Added JOSS paper to source tree

Author: Martin D. Weinberg

Paper/README.md

@@ -0,0 +1,20 @@
+# Paper
+
+This is the JOSS abstract/paper describing the EXP release
+
+## Contents
+
+All of the text is in the `paper` directory.  Contents are:
+
+| File      | Description |
+| ---       | ---         |
+| paper.md  | The primary markdown text file |
+| paper.bib | The bibliography file |
+| paper.pdf | The compiled PDF file |
+
+
+## Compile to PDF with Docker as follows
+
+```
+docker run --rm --volume $PWD/paper:/data --user $(id -u):$(id -g) --env JOURNAL=joss openjournals/inara
+```

Paper/paper/examplefunctions.png

@@ -0,0 +1,322 @@
+@book{Binney:2008,
+  	url = {http://adsabs.harvard.edu/abs/2008gady.book.....B},
+  	Author = {{Binney}, J. and {Tremaine}, S.},
+  	Booktitle = {Galactic Dynamics: Second Edition, by James Binney and Scott Tremaine.~ISBN 978-0-691-13026-2 (HB).~Published by Princeton University Press, Princeton, NJ USA, 2008.},
+  	Publisher = {Princeton University Press},
+  	Title = {{Galactic Dynamics: Second Edition}},
+  	Year = 2008
+}
+
+@article{gaia,
+    author = {{Gaia Collaboration}},
+    title = "{The Gaia mission}",
+    journal = {Astronomy and Astrophysics},
+    archivePrefix = "arXiv",
+    eprint = {1609.04153},
+    primaryClass = "astro-ph.IM",
+    keywords = {space vehicles: instruments, Galaxy: structure, astrometry, parallaxes, proper motions, telescopes},
+    year = 2016,
+    month = nov,
+    volume = 595,
+    doi = {10.1051/0004-6361/201629272},
+    url = {http://adsabs.harvard.edu/abs/2016A%26A...595A...1G},
+}
+
+@article{gaia_DR2_disk,
+	Title = {{Gaia Data Release 2. Mapping the Milky Way disc kinematics}},
+	Author = {{Gaia Collaboration}},
+	Doi = {10.1051/0004-6361/201832865},
+	Eid = {A11},
+	Eprint = {1804.09380},
+	Journal = {A\&Ap},
+	Month = {Aug},
+	Pages = {A11},
+	Primaryclass = {astro-ph.GA},
+	Volume = {616},
+	Year = {2018},
+        Archiveprefix = {arXiv}
+}
+
+@article{astropy,
+    author = {{Astropy Collaboration}},
+    title = "{Astropy: A community Python package for astronomy}",
+    journal = {Astronomy and Astrophysics},
+    archivePrefix = "arXiv",
+    eprint = {1307.6212},
+    primaryClass = "astro-ph.IM",
+    keywords = {methods: data analysis, methods: miscellaneous, virtual observatory tools},
+    year = 2013,
+    month = oct,
+    volume = 558,
+    doi = {10.1051/0004-6361/201322068},
+    url = {http://adsabs.harvard.edu/abs/2013A%26A...558A..33A}
+}
+
+@article{gala,
+  doi = {10.21105/joss.00388},
+  url = {https://doi.org/10.21105%2Fjoss.00388},
+  year = 2017,
+  month = {oct},
+  publisher = {The Open Journal},
+  volume = {2},
+  number = {18},
+  author = {Adrian M. Price-Whelan},
+  title = {Gala: A Python package for galactic dynamics},
+  journal = {The Journal of Open Source Software}}
+
+
+@misc{hdf5,
+    author = {{The HDF Group}},
+    title = "{Hierarchical data format version 5}",
+    year = {2000-2010},
+    howpublished = {http://www.hdfgroup.org/HDF5}
+}
+
+@misc{pybind11,
+   author = {Wenzel Jakob and Jason Rhinelander and Dean Moldovan},
+   year = {2017},
+   note = {https://github.com/pybind/pybind11},
+   title = {pybind11 -- Seamless operability between C++11 and Python}
+}
+
