Finish adding citations correctly + Fix paper compile workflow

.github/workflows/draft-pdf.yml

@@ -6,18 +6,14 @@ jobs:
     name: Paper Draft
     steps:
       - name: Checkout
-        uses: actions/checkout@v2
+        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/JOSS_gollum/paper.md
+          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/JOSS_gollum/paper.pdf
+          path: paper/paper.pdf

paper/paper.bib

@@ -1,4 +1,4 @@
-@MISC{lightkurve,
+@MISC{lightkurve:2018,
   author = {{Lightkurve Collaboration} and {Cardoso}, J.~V.~d.~M. and
             {Hedges}, C. and {Gully-Santiago}, M. and {Saunders}, N. and
             {Cody}, A.~M. and {Barclay}, T. and {Hall}, O. and
@@ -16,14 +16,14 @@ @MISC{lightkurve
   adsurl = {http://adsabs.harvard.edu/abs/2018ascl.soft12013L},
 }
 
-@Manual{bokeh,
+@Manual{bokeh2018,
   title = {Bokeh: Python library for interactive visualization},
   author = {{Bokeh Development Team}},
   year = {2018},
   url = {https://bokeh.pydata.org/en/latest/},
 }
 
-@Article{numpy,
+@Article{harris:2020,
  title = {Array programming with {NumPy}},
  author = {Charles R. Harris and K. Jarrod Millman and St{\'{e}}fan J.
           van der Walt and Ralf Gommers and Pauli Virtanen and David
@@ -46,7 +46,7 @@ @Article{numpy
  url = {https://doi.org/10.1038/s41586-020-2649-2}
 }
 
-@ARTICLE{scipy,
+@ARTICLE{virtanen:2020,
   author = {Virtanen, Pauli and Gommers, Ralf and Oliphant, Travis E. and
             Haberland, Matt and Reddy, Tyler and Cournapeau, David and
             Burovski, Evgeni and Peterson, Pearu and Weckesser, Warren and
@@ -70,7 +70,7 @@ @ARTICLE{scipy
   doi = {10.1038/s41592-019-0686-2},
 }
 
