diff --git a/papers/joss_paper/.gitignore b/papers/joss_paper/.gitignore
new file mode 100644
index 0000000000000000000000000000000000000000..d578a788ec47e9224c23521a893e1c3f7e15896f
--- /dev/null
+++ b/papers/joss_paper/.gitignore
@@ -0,0 +1,2 @@
+inara/
+*~
diff --git a/papers/joss_paper/generate.rb b/papers/joss_paper/generate.rb
new file mode 100644
index 0000000000000000000000000000000000000000..d56d7f7d6bab810b5d2c15843fe8b2205af39a4c
--- /dev/null
+++ b/papers/joss_paper/generate.rb
@@ -0,0 +1,146 @@
+#!/usr/bin/ruby
+
+# For an OO language, this is distinctly procedural. Should probably fix that.
+require 'json'
+
+details = Hash.new({})
+
+capture_params = [
+ { :name => "title", :message => "Enter project name." },
+ { :name => "url", :message => "Enter the URL of the project repository." },
+ { :name => "description", :message => "Enter the (short) project description." },
+ { :name => "license", :message => "Enter the license this software shared under. (hit enter to skip)\nFor example MIT, BSD, GPL v3.0, Apache 2.0" },
+ { :name => "doi", :message => "Enter the DOI of the archived version of this code. (hit enter to skip)\nFor example http://dx.doi.org/10.6084/m9.figshare.828487" },
+ { :name => "keywords", :message => "Enter keywords that should be associated with this project (hit enter to skip)\nComma-separated, for example: turkey, chicken, pot pie" },
+ { :name => "version", :message => "Enter the version of your software (hit enter to skip)\nSEMVER preferred: http://semver.org e.g. v1.0.0" }
+]
+
+puts "I'm going to try and help you prepare some things for your JOSS submission"
+puts "If all goes well then we'll have a nice codemeta.json file soon..."
+puts ""
+puts "************************************"
+puts "* First, some basic details *"
+puts "************************************"
+puts ""
+
+# Loop through the desired captures and print out for clarity
+capture_params.each do |param|
+ puts param[:message]
+ print "> "
+ input = gets
+
+ details[param[:name]] = input.chomp
+
+ puts ""
+ puts "OK, your project has #{param[:name]}: #{input}"
+ puts ""
+end
+
+puts ""
+puts "************************************"
+puts "* Experimental stuff *"
+puts "************************************"
+puts ""
+
+puts "Would you like me to try and build a list of authors for you?"
+puts "(You need to be running this script in a git repository for this to work)"
+print "> (Y/N)"
+answer = gets.chomp
+
+case answer.downcase
+when "y", "yes"
+
+ # Use git shortlog to extract a list of author names and commit counts.
+ # Note we don't extract emails here as there's often different emails for
+ # each user. Instead we capture emails at the end.
+
+ git_log = `git shortlog --summary --numbered --no-merges`
+
+ # ["252\tMichael Jackson", "151\tMC Hammer"]
+ authors_and_counts = git_log.split("\n").map(&:strip)
+
+ authors_and_counts.each do |author_count|
+ count, author = author_count.split("\t").map(&:strip)
+
+ puts "Looks like #{author} made #{count} commits"
+ puts "Add them to the output?"
+ print "> (Y/N)"
+ answer = gets.chomp
+
+ # If a user chooses to add this author to the output then we ask for some
+ # additional information including their email, ORCID and affiliation.
+ case answer.downcase
+ when "y", "yes"
+ puts "What is #{author}'s email address? (hit enter to skip)"
+ print "> "
+ email = gets.chomp
+
+ puts "What is #{author}'s ORCID? (hit enter to skip)"
+ puts "For example: http://orcid.org/0000-0000-0000-0000"
+ print "> "
+ orcid = gets.chomp
+
+ puts "What is #{author}'s affiliation? (hit enter to skip)"
+ print "> "
+ affiliation = gets.chomp
+
+
+ details['authors'].merge!(author => { 'commits' => count,
+ 'email' => email,
+ 'orcid' => orcid,
+ 'affiliation' => affiliation })
+
+ when "n", "no"
+ puts "OK boss..."
+ puts ""
+ end
+ end
+when "n", "no"
+ puts "OK boss..."
+ puts ""
+end
+
+puts "Reticulating splines"
+
+5.times do
+ print "."
+ sleep 0.5
+end
+
+puts ""
+puts "Generating some JSON goodness..."
+
+# TODO: work out how to use some kind of JSON template here.
+# Build the output list of authors from the inputs we've collected.
+output_authors = []
+
+details['authors'].each do |author_name, values|
+ entry = {
+ "@id" => values['orcid'],
+ "@type" => "Person",
+ "email" => values['email'],
+ "name" => author_name,
+ "affiliation" => values['affiliation']
+ }
+ output_authors << entry
+end
+
+# TODO: this is currently a static template (written out here). It would be good
+# to do something smarter here.
+output = {
+ "@context" => "https://raw.githubusercontent.com/codemeta/codemeta/master/codemeta.jsonld",
+ "@type" => "Code",
+ "author" => output_authors,
+ "identifier" => details['doi'],
+ "codeRepository" => details['url'],
+ "datePublished" => Time.now.strftime("%Y-%m-%d"),
+ "dateModified" => Time.now.strftime("%Y-%m-%d"),
+ "dateCreated" => Time.now.strftime("%Y-%m-%d"),
+ "description" => details['description'],
+ "keywords" => details['keywords'],
+ "license" => details['license'],
+ "title" => details['title'],
+ "version" => details['version']
+}
+
+File.open('codemeta.json', 'w') {|f| f.write(JSON.pretty_generate(output)) }
diff --git a/papers/joss_paper/paper.bib b/papers/joss_paper/paper.bib
new file mode 100644
index 0000000000000000000000000000000000000000..a4ab8faaa9b869b7bbeaf633f9d24b6f6bd690c7
--- /dev/null
+++ b/papers/joss_paper/paper.bib
@@ -0,0 +1,144 @@
+@article{izzardNewSyntheticModel2004,
+ title = {A New Synthetic Model for Asymptotic Giant Branch Stars},
+ author = {Izzard, Robert G. and Tout, Christopher A. and Karakas, Amanda I. and Pols, Onno R.},
+ year = {2004},
+ month = may,
+ journal = {Monthly Notices of the Royal Astronomical Society},
+ volume = {350},
+ number = {2},
+ pages = {407--426},
+ issn = {0035-8711},
+ doi = {10.1111/j.1365-2966.2004.07446.x},
+ abstract = {Abstract. We present a synthetic model for thermally pulsing asymptotic giant branch (TPAGB) evolution constructed by fitting expressions to full evolutionary},
+ langid = {english},
+ keywords = {masterthesis},
+ file = {/home/david/pdfs/Zotero/Izzard et al_2004_A new synthetic model for asymptotic giant branch stars.pdf;/home/david/Zotero/storage/DNNTAJQF/1113239.html}
+}
+
+@article{izzardPopulationNucleosynthesisSingle2006,
+ title = {Population Nucleosynthesis in Single and Binary Stars - {{I}}. {{Model}}},
+ author = {Izzard, R. G. and Dray, L. M. and Karakas, A. I. and Lugaro, M. and Tout, C. A.},
+ year = {2006},
+ month = dec,
+ journal = {Astronomy \& Astrophysics},
+ volume = {460},
+ number = {2},
+ pages = {565--572},
+ issn = {0004-6361, 1432-0746},
+ doi = {10.1051/0004-6361:20066129},
+ abstract = {We present a synthetic algorithm to rapidly calculate nucleosynthetic yields from populations of single and binary stars for use in population synthesis, globular cluster and Galactic chemical evolution simulations. Single star nucleosynthesis is fitted directly to full evolution models and our model includes first, second and third dredge-ups with \emph{s{$<$}i/{$>$}-process enhancements, an analytic calculation for hot-bottom burning of CNO, NeNa and MgAl isotopes, surface enhancements due to wind loss in massive stars and core-collapse supernova yields. Even though this algorithm operates about 10\textsuperscript{7{$<$}sup/{$>$} times faster than full evolution and nucleosynthesis calculations, agreement with such models is good. We extend the single star model to include prescriptions of binary star interactions, notably mass loss and gain by stellar winds and Roche-lobe overflow, novae and type Ia supernovae. As examples of the application of our algorithm we present models of some interesting systems containing chemically peculiar stars that may occur in binaries.}}},
+ copyright = {\textcopyright{} ESO, 2006},
+ langid = {english},
+ keywords = {masterthesis},
+ file = {/home/david/pdfs/Zotero/Izzard et al_2006_Population nucleosynthesis in single and binary stars - I.pdf;/home/david/Zotero/storage/8EB73LN9/aa6129-06.html}
+}
+
+@article{izzardPopulationSynthesisBinary2009,
+ ids = {izzardPopulationSynthesisBinary2009a},
+ title = {Population Synthesis of Binary Carbon-Enhanced Metal-Poor Stars},
+ author = {Izzard, R. G. and Glebbeek, E. and Stancliffe, R. J. and Pols, O. R.},
+ year = {2009},
+ month = dec,
+ journal = {Astronomy and Astrophysics},
+ volume = {508},
+ number = {3},
+ pages = {1359--1374},
+ publisher = {{EDP Sciences}},
+ issn = {0004-6361},
+ doi = {10.1051/0004-6361/200912827},
+ abstract = {The carbon-enhanced metal-poor (CEMP) stars constitute approximately one fifth of the metal-poor ([Fe/H] {$\lnapprox$} -2) population but their origin is not well understood. The most widely accepted formation scenario, at least for the majority of CEMP stars which are also enriched in s-process elements, invokes mass-transfer of carbon-rich material from a thermally-pulsing asymptotic giant branch (TPAGB) primary star to a less massive main-sequence companion which is seen today. Recent studies explore the possibility that an initial mass function biased toward intermediate-mass stars is required to reproduce the observed CEMP fraction in stars with metallicity [Fe/H]{$<$}-2.5. These models also implicitly predict a large number of nitrogen-enhanced metal-poor (NEMP) stars which is not seen. In this paper we investigate whether the observed CEMP and NEMP to extremely metal-poor (EMP) ratios can be explained without invoking a change in the initial mass function. We construct binary-star populations in an attempt to reproduce the observed number and chemical abundance patterns of CEMP stars at a metallicity [Fe/H]\texttildelow -2.3. Our binary-population models include synthetic nucleosynthesis in TPAGB stars and account for mass transfer and other forms of binary interaction. This approach allows us to explore uncertainties in the CEMP-star formation scenario by parameterization of uncertain input physics. In particular, we consider the uncertainty in the physics of third dredge up in the TPAGB primary, binary mass transfer and mixing in the secondary star. We confirm earlier findings that with current detailed TPAGB models, in which third dredge up is limited to stars more massive than about 1.25\textasciitilde M{$\odot$}, the large observed CEMP fraction cannot be accounted for. We find that efficient third dredge up in low-mass (less than 1.25\textasciitilde M{$\odot$}), low-metallicity stars may offer at least a partial explanation for the large observed CEMP fraction while remaining consistent with the small observed NEMP fraction. Appendices A-E are only available in electronic form at http://www.aanda.org},
