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JOSS documentation; example: Kolby's paper

JOSS Submission draft:

paper.md:

---
title: 'aesop: ARC Echelle Spectroscopic Observation Pipeline'
tags:
  - Python
  - astronomy
  - spectroscopy
authors:
  - name: Brett M. Morris
    orcid: 0000-0003-2528-3409
    affiliation: 1
  - name: Trevor Dorn-Wallenstein
    orcid: 0000-0003-3601-3180
    affiliation: 1
affiliations:
 - name: Astronomy Department, University of Washington, Seattle, WA, USA
   index: 1
date: XX July 2018
bibliography: paper.bib
---

# Summary

The ARC Echelle Spectroscopic Observation Pipeline, or ``aesop``, is a high resolution 
spectroscopy software toolkit tailored for observations from the Astrophysics Research 
Consortium (ARC) Echelle Spectrograph mounted on the ARC 3.5 m Telescope at Apache 
Point Observatory. ``aesop`` picks up where the traditional IRAF reduction scripts leave 
off, offering an open development, object-oriented Pythonic analysis framework for echelle
spectra. 

Basic functionality of ``aesop`` includes: (1) blaze function normalization by polynomial 
fits to observations of early-type stars, (2) an additional/alternative robust least-squares 
normalization method, (3) radial velocity measurements (or offset removals) via 
cross-correlation with model spectra, including barycentric radial velocity calculations, 
(4) concatenation of multiple echelle orders into a simple 1D spectrum, and (5) approximate
flux calibration. 

Some handy additional utilities include methods for download PHOENIX model spectra
[@Husser:2013], and methods for measuring the Mount Wilson Observatory-calibrated 
CaII H & K "S" index [@Morris:2017]. aesop was built from the Astropy 
package-template, and thus includes self-building documentation and continuous integration
[@astropy:2018].

# Acknowledgements

We acknowledge guidance from Suzanne L. Hawley and Emily Levesque, and the invaluable 
framework and dev team behind the astropy package-template.

# References

paper.bib:

@ARTICLE{Morris:2017,
       author = {{Morris}, Brett M. and {Hawley}, Suzanne L. and {Hebb}, Leslie and
        {Sakari}, Charli and {Davenport}, James. R.~A. and {Isaacson},
        Howard and {Howard}, Andrew W. and {Montet}, Benjamin T. and
        {Agol}, Eric},
        title = "{Chromospheric Activity of HAT-P-11: An Unusually Active Planet-hosting K
        Star}",
      journal = {\apj},
     keywords = {methods: observational, planet─star interactions, stars: activity,
        stars: chromospheres, starspots, Astrophysics - Solar and
        Stellar Astrophysics, Astrophysics - Earth and Planetary
        Astrophysics},
         year = 2017,
        month = Oct,
       volume = {848},
          eid = {58},
        pages = {58},
          doi = {10.3847/1538-4357/aa8cca},
       adsurl = {https://ui.adsabs.harvard.edu/#abs/2017ApJ...848...58M},
      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},
       adsurl = {https://ui.adsabs.harvard.edu/#abs/2013A&A...553A...6H},
      adsnote = {Provided by the SAO/NASA Astrophysics Data System}
}
@ARTICLE{astropy:2018,
       author = {{The Astropy Collaboration} and {Price-Whelan}, A.~M. and
        {Sip{\'{o}}cz}, B.~M. and {G{\"u}nther}, H.~M. and {Lim}, P.~L.
        and {Crawford}, S.~M. and {Conseil}, S. and {Shupe}, D.~L. and
        {Craig}, M.~W. and {Dencheva}, N. and {Ginsburg}, A. and
        {VanderPlas}, J.~T. and {Bradley}, L.~D. and {P{\'e}rez-
        Su{\'a}rez}, D. and {de Val-Borro}, M. and {Aldcroft}, T.~L. and
        {Cruz}, K.~L. and {Robitaille}, T.~P. and {Tollerud}, E.~J. and
        {Ardelean}, C. and {Babej}, T. and {Bachetti}, M. and {Bakanov},
        A.~V. and {Bamford}, S.~P. and {Barentsen}, G. and {Barmby}, P.
        and {Baumbach}, A. and {Berry}, K.~L. and {Biscani}, F. and
        {Boquien}, M. and {Bostroem}, K.~A. and {Bouma}, L.~G. and
        {Brammer}, G.~B. and {Bray}, E.~M. and {Breytenbach}, H. and
        {Buddelmeijer}, H. and {Burke}, D.~J. and {Calderone}, G. and
        {Cano Rodr{\'\i}guez}, J.~L. and {Cara}, M. and {Cardoso},
        J.~V.~M. and {Cheedella}, S. and {Copin}, Y. and {Crichton}, D.
        and {D{\'A}vella}, D. and {Deil}, C. and {Depagne}, {\'E}. and
        {Dietrich}, J.~P. and {Donath}, A. and {Droettboom}, M. and
        {Earl}, N. and {Erben}, T. and {Fabbro}, S. and {Ferreira},
        L.~A. and {Finethy}, T. and {Fox}, R.~T. and {Garrison}, L.~H.
        and {Gibbons}, S.~L.~J. and {Goldstein}, D.~A. and {Gommers}, R.
        and {Greco}, J.~P. and {Greenfield}, P. and {Groener}, A.~M. and
        {Grollier}, F. and {Hagen}, A. and {Hirst}, P. and {Homeier}, D.
        and {Horton}, A.~J. and {Hosseinzadeh}, G. and {Hu}, L. and
        {Hunkeler}, J.~S. and {Ivezi{\'c}}, {\v{Z}}. and {Jain}, A. and
        {Jenness}, T. and {Kanarek}, G. and {Kendrew}, S. and {Kern},
        N.~S. and {Kerzendorf}, W.~E. and {Khvalko}, A. and {King}, J.
        and {Kirkby}, D. and {Kulkarni}, A.~M. and {Kumar}, A. and
        {Lee}, A. and {Lenz}, D. and {Littlefair}, S.~P. and {Ma}, Z.
        and {Macleod}, D.~M. and {Mastropietro}, M. and {McCully}, C.
        and {Montagnac}, S. and {Morris}, B.~M. and {Mueller}, M. and
        {Mumford}, S.~J. and {Muna}, D. and {Murphy}, N.~A. and
        {Nelson}, S. and {Nguyen}, G.~H. and {Ninan}, J.~P. and
        {N{\"o}the}, M. and {Ogaz}, S. and {Oh}, S. and {Parejko}, J.~K.
        and {Parley}, N. and {Pascual}, S. and {Patil}, R. and {Patil},
        A.~A. and {Plunkett}, A.~L. and {Prochaska}, J.~X. and
        {Rastogi}, T. and {Reddy Janga}, V. and {Sabater}, J. and
        {Sakurikar}, P. and {Seifert}, M. and {Sherbert}, L.~E. and
        {Sherwood-Taylor}, H. and {Shih}, A.~Y. and {Sick}, J. and
        {Silbiger}, M.~T. and {Singanamalla}, S. and {Singer}, L.~P. and
        {Sladen}, P.~H. and {Sooley}, K.~A. and {Sornarajah}, S. and
        {Streicher}, O. and {Teuben}, P. and {Thomas}, S.~W. and
        {Tremblay}, G.~R. and {Turner}, J.~E.~H. and {Terr{\'o}n}, V.
        and {van Kerkwijk}, M.~H. and {de la Vega}, A. and {Watkins},
        L.~L. and {Weaver}, B.~A. and {Whitmore}, J.~B. and {Woillez},
        J. and {Zabalza}, V.},
        title = "{The Astropy Project: Building an inclusive, open-science project and
        status of the v2.0 core package}",
      journal = {ArXiv e-prints},
     keywords = {Astrophysics - Instrumentation and Methods for Astrophysics},
         year = 2018,
        month = Jan,
          eid = {arXiv:1801.02634},
        pages = {arXiv:1801.02634},
archivePrefix = {arXiv},
       eprint = {1801.02634},
       adsurl = {https://ui.adsabs.harvard.edu/#abs/2018arXiv180102634T},
      adsnote = {Provided by the SAO/NASA Astrophysics Data System}
}