-@ARTICLE{astropy,
+@ARTICLE{astropy:2022,
   author = {{Astropy Collaboration} and {Price-Whelan}, Adrian M. and {Lim}, Pey Lian and {Earl}, Nicholas and {Starkman}, Nathaniel and {Bradley}, Larry and {Shupe}, David L. and {Patil}, Aarya A. and {Corrales}, Lia and {Brasseur}, C.~E. and {N{\"o}the}, Maximilian and {Donath}, Axel and {Tollerud}, Erik and {Morris}, Brett M. and {Ginsburg}, Adam and {Vaher}, Eero and {Weaver}, Benjamin A. and {Tocknell}, James and {Jamieson}, William and {van Kerkwijk}, Marten H. and {Robitaille}, Thomas P. and {Merry}, Bruce and {Bachetti}, Matteo and {G{\"u}nther}, H. Moritz and {Aldcroft}, Thomas L. and {Alvarado-Montes}, Jaime A. and {Archibald}, Anne M. and {B{\'o}di}, Attila and {Bapat}, Shreyas and {Barentsen}, Geert and {Baz{\'a}n}, Juanjo and {Biswas}, Manish and {Boquien}, M{\'e}d{\'e}ric and {Burke}, D.~J. and {Cara}, Daria and {Cara}, Mihai and {Conroy}, Kyle E. and {Conseil}, Simon and {Craig}, Matthew W. and {Cross}, Robert M. and {Cruz}, Kelle L. and {D'Eugenio}, Francesco and {Dencheva}, Nadia and {Devillepoix}, Hadrien A.~R. and {Dietrich}, J{\"o}rg P. and {Eigenbrot}, Arthur Davis and {Erben}, Thomas and {Ferreira}, Leonardo and {Foreman-Mackey}, Daniel and {Fox}, Ryan and {Freij}, Nabil and {Garg}, Suyog and {Geda}, Robel and {Glattly}, Lauren and {Gondhalekar}, Yash and {Gordon}, Karl D. and {Grant}, David and {Greenfield}, Perry and {Groener}, Austen M. and {Guest}, Steve and {Gurovich}, Sebastian and {Handberg}, Rasmus and {Hart}, Akeem and {Hatfield-Dodds}, Zac and {Homeier}, Derek and {Hosseinzadeh}, Griffin and {Jenness}, Tim and {Jones}, Craig K. and {Joseph}, Prajwel and {Kalmbach}, J. Bryce and {Karamehmetoglu}, Emir and {Ka{\l}uszy{\'n}ski}, Miko{\l}aj and {Kelley}, Michael S.~P. and {Kern}, Nicholas and {Kerzendorf}, Wolfgang E. and {Koch}, Eric W. and {Kulumani}, Shankar and {Lee}, Antony and {Ly}, Chun and {Ma}, Zhiyuan and {MacBride}, Conor and {Maljaars}, Jakob M. and {Muna}, Demitri and {Murphy}, N.~A. and {Norman}, Henrik and {O'Steen}, Richard and {Oman}, Kyle A. and {Pacifici}, Camilla and {Pascual}, Sergio and {Pascual-Granado}, J. and {Patil}, Rohit R. and {Perren}, Gabriel I. and {Pickering}, Timothy E. and {Rastogi}, Tanuj and {Roulston}, Benjamin R. and {Ryan}, Daniel F. and {Rykoff}, Eli S. and {Sabater}, Jose and {Sakurikar}, Parikshit and {Salgado}, Jes{\'u}s and {Sanghi}, Aniket and {Saunders}, Nicholas and {Savchenko}, Volodymyr and {Schwardt}, Ludwig and {Seifert-Eckert}, Michael and {Shih}, Albert Y. and {Jain}, Anany Shrey and {Shukla}, Gyanendra and {Sick}, Jonathan and {Simpson}, Chris and {Singanamalla}, Sudheesh and {Singer}, Leo P. and {Singhal}, Jaladh and {Sinha}, Manodeep and {Sip{\H{o}}cz}, Brigitta M. and {Spitler}, Lee R. and {Stansby}, David and {Streicher}, Ole and {{\v{S}}umak}, Jani and {Swinbank}, John D. and {Taranu}, Dan S. and {Tewary}, Nikita and {Tremblay}, Grant R. and {de Val-Borro}, Miguel and {Van Kooten}, Samuel J. and {Vasovi{\'c}}, Zlatan and {Verma}, Shresth and {de Miranda Cardoso}, Jos{\'e} Vin{\'\i}cius and {Williams}, Peter K.~G. and {Wilson}, Tom J. and {Winkel}, Benjamin and {Wood-Vasey}, W.~M. and {Xue}, Rui and {Yoachim}, Peter and {Zhang}, Chen and {Zonca}, Andrea and {Astropy Project Contributors}},
   title = "{The Astropy Project: Sustaining and Growing a Community-oriented Open-source Project and the Latest Major Release (v5.0) of the Core Package}",
   journal = {\apj},
@@ -89,7 +89,7 @@ @ARTICLE{astropy
   adsnote = {Provided by the SAO/NASA Astrophysics Data System}
 }
 
-@software{specutils,
+@software{earl:2023,
   author = {Nicholas Earl and Erik Tollerud and Ricky O'Steen and brechmos and Wolfgang Kerzendorf and Ivo Busko and shaileshahuja and Dan D'Avella and Thomas Robitaille and P. L. Lim and Adam Ginsburg and Derek Homeier and Brigitta Sipőcz and Jesse Averbukh and James Tocknell and Brian Cherinka and Sara Ogaz and Robel Geda and James Davies and Kyle Conroy and Hans Moritz Günther and Kyle Barbary and Jonathan Foster and Michael Droettboom and Duy Tuong Nguyen and E. M. Bray and Andy Casey and Peter Teuben and Steve Crawford and Henry Ferguson},
   title = {astropy/specutils: v1.12.0},
   month = oct,
@@ -100,21 +100,182 @@ @software{specutils
   url = {https://doi.org/10.5281/zenodo.10016569}
 }
 