+ keywords = {abundances,binaries: close,Galaxy: halo,Galaxy: stellar content,masterthesis,nuclear reactions,nucleosynthesis,project_core,stars: carbon,stars: chemically peculiar,to_read},
+ file = {/home/david/pdfs/Zotero/Izzard et al_2009_Population synthesis of binary carbon-enhanced metal-poor stars.pdf;/home/david/Zotero/storage/BAXNURKG/aa12827-09.html}
+}
+
+@article{izzardBinaryStarsGalactic2018,
+ title = {Binary Stars in the {{Galactic}} Thick Disc},
+ author = {Izzard, Robert G. and Preece, Holly and Jofre, Paula and Halabi, Ghina M. and Masseron, Thomas and Tout, Christopher A.},
+ year = {2018},
+ month = jan,
+ journal = {Monthly Notices of the Royal Astronomical Society},
+ volume = {473},
+ pages = {2984--2999},
+ issn = {0035-8711},
+ doi = {10.1093/mnras/stx2355},
+ abstract = {The combination of asteroseismologically measured masses with abundances from detailed analyses of stellar atmospheres challenges our fundamental knowledge of stars and our ability to model them. Ancient red-giant stars in the Galactic thick disc are proving to be most troublesome in this regard. They are older than 5 Gyr, a lifetime corresponding to an initial stellar mass of about 1.2 M{$\odot$}. So why do the masses of a sizeable fraction of thick-disc stars exceed 1.3 M{$\odot$}, with some as massive as 2.3 M{$\odot$}? We answer this question by considering duplicity in the thick-disc stellar population using a binary population-nucleosynthesis model. We examine how mass transfer and merging affect the stellar mass distribution and surface abundances of carbon and nitrogen. We show that a few per cent of thick-disc stars can interact in binary star systems and become more massive than 1.3 M{$\odot$}. Of these stars, most are single because they are merged binaries. Some stars more massive than 1.3 M{$\odot$} form in binaries by wind mass transfer. We compare our results to a sample of the APOKASC data set and find reasonable agreement except in the number of these thick-disc stars more massive than 1.3 M{$\odot$}. This problem is resolved by the use of a logarithmically flat orbital-period distribution and a large binary fraction.},
+ keywords = {binaries: general,binary,Galaxy: disc,Galaxy: stellar content,masterthesis,surrey,to_Read},
+ file = {/home/david/pdfs/Zotero/Izzard et al_2018_Binary stars in the Galactic thick disc2.pdf}
+}
+
+@article{foreman-mackeyEmceeMCMCHammer2013,
+ title = {Emcee: {{The MCMC Hammer}}},
+ shorttitle = {Emcee},
+ author = {{Foreman-Mackey}, Daniel and Hogg, David W. and Lang, Dustin and Goodman, Jonathan},
+ year = {2013},
+ month = mar,
+ journal = {Publications of the Astronomical Society of the Pacific},
+ volume = {125},
+ number = {925},
+ eprint = {1202.3665},
+ eprinttype = {arxiv},
+ pages = {306--312},
+ issn = {00046280, 15383873},
+ doi = {10.1086/670067},
+ abstract = {We introduce a stable, well tested Python implementation of the affine-invariant ensemble sampler for Markov chain Monte Carlo (MCMC) proposed by Goodman \& Weare (2010). The code is open source and has already been used in several published projects in the astrophysics literature. The algorithm behind emcee has several advantages over traditional MCMC sampling methods and it has excellent performance as measured by the autocorrelation time (or function calls per independent sample). One major advantage of the algorithm is that it requires hand-tuning of only 1 or 2 parameters compared to \$\textbackslash sim N\^2\$ for a traditional algorithm in an N-dimensional parameter space. In this document, we describe the algorithm and the details of our implementation and API. Exploiting the parallelism of the ensemble method, emcee permits any user to take advantage of multiple CPU cores without extra effort. The code is available online at http://dan.iel.fm/emcee under the MIT License.},
+ archiveprefix = {arXiv},
+ keywords = {Astrophysics - Instrumentation and Methods for Astrophysics,Physics - Computational Physics,Statistics - Computation},
+ file = {/home/david/pdfs/Zotero/Foreman-Mackey et al_2013_emcee.pdf;/home/david/Zotero/storage/SSM96UY2/1202.html}
+}
+
+@article{speagleDynestyDynamicNested2020,
+ title = {Dynesty: A Dynamic Nested Sampling Package for Estimating {{Bayesian}} Posteriors and Evidences},
+ shorttitle = {Dynesty},
+ author = {Speagle, Joshua S},
+ year = {2020},
+ month = apr,
+ journal = {Monthly Notices of the Royal Astronomical Society},
+ volume = {493},
+ number = {3},
+ pages = {3132--3158},
+ issn = {0035-8711},
+ doi = {10.1093/mnras/staa278},
+ abstract = {We present dynesty, a public, open-source, python package to estimate Bayesian posteriors and evidences (marginal likelihoods) using the dynamic nested sampling methods developed by Higson et~al. By adaptively allocating samples based on posterior structure, dynamic nested sampling has the benefits of Markov chain Monte Carlo (MCMC) algorithms that focus exclusively on posterior estimation while retaining nested sampling's ability to estimate evidences and sample from complex, multimodal distributions. We provide an overview of nested sampling, its extension to dynamic nested sampling, the algorithmic challenges involved, and the various approaches taken to solve them in this and previous work. We then examine dynesty's performance on a variety of toy problems along with several astronomical applications. We find in particular problems dynesty can provide substantial improvements in sampling efficiency compared to popular MCMC approaches in the astronomical literature. More detailed statistical results related to nested sampling are also included in the appendix.},
+ file = {/home/david/pdfs/Zotero/Speagle_2020_dynesty.pdf;/home/david/Zotero/storage/PZBMLD2H/5721521.html}
+}
+
+@article{astropycollaborationAstropyCommunityPython2013,
+ title = {Astropy: {{A}} Community {{Python}} Package for Astronomy},
+ shorttitle = {Astropy},
+ author = {{Astropy Collaboration} and Robitaille, Thomas P. and Tollerud, Erik J. and Greenfield, Perry and Droettboom, Michael and Bray, Erik and Aldcroft, Tom and Davis, Matt and Ginsburg, Adam and {Price-Whelan}, Adrian M. and Kerzendorf, Wolfgang E. and Conley, Alexander and Crighton, Neil and Barbary, Kyle and Muna, Demitri and Ferguson, Henry and Grollier, Fr{\'e}d{\'e}ric and Parikh, Madhura M. and Nair, Prasanth H. and Unther, Hans M. and Deil, Christoph and Woillez, Julien and Conseil, Simon and Kramer, Roban and Turner, James E. H. and Singer, Leo and Fox, Ryan and Weaver, Benjamin A. and Zabalza, Victor and Edwards, Zachary I. and Azalee Bostroem, K. and Burke, D. J. and Casey, Andrew R. and Crawford, Steven M. and Dencheva, Nadia and Ely, Justin and Jenness, Tim and Labrie, Kathleen and Lim, Pey Lian and Pierfederici, Francesco and Pontzen, Andrew and Ptak, Andy and Refsdal, Brian and Servillat, Mathieu and Streicher, Ole},
+ year = {2013},
+ month = oct,
+ journal = {Astronomy and Astrophysics},
+ volume = {558},
+ pages = {A33},
+ issn = {0004-6361},
+ doi = {10.1051/0004-6361/201322068},
+ abstract = {We present the first public version (v0.2) of the open-source and community-developed Python package, Astropy. This package provides core astronomy-related functionality to the community, including support for domain-specific file formats such as flexible image transport system (FITS) files, Virtual Observatory (VO) tables, and common ASCII table formats, unit and physical quantity conversions, physical constants specific to astronomy, celestial coordinate and time transformations, world coordinate system (WCS) support, generalized containers for representing gridded as well as tabular data, and a framework for cosmological transformations and conversions. Significant functionality is under activedevelopment, such as a model fitting framework, VO client and server tools, and aperture and point spread function (PSF) photometry tools. The core development team is actively making additions and enhancements to the current code base, and we encourage anyone interested to participate in the development of future Astropy versions.},
+ langid = {english},
+ file = {/home/david/pdfs/Zotero/Collaboration et al_2013_Astropy.pdf;/home/david/Zotero/storage/VXZP754H/abstract.html}
+}
+
+@article{astropycollaborationAstropyProjectBuilding2018,
+ title = {The {{Astropy Project}}: {{Building}} an {{Open-science Project}} and {{Status}} of the v2.0 {{Core Package}}},
+ shorttitle = {The {{Astropy Project}}},