+@ARTICLE{Weinberg:23,
+       author = {{Weinberg}, Martin D.},
+        title = "{New dipole instabilities in spherical stellar systems}",
+      journal = {MNRAS},
+         year = 2023,
+        month = nov,
+       volume = {525},
+       number = {4},
+        pages = {4962-4975},
+          doi = {10.1093/mnras/stad2591},
+archivePrefix = {arXiv},
+       eprint = {2209.06846},
+ primaryClass = {astro-ph.GA}
+}
+
+@ARTICLE{Weinberg:21,
+       author = {{Weinberg}, Martin D. and {Petersen}, Michael S.},
+        title = "{Using multichannel singular spectrum analysis to study galaxy dynamics}",
+      journal = {MNRAS},
+         year = 2021,
+        month = mar,
+       volume = {501},
+       number = {4},
+        pages = {5408-5423},
+          doi = {10.1093/mnras/staa3997},
+archivePrefix = {arXiv},
+       eprint = {2009.07870},
+ primaryClass = {astro-ph.GA}
+}
+
+@ARTICLE{Petersen:22,
+       author = {{Petersen}, Michael S. and {Weinberg}, Martin D. and {Katz}, Neal},
+        title = "{EXP: N-body integration using basis function expansions}",
+      journal = {\mnras},
+     keywords = {methods: numerical, Galaxy: halo, galaxies: haloes, galaxies: kinematics and dynamics, galaxies: structure, Astrophysics - Astrophysics of Galaxies, Astrophysics - Instrumentation and Methods for Astrophysics},
+         year = 2022,
+        month = mar,
+       volume = {510},
+       number = {4},
+        pages = {6201-6217},
+          doi = {10.1093/mnras/stab3639},
+archivePrefix = {arXiv},
+       eprint = {2104.14577},
+ primaryClass = {astro-ph.GA}
+}
+
+@ARTICLE{Johnson:23,
+       author = {{Johnson}, Alexander C. and {Petersen}, Michael S. and {Johnston}, Kathryn V. and {Weinberg}, Martin D.},
+        title = "{Dynamical data mining captures disc-halo couplings that structure galaxies}",
+      journal = {MNRAS},
+     keywords = {galaxies: disc, galaxies: haloes, galaxies: structure, Astrophysics - Astrophysics of Galaxies, Astrophysics - Instrumentation and Methods for Astrophysics},
+         year = 2023,
+        month = may,
+       volume = {521},
+       number = {2},
+        pages = {1757-1774},
+          doi = {10.1093/mnras/stad485},
+archivePrefix = {arXiv},
+       eprint = {2301.02256},
+ primaryClass = {astro-ph.GA}
+}
+
+@book{SSA,
+  title={Analysis of time series structure: SSA and related techniques},
+  author={Golyandina, Nina and Nekrutkin, Vladimir and Zhigljavsky, Anatoly A},
+  year={2001},
+  publisher={CRC press}
+}
+                  
+@Article{numpy,
+ 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
+                 Cournapeau and Eric Wieser and Julian Taylor and Sebastian
+                 Berg and Nathaniel J. Smith and Robert Kern and Matti Picus
+                 and Stephan Hoyer and Marten H. van Kerkwijk and Matthew
+                 Brett and Allan Haldane and Jaime Fern{\'{a}}ndez del
+                 R{\'{i}}o and Mark Wiebe and Pearu Peterson and Pierre
+                 G{\'{e}}rard-Marchant and Kevin Sheppard and Tyler Reddy and
+                 Warren Weckesser and Hameer Abbasi and Christoph Gohlke and
+                 Travis E. Oliphant},
+ year          = {2020},
+ month         = sep,
+ journal       = {Nature},
+ volume        = {585},
