fixing some formatting bugs in joss paper

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}}
+

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