+ author = {{Astropy Collaboration} and {Price-Whelan}, A. M. and Sip{\H 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 Bach, Y. P. 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 Corrales, L. and Crichton, D. and D'Avella, 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. and {Astropy Contributors}},
+ year = {2018},
+ month = sep,
+ journal = {The Astronomical Journal},
+ volume = {156},
+ pages = {123},
+ issn = {0004-6256},
+ doi = {10.3847/1538-3881/aabc4f},
+ abstract = {The Astropy Project supports and fosters the development of open-source and openly developed Python packages that provide commonly needed functionality to the astronomical community. A key element of the Astropy Project is the core package astropy, which serves as the foundation for more specialized projects and packages. In this article, we provide an overview of the organization of the Astropy project and summarize key features in the core package, as of the recent major release, version 2.0. We then describe the project infrastructure designed to facilitate and support development for a broader ecosystem of interoperable packages. We conclude with a future outlook of planned new features and directions for the broader Astropy Project. .},
+ keywords = {Astrophysics - Instrumentation and Methods for Astrophysics,methods: data analysis,methods: miscellaneous,methods: statistical,reference systems},
+ annotation = {ADS Bibcode: 2018AJ....156..123A},
+ file = {/home/david/pdfs/Zotero/Astropy Collaboration et al_2018_The Astropy Project2.pdf}
+}
+
+
+@article{mirouh_etal22,
+ author = {{Mirouh}, Giovanni M. and {Hendriks}, David D. and {Dykes}, Sophie and {Moe}, Maxwell and {Izzard}, Robert G.},
+ title = "{Detailed equilibrium and dynamical tides: impact on circularization and synchronization in open clusters}",
+ journal = {\mnras},
+ year = "submitted",
+}
\ No newline at end of file
diff --git a/papers/joss_paper/paper.crossref b/papers/joss_paper/paper.crossref
new file mode 100644
index 0000000000000000000000000000000000000000..46062ee5c9bf15c4b044008064e1b7fd3f207ac7
--- /dev/null
+++ b/papers/joss_paper/paper.crossref
@@ -0,0 +1,237 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<doi_batch xmlns="http://www.crossref.org/schema/5.3.1"
+ xmlns:ai="http://www.crossref.org/AccessIndicators.xsd"
+ xmlns:rel="http://www.crossref.org/relations.xsd"
+ xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+ version="5.3.1"
+ xsi:schemaLocation="http://www.crossref.org/schema/5.3.1 http://www.crossref.org/schemas/crossref5.3.1.xsd">
+ <head>
+ <doi_batch_id>20220618T102130-31c226c27c5bafd915ddd929fd270d6cd13f2bf3</doi_batch_id>
+ <timestamp>20220618102130</timestamp>
+ <depositor>
+ <depositor_name>JOSS Admin</depositor_name>
+ <email_address>admin@theoj.org</email_address>
+ </depositor>
+ <registrant>The Open Journal</registrant>
+ </head>
+ <body>
+ <journal>
+ <journal_metadata>
+ <full_title>Journal of Open Source Software</full_title>
+ <abbrev_title>JOSS</abbrev_title>
+ <issn media_type="electronic">2475-9066</issn>
+ <doi_data>
+ <doi>10.21105/joss</doi>
+ <resource>https://joss.theoj.org/</resource>
+ </doi_data>
+ </journal_metadata>
+ <journal_issue>
+ <publication_date media_type="online">
+ <month>01</month>
+ <year>1970</year>
+ </publication_date>
+ <journal_volume>
+ <volume>¿VOL?</volume>
+ </journal_volume>
+ <issue>¿ISSUE?</issue>
+ </journal_issue>
+ <journal_article publication_type="full_text">
+ <titles>
+ <title>binary_c-python: A python-based stellar population
+synthesis tool and interface to binary_c</title>
+ </titles>
+ <contributors>
+ <person_name sequence="first" contributor_role="author">
+ <given_name>D. D.</given_name>
+ <surname>Hendriks</surname>
+ <ORCID>https://orcid.org/0000-0002-8717-6046</ORCID>
+ </person_name>
+ <person_name sequence="additional"
+ contributor_role="author">
+ <given_name>R. G.</given_name>
+ <surname>Izzard</surname>
+ <ORCID>https://orcid.org/0000-0003-0378-4843</ORCID>
+ </person_name>
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+ <citation_list>
+ <citation key="izzardNewSyntheticModel2004">
+ <article_title>A new synthetic model for asymptotic giant
+branch stars</article_title>
+ <author>Izzard</author>
+ <journal_title>Monthly Notices of the Royal Astronomical
+Society</journal_title>
+ <issue>2</issue>
+ <volume>350</volume>
+ <doi>10.1111/j.1365-2966.2004.07446.x</doi>
+ <issn>0035-8711</issn>
+ <cYear>2004</cYear>
+ <unstructured_citation>Izzard, R. G., Tout, C. A., Karakas,
+A. I., & Pols, O. R. (2004). A new synthetic model for asymptotic
+giant branch stars. Monthly Notices of the Royal Astronomical Society,
+350(2), 407–426.
+https://doi.org/10.1111/j.1365-2966.2004.07446.x</unstructured_citation>
+ </citation>
+ <citation key="izzardPopulationNucleosynthesisSingle2006">
+ <article_title>Population nucleosynthesis in single and
+binary stars - I. Model</article_title>
+ <author>Izzard</author>
+ <journal_title>Astronomy & Astrophysics</journal_title>
+ <issue>2</issue>
+ <volume>460</volume>
+ <doi>10.1051/0004-6361:20066129</doi>
+ <issn>0004-6361</issn>
+ <cYear>2006</cYear>
+ <unstructured_citation>Izzard, R. G., Dray, L. M., Karakas,
+A. I., Lugaro, M., & Tout, C. A. (2006). Population nucleosynthesis
+in single and binary stars - I. Model. Astronomy & Astrophysics,
+460(2), 565–572.
+https://doi.org/10.1051/0004-6361:20066129</unstructured_citation>
+ </citation>
+ <citation key="izzardPopulationSynthesisBinary2009">
+ <article_title>Population synthesis of binary
+carbon-enhanced metal-poor stars</article_title>
+ <author>Izzard</author>
+ <journal_title>Astronomy and Astrophysics</journal_title>
+ <issue>3</issue>
+ <volume>508</volume>
+ <doi>10.1051/0004-6361/200912827</doi>
+ <issn>0004-6361</issn>
+ <cYear>2009</cYear>
+ <unstructured_citation>Izzard, R. G., Glebbeek, E.,
+Stancliffe, R. J., & Pols, O. R. (2009). Population synthesis of
+binary carbon-enhanced metal-poor stars. Astronomy and Astrophysics,
+508(3), 1359–1374.
+https://doi.org/10.1051/0004-6361/200912827</unstructured_citation>
+ </citation>
+ <citation key="izzardBinaryStarsGalactic2018">
+ <article_title>Binary stars in the Galactic thick
+disc</article_title>
+ <author>Izzard</author>
+ <journal_title>Monthly Notices of the Royal Astronomical
+Society</journal_title>
+ <volume>473</volume>
+ <doi>10.1093/mnras/stx2355</doi>
+ <issn>0035-8711</issn>
+ <cYear>2018</cYear>
+ <unstructured_citation>Izzard, R. G., Preece, H., Jofre, P.,
+Halabi, G. M., Masseron, T., & Tout, C. A. (2018). Binary stars in
+the Galactic thick disc. Monthly Notices of the Royal Astronomical
+Society, 473, 2984–2999.
+https://doi.org/10.1093/mnras/stx2355</unstructured_citation>
+ </citation>
+ <citation key="foreman-mackeyEmceeMCMCHammer2013">
+ <article_title>Emcee: The MCMC Hammer</article_title>
+ <author>Foreman-Mackey</author>
+ <journal_title>Publications of the Astronomical Society of
+the Pacific</journal_title>
+ <issue>925</issue>
+ <volume>125</volume>
+ <doi>10.1086/670067</doi>
+ <cYear>2013</cYear>
+ <unstructured_citation>Foreman-Mackey, D., Hogg, D. W.,
+Lang, D., & Goodman, J. (2013). Emcee: The MCMC Hammer. Publications
+of the Astronomical Society of the Pacific, 125(925), 306–312.
+https://doi.org/10.1086/670067</unstructured_citation>
+ </citation>
+ <citation key="speagleDynestyDynamicNested2020">
+ <article_title>Dynesty: A dynamic nested sampling package
+for estimating Bayesian posteriors and evidences</article_title>
+ <author>Speagle</author>
+ <journal_title>Monthly Notices of the Royal Astronomical
+Society</journal_title>
+ <issue>3</issue>
+ <volume>493</volume>
+ <doi>10.1093/mnras/staa278</doi>
+ <issn>0035-8711</issn>
+ <cYear>2020</cYear>
+ <unstructured_citation>Speagle, J. S. (2020). Dynesty: A
+dynamic nested sampling package for estimating Bayesian posteriors and
+evidences. Monthly Notices of the Royal Astronomical Society, 493(3),
+3132–3158. https://doi.org/10.1093/mnras/staa278</unstructured_citation>
+ </citation>
+ <citation key="astropycollaborationAstropyCommunityPython2013">
+ <article_title>Astropy: A community Python package for
+astronomy</article_title>
+ <author>Astropy Collaboration</author>
+ <journal_title>Astronomy and Astrophysics</journal_title>
+ <volume>558</volume>
+ <doi>10.1051/0004-6361/201322068</doi>
+ <issn>0004-6361</issn>
+ <cYear>2013</cYear>
+ <unstructured_citation>Astropy Collaboration, Robitaille, T.
+P., Tollerud, E. J., Greenfield, P., Droettboom, M., Bray, E., Aldcroft,
+T., Davis, M., Ginsburg, A., Price-Whelan, A. M., Kerzendorf, W. E.,
+Conley, A., Crighton, N., Barbary, K., Muna, D., Ferguson, H., Grollier,
+F., Parikh, M. M., Nair, P. H., … Streicher, O. (2013). Astropy: A
+community Python package for astronomy. Astronomy and Astrophysics, 558,
+A33. https://doi.org/10.1051/0004-6361/201322068</unstructured_citation>
+ </citation>
+ <citation key="astropycollaborationAstropyProjectBuilding2018">
+ <article_title>The Astropy Project: Building an Open-science
+Project and Status of the v2.0 Core Package</article_title>
+ <author>Astropy Collaboration</author>
+ <journal_title>The Astronomical Journal</journal_title>
+ <volume>156</volume>
+ <doi>10.3847/1538-3881/aabc4f</doi>
+ <issn>0004-6256</issn>
+ <cYear>2018</cYear>
+ <unstructured_citation>Astropy Collaboration, Price-Whelan,
+A. M., Sipőcz, B. M., Günther, H. M., Lim, P. L., Crawford, S. M.,
+Conseil, S., Shupe, D. L., Craig, M. W., Dencheva, N., Ginsburg, A.,
+VanderPlas, J. T., Bradley, L. D., Pérez-Suárez, D., de Val-Borro, M.,
+Aldcroft, T. L., Cruz, K. L., Robitaille, T. P., Tollerud, E. J., …
+Astropy Contributors. (2018). The Astropy Project: Building an
+Open-science Project and Status of the v2.0 Core Package. The
+Astronomical Journal, 156, 123.
