords = {planets and satellites: detection, astrometry, instrumentation: interferometers, instrumentation: high angular resolution, Astrophysics - Earth and Planetary Astrophysics, Astrophysics - Instrumentation and Methods for Astrophysics}, year = 2021, month = oct, @@ -273,7 +273,7 @@ @ARTICLE{Lacour:2021 @ARTICLE{Bowler:2020, author = {{Bowler}, Brendan P. and {Blunt}, Sarah C. and {Nielsen}, Eric L.}, title = "{Population-level Eccentricity Distributions of Imaged Exoplanets and Brown Dwarf Companions: Dynamical Evidence for Distinct Formation Channels}", - journal = {\aj}, + journal = {The Astronomical Journal}, keywords = {Exoplanet formation, Brown dwarfs, Extrasolar gaseous giant planets, 492, 185, 509, Astrophysics - Earth and Planetary Astrophysics, Astrophysics - Solar and Stellar Astrophysics}, year = 2020, month = feb, diff --git a/paper/paper.md b/paper/paper.md index 2952a2ee..e9bf8046 100644 --- a/paper/paper.md +++ b/paper/paper.md @@ -1,9 +1,9 @@ --- -title: 'orbitize! v3: Orbit-fitting for the High-contrast Imaging Community' +title: 'orbitize! v3: Orbit fitting for the High-contrast Imaging Community' tags: - Python - astronomy - - orbit-fitting + - Orbit fitting - exoplanets - high-contrast imaging authors: @@ -106,13 +106,13 @@ bibliography: paper.bib # Summary `orbitize!` is a package for Bayesian modeling of the orbital parameters of resolved binary -objects from timeseries measurements. It was developed with the needs of the high-contrast +objects from time series measurements. It was developed with the needs of the high-contrast imaging community in mind, and has since also become widely used in the binary star community. -A generic `orbitize!` use case involves translating relative astrometric timeseries, optionally -combined with radial velocity or astrometric timeseries, into a set of derived orbital posteriors. +A generic `orbitize!` use case involves translating relative astrometric time series, optionally +combined with radial velocity or astrometric time series, into a set of derived orbital posteriors. This paper is published alongside the release of `orbitize!` version 3.0, which -has seen significant expansions in functionality and accessibility since the +has seen significant enhancements in functionality and accessibility since the release of version 1.0 [@Blunt:2020]. # Statement of need @@ -122,8 +122,7 @@ their present-day dynamics and formation histories [@Bowler:2016], as well as ab their inherent physical characteristics (particularly mass, generally called "dynamical mass" when derived from orbital constraints, e.g. @Brandt:2021, @Lacour:2021). -`orbitize!` is used widely in the exoplanet imaging and binary star communities for -translating astrometric data to information about eccentricities [@Bowler:2020], obliquities [@Bryan:2020], +`orbitize!` is widely used in the exoplanet imaging and binary star communities to translate astrometric data to information about eccentricities [@Bowler:2020], obliquities [@Bryan:2020], dynamical masses [@Lacour:2021], and more. Each new released version of the `orbitize!` source code is automatically archived on Zenodo [@orbitize]. @@ -131,71 +130,69 @@ Each new released version of the `orbitize!` source code is automatically archiv # Major features added since v1 For a detailed overview of the `orbitize!` API, core functionality (including information -about our Kepler solver), and initial verification, we refer readers to @Blunt:2020. +about our Kepler solver), and initial verification, we refer the reader to @Blunt:2020. This section lists major new features that have been added to the -code since the release of version 1.0 and directs readers to more information about each. -A complete descriptive list of modifications to the code is maintained in our +code since the release of version 1.0 and directs the reader to more information about each of them. +A full descriptive list of modifications to the code is maintained in our [changelog](https://orbitize.readthedocs.io/en/latest/#changelog). Major new features since v1 include: -1. The ability to jointly fit radial velocity (RV) timeseries, both RVs of the secondary - companion (see Section 3 of @Blunt:2023a) and RVs of the primary - star. RVs of the primary star can either be passed into `orbitize!