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Merge pull request #48 from sourceryinstitute/paper
Add example JOSS paper as template
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.github/workflows/draft-pdf.yml

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on: [push]
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jobs:
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paper:
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runs-on: ubuntu-latest
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name: Paper Draft
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steps:
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- name: Checkout
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uses: actions/checkout@v2
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- name: Build draft PDF
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uses: openjournals/openjournals-draft-action@master
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with:
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journal: joss
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# This should be the path to the paper within your repo.
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paper-path: doc/paper.md
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- name: Upload
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uses: actions/upload-artifact@v1
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with:
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name: paper
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# This is the output path where Pandoc will write the compiled
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# PDF. Note, this should be the same directory as the input
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# paper.md
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path: doc/

doc/paper.bib

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@article{Pearson:2017,
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url = {http://adsabs.harvard.edu/abs/2017arXiv170304627P},
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Archiveprefix = {arXiv},
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Author = {{Pearson}, S. and {Price-Whelan}, A.~M. and {Johnston}, K.~V.},
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Eprint = {1703.04627},
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Journal = {ArXiv e-prints},
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Keywords = {Astrophysics - Astrophysics of Galaxies},
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Month = mar,
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Title = {{Gaps in Globular Cluster Streams: Pal 5 and the Galactic Bar}},
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Year = 2017
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}
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@book{Binney:2008,
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url = {http://adsabs.harvard.edu/abs/2008gady.book.....B},
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Author = {{Binney}, J. and {Tremaine}, S.},
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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.},
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Publisher = {Princeton University Press},
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Title = {{Galactic Dynamics: Second Edition}},
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Year = 2008
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}
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@article{gaia,
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author = {{Gaia Collaboration}},
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title = "{The Gaia mission}",
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journal = {Astronomy and Astrophysics},
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archivePrefix = "arXiv",
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eprint = {1609.04153},
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primaryClass = "astro-ph.IM",
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keywords = {space vehicles: instruments, Galaxy: structure, astrometry, parallaxes, proper motions, telescopes},
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year = 2016,
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month = nov,
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volume = 595,
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doi = {10.1051/0004-6361/201629272},
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url = {http://adsabs.harvard.edu/abs/2016A%26A...595A...1G},
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}
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@article{astropy,
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author = {{Astropy Collaboration}},
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title = "{Astropy: A community Python package for astronomy}",
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journal = {Astronomy and Astrophysics},
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archivePrefix = "arXiv",
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eprint = {1307.6212},
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primaryClass = "astro-ph.IM",
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keywords = {methods: data analysis, methods: miscellaneous, virtual observatory tools},
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year = 2013,
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month = oct,
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volume = 558,
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doi = {10.1051/0004-6361/201322068},
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url = {http://adsabs.harvard.edu/abs/2013A%26A...558A..33A}
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}
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@misc{fidgit,
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author = {A. M. Smith and K. Thaney and M. Hahnel},
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title = {Fidgit: An ungodly union of GitHub and Figshare},
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year = {2020},
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publisher = {GitHub},
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journal = {GitHub repository},
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url = {https://github.com/arfon/fidgit}
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}