+https://doi.org/10.3847/1538-3881/aabc4f</unstructured_citation>
+ </citation>
+ <citation key="mirouh_etal22">
+ <article_title>Detailed equilibrium and dynamical tides:
+impact on circularization and synchronization in open
+clusters</article_title>
+ <author>Mirouh</author>
+ <unstructured_citation>Mirouh, G. M., Hendriks, D. D.,
+Dykes, S., Moe, M., & Izzard, R. G. (submitted). Detailed
+equilibrium and dynamical tides: impact on circularization and
+synchronization in open clusters.</unstructured_citation>
+ </citation>
+ </citation_list>
+ </journal_article>
+ </journal>
+ </body>
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diff --git a/papers/joss_paper/paper.md b/papers/joss_paper/paper.md
new file mode 100644
index 0000000000000000000000000000000000000000..a4dc41770c8a0142773903ecc304ce2a41bcfe83
--- /dev/null
+++ b/papers/joss_paper/paper.md
@@ -0,0 +1,135 @@
+---
+title: '[binary\_c-python]{.smallcaps}: A python-based stellar population synthesis tool and interface to [binary\_c]{.smallcaps}'
+tags:
+ - Python
+ - astronomy
+authors:
+ - name: D. D. Hendriks[^1]
+ orcid: 0000-0002-8717-6046
+ affiliation: 1
+ - name: R. G. Izzard
+ orcid: 0000-0003-0378-4843
+ affiliation: 1
+affiliations:
+ - name: Department of Physics, University of Surrey, Guildford, GU2 7XH, Surrey, UK
+ index: 1
+date: 18 June 2022
+bibliography: paper.bib
+---
+
+Summary {#sec:summary}
+=======
+
+We present our package
+[[binary\_c-python]{.smallcaps}](https://ri0005.pages.surrey.ac.uk/binary_c-python/),
+which is aimed to provide a convenient and easy-to-use interface to the
+[[binary\_c]{.smallcaps}](http://personal.ph.surrey.ac.uk/~ri0005/doc/binary_c/binary_c.html)Â [@izzardNewSyntheticModel2004; @izzardPopulationNucleosynthesisSingle2006; @izzardPopulationSynthesisBinary2009; @izzardBinaryStarsGalactic2018]
+framework, allowing the user to rapidly evolve individual systems and
+populations of stars. [binary\_c-python]{.smallcaps}Â is available on
+[Pip](https://pypi.org/project/binarycpython/) and on
+[Gitlab](https://gitlab.com/binary_c/binary_c-python).
+
+The user can control output from [binary\_c]{.smallcaps}by providing
+[binary\_c-python]{.smallcaps}Â with logging statements that are
+dynamically compiled and loaded into [binary\_c]{.smallcaps}.
+[binary\_c-python]{.smallcaps}Â uses multiprocessing to utilise all the
+cores on a particular machine, and can run populations with HPC cluster
+workload managers like [HTCondor]{.smallcaps} and [Slurm]{.smallcaps},
+allowing the user to run simulations on very large computing clusters.
+
+[binary\_c-python]{.smallcaps}Â is easily interfaced or integrated with
+other Python-based codes, e.g. sampling codes like [Emcee]{.smallcaps}
+or [Dynesty]{.smallcaps}, or the astrophysics oriented package
+[Astropy]{.smallcaps}Â [@astropycollaborationAstropyCommunityPython2013; @foreman-mackeyEmceeMCMCHammer2013; @astropycollaborationAstropyProjectBuilding2018; @speagleDynestyDynamicNested2020].
+Moreover, it is possible to provide custom system-generating functions
+through our function hooks, allowing third-party packages to control the
+populations of stars and evolve them through
+[binary\_c-python]{.smallcaps}.
+
+Recent developments in [binary\_c]{.smallcaps}Â include standardised
+output datasets called *ensembles*.
+[binary\_c-python]{.smallcaps}Â easily processes these datasets and
+provides a suite of utility functions to handle them. Furthermore,
+[binary\_c]{.smallcaps}Â now includes the *ensemble-manager* class, which
+makes use of the core functions and classes of
+[binary\_c-python]{.smallcaps}Â to evolve a grid of stellar populations
+of stars with varying input physics, allowing for huge, automated
+parameter studies through a single interface.
+
+We provide
+[documentation](https://ri0005.pages.surrey.ac.uk/binary_c-python/index.html)
+that is automatically generated based on docstrings and a suite of
+[Jupyter]{.smallcaps}
+[notebooks](https://ri0005.pages.surrey.ac.uk/binary_c-python/example_notebooks.html).
+These notebooks consist of technical tutorials on how to use
+[binary\_c-python]{.smallcaps}, and use-case scenarios aimed at doing
+science. Much of [binary\_c-python]{.smallcaps}Â is covered by unit tests
+to ensure reliability and correctness, and the test coverage is
+continually increased as the package is being improved.
+
+Statement of need {#sec:statement}
+=================
+
+In the current scientific climate [Python]{.smallcaps} is ubiquitous,
+and while lower-level codes written in e.g. [Fortran]{.smallcaps} or
+[C]{.smallcaps} are still widely used, much of the newer software is
+written in [Python]{.smallcaps}, either entirely or as a wrapper around
+other codes. Education in programming also often includes
+[Python]{.smallcaps} courses because of its ease of use and its
+flexibility. Moreover, [Python]{.smallcaps} has a large community with
+many resources and tutorials. We have created
+[binary\_c-python]{.smallcaps}Â to allow students and scientists alike to
+explore current scientific issues while enjoying the familiar syntax,
+and at the same time make use of the plentiful scientific and
+astrophysical packages like [Numpy]{.smallcaps}, [Scipy]{.smallcaps},
+[Pandas]{.smallcaps}, [Astropy]{.smallcaps}Â and platforms like
+[Jupyter]{.smallcaps}.
+
+Earlier versions of [binary\_c-python]{.smallcaps}Â were written in Perl,
+where much of the debugging and the logic and structure developments
+were done. This greatly made porting to [Python]{.smallcaps} relatively
+easy.
+
+Projects that use [binary\_c-python]{.smallcaps} {#sec:projects}
+================================================
+
+[binary\_c-python]{.smallcaps}Â has already been used in a variety of
+situations, ranging from pure research to educational purposes, as well
+as in outreach events. In the summer of 2021 we used
+[binary\_c-python]{.smallcaps}Â as the basis for the interactive classes
+on stellar ecosystems during the [International Max-Planck Research
+School summer school 2021 in
+Heidelberg](https://www2.mpia-hd.mpg.de/imprs-hd/SummerSchools/2021/),
+where students were introduced to the topic of population synthesis and
+were able to use our notebooks to perform their own calculations.
+[binary\_c-python]{.smallcaps}Â has been used in @mirouh_etal22, where
+improvements to tidal interactions between stars were implemented, and
+initial birth parameter distributions were varied to match to observed
+binary systems in star clusters. A Master's thesis project, aimed at
+finding the birth system parameters of the V106 stellar system,
+comparing observations to results of [binary\_c]{.smallcaps}Â and
+calculating the maximum likelihood with Bayesian inference through
+Markov chain Monte Carlo sampling. The project made use of
+[binary\_c-python]{.smallcaps}Â and the [Emcee]{.smallcaps} package.
+
+Currently [binary\_c-python]{.smallcaps}Â is used in several ongoing
+projects that study the effect of birth distributions on the occurrence
+of carbon-enhanced metal-poor (CEMP) stars, the occurrence and
+properties of accretion disks in main-sequence stars and the predicted
+observable black hole distribution by combining star formation and
+metallicity distributions with the output of [binary\_c]{.smallcaps}.
+Moreover, we use the *ensemble* output structure to generate datasets
+for galactic chemical evolution on cosmological timescales, where we
+rely heavily on the utilities of [binary\_c-python]{.smallcaps}.
+
+Acknowledgements {#sec:orgf6f5520}
+================
+
+We acknowledge the helpful discussions and early testing efforts from M.
+Delorme, G. Mirouh, and D. Tracey, and the early work of J. Andrews
+which inspired our Python-C interface code. DDH thanks the UKRI/UoS for
+the funding grant H120341A. RGI thanks STFC for funding grants
+[ST/R000603/1](https://gtr.ukri.org/projects?ref=ST%2FR000603%2F1) and
+[ST/L003910/2](https://gtr.ukri.org/projects?ref=ST/L003910/2).
+
+[^1]: E-mail: <dh00601@surrey.ac.uk>Â (DDH)
diff --git a/papers/joss_paper/paper_tex/auto/paper.el b/papers/joss_paper/paper_tex/auto/paper.el
new file mode 100644
index 0000000000000000000000000000000000000000..52d0c5f7ad6bc4985be28a1bd4ce943d1b473e07
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+(TeX-add-style-hook
+ "paper"
+ (lambda ()
+ (TeX-add-to-alist 'LaTeX-provided-class-options
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+ (TeX-add-to-alist 'LaTeX-provided-package-options
+ '(("inputenc" "utf8") ("fontenc" "T1") ("ulem" "normalem")))
+ (add-to-list 'LaTeX-verbatim-environments-local "lstlisting")
+ (add-to-list 'LaTeX-verbatim-macros-with-braces-local "path")
+ (add-to-list 'LaTeX-verbatim-macros-with-braces-local "url")
+ (add-to-list 'LaTeX-verbatim-macros-with-braces-local "nolinkurl")
+ (add-to-list 'LaTeX-verbatim-macros-with-braces-local "hyperbaseurl")
+ (add-to-list 'LaTeX-verbatim-macros-with-braces-local "hyperimage")
+ (add-to-list 'LaTeX-verbatim-macros-with-braces-local "hyperref")
+ (add-to-list 'LaTeX-verbatim-macros-with-braces-local "href")
+ (add-to-list 'LaTeX-verbatim-macros-with-braces-local "lstinline")
+ (add-to-list 'LaTeX-verbatim-macros-with-delims-local "path")
+ (add-to-list 'LaTeX-verbatim-macros-with-delims-local "lstinline")
+ (TeX-run-style-hooks
+ "latex2e"
+ "mnras"
+ "mnras10"
+ "inputenc"
+ "fontenc"
+ "graphicx"
+ "grffile"
+ "longtable"
+ "wrapfig"
+ "rotating"
+ "ulem"
+ "amsmath"
+ "textcomp"
+ "amssymb"
+ "capt-of"
+ "hyperref"
+ "color"
+ "listings"
+ "natbib"
+ "hypernat"
+ "/home/david/projects/latex_todo_upgrade/tex_todo"
+ "/home/david/projects/latex_editing_colors/editing_colors")
+ (TeX-add-symbols
+ '("VAN" 3)
+ "binaryc"
+ "binarycpython"
+ "mytitle"
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+ "thebibliography")
+ (LaTeX-add-labels
+ "sec:summary"
+ "sec:statement"
+ "sec:projects"
+ "sec:orgf6f5520")
+ (LaTeX-add-bibliographies
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+ :latex)
+
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+%% Invocation:
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+%% LaTeX2e class file (mnras.cls).