-@software{muler,
-  author = {Michael A. Gully-Santiago and
-            Jessica L. Luna and
-            Caroline V. Morley and
-            Kyle Kaplan and
-            Aishwarya Ganesh and
-            Erica A. Sawczynec and
-            Joel Burke and
-            Daniel M. Krolikowski},
-  title = {{Astronomical échelle spectroscopy data analysis 
-                   with muler}},
+@misc{kimani-stewart:2021,
+  author = {Karina Kimani-Stewart and Diana Gonzalez-Argúeta and Michael Gully-Santiago},
+  title = {bdexda: Interactive brown dwarf NIR spectral analysis},
+  year = {2021},
+  publisher = {GitHub},
+  journal = {GitHub repository},
+  url = {https://github.com/karina-ks/bdexda}
+}
+
+@misc{cao:2022,
+  author = {Jiayi Cao and Michael Gully-Santiago and Ben Montet and Sujay Shankar},
+  title = {acdc: Disentangling AC and DC signals in spotted young stars},
+  year = {2022},
+  publisher = {GitHub},
+  journal = {GitHub repository},
+  url = {https://github.com/gully/acdc}
+}
+
+@misc{kaplan2023,
+  author = {Kyle Kaplan},
+  title = {plotspec: Python code for analyzing reduced 1D and 2D IGRINS spectra},
+  year = {2023},
+  publisher = {GitHub},
+  journal = {GitHub repository},
+  url = {https://github.com/kfkaplan/plotspec}
+}
+
+@software{gully-santiago:2022a,
+  author = {Michael A. Gully-Santiago and Jessica L. Luna and Caroline V. Morley and Kyle Kaplan and Aishwarya Ganesh and Erica A. Sawczynec and Joel Burke and Daniel M. Krolikowski},
+  title = {{Astronomical échelle spectroscopy data analysis with muler}},
   month = may,
   year = 2022,
   publisher = {Zenodo},
   version = {v0.3.4},
   doi = {10.5281/zenodo.6539458},
   url = {https://doi.org/10.5281/zenodo.6539458}
+}
+
+@ARTICLE{gully-santiago:2022b,
+  author = {{Gully-Santiago}, Michael and {Morley}, Caroline V.},
+  title = "{An Interpretable Machine-learning Framework for Modeling High-resolution Spectroscopic Data}",
+  journal = {\apj},
+  keywords = {High resolution spectroscopy, Stellar spectral lines, Astronomy data modeling, GPU computing, Calibration, Radial velocity, Maximum likelihood estimation, Deconvolution, Stellar photospheres, Atomic spectroscopy, Brown dwarfs, Earth atmosphere, 2096, 1630, 1859, 1969, 2179, 1332, 1901, 1910, 1237, 2099, 185, 437, Astrophysics - Instrumentation and Methods for Astrophysics, Astrophysics - Solar and Stellar Astrophysics},
+  year = 2022,
+  month = dec,
+  volume = {941},
+  number = {2},
+  eid = {200},
+  pages = {200},
+  doi = {10.3847/1538-4357/aca0a2},
+  archivePrefix = {arXiv},
+  eprint = {2210.01827},
+  primaryClass = {astro-ph.IM},
+  adsurl = {https://ui.adsabs.harvard.edu/abs/2022ApJ...941..200G},
+  adsnote = {Provided by the SAO/NASA Astrophysics Data System}
+}
+
+@ARTICLE{czekala:2015,
+  author = {{Czekala}, Ian and {Andrews}, Sean M. and {Mandel}, Kaisey S. and {Hogg}, David W. and {Green}, Gregory M.},