+ number        = {7825},
+ pages         = {357--362},
+ doi           = {10.1038/s41586-020-2649-2},
+ publisher     = {Springer Science and Business Media {LLC}},
+ url           = {https://doi.org/10.1038/s41586-020-2649-2}
+}
+@Article{matplotlib,
+  Author    = {Hunter, J. D.},
+  Title     = {Matplotlib: A 2D graphics environment},
+  Journal   = {Computing in Science \& Engineering},
+  Volume    = {9},
+  Number    = {3},
+  Pages     = {90--95},
+  abstract  = {Matplotlib is a 2D graphics package used for Python for
+  application development, interactive scripting, and publication-quality
+  image generation across user interfaces and operating systems.},
+  publisher = {IEEE COMPUTER SOC},
+  doi       = {10.1109/MCSE.2007.55},
+  year      = 2007
+}
+
+@ARTICLE{Weinberg:99,
+       author = {{Weinberg}, Martin D.},
+        title = "{An Adaptive Algorithm for N-Body Field Expansions}",
+      journal = {\aj},
+     keywords = {CELESTIAL MECHANICS, STELLAR DYNAMICS, GALAXIES: STRUCTURE, GALAXY: STRUCTURE, METHODS: NUMERICAL, Astrophysics},
+         year = 1999,
+        month = jan,
+       volume = {117},
+       number = {1},
+        pages = {629-637},
+          doi = {10.1086/300669},
+archivePrefix = {arXiv},
+       eprint = {astro-ph/9805357},
+ primaryClass = {astro-ph},
+       adsurl = {https://ui.adsabs.harvard.edu/abs/1999AJ....117..629W},
+      adsnote = {Provided by the SAO/NASA Astrophysics Data System}
+}
+
+ @MISC{Eigen,
+  author = {Ga\"{e}l Guennebaud and Beno\^{i}t Jacob and others},
+  title = {Eigen v3},
+  howpublished = {http://eigen.tuxfamily.org},
+  year = {2010}
+ }
+
+@Article{iPython,
+  Author    = {P\'erez, Fernando and Granger, Brian E.},
+  Title     = {{IP}ython: a System for Interactive Scientific Computing},
+  Journal   = {Computing in Science and Engineering},
+  Volume    = {9},
+  Number    = {3},
+  Pages     = {21--29},
+  month     = may,
+  year      = 2007,
+  url       = "https://ipython.org",
+  ISSN      = "1521-9615",
+  doi       = {10.1109/MCSE.2007.53},
+  publisher = {IEEE Computer Society},
+}
+
+@INCOLLECTION{jupyter,
+       author = {{Kluyver}, Thomas and {Ragan-Kelley}, Benjain and {P{\'e}rez}, Fernando and {Granger}, Brian and {Bussonnier}, Matthias and {Frederic}, Jonathan and {Kelley}, Kyle and {Hamrick}, Jessica and {Grout}, Jason and {Corlay}, Sylvain and {Ivanov}, Paul and {Avila}, Dami{\'a}n and {Abdalla}, Safia and {Willing}, Carol and {Jupyter Development Team}},
+        title = "{Jupyter Notebooks{\textemdash}a publishing format for reproducible computational workflows}",
+     keywords = {Notebook, reproducibility, research code},
+    booktitle = {IOS Press},
+         year = 2016,
+        pages = {87-90},
+          doi = {10.3233/978-1-61499-649-1-87},
+       adsurl = {https://ui.adsabs.harvard.edu/abs/2016ppap.book...87K},
+      adsnote = {Provided by the SAO/NASA Astrophysics Data System}
+}
+
+@misc{cuda, 
+  author={NVIDIA and Vingelmann, Péter and Fitzek, Frank H.P.}, 
+  title={CUDA, release: 10.2.89}, 
+  year={2020}, 
+  url={https://developer.nvidia.com/cuda-toolkit}, 
+}
+
+@manual{mpi41,
+    author = "{Message Passing Interface Forum}",
+    title  = "{MPI}: A Message-Passing Interface Standard Version 4.1",