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+%% Hyperlinks:
+%% To make the eprint and doi bibtex fields hyperlinks, you need
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+%% Authors:
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+%% Sake J. Hogeveen
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+%% At the request of Keith Smith this file has been renamed to be mnras.bst
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+%%
+%% License:
+%% This work may be distributed and/or modified under the
+%% conditions of the LaTeX Project Public License, either version 1.3
+%% of this license or (at your option) any later version.
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+ }
+ if$
+ mid.sentence 'output.state :=
+ }
+ if$
+ s
+}
+
+% output.nonnull.extra is like output.nonnull, except that the thing
+% we output is 'extra' to a block, so if we're in the after.block
+% state, we append it rather than starting a new block.
+FUNCTION {output.nonnull.extra}
+{ 's :=
+ output.state mid.sentence =
+ { ", " * write$ }
+ { output.state after.block =
+ { ", " * write$
+ newline$
+ "\newblock " write$
+ }
+ { output.state before.all =
+ 'write$
+ { ", " * write$ }
+ if$
+ }
+ if$
+ mid.sentence 'output.state :=
+ }
+ if$
+ s
+}
+
+FUNCTION {output.nonnull.nocomma}
+{'s :=
+ output.state mid.sentence =
+ { write$ }
+ { output.state after.block =
+ { ". " * write$
+ newline$
+% "\newblock " write$
+ }
+ { output.state before.all =
+ 'write$
+ { ", " * write$ }
+ if$
+ }
+ if$
+ mid.sentence 'output.state :=
+ }
+ if$
+ s
+}
+
+FUNCTION {output}
+{ duplicate$ empty$
+ 'pop$
+ 'output.nonnull
+ if$
+}
+
+FUNCTION {output.extra}
+{ duplicate$ empty$
+ 'pop$
+ 'output.nonnull.extra
+ if$
+}
+
+FUNCTION {output.check}
+{ 't :=
+ duplicate$ empty$
+ { pop$ "empty " t * " in " * cite$ * warning$ }
+ 'output.nonnull
+ if$
+}
+
+FUNCTION {output.check.nocomma}
+{ 't :=
+ duplicate$ empty$
+ 'pop$ % or warn with { pop$ "empty " t * " in " * cite$ * warning$ }
+ 'output.nonnull.nocomma
+ if$
+}
+
+FUNCTION {output.check.extra}
+{ 't :=
+ duplicate$ empty$
+ { pop$ "empty " t * " in " * cite$ * warning$ }
+ 'output.nonnull.extra
+ if$
+}
+
+FUNCTION {output.year.check}
+{ year empty$
+ { "empty year in " cite$ * warning$ }
+ { write$
+ " " year * extra.label *
+ mid.sentence 'output.state :=
+ }
+ if$
+}
+
+FUNCTION {output.bibitem}
+{ newline$
+ "\bibitem[" write$
+ label write$
+ "]{" write$
+ cite$ write$
+ "}" write$
+ % debugging: define eg \def\logsortkey#1{{[\tiny #1]}} to see this
+ %"\logsortkey{" presort.key * "/" * sort.key$ * "}" * write$
+ newline$
+ ""
+ before.all 'output.state :=
+}
+
+FUNCTION {fin.entry}
+{ write$
+ newline$
+}
+
+FUNCTION {new.block}
+{ output.state before.all =
+ 'skip$
+ { after.block 'output.state := }
+ if$
+}
+
+FUNCTION {new.sentence}
+{ output.state after.block =
+ 'skip$
+ { output.state before.all =
+ 'skip$
+ { after.sentence 'output.state := }
+ if$
+ }
+ if$
+}
+
+FUNCTION {not}
+{ { #0 }
+ { #1 }
+ if$
+}
+
+FUNCTION {and}
+{ 'skip$
+ { pop$ #0 }
+ if$
+}
+
+FUNCTION {or}
+{ { pop$ #1 }
+ 'skip$
+ if$
+}
+
+FUNCTION {new.block.checkb}
+{ empty$
+ swap$ empty$
+ and
+ 'skip$
+ 'new.block
+ if$
+}
+
+FUNCTION {field.or.null}
+{ duplicate$ empty$
+ { pop$ "" }
+ 'skip$
+ if$
+}
+
+FUNCTION {boldface}
+{ duplicate$ empty$
+ { pop$ "" }
+ { "{ " swap$ * "}" * }
+ if$
+}
+
+FUNCTION {emphasize}
+{ duplicate$ empty$
+ { pop$ "" }
+ { "{ " swap$ * "}" * }
+ if$
+}
+
+% Make hyperref links.
+% The LaTeX hyperref package supports a macro \href{URL}{text}
+%
+% On call, the stack contains
+% href-url
+% link-text
+FUNCTION {make.href.hyperref}
+{
+ "\href {" swap$ * "} {" * swap$ * "}" *
+}
+
+INTEGERS { nameptr namesleft numnames }
+
+% Helper functions for print.all.names: print the last or 'others' name.
+%
+% On call, the stack contains
+% a formatted name,
+% and the built-up string of names so far.
+FUNCTION {print.all.names.plain.trailer}
+{ duplicate$ "others" =
+ { pop$ " et~al.," * }
+ { " " swap$ * * }
+ if$
+}
+
+% as above
+FUNCTION {print.all.names.label.trailer}
+{ duplicate$ "others" =
+ { pop$ " et~al." * }
+ { " \& " swap$ * * }
+ if$
+}
+
+% Print out the complete author list
+% (because we have maxauthors or fewer).
+%
+% On call, the stack contains
+% a format string (for format.name$),
+% a name-separator string (such as ", "),
+% an author or editor field,
+% and one of the 'trailer' functions above.
+FUNCTION {print.all.names}
+{ 'fmt :=
+ 'sep :=
+ 's :=
+ s num.names$ 'namesleft :=
+ namesleft #2 < % we're not going to need the trailer function, so discard it
+ 'pop$
+ 'skip$
+ if$
+ #1 'nameptr :=
+ { namesleft #0 > }
+ { s nameptr fmt format.name$ 't := % last name first
+ nameptr #1 >
+ { namesleft #1 >
+ { sep * t * }
+ { % namesleft == 1: this is the last name.
+ % Invoke the trailer function.
+ s num.names$ #2 > % _why_ do we add this extra space for long lists?
+ { " " * }
+ 'skip$
+ if$
+ % This next line is a bit clever.
+ %
+ % We start with a stack
+ % string containing the list of names so far
+ % trailer function
+ %
+ % Rearrange the stack so that we have
+ % 'skip
+ % trailer function
+ % #1
+ % t
+ % names so far
+ % then call if$. This is a rather indirect way of
+ % invoking the trailer function on the stack
+ % t
+ % names so far
+ %
+ % Ta dahhhh!
+ swap$ t swap$ #1 swap$ 'skip$ if$
+ }
+ if$
+ }
+ 't
+ if$
+ nameptr #1 + 'nameptr :=
+ namesleft #1 - 'namesleft :=
+ }
+ while$
+}
+
+% Name formatting. According to the MN instructions for authors, `In
+% the references list [...] List all authors if eight or fewer,
+% otherwise et al.'. This means (according to a ruling from the MN
+% editors) that if there are eight or more authors, they should be
+% listed as "first one plus et al."
+%
+% On call, the stack contains
+% an author or editor field.
+FUNCTION {format.names}
+{ duplicate$ num.names$ maxauthors >
+ { % Too many authors -- format as First author et al.
+ #1 "{vv }{ll}{ jj}{ f., }" format.name$ % last name first
+ " et~al.," *
+ }
+ { 'print.all.names.plain.trailer swap$ " " "{vv }{ll}{ jj}{ f., }" print.all.names }
+ if$
+}
+
+% Format an author/editor field, for inclusion in a label
+% (ie, "Surname, Surname \& Surname")
+%
+% On call, the stack contains an author/editor field.
+FUNCTION {format.names.label}
+{ duplicate$ num.names$ maxauthors >
+ { % Too many authors -- format as First author et al.
+ #1 "{vv }{ll}{ jj}" format.name$ % last name first
+ " et~al.," *
+ }
+ { 'print.all.names.label.trailer swap$ ", " "{vv }{ll}" print.all.names }
+ if$
+}
+
+FUNCTION {format.authors}
+{ author empty$
+ { "" }
+ { author format.names }
+ if$
+}
+
+FUNCTION {format.key} % this function is just for apalike
+{ empty$
+ { key field.or.null }
+ { "" }
+ if$
+}
+
+FUNCTION {format.editors}
+{ editor empty$
+ { "" }
+ { editor format.names
+ editor num.names$ #1 >
+ { " eds," * }
+ { " ed." * }
+ if$
+ }
+ if$
+}
+
+FUNCTION {format.editors.extra}
+{ editor empty$
+ { "" }
+ { editor format.names
+ editor num.names$ #1 >
+ { " eds" * }
+ { " ed." * }
+ if$
+ }
+ if$
+}
+
+FUNCTION {format.title}
+{ title empty$
+ { "" }
+ { title "t" change.case$ }
+ if$
+}
+
+FUNCTION {format.eprint}
+{ eprint empty$
+ { "" }
+ { " (\mn@eprint {"
+ archiveprefix empty$
+ { "" }
+ { archiveprefix }
+ if$
+ * "} {" * eprint * "})" * }
+ if$
+}
+
+FUNCTION {format.doi}
+{ doi empty$
+ { "" }
+ { ", \mn@doi{" * doi * "}" }
+ if$
+}
+
+FUNCTION {n.dashify}
+{ 't :=
+ ""
+ { t empty$ not }
+ { t #1 #1 substring$ "-" =
+ { t #1 #2 substring$ "--" = not
+ { "--" *
+ t #2 global.max$ substring$ 't :=
+ }
+ { { t #1 #1 substring$ "-" = }
+ { "-" *
+ t #2 global.max$ substring$ 't :=
+ }
+ while$
+ }
+ if$
+ }
+ { t #1 #1 substring$ *
+ t #2 global.max$ substring$ 't :=
+ }
+ if$
+ }
+ while$
+}
+
+FUNCTION {first.page.number}
+{ 't :=
+ ""
+ { t "" =
+ { #0 }
+ { t #1 #1 substring$ "-" = not }
+ if$
+ }
+ { t #1 #1 substring$ *
+ t #2 global.max$ substring$ 't :=
+ }
+ while$
+}
+
+FUNCTION {format.btitle}
+{ title
+}
+
+FUNCTION {tie.or.space.connect}
+{ duplicate$ text.length$ #5 <
+ { "~" }
+ { " " }
+ if$
+ swap$ * *
+}
+
+FUNCTION {either.or.check}
+{ empty$
+ 'pop$
+ { "can't use both " swap$ * " fields in " * cite$ * warning$ }
+ if$
+}
+
+FUNCTION {format.bvolume}
+{ volume empty$
+ { "" }
+ { "" series tie.or.space.connect
+ volume empty$
+ 'skip$
+ { " Vol. " * volume * }
+ if$
+ "volume and number" number either.or.check
+ }
+ if$
+}
+
+FUNCTION {format.number.series}
+{ volume empty$
+ { number empty$
+ { series field.or.null }
+ { output.state mid.sentence =
+ { "No." }
+ { "No." }
+ if$
+ number tie.or.space.connect
+ series empty$
+ { "there's a number but no series in " cite$ * warning$ }
+ { " in " * series * }
+ if$
+ }
+ if$
+ }
+ { "" }
+ if$
+}
+
+FUNCTION {format.edition}
+{ edition empty$
+ { "" }
+ { output.state mid.sentence =
+ { edition "l" change.case$ " edn" * }
+ { edition "t" change.case$ " edn" * }
+ if$
+ }
+ if$
+}
+
+INTEGERS { multiresult }
+
+FUNCTION {multi.page.check}
+{ 't :=
+ #0 'multiresult :=
+ { multiresult not
+ t empty$ not
+ and
+ }
+ { t #1 #1 substring$
+ duplicate$ "-" =
+ swap$ duplicate$ "," =
+ swap$ "+" =
+ or or
+ { #1 'multiresult := }
+ { t #2 global.max$ substring$ 't := }
+ if$
+ }
+ while$
+ multiresult
+}
+
+FUNCTION {format.pages}
+{ pages empty$
+ { "" }
+ { pages multi.page.check
+ { "pp" pages n.dashify tie.or.space.connect }
+ { "p." pages tie.or.space.connect }
+ if$
+ }
+ if$
+}
+
+FUNCTION {format.page}
+{ pages empty$
+ { "" }
+ { "p.~" pages first.page.number * }
+ if$
+}
+
+% If a paper is available as a preprint only, ADS will call the
+% journal "ArXiv e-print". In this case MN suggests the journal
+% should be called "preprint".