doc/paper.md

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---
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title: 'Gala: A Python package for galactic dynamics'
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tags:
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- Python
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- astronomy
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- dynamics
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- galactic dynamics
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- milky way
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authors:
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- name: Adrian M. Price-Whelan
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orcid: 0000-0000-0000-0000
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equal-contrib: true
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affiliation: "1, 2" # (Multiple affiliations must be quoted)
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- name: Author Without ORCID
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equal-contrib: true # (This is how you can denote equal contributions between multiple authors)
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affiliation: 2
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- name: Author with no affiliation
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corresponding: true # (This is how to denote the corresponding author)
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affiliation: 3
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affiliations:
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- name: Lyman Spitzer, Jr. Fellow, Princeton University, USA
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index: 1
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- name: Institution Name, Country
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index: 2
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- name: Independent Researcher, Country
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index: 3
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date: 13 August 2017
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bibliography: paper.bib
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# Optional fields if submitting to a AAS journal too, see this blog post:
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# https://blog.joss.theoj.org/2018/12/a-new-collaboration-with-aas-publishing
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aas-doi: 10.3847/xxxxx <- update this with the DOI from AAS once you know it.
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aas-journal: Astrophysical Journal <- The name of the AAS journal.
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---
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# Summary
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The forces on stars, galaxies, and dark matter under external gravitational
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fields lead to the dynamical evolution of structures in the universe. The orbits
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of these bodies are therefore key to understanding the formation, history, and
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future state of galaxies. The field of "galactic dynamics," which aims to model
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the gravitating components of galaxies to study their structure and evolution,
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is now well-established, commonly taught, and frequently used in astronomy.
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Aside from toy problems and demonstrations, the majority of problems require
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efficient numerical tools, many of which require the same base code (e.g., for
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performing numerical orbit integration).
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# Statement of need
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`Gala` is an Astropy-affiliated Python package for galactic dynamics. Python
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enables wrapping low-level languages (e.g., C) for speed without losing
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flexibility or ease-of-use in the user-interface. The API for `Gala` was
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designed to provide a class-based and user-friendly interface to fast (C or
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Cython-optimized) implementations of common operations such as gravitational
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potential and force evaluation, orbit integration, dynamical transformations,
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and chaos indicators for nonlinear dynamics. `Gala` also relies heavily on and
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interfaces well with the implementations of physical units and astronomical
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coordinate systems in the `Astropy` package [@astropy] (`astropy.units` and
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`astropy.coordinates`).
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`Gala` was designed to be used by both astronomical researchers and by
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students in courses on gravitational dynamics or astronomy. It has already been
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used in a number of scientific publications [@Pearson:2017] and has also been
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used in graduate courses on Galactic dynamics to, e.g., provide interactive
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visualizations of textbook material [@Binney:2008]. The combination of speed,
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design, and support for Astropy functionality in `Gala` will enable exciting
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scientific explorations of forthcoming data releases from the *Gaia* mission
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[@gaia] by students and experts alike.
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# Mathematics
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Single dollars ($) are required for inline mathematics e.g. $f(x) = e^{\pi/x}$
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Double dollars make self-standing equations:
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$$\Theta(x) = \left\{\begin{array}{l}
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0\textrm{ if } x < 0\cr
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1\textrm{ else}
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\end{array}\right.$$
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You can also use plain \LaTeX for equations
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\begin{equation}\label{eq:fourier}
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\hat f(\omega) = \int_{-\infty}^{\infty} f(x) e^{i\omega x} dx
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\end{equation}
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and refer to \autoref{eq:fourier} from text.
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# Citations
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Citations to entries in paper.bib should be in
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[rMarkdown](http://rmarkdown.rstudio.com/authoring_bibliographies_and_citations.html)
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format.
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If you want to cite a software repository URL (e.g. something on GitHub without a preferred
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citation) then you can do it with the example BibTeX entry below for @fidgit.
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For a quick reference, the following citation commands can be used:
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- `@author:2001` -> "Author et al. (2001)"
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- `[@author:2001]` -> "(Author et al., 2001)"
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- `[@author1:2001; @author2:2001]` -> "(Author1 et al., 2001; Author2 et al., 2002)"
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# Figures
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Figures can be included like this:
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![Caption for example figure.\label{fig:example}](figure.png)
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and referenced from text using \autoref{fig:example}.
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Figure sizes can be customized by adding an optional second parameter:
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![Caption for example figure.](figure.png){ width=20% }
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# Acknowledgements
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We acknowledge contributions from Brigitta Sipocz, Syrtis Major, and Semyeong
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Oh, and support from Kathryn Johnston during the genesis of this project.
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# References

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