+    url    = "https://www.mpi-forum.org/docs/mpi-4.1/mpi41-report.pdf",
+    year   = 2023,
+    month  = nov
+}
+
+
+@ARTICLE{GaravitoCamargo:21,
+       author = {{Garavito-Camargo}, Nicol{\'a}s and {Besla}, Gurtina and {Laporte}, Chervin F.~P. and {Price-Whelan}, Adrian M. and {Cunningham}, Emily C. and {Johnston}, Kathryn V. and {Weinberg}, Martin and {G{\'o}mez}, Facundo A.},
+        title = "{Quantifying the Impact of the Large Magellanic Cloud on the Structure of the Milky Way's Dark Matter Halo Using Basis Function Expansions}",
+      journal = {\apj},
+     keywords = {Milky Way dynamics, Large Magellanic Cloud, Milky Way dark matter halo, 1051, 903, 1049, Astrophysics - Astrophysics of Galaxies},
+         year = 2021,
+        month = oct,
+       volume = {919},
+       number = {2},
+          eid = {109},
+        pages = {109},
+          doi = {10.3847/1538-4357/ac0b44},
+archivePrefix = {arXiv},
+       eprint = {2010.00816},
+ primaryClass = {astro-ph.GA},
+       adsurl = {https://ui.adsabs.harvard.edu/abs/2021ApJ...919..109G},
+      adsnote = {Provided by the SAO/NASA Astrophysics Data System}
+}
+
+@ARTICLE{Hernquist:90,
+       author = {{Hernquist}, Lars},
+        title = "{An Analytical Model for Spherical Galaxies and Bulges}",
+      journal = {\apj},
+     keywords = {Computational Astrophysics, Elliptical Galaxies, Galactic Bulge, Galactic Structure, Astronomical Models, Astronomical Photometry, Brightness Distribution, Distribution Functions, Astrophysics, GALAXIES: PHOTOMETRY, GALAXIES: STRUCTURE},
+         year = 1990,
+        month = jun,
+       volume = {356},
+        pages = {359},
+          doi = {10.1086/168845},
+       adsurl = {https://ui.adsabs.harvard.edu/abs/1990ApJ...356..359H},
+      adsnote = {Provided by the SAO/NASA Astrophysics Data System}
+}
+
+
+
+@ARTICLE{Hernquist:92,
+       author = {{Hernquist}, Lars and {Ostriker}, Jeremiah P.},
+        title = "{A Self-consistent Field Method for Galactic Dynamics}",
+      journal = {\apj},
+     keywords = {Celestial Mechanics, Computational Astrophysics, Galaxies, Stellar Motions, Algorithms, Astronomical Models, Dynamical Systems, Numerical Analysis, Astrophysics, CELESTIAL MECHANICS, STELLAR DYNAMICS, METHODS: NUMERICAL},
+         year = 1992,
+        month = feb,
+       volume = {386},
+        pages = {375},
+          doi = {10.1086/171025},
+       adsurl = {https://ui.adsabs.harvard.edu/abs/1992ApJ...386..375H},
+      adsnote = {Provided by the SAO/NASA Astrophysics Data System}
+}
+
+@ARTICLE{NFW,
+       author = {{Navarro}, Julio F. and {Frenk}, Carlos S. and {White}, Simon D.~M.},
+        title = "{A Universal Density Profile from Hierarchical Clustering}",
+      journal = {\apj},
+     keywords = {Cosmology: Theory, Cosmology: Dark Matter, Galaxies: Halos, Methods: Numerical, Astrophysics},
+         year = 1997,
+        month = dec,
+       volume = {490},
+       number = {2},
+        pages = {493-508},
+          doi = {10.1086/304888},
+archivePrefix = {arXiv},
+       eprint = {astro-ph/9611107},
+ primaryClass = {astro-ph},
+       adsurl = {https://ui.adsabs.harvard.edu/abs/1997ApJ...490..493N},
+      adsnote = {Provided by the SAO/NASA Astrophysics Data System}
+}
+