+FUNCTION {format.journal.doi}
+{ doi empty$
+ { journal "ArXiv e-prints" =
+ { "preprint" }
+ { journal }
+ if$
+ }
+ { journal "ArXiv e-prints" =
+ { "preprint" }
+ { "\mn@doi [" journal * "] {" * doi * "}" * }
+ if$
+ }
+ if$
+}
+
+FUNCTION {format.vol.num.pages}
+{ volume field.or.null
+ number empty$
+ 'skip$
+ { "(" number * ")" * *
+ volume empty$
+ { "there's a number but no volume in " cite$ * warning$ }
+ 'skip$
+ if$
+ }
+ if$
+ pages empty$
+ 'skip$
+ { duplicate$ empty$
+ { pop$ format.pages }
+ { ", " * pages n.dashify * }
+ if$
+ }
+ if$
+}
+
+FUNCTION {format.vol.page}
+{ volume field.or.null
+ pages empty$
+ 'skip$
+ { duplicate$ empty$
+ { pop$ format.pages }
+ { ", " * pages first.page.number * }
+ if$
+ }
+ if$
+}
+
+FUNCTION {format.vol.num.page}
+{ volume field.or.null
+ number empty$
+ 'skip$
+ { "(" number * ")" * *
+ volume empty$
+ { "there's a number but no volume in " cite$ * warning$ }
+ 'skip$
+ if$
+ }
+ if$
+ pages empty$
+ 'skip$
+ { duplicate$ empty$
+ { pop$ format.pages }
+ { ", " * pages first.page.number * }
+ if$
+ }
+ if$
+}
+FUNCTION {format.chapter.pages}
+{ chapter empty$
+ 'format.pages
+ { type empty$
+ { "Chapt." }
+ { type "l" change.case$ }
+ if$
+ chapter tie.or.space.connect
+ pages empty$
+ 'skip$
+ { ", " * format.pages * }
+ if$
+ }
+ if$
+}
+
+FUNCTION {format.in.ed.booktitle}
+{ booktitle empty$
+ { "" }
+ { editor empty$
+ { "in " booktitle * }
+ { format.bvolume empty$
+ { "in " format.editors.extra * ", " * booktitle * }
+ { "in " format.editors.extra * ", " * format.bvolume * ", " * booktitle * }
+ if$
+ }
+ if$
+ }
+ if$
+}
+
+FUNCTION {format.in.ed.collect}
+{ booktitle empty$
+ { "" }
+ { editor empty$
+ { "in " }
+ { "in " format.editors.extra * ", " * }
+ if$
+ series empty$
+ { skip$ }
+ { series * }
+ if$
+ volume empty$
+ { number empty$
+ { }
+ { output.state mid.sentence =
+ { "No." }
+ { "No." }
+ if$
+ number tie.or.space.connect *
+ }
+ if$
+ }
+ {
+ output.state mid.sentence =
+ { ", " * }
+ { skip$ }
+ if$
+ "Vol." volume tie.or.space.connect *
+ }
+ if$
+ output.state mid.sentence =
+ { ", " * }
+ { skip$ }
+ if$
+ booktitle *
+ }
+ if$
+}
+
+FUNCTION {format.thesis.type}
+{ type empty$
+ 'skip$
+ { pop$
+ type "t" change.case$
+ }
+ if$
+}
+
+% the \url{} macro is supplied by hyperref
+FUNCTION {format.url}
+{
+ url empty$
+ { "" }
+ { "\url {" url * "}" * }
+ if$
+}
+
+FUNCTION {format.tr.number}
+{
+ type empty$
+ { "Technical Report" }
+ { type }
+ if$
+ number empty$
+ { "t" change.case$ }
+ { number tie.or.space.connect }
+ if$
+}
+
+FUNCTION {format.article.crossref}
+{ "in" % this is for apalike
+ " \cite{" * crossref * "}" *
+}
+
+FUNCTION {format.book.crossref}
+{ volume empty$
+ { "empty volume in " cite$ * "'s crossref of " * crossref * warning$
+ "in "
+ }
+ { "Vol." volume tie.or.space.connect
+ " of " *
+ }
+ if$
+ "\cite{" * crossref * "}" * % this is for apalike
+}
+
+FUNCTION {format.incoll.inproc.crossref}
+{ "in" % this is for apalike
+ " \cite{" * crossref * "}" *
+}
+
+FUNCTION {article}
+{ output.bibitem
+ format.authors "author" output.check
+ author format.key output % special for
+ output.year.check % apalike
+ % MN style does not display eprints or DOIs on published articles,
+ % but does link the journal name to any available DOI.
+ crossref missing$
+ { format.journal.doi "journal" output.check.extra
+ % ...and links volume and page information to any available adsurl
+ adsurl empty$
+ { format.vol.page }
+ { format.vol.page adsurl make.href.hyperref }
+ if$
+ output.extra
+ }
+ { format.article.crossref output.nonnull
+ format.page output
+ }
+ if$
+
+ % If the "journal" field is the arXiv, then print out the arXiv identifier
+ journal "ArXiv e-prints" =
+ { format.eprint "eprint" output.check.nocomma }
+ { }
+ if$
+
+ fin.entry
+}
+
+FUNCTION {book}
+{ output.bibitem
+ author empty$
+ { format.editors "author and editor" output.check
+ editor format.key output
+ }
+ { format.authors output.nonnull
+ crossref missing$
+ { "author and editor" editor either.or.check }
+ 'skip$
+ if$
+ }
+ if$
+ output.year.check % special for apalike
+ format.btitle "title" output.check
+ format.edition output
+ new.block
+ crossref missing$
+ { format.bvolume output
+ format.number.series output
+ new.sentence
+ publisher "publisher" output.check
+ address output
+ }
+ {format.book.crossref output.nonnull}
+ if$
+ format.eprint "eprint" output.check.nocomma
+ format.doi "doi" output.check.nocomma
+ format.url output
+ fin.entry
+}
+
+FUNCTION {booklet}
+{ output.bibitem
+ format.authors output
+ author format.key output % special for
+ output.year.check % apalike
+ format.btitle "title" output.check
+ howpublished output
+ address output
+ format.eprint "eprint" output.check.nocomma
+ format.doi "doi" output.check.nocomma
+ format.url output
+ fin.entry
+}
+
+FUNCTION {inbook}
+{ output.bibitem
+ author empty$
+ { format.editors "author and editor" output.check
+ editor format.key output
+ }
+ { format.authors output.nonnull
+ crossref missing$
+ { "author and editor" editor either.or.check }
+ 'skip$
+ if$
+ }
+ if$
+ output.year.check % special for apalike
+ format.btitle "title" output.check
+ format.edition output
+ new.block
+ crossref missing$
+ {
+ new.sentence
+ publisher "publisher" output.check
+ address output
+ format.pages output
+ }
+ { format.chapter.pages "chapter and pages" output.check
+ format.book.crossref output.nonnull
+ }
+ if$
+ format.eprint "eprint" output.check.nocomma
+ format.doi "doi" output.check.nocomma
+ format.url output
+ fin.entry
+}
+
+FUNCTION {incollection}
+{ output.bibitem
+ format.authors "author" output.check
+ author format.key output % special for
+ output.year.check % apalike
+ crossref missing$
+ {
+ format.in.ed.collect "booktitle" output.check
+ format.edition output
+ booktitle empty$ edition empty$ =
+ { } { new.block } if$
+ new.sentence
+ publisher "publisher" output.check
+ address output
+ }
+ { format.incoll.inproc.crossref output.nonnull
+ format.chapter.pages output
+ }
+ if$
+ format.chapter.pages output
+ format.eprint "eprint" output.check.nocomma
+ format.doi "doi" output.check.nocomma
+ format.url output
+ fin.entry
+}
+
+FUNCTION {inproceedings}
+{ output.bibitem
+ format.authors "author" output.check
+ author format.key output % special for
+ output.year.check % apalike
+ crossref missing$
+ {
+
+ format.in.ed.booktitle "booktitle" output.check
+ ". " *
+% format.bvolume output
+ before.all 'output.state :=
+ new.block
+% format.title "title" output.check
+ format.number.series output
+ new.block
+% organization output
+ publisher output
+ address output
+ format.pages output
+ }
+ { format.incoll.inproc.crossref output.nonnull
+ format.pages output
+ }
+ if$
+ format.eprint "eprint" output.check.nocomma
+ format.doi "doi" output.check.nocomma
+ format.url output
+ fin.entry
+}
+
+FUNCTION {conference} { inproceedings }
+
+FUNCTION {manual}
+{ output.bibitem
+ format.authors output
+ author format.key output % special for
+ output.year.check % apalike
+ format.btitle "title" output.check
+ new.block
+ organization address new.block.checkb
+ organization output
+ address output
+ format.edition output
+ format.eprint "eprint" output.check.nocomma
+ format.doi "doi" output.check.nocomma
+ format.url output
+ fin.entry
+}
+
+FUNCTION {mastersthesis}
+{ output.bibitem
+ format.authors "author" output.check
+ author format.key output % special for
+ output.year.check % apalike
+ "Master's thesis" format.thesis.type output.nonnull