` directly (see the [radial velocity tutorial](https://orbitize.readthedocs.io/en/latest/tutorials/RV_MCMC_Tutorial.html)), or fit separately and passed in as prior - information (see the [non-orbitize! posteriors as priors tutorial](https://orbitize.readthedocs.io/en/latest/tutorials/Using_nonOrbitize_Posteriors_as_Priors.html).) +1. The functionality to jointly fit the radial velocity (RV) time series for the primary star together and the secondary companion (see Section 3 of @Blunt:2023a). For the primary star, the RV data can either be directly input into orbitize! (as explained in the [Radial Velocity Tutorial](https://orbitize.readthedocs.io/en/latest/tutorials/RV_MCMC_Tutorial.html)) or be fitted separately and then used as priors (as detailed in the [Non-orbitize! Posteriors as Priors Tutorial](https://orbitize.readthedocs.io/en/latest/tutorials/Using_nonOrbitize_Posteriors_as_Priors.html)). 2. The ability to jointly fit absolute astrometry of the primary star. `orbitize!` can fit - the Hipparcos-Gaia catalog of accelerations (@Brandt:2021; see the [HGCA tutorial](https://github.com/sblunt/orbitize/blob/v3/docs/tutorials/HGCA_tutorial.ipynb)), as well as Hipparcos intermediate astrometric data and Gaia - astrometry, following @Nielsen:2020 (see the [Hipparcos IAD tutorial](https://orbitize.readthedocs.io/en/latest/tutorials/Hipparcos_IAD.html)). It can also handle arbitrary absolute astrometry (see the [Fitting Arbitrary Astrometry tutorial](https://orbitize.readthedocs.io/en/latest/tutorials/abs_astrometry.html)). + the Hipparcos-Gaia catalog of accelerations (@Brandt:2021; see the [HGCA Tutorial](https://github.com/sblunt/orbitize/blob/v3/docs/tutorials/HGCA_tutorial.ipynb)), as well as Hipparcos intermediate astrometric data and Gaia + astrometry, following @Nielsen:2020 (see the [Hipparcos IAD Tutorial](https://orbitize.readthedocs.io/en/latest/tutorials/Hipparcos_IAD.html)). It can also handle arbitrary absolute astrometry (see the [Fitting Arbitrary Astrometry Tutorial](https://orbitize.readthedocs.io/en/latest/tutorials/abs_astrometry.html)). 3. In addition to the MCMC and OFTI posterior computation algorithms documented in @Blunt:2020, - `orbitize!` version 3 also implements a nested sampling backend, via `dynesty` (@Speagle:2020; see the [`dynesty` tutorial](https://github.com/sblunt/orbitize/blob/dynesty/docs/tutorials/dynesty_tutorial.ipynb).) + `orbitize!` version 3 also implements a nested sampling backend, via `dynesty` (@Speagle:2020; see the [`dynesty` Tutorial](https://github.com/sblunt/orbitize/blob/dynesty/docs/tutorials/dynesty_tutorial.ipynb).) 4. `orbitize!` version 3 implements two prescriptions for handling multi-planet effects. Keplerian epicyclic motion of the primary star due to multiple orbiting bodies, - following @Lacour:2021, is discussed in the [multi-planet tutorial](https://orbitize.readthedocs.io/en/latest/tutorials/Multiplanet_Tutorial.html), and N-body interactions are discussed in @Covarrubias:2022. The Keplerian epicyclic motion - prescription only accounts for star-planet interactions, treating the motion of the star as a sum of Keplerians, + following @Lacour:2021, is discussed in the [Multi-planet Tutorial](https://orbitize.readthedocs.io/en/latest/tutorials/Multiplanet_Tutorial.html), and N-body interactions are discussed in @Covarrubias:2022. The Keplerian epicyclic motion + prescription only accounts for star-planet interactions, treating the motion of the star as a sum of Keplerian orbit signals, while the N-body prescription models this effect as well as planet-planet interactions. 5. The ability to fit in different orbital bases (@Ferrer-Chavez:2021, @Surti:2023; see the - [changing basis](https://orbitize.readthedocs.io/en/latest/tutorials/Changing_bases_tutorial.html) tutorial), as well - as the ability to apply the observation-based priors derived in @ONeil:2019 (see the [observation-based priors tutorial](https://github.com/sblunt/orbitize/blob/main/docs/tutorials/ONeil-ObsPriors.ipynb)). + [Changing Bases](https://orbitize.readthedocs.io/en/latest/tutorials/Changing_bases_tutorial.html) tutorial), as well + as the ability to apply the observation-based priors derived in @ONeil:2019 (see the [Observation-based Priors Tutorial](https://github.com/sblunt/orbitize/blob/main/docs/tutorials/ONeil-ObsPriors.ipynb)). # Verification and Documentation `orbitize!