+  title = "{Constructing a Flexible Likelihood Function for Spectroscopic Inference}",
+  journal = {\apj},
+  keywords = {methods: data analysis, methods: statistical, stars: fundamental parameters, stars: late-type, stars: statistics, techniques: spectroscopic, Astrophysics - Solar and Stellar Astrophysics, Astrophysics - Earth and Planetary Astrophysics, Astrophysics - Instrumentation and Methods for Astrophysics},
+  year = 2015,
+  month = oct,
+  volume = {812},
+  number = {2},
+  eid = {128},
+  pages = {128},
+  doi = {10.1088/0004-637X/812/2/128},
+  archivePrefix = {arXiv},
+  eprint = {1412.5177},
+  primaryClass = {astro-ph.SR},
+  adsurl = {https://ui.adsabs.harvard.edu/abs/2015ApJ...812..128C},
+  adsnote = {Provided by the SAO/NASA Astrophysics Data System}
+}
+
+@ARTICLE{husser:2013,
+  author = {{Husser}, T. -O. and {Wende-von Berg}, S. and {Dreizler}, S. and {Homeier}, D. and {Reiners}, A. and {Barman}, T. and {Hauschildt}, P.~H.},
+  title = "{A new extensive library of PHOENIX stellar atmospheres and synthetic spectra}",
+  journal = {\aap},
+  keywords = {stars: atmospheres, convection, stars: late-type, Astrophysics - Solar and Stellar Astrophysics},
+  year = 2013,
+  month = may,
+  volume = {553},
+  eid = {A6},
+  pages = {A6},
+  doi = {10.1051/0004-6361/201219058},
+  archivePrefix = {arXiv},
+  eprint = {1303.5632},
+  primaryClass = {astro-ph.SR},
+  adsurl = {https://ui.adsabs.harvard.edu/abs/2013A&A...553A...6H},
+  adsnote = {Provided by the SAO/NASA Astrophysics Data System}
+}
+
+@INPROCEEDINGS{marley:2017,
+  author = {{Marley}, Mark S. and {Saumon}, Didier and {Fortney}, Jonathan J. and {Morley}, Caroline and {Lupu}, Roxana E. and {Freedman}, Richard and {Visscher}, Channon},
+  title = "{Sonora: A New Generation Model Atmosphere Grid for Brown Dwarfs and Young Extrasolar Giant Planets}",
+  booktitle = {American Astronomical Society Meeting Abstracts \#230},
+  year = 2017,
+  series = {American Astronomical Society Meeting Abstracts},
+  volume = {230},
+  month = jun,
+  eid = {315.07},
+  pages = {315.07},
+  adsurl = {https://ui.adsabs.harvard.edu/abs/2017AAS...23031507M},
+  adsnote = {Provided by the SAO/NASA Astrophysics Data System}
+}
+
+@ARTICLE{marley:2021,
+  author = {{Marley}, Mark S. and {Saumon}, Didier and {Visscher}, Channon and {Lupu}, Roxana and {Freedman}, Richard and {Morley}, Caroline and {Fortney}, Jonathan J. and {Seay}, Christopher and {Smith}, Adam J.~R.~W. and {Teal}, D.~J. and {Wang}, Ruoyan},
+  title = "{The Sonora Brown Dwarf Atmosphere and Evolution Models. I. Model Description and Application to Cloudless Atmospheres in Rainout Chemical Equilibrium}",
+  journal = {\apj},
+  keywords = {Brown dwarfs, T dwarfs, L dwarfs, L subdwarfs, T subdwarfs, Y dwarfs, Stellar atmospheres, 185, 1679, 894, 896, 1680, 1827, 1584, Astrophysics - Solar and Stellar Astrophysics, Astrophysics - Earth and Planetary Astrophysics},
+  year = 2021,
+  month = oct,
+  volume = {920},