+ school "school" output.check
+ address output
+ format.eprint "eprint" output.check.nocomma
+ format.doi "doi" output.check.nocomma
+ format.url output
+ fin.entry
+}
+
+FUNCTION {misc}
+{ output.bibitem
+ format.authors output
+ author format.key output % special for apalike
+ output.year.check
+ format.btitle output
+ howpublished output
+ format.eprint "eprint" output.check.nocomma
+ format.doi "doi" output.check.nocomma
+ format.url output
+ fin.entry
+}
+
+FUNCTION {phdthesis}
+{ output.bibitem
+ format.authors "author" output.check
+ author format.key output % special for
+ output.year.check % apalike
+ "PhD thesis" format.thesis.type output.nonnull
+ school "school" output.check
+ address output
+ format.eprint "eprint" output.check.nocomma
+ format.doi "doi" output.check.nocomma
+ format.url output
+ fin.entry
+}
+
+FUNCTION {proceedings}
+{ output.bibitem
+ format.editors output
+ editor format.key output % special for
+ mid.sentence 'output.state :=
+ output.year.check % apalike
+ format.btitle "title" output.check
+ " " *
+ before.all 'output.state :=
+% new.block
+ format.bvolume output
+ format.number.series output
+ new.block
+% organization output % a nonempty organization
+ publisher output
+ address output
+ format.eprint "eprint" output.check.nocomma
+ format.doi "doi" output.check.nocomma
+ format.url output
+ fin.entry
+}
+
+FUNCTION {techreport}
+{ output.bibitem
+ format.authors "author" output.check
+ author format.key output % special for
+ output.year.check % apalike
+ format.tr.number output.nonnull
+ format.btitle "title" output.check
+ format.url output
+ new.block
+ institution "institution" output.check
+ address output
+ format.eprint "eprint" output.check.nocomma
+ format.doi "doi" output.check.nocomma
+ format.url output
+ fin.entry
+}
+
+FUNCTION {unpublished}
+{ output.bibitem
+ format.authors "author" output.check
+ author format.key output % special for
+ output.year.check % apalike
+ format.btitle "title" output.check
+ note "note" output.check
+ % the following are presumably redundant for 'unpublished'
+ format.eprint "eprint" output.check.nocomma
+ format.doi "doi" output.check.nocomma
+ format.url output
+ fin.entry
+}
+
+FUNCTION {default.type} { misc }
+
+MACRO {jan} {"Jan."}
+
+MACRO {feb} {"Feb."}
+
+MACRO {mar} {"Mar."}
+
+MACRO {apr} {"Apr."}
+
+MACRO {may} {"May"}
+
+MACRO {jun} {"June"}
+
+MACRO {jul} {"July"}
+
+MACRO {aug} {"Aug."}
+
+MACRO {sep} {"Sept."}
+
+MACRO {oct} {"Oct."}
+
+MACRO {nov} {"Nov."}
+
+MACRO {dec} {"Dec."}
+
+%% Journal macros for bib files. Should be kept synchronized with
+%% the entries in the class file.
+
+%% Astronomy and Astrophysics
+MACRO {aap} {"A\&A"}
+
+%% Astronomy and Astrophysics
+MACRO {astap} {"A\&A"}
+
+%% Astronomy and Astrophysics Review (the)
+MACRO {aapr} {"A\&ARv"}
+
+%% Astronomy and Astrophysics Supplement Series
+MACRO {aaps} {"A\&AS"}
+
+%% Acta Astronomica
+MACRO {actaa} {"Acta Astron."}
+
+%% Astrofizika
+MACRO {afz} {"Afz"}
+
+%% Astronomical Journal (the)
+MACRO {aj} {"AJ"}
+
+%% Applied Optics
+MACRO {ao} {"Appl. Opt."}
+
+%% Applied Optics
+MACRO {applopt} {"Appl. Opt."}
+
+%% Astrophysics Letters
+MACRO {aplett} {"Astrophys.~Lett."}
+
+%% Astrophysical Journal
+MACRO {apj} {"ApJ"}
+
+%% Astrophysical Journal, Letters
+MACRO {apjl} {"ApJ"}
+
+%% Astrophysical Journal, Letters
+MACRO {apjlett} {"ApJ"}
+
+%% Astrophysical Journal, Supplement
+MACRO {apjs} {"ApJS"}
+
+%% Astrophysical Journal, Supplement
+MACRO {apjsupp} {"ApJS"}
+
+%% Astrophysics and Space Science
+MACRO {apss} {"Ap\&SS"}
+
+%% Annual Review of Astronomy and Astrophysics
+MACRO {araa} {"ARA\&A"}
+
+%% Astronomicheskii Zhurnal
+MACRO {azh} {"Azh"}
+
+%% Bulletin of the American Astronomical Society
+MACRO {baas} {"BAAS"}
+
+%% Bulletin of the Astronomical Institutes of Czechoslovakia
+MACRO {bac} {"Bull. Astron. Inst. Czechoslovakia"}
+
+%% Bulletin Astronomical Institute of the Netherlands
+MACRO {bain} {"Bull. Astron. Inst. Netherlands"}
+
+%% Chinese Astronomy and Astrophysics
+MACRO {caa} {"Chinese Astron. Astrophys."}
+
+%% Chinese Journal of Astronomy and Astrophysics
+MACRO {cjaa} {"Chinese J.~Astron. Astrophys."}
+
+%% Fundamentals of Cosmic Physics
+MACRO {fcp} {"Fundamentals Cosmic Phys."}
+
+%% Geochimica Cosmochimica Acta
+MACRO {gca} {"Geochimica Cosmochimica Acta"}
+
+%% Geophysics Research Letters
+MACRO {grl} {"Geophys. Res. Lett."}
+
+%% IAU Cirulars
+MACRO {iaucirc} {"IAU~Circ."}
+
+%% Icarus
+MACRO {icarus} {"Icarus"}
+
+%% Journal of Astrophysics and Astronomy
+MACRO {japa} {"J.~Astrophys. Astron."}
+
+%% Journal of Cosmology and Astroparticle Physics
+MACRO {jcap} {"J.~Cosmology Astropart. Phys."}
+
+%% Journal of Chemical Physics
+MACRO {jcp} {"J.~Chem.~Phys."}
+
+%% Journal of Geophysics Research
+MACRO {jgr} {"J.~Geophys.~Res."}
+
+%% Journal of Quantitiative Spectroscopy and Radiative Transfer
+MACRO {jqsrt} {"J.~Quant. Spectrosc. Radiative Transfer"}
+
+%% Journal of the RAS of Canada
+MACRO {jrasc} {"J.~R.~Astron. Soc. Canada"}
+
+%% Memoirs of the RAS
+MACRO {memras} {"Mem.~RAS"}
+
+%% Memoire della Societa Astronomica Italiana
+MACRO {memsai} {"Mem. Soc. Astron. Italiana"}
+
+%% Monthly Notes of the Astronomical Society of Southern Africa
+MACRO {mnassa} {"MNASSA"}
+
+%% Monthly Notices of the Royal Astronomical Society
+MACRO {mnras} {"MNRAS"}
+
+%% New Astronomy
+MACRO {na} {"New~Astron."}
+
+%% New Astronomy Review
+MACRO {nar} {"New~Astron.~Rev."}
+
+%% Nature
+MACRO {nat} {"Nature"}
+
+%% Nuclear Physics A
+MACRO {nphysa} {"Nuclear Phys.~A"}
+
+%% Physical Review A: General Physics
+MACRO {pra} {"Phys. Rev.~A"}
+
+%% Physical Review B: Solid State
+MACRO {prb} {"Phys. Rev.~B"}
+
+%% Physical Review C
+MACRO {prc} {"Phys. Rev.~C"}
+
+%% Physical Review D
+MACRO {prd} {"Phys. Rev.~D"}
+
+%% Physical Review E
+MACRO {pre} {"Phys. Rev.~E"}
+
+%% Physical Review Letters
+MACRO {prl} {"Phys. Rev.~Lett."}
+
+%% Publications of the Astronomical Society of Australia
+MACRO {pasa} {"PASA"}
+
+%% Publications of the Astronomical Society of the Pacific
+MACRO {pasp} {"PASP"}
+
+%% Publications of the Astronomical Society of Japan
+MACRO {pasj} {"PASJ"}
+
+%% Physics Reports
+MACRO {physrep} {"Phys.~Rep."}
+
+%% Physica Scripta
+MACRO {physscr} {"Phys.~Scr."}
+
+%% Planetary Space Science
+MACRO {planss} {"Planet. Space~Sci."}
+
+%% Proceedings of the Society of Photo-Optical Instrumentation Engineers
+MACRO {procspie} {"Proc.~SPIE"}
+
+%% Revista Mexicana de Astronomia y Astrofisica
+MACRO {rmxaa} {"Rev. Mex. Astron. Astrofis."}
+
+%% Quarterly Journal of the RAS
+MACRO {qjras} {"QJRAS"}
+
+%% Science
+MACRO {sci} {"Science"}
+
+%% Sky and Telescope
+MACRO {skytel} {"Sky \& Telesc."}
+
+%% Solar Physics
+MACRO {solphys} {"Sol.~Phys."}
+
+%% Soviet Astronomy (aka Astronomy Reports)
+MACRO {sovast} {"Soviet~Ast."}
+
+%% Space Science Reviews
+MACRO {ssr} {"Space Sci. Rev."}
+
+%% Zeitschrift fuer Astrophysik
+MACRO {zap} {"Z.~Astrophys."}
+
+%% Astronomical Society of the Pacific Conference Series
+MACRO {aspconf} {"ASP Conf. Ser."}
+
+%% Astronomische Nachrichten
+MACRO {astnach} {"Astron. Nachr."}
+
+%% Astronomy & Computing
+MACRO {astcomp} {"Astron. Comput."}
+
+READ
+
+FUNCTION {sortify}
+{ purify$
+ "l" change.case$
+}
+
+INTEGERS { len }
+
+FUNCTION {chop.word}
+{ 's :=
+ 'len :=
+ s #1 len substring$ =
+ { s len #1 + global.max$ substring$ }
+ 's
+ if$
+}
+
+% There are three apalike cases: one person (Jones),
+% two (Jones and de~Bruijn), and more (Jones et~al.).