` implements a full stack of automated testing and documentation building practices. We use GitHub Actions to automatically run a suite of unit tests, maintained in [orbitize/tests](https://github.com/sblunt/orbitize/tree/main/tests), -each time code is committed to the public repository or a pull request is opened. The jupyter notebook -tutorials, maintained in [orbitize/docs/tutorials](https://github.com/sblunt/orbitize/tree/main/docs/tutorials), are also automatically run when a +each time code is committed to the public repository or a pull request is opened. The Jupyter notebook +tutorials, maintained in [orbitize/docs/tutorials](https://github.com/sblunt/orbitize/tree/main/docs/tutorials), are also run automatically when a pull request to the `main` branch is opened. Documentation is built using `sphinx`, and hosted on readthedocs.org at [orbitize.info](https://orbitize.readthedocs.io/en/latest/). We also maintain a set of longer-running tests in [orbitize/tests/end-to-end-tests](https://github.com/sblunt/orbitize/tree/main/tests/end-to-end-tests) that show real scientific use cases of the code. These tests are not automatically run. -`orbitize!` is documented through API docstrings describing individual functions, which are accessible on [our readthedocs page](https://orbitize.readthedocs.io/en/latest/api.html), a set of [jupyter notebook tutorials](https://orbitize.readthedocs.io/en/latest/tutorials.html) walking the user through a particular application, a set of [frequently asked questions](https://orbitize.readthedocs.io/en/latest/faq.html), -and an in-progress ["manual"](https://orbitize.readthedocs.io/en/orbitize-manual/manual.html) describing orbit-fitting with `orbitize!` from first principles. +`orbitize!` is documented through API docstrings describing individual functions, which are accessible on [our readthedocs page](https://orbitize.readthedocs.io/en/latest/api.html), a set of [Jupyter notebook tutorials](https://orbitize.readthedocs.io/en/latest/tutorials.html) walking the user through a particular application, a set of [frequently asked questions](https://orbitize.readthedocs.io/en/latest/faq.html), +and an in-progress ["manual"](https://orbitize.readthedocs.io/en/orbitize-manual/manual.html) describing orbit fitting with `orbitize!` from first principles. # Comparison to Similar Packages -Since the release of `orbitize!` version 1, other open-source packages have been released that have -similar goals to `orbitize!`, notably `orvara` [@Brandt:2021] and `octofitter` [@Thompson:2023]. This is a wonderful development, since all packages benefit from open sharing of knowledge! `orbitize!`, `orvara`, and `octofitter` can +Since the release of `orbitize!` version 1, other open source packages have been released that have +similar goals to `orbitize!`, notably `orvara` [@Brandt:2021] and `octofitter` [@Thompson:2023]. This is a wonderful development, as all packages benefit from open sharing of knowledge! `orbitize!`, `orvara`, and `octofitter` can do many similar things, but each has unique features and strengths; as an example, `octofitter` is extraordinarily fast, and enables joint astrometry extraction and orbit modeling, while `orbitize!` has unique abilities to fit arbitrary absolute astrometry (i.e. not from Hipparcos or Gaia) and model data using an N-body backend. `orvara` analytically marginalizes over parallax assuming a prior informed by Gaia, a significant speed advantage, while -`orbitize!` allows different parallax priors to be used. We recommend users of each package compare the implementations +`orbitize!` allows different parallax priors to be used. We recommend that users of each package compare the implementations of the particular features they wish to use. -Best practices for orbit-fitting, particularly using radial velocities, for which treatment of stellar -activity is an active area of research, and absolute astrometry with Gaia and Hipparcos, for which -correlated error treatment is an active area of research, evolve quickly. The philosophy of `orbitize!` +Best practices for orbit fitting, particularly using radial velocities, for which the treatment of stellar +activity is an active area of research, and absolute astrometry with Gaia and Hipparcos, for which the treatment of +correlated errors is an active area of research, evolve quickly. The philosophy of `orbitize!