+  number = {2},
+  eid = {85},
+  pages = {85},
+  doi = {10.3847/1538-4357/ac141d},
+  archivePrefix = {arXiv},
+  eprint = {2107.07434},
+  primaryClass = {astro-ph.SR},
+  adsurl = {https://ui.adsabs.harvard.edu/abs/2021ApJ...920...85M},
+  adsnote = {Provided by the SAO/NASA Astrophysics Data System}
+}
+
+@ARTICLE{morley:2024,
+  author = {{Morley}, Caroline V. and {Mukherjee}, Sagnick and {Marley}, Mark S. and {Fortney}, Jonathan J. and {Visscher}, Channon and {Lupu}, Roxana and {Gharib-Nezhad}, Ehsan and {Thorngren}, Daniel and {Freedman}, Richard and {Batalha 7}, Natasha},
+  title = "{The Sonora Substellar Atmosphere Models. III. Diamondback: Atmospheric Properties, Spectra, and Evolution for Warm Cloudy Substellar Objects}",
+  journal = {arXiv e-prints},
+  keywords = {Astrophysics - Solar and Stellar Astrophysics, Astrophysics - Earth and Planetary Astrophysics},
+  year = 2024,
+  month = feb,
+  eid = {arXiv:2402.00758},
+  pages = {arXiv:2402.00758},
+  doi = {10.48550/arXiv.2402.00758},
+  archivePrefix = {arXiv},
+  eprint = {2402.00758},
+  primaryClass = {astro-ph.SR},
+  adsurl = {https://ui.adsabs.harvard.edu/abs/2024arXiv240200758M},
+  adsnote = {Provided by the SAO/NASA Astrophysics Data System}
+}
+
+@ARTICLE{lacy:2023,
+  author = {{Lacy}, Brianna and {Burrows}, Adam},
+  title = "{Self-consistent Models of Y Dwarf Atmospheres with Water Clouds and Disequilibrium Chemistry}",
+  journal = {\apj},
+  keywords = {Brown dwarfs, Y dwarfs, Atmospheric structure, Exoplanet atmospheres, 185, 1827, 2309, 487, Astrophysics - Earth and Planetary Astrophysics, Astrophysics - Solar and Stellar Astrophysics},
+  year = 2023,
+  month = jun,
+  volume = {950},
+  number = {1},
+  eid = {8},
+  pages = {8},
+  doi = {10.3847/1538-4357/acc8cb},
+  archivePrefix = {arXiv},
+  eprint = {2303.16295},
+  primaryClass = {astro-ph.EP},
+  adsurl = {https://ui.adsabs.harvard.edu/abs/2023ApJ...950....8L},
+  adsnote = {Provided by the SAO/NASA Astrophysics Data System}
+}
+
+@ARTICLE{mukherjee:2024,
+  author = {{Mukherjee}, Sagnick and {Fortney}, Jonathan J. and {Morley}, Caroline V. and {Batalha}, Natasha E. and {Marley}, Mark S. and {Karalidi}, Theodora and {Visscher}, Channon and {Lupu}, Roxana and {Freedman}, Richard and {Gharib-Nezhad}, Ehsan},
+  title = "{The Sonora Substellar Atmosphere Models. IV. Elf Owl: Atmospheric Mixing and Chemical Disequilibrium with Varying Metallicity and C/O Ratios}",
+  journal = {arXiv e-prints},
+  keywords = {Astrophysics - Earth and Planetary Astrophysics, Astrophysics - Solar and Stellar Astrophysics},
+  year = 2024,
+  month = feb,
+  eid = {arXiv:2402.00756},
+  pages = {arXiv:2402.00756},
+  doi = {10.48550/arXiv.2402.00756},
+  archivePrefix = {arXiv},
+  eprint = {2402.00756},
+  primaryClass = {astro-ph.EP},
+  adsurl = {https://ui.adsabs.harvard.edu/abs/2024arXiv240200756M},
+  adsnote = {Provided by the SAO/NASA Astrophysics Data System}
 }