` is to, as much as possible, implement multiple approaches to a problem, evidenced by our multiple implementations of radial velocity joint fitting and absolute astrometry joint fitting (described above). -For detailed information about our particular implementations, we direct the reader to our [documentation](https://orbitize.readthedocs.io/en/latest/). +For detailed information about our particular implementations, we refer the reader to our [documentation](https://orbitize.readthedocs.io/en/latest/). # Acknowledgements -Our team gratefully acknowledges support the Heising-Simons Foundation. S.B. and J.J.W. are supported -by NASA Grant 80NSSC23K0280. +Our team gratefully acknowledges support the Heising-Simons Foundation. S.B. and J.J.W. are supported by NASA Grant 80NSSC23K0280. + +This paper describes additions made to `orbitize!` between versions 1.0.0 and 3.0.0. We are extremely grateful to Isabel Angelo, Henry Ngo, James Graham, Logan Pearce, and Malena Rice, who contribtued code to version 1.0.0, and are included as authors in @Blunt:2020. # References From 54ae9df30b1b36b31cd3327b3887e2bd168c24ca Mon Sep 17 00:00:00 2001 From: Sarah Blunt Date: Mon, 26 Aug 2024 17:03:40 -0700 Subject: [PATCH 26/30] fix broken links --- paper/paper.md | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/paper/paper.md b/paper/paper.md index e9bf8046..0f590d26 100644 --- a/paper/paper.md +++ b/paper/paper.md @@ -78,7 +78,7 @@ affiliations: index: 7 - name: NASA Goddard Space Flight Center, Code 698 index: 8 - - name: Google, Inc. + - name: Google LLC index: 9 - name: Department of Astronomy & Astrophysics, University of California San Diego index: 10 @@ -141,11 +141,11 @@ Major new features since v1 include: 1. The functionality to jointly fit the radial velocity (RV) time series for the primary star together and the secondary companion (see Section 3 of @Blunt:2023a). For the primary star, the RV data can either be directly input into orbitize! (as explained in the [Radial Velocity Tutorial](https://orbitize.readthedocs.io/en/latest/tutorials/RV_MCMC_Tutorial.html)) or be fitted separately and then used as priors (as detailed in the [Non-orbitize! Posteriors as Priors Tutorial](https://orbitize.readthedocs.io/en/latest/tutorials/Using_nonOrbitize_Posteriors_as_Priors.html)). 2. The ability to jointly fit absolute astrometry of the primary star. `orbitize!` can fit - the Hipparcos-Gaia catalog of accelerations (@Brandt:2021; see the [HGCA Tutorial](https://github.com/sblunt/orbitize/blob/v3/docs/tutorials/HGCA_tutorial.ipynb)), as well as Hipparcos intermediate astrometric data and Gaia + the Hipparcos-Gaia catalog of accelerations (@Brandt:2021; see the [HGCA Tutorial](https://orbitize.readthedocs.io/en/latest/tutorials/HGCA_tutorial.html)), as well as Hipparcos intermediate astrometric data and Gaia astrometry, following @Nielsen:2020 (see the [Hipparcos IAD Tutorial](https://orbitize.readthedocs.io/en/latest/tutorials/Hipparcos_IAD.html)). It can also handle arbitrary absolute astrometry (see the [Fitting Arbitrary Astrometry Tutorial](https://orbitize.readthedocs.io/en/latest/tutorials/abs_astrometry.html)). 3. In addition to the MCMC and OFTI posterior computation algorithms documented in @Blunt:2020, - `orbitize!` version 3 also implements a nested sampling backend, via `dynesty` (@Speagle:2020; see the [`dynesty` Tutorial](https://github.com/sblunt/orbitize/blob/dynesty/docs/tutorials/dynesty_tutorial.ipynb).) + `orbitize!` version 3 also implements a nested sampling backend, via `dynesty` (@Speagle:2020; see the [`dynesty` Tutorial](https://github.com/sblunt/orbitize/blob/main/docs/tutorials/dynesty_tutorial.ipynb).) 4. `orbitize!` version 3 implements two prescriptions for handling multi-planet effects. Keplerian epicyclic motion of the primary star due to multiple orbiting bodies, @@ -191,7 +191,7 @@ For detailed information about our particular implementations, we refer the read # Acknowledgements -Our team gratefully acknowledges support the Heising-Simons Foundation. S.B. and J.J.W. are supported by NASA Grant 80NSSC23K0280. +Our team gratefully acknowledges support from the Heising-Simons Foundation. S.B. and J.J.W. are supported by NASA Grant 80NSSC23K0280. This paper describes additions made to `orbitize!