paper/paper.md

@@ -34,7 +34,7 @@ affiliations:
     index: 2
   - name: New Jersey Institute of Technology | Department of Physics, Newark, NJ, USA
     index: 3
-date: 6 February 2024
+date: 7 February 2024
 bibliography: paper.bib
 ---
 
@@ -44,9 +44,9 @@ The spectra of stars, brown dwarfs, and planets are incredibly complex and infor
 
 # Statement of need
 
-`gollum` is a Python package for intuitive analysis and visualization of precomputed synthetic spectra. Its API is designed to have modules dedicated to each model grid it supports, with each module then containing classes for both individual spectra and bulk grid access. The programmatic interface to spectral analysis uses method-chaining to make `gollum` code very readable, taking inspiration from frameworks like lightkurve [@lightkurve]. The visual interface in the form of interactive dashboards powered by `bokeh` sports low-latency sliders and toggles that allow users to tweak both fundamental stellar parameters and extrinsic parameters such as radial velocity and rotational broadening, building intuition [@bokeh]. `gollum`'s modularity allows for a wide range of model grids to potentially be supported, and its performance is optimized with libraries such as `numpy`, `scipy`, `astropy`, and `specutils` to allow for quick loading and processing of large amounts of data [@numpy; @scipy; @astropy; @specutils].
+`gollum` is a Python package for intuitive analysis and visualization of precomputed synthetic spectra. Its API is designed to have modules dedicated to each model grid it supports, with each module then containing classes for both individual spectra and bulk grid access. The programmatic interface to spectral analysis uses method-chaining to make `gollum` code very readable, taking inspiration from frameworks like lightkurve [@lightkurve:2018]. The visual interface in the form of interactive dashboards powered by `bokeh` sports low-latency sliders and toggles that allow users to tweak both fundamental stellar parameters and extrinsic parameters such as radial velocity and rotational broadening, building intuition [@bokeh2018]. `gollum`'s modularity allows for a wide range of model grids to potentially be supported, and its performance is optimized with libraries such as `numpy`, `scipy`, `astropy`, and `specutils` to allow for quick loading and processing of large amounts of data [@harris:2020; @virtanen:2020; @astropy:2022; @earl:2023].
 
-`gollum` appeals to use cases ranging from entry-level astronomers to seasoned researchers with its combination of intuition-building and performance. The framework has been demonstrated on high-resolution spectra of brown dwarfs from Keck-NIRSPEC using [`bdexda`](https://github.com/karina-ks/bdexda), has experimental support for starspots, used in [`acdc`](https://github.com/gully/acdc), and its programmatic interface has been used in the analysis of IGRINS spectra with [`plotspec`](https://github.com/kfkaplan/plotspec). It interoperates with `muler`, a similar framework designed for observed data from échelle spectrographs, and thanks to its dashboard, can also be used for by-eye fitting of models to data [@muler]. `gollum`'s programmatic interface is being used to create an extension to the `blase` framework that will allow for inference of fundamental stellar parameters from observed spectra using interpretable machine learning and interpolation techniques, taking inspiration from other frameworks such as `starfish` that also specialize in spectroscopic inference [@blase2022; @czekala15]. `gollum` currently supports PHOENIX, Sonora (Alpha, Bobcat, and Diamondback), and CoolTLUSTY model grids, and support for other model grids is planned [@husser2013; @alpha; @bobcat; @diamondback; @lacy2023].
+`gollum` appeals to use cases ranging from entry-level astronomers to seasoned researchers with its combination of intuition-building and performance. The framework has been demonstrated on high-resolution spectra of brown dwarfs from Keck-NIRSPEC using `bdexda`, has experimental support for starspots, used in `acdc`, and its programmatic interface has been used in the analysis of IGRINS spectra with `plotspec` [@kimani-stewart:2021; @cao:2022; @kaplan2023]. It interoperates with `muler`, a similar framework designed for observed data from échelle spectrographs, and thanks to its dashboard, can also be used for by-eye fitting of models to data [@gully-santiago:2022a]. `gollum`'s programmatic interface is being used to create an extension to the `blase` framework that will allow for inference of fundamental stellar parameters from observed spectra using interpretable machine learning and interpolation techniques, taking inspiration from other frameworks such as `starfish` that also specialize in spectroscopic inference [@gully-santiago:2022b; @czekala:2015]. `gollum` currently supports PHOENIX, Sonora (Alpha, Bobcat, and Diamondback), and CoolTLUSTY model grids, and support for other model grids such as Sonora Elf Owl is planned [@husser:2013; @marley:2017; @marley:2021; @morley:2024; @lacy:2023; @mukherjee:2024].
 
 # Acknowledgements