` between versions 1.0.0 and 3.0.0. We are extremely grateful to Isabel Angelo, Henry Ngo, James Graham, Logan Pearce, and Malena Rice, who contribtued code to version 1.0.0, and are included as authors in @Blunt:2020. From 051da8299c3e21eedb0f8066c564a68c2b4e801d Mon Sep 17 00:00:00 2001 From: Sarah Blunt Date: Tue, 27 Aug 2024 09:08:49 -0700 Subject: [PATCH 27/30] add eric grant info & middle initial --- paper/paper.md | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/paper/paper.md b/paper/paper.md index 0f590d26..b6ed9c56 100644 --- a/paper/paper.md +++ b/paper/paper.md @@ -55,7 +55,7 @@ authors: - name: Clarissa R. Do Ó orcid: 0000-0001-5173-2947 affiliation: "10" - - name: Eric Nielsen + - name: Eric L. Nielsen affiliation: "15" - name: Robert J. De Rosa orcid: 0000-0002-4918-0247 @@ -191,7 +191,8 @@ For detailed information about our particular implementations, we refer the read # Acknowledgements -Our team gratefully acknowledges support from the Heising-Simons Foundation. S.B. and J.J.W. are supported by NASA Grant 80NSSC23K0280. +Our team gratefully acknowledges support from the Heising-Simons Foundation. S.B. and J.J.W. are supported by NASA Grant 80NSSC23K0280. E.L.N. is supported by NASA Grants 21-ADAP21-0130 and 80NSSC21K0958. + This paper describes additions made to `orbitize!` between versions 1.0.0 and 3.0.0. We are extremely grateful to Isabel Angelo, Henry Ngo, James Graham, Logan Pearce, and Malena Rice, who contribtued code to version 1.0.0, and are included as authors in @Blunt:2020. From 11849296d30fb0ffb97cff805d0e18d0be3ac169 Mon Sep 17 00:00:00 2001 From: Sarah Blunt Date: Mon, 9 Sep 2024 09:55:37 -0700 Subject: [PATCH 28/30] typo fix --- paper/paper.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/paper/paper.md b/paper/paper.md index b6ed9c56..fb4d4b1f 100644 --- a/paper/paper.md +++ b/paper/paper.md @@ -138,7 +138,7 @@ A full descriptive list of modifications to the code is maintained in our Major new features since v1 include: -1. The functionality to jointly fit the radial velocity (RV) time series for the primary star together and the secondary companion (see Section 3 of @Blunt:2023a). For the primary star, the RV data can either be directly input into orbitize! (as explained in the [Radial Velocity Tutorial](https://orbitize.readthedocs.io/en/latest/tutorials/RV_MCMC_Tutorial.html)) or be fitted separately and then used as priors (as detailed in the [Non-orbitize! Posteriors as Priors Tutorial](https://orbitize.readthedocs.io/en/latest/tutorials/Using_nonOrbitize_Posteriors_as_Priors.html)). +1. The functionality to jointly fit the radial velocity (RV) time series for the primary star together with the secondary companion (see Section 3 of @Blunt:2023a). For the primary star, the RV data can either be directly input into orbitize! (as explained in the [Radial Velocity Tutorial](https://orbitize.readthedocs.io/en/latest/tutorials/RV_MCMC_Tutorial.html)) or be fitted separately and then used as priors (as detailed in the [Non-orbitize! Posteriors as Priors Tutorial](https://orbitize.readthedocs.io/en/latest/tutorials/Using_nonOrbitize_Posteriors_as_Priors.html)). 2. The ability to jointly fit absolute astrometry of the primary star. `orbitize!` can fit the Hipparcos-Gaia catalog of accelerations (@Brandt:2021; see the [HGCA Tutorial](https://orbitize.readthedocs.io/en/latest/tutorials/HGCA_tutorial.html)), as well as Hipparcos intermediate astrometric data and Gaia From 85e23644c6f1a72ea2cd2798b43b57304d22779d Mon Sep 17 00:00:00 2001 From: Sarah Blunt Date: Mon, 9 Sep 2024 09:58:17 -0700 Subject: [PATCH 29/30] increment version --- orbitize/__init__.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/orbitize/__init__.py b/orbitize/__init__.py index 1bebb014..1eff7b10 100644 --- a/orbitize/__init__.py +++ b/orbitize/__init__.py @@ -1,6 +1,6 @@ import os -__version__ = "3.0.1" +__version__ = "3.1.0" # set Python env variable to keep track of example data dir orbitize_dir = os.path.dirname(__file__) From f6c1018cf8f7ffeca1e0e7a194e3f6dea7dcae2f Mon Sep 17 00:00:00 2001 From: Sarah Blunt Date: Mon, 9 Sep 2024 09:59:22 -0700 Subject: [PATCH 30/30] update changelog --- docs/index.rst | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/docs/index.rst b/docs/index.rst index 327fb51f..54f5f8c5 100644 --- a/docs/index.rst +++ b/docs/index.rst @@ -55,6 +55,10 @@ User Guide: Changelog: ++++++++++ +**3.1.0 (2024-9-09)** + +- JOSS paper published! (@sblunt et al) + **3.0.1 (2024-8-19)** - bugfix for issue #370 involving saving and loading hipparcos.py objects (@sblunt)