+% This function is much like format.crossref.editors.
+%
+% The goal here is to be compatible with the MN style prescription that:
+% If there are several references with the same first author,
+% arrange in the following order:
+% firstly single-author papers (by date);
+% then two-author papers (alphabetically by co-author, then by date);
+% then multi-author papers (by date).
+% We deem 'Jones and others' to be a multi-author paper, in this sense,
+% so that it sorts, by date, with the three-or-more author papers.
+% An alternative is to deem 'Jones and others' to sort just after the single-author papers
+% (this case isn't really covered by the above rules, but this position looks sensible);
+% we can get that by putting extra spaces before the 'et~al.', as noted below.
+% Note: we can't put arbitrary characters here, to force the order,
+% because the result of this function appears as the citation label in the typeset result.
+FUNCTION {format.lab.names}
+{ 's :=
+ s #1 "{vv~}{ll}" format.name$
+ s num.names$ duplicate$
+ #2 >
+ { pop$ " et~al." * }
+ { #2 <
+ 'skip$
+ { s #2 "{ff }{vv }{ll}{ jj}" format.name$ "others" =
+ { " et~al." * } % <-----+-- alternate sortings
+ %{ " et~al." * } % <--+
+ { " \& " * s #2 "{vv~}{ll}" format.name$ * }
+ if$
+ }
+ if$
+ }
+ if$
+}
+
+% Format names in full
+%
+FUNCTION {format.lab.names.full}
+{ 's :=
+ s #1 "{vv~}{ll}" format.name$
+ s num.names$ duplicate$
+ #2 <
+ 'skip$
+ { s #2 "{ff }{vv }{ll}{ jj}" format.name$ "others" =
+ 'skip$
+ { " \& " * s #2 "{vv~}{ll}" format.name$ * }
+ if$
+ }
+ if$
+}
+
+FUNCTION {author.key.label}
+{ author empty$
+ { key empty$
+ { cite$ #1 #3 substring$ }
+ 'key % apalike uses the whole key
+ if$
+ }
+ { author format.lab.names }
+ if$
+}
+
+
+FUNCTION {author.editor.key.label}
+{ author empty$
+ { editor empty$
+ { key empty$
+ { cite$ #1 #3 substring$ }
+ 'key % apalike uses the whole key
+ if$
+ }
+ { editor format.lab.names }
+ if$
+ }
+ { author format.lab.names }
+ if$
+}
+
+FUNCTION {author.editor.key.label.full}
+{ author empty$
+ { editor empty$
+ { key empty$
+ { cite$ #1 #3 substring$ }
+ 'key
+ if$
+ }
+ { editor format.names.label }
+ if$
+ }
+ { author format.names.label }
+ if$
+}
+
+FUNCTION {editor.key.label}
+{ editor empty$
+ { key empty$
+ { cite$ #1 #3 substring$ }
+ 'key % apalike uses the whole key, no organization
+ if$
+ }
+ { editor format.lab.names }
+ if$
+}
+
+% Calculate the 'label' for the entry, which is used for sorting.
+% Note that this does not include the a/b/c... for disambiguating
+% years (that's added later, in forward.pass).
+FUNCTION {calc.label}
+{ % Define t: this is the 'full' set of names
+ type$ "book" =
+ type$ "inbook" =
+ or
+ 'author.editor.key.label.full
+ { type$ "proceedings" =
+ { editor format.names.label }
+ { author format.names.label }
+ if$
+ }
+ if$
+ 't :=
+ % Define s: this is the 'shortened' set of names, with 'et al.',
+ % which are to appear in citations
+ type$ "book" =
+ type$ "inbook" =
+ or
+ 'author.editor.key.label
+ { type$ "proceedings" =
+ 'editor.key.label % apalike ignores organization
+ 'author.key.label % for labeling and sorting
+ if$
+ }
+ if$
+ 's :=
+ % the '\protect... is for apalike
+ "\protect\citeauthoryear{" t * "}{" *
+ threeauthorvar
+ numnames #3 =
+ and
+ { "\protect\mniiiauthor{" cite$ * "}{" *
+ t * "}{" * s * "}" * }
+ { s }
+ if$
+ *
+ "}{" *
+ year field.or.null
+ *
+ % the matching closing "}" comes in at the reverse.pass
+ 'label :=
+}
+
+FUNCTION {sort.format.names}
+{ 's :=
+ #1 'nameptr :=
+ ""
+ s num.names$ 'numnames :=
+ numnames 'namesleft :=
+ { namesleft #0 > }
+ { nameptr #1 >
+ { " " * }
+ 'skip$
+ if$ % apalike uses initials
+ s nameptr "{vv{ } }{ll{ }}{ f{ }}{ jj{ }}" format.name$ 't := % <= here
+ "Mc" t #2 text.prefix$ =
+ { "mac" t #3 t text.length$ substring$ * 't := }
+ 'skip$
+ if$
+ nameptr numnames = t "others" = and
+ { " et~al." * }
+ { t sortify * }
+ if$
+ nameptr #1 + 'nameptr :=
+ namesleft #1 - 'namesleft :=
+ }
+ while$
+}
+
+FUNCTION {sort.format.title}
+{ 't :=
+ "A " #2
+ "An " #3
+ "The " #4 t chop.word
+ chop.word
+ chop.word
+ sortify
+ #1 global.max$ substring$
+}
+
+FUNCTION {author.sort}
+{ author empty$
+ { key empty$
+ { "to sort, need author or key in " cite$ * warning$
+ ""
+ }
+ { key sortify }
+ if$
+ }
+ { author sort.format.names }
+ if$
+}
+
+FUNCTION {author.editor.sort}
+{ author empty$
+ { editor empty$
+ { key empty$
+ { "to sort, need author, editor, or key in " cite$ * warning$
+ ""
+ }
+ { key sortify }
+ if$
+ }
+ { editor sort.format.names }
+ if$
+ }
+ { author sort.format.names }
+ if$
+}
+
+FUNCTION {editor.sort}
+{ editor empty$
+ { key empty$
+ { "to sort, need editor or key in " cite$ * warning$
+ ""
+ }
+ { key sortify }
+ if$
+ }
+ { editor sort.format.names }
+ if$
+}
+
+% Format numbers (eg volume, number, pages) into a fixed-width string,
+% for sorting.
+FUNCTION {number.for.presort}
+{ field.or.null
+ duplicate$ text.length$ 'len :=
+ ""
+ { #5 len > }
+ { "0" *
+ len #1 + 'len := }
+ while$
+ swap$ *
+}
+
+% apalike uses two sorting passes; the first one sets the
+% labels so that the `a's, `b's, etc. can be computed;
+% the second pass puts the references in "correct" order.
+% The presort function is for the first pass. It computes
+% presort.key, sort.label, and sort.key$
+FUNCTION {presort}
+{ calc.label
+ type$ "book" =
+ type$ "inbook" =
+ or
+ 'author.editor.key.label
+ { type$ "proceedings" =
+ 'editor.key.label % apalike ignores organization
+ 'author.key.label % for labeling and sorting
+ if$
+ }
+ if$
+ purify$ % remove {braces} round names, to avoid confusing sorting
+ " "
+ *
+ year number.for.presort *
+ #1 entry.max$ substring$
+ 'presort.key :=
+ presort.key
+ " "
+ *
+ % Style apalike prefers 'title field.or.null sort.format.title *' here.
+ % We don't, because we will predominantly be sorting articles in
+ % this style, and we don't include their titles in the final bibliography.
+ volume number.for.presort *
+ number number.for.presort *
+ pages empty$
+ { "0" }
+ { pages first.page.number }
+ if$
+ number.for.presort *
+ #1 entry.max$ substring$
+ 'sort.key$ :=
+ sort.key$ 'sort.label :=
+}
+
+EXECUTE {initialise.mn2e}
+
+ITERATE {presort}
+
+SORT % by label, sort.label, title---for final label calculation
+
+% Manage the construction of the 'extra' labels for references. These
+% are the a/b/c/... year suffixes which distinguish different
+% publications by the same author.
+%
+% These apalike labels are only for the text; the 'label' does not
+% appear in the bibiliography, so that the 'longest.label' variable is
+% unnecessary in this style.
+STRINGS { last.key next.extra }
+
+INTEGERS { last.extra.num }
+
+FUNCTION {initialize.extra.label.stuff}
+{ #0 int.to.chr$ 'last.key :=
+ "" 'next.extra :=
+ #0 'last.extra.num :=
+}
+
+% By the time that this function is iterated over, the entries have
+% had presort.key assigned, and have been presorted. However these labels
+% do not (by design) respect the presence of multiple entries in the
+% same year, so that there are duplicates. Detect successive
+% duplicates, and add an extra a/b/c... suffix.
+%
+% At the end of this forward.pass, each entry with a duplicate presort.key
+% will have an extra.label, starting with 'b' for the first duplicate,
+% 'c' for the second, and so on. That is, only the first
+% soon-to-be-discovered-to-be-duplicate label will not have an
+% extra.label.
+FUNCTION {forward.pass}
+{ last.key presort.key =
+ { last.extra.num #1 + 'last.extra.num :=
+ last.extra.num int.to.chr$ 'extra.label :=
+ }
+ { % first time we've seen this key
+ "a" chr.to.int$ 'last.extra.num :=
+ "" 'extra.label :=
+ presort.key 'last.key :=
+ }
+ if$
+}
+
+% Work back through the labels. If, on this pass we discover that the
+% next entry in the sequence (which is the last entry processed in
+% this reverse pass) had an extra.label of 'b', then this tells us
+% that _this_ entry should have an extra.label of 'a', which we were
+% unable to detect in the forward.pass above.
+%
+% We also close the brace pair {...} opened in calc.label
+FUNCTION {reverse.pass}
+{ next.extra "b" =
+ { "a" 'extra.label := }
+ 'skip$
+ if$
+ label extra.label * "}" * 'label :=
+ extra.label 'next.extra :=
+}
+
+EXECUTE {initialize.extra.label.stuff}
+
+ITERATE {forward.pass}
+
+REVERSE {reverse.pass}
+
+% Now that the label is right we sort for real. We sort on sort.label
+% then year then title. Since sort.label starts with presort.key,
+% this sorting is compatible with the letter suffixes added to years.
+%
+% This is for the second sorting pass.
+FUNCTION {bib.sort.order}
+{ sort.label
+ " "
+ *
+ year field.or.null sortify
+ *
+ " "
+ *
+ title field.or.null
+ sort.format.title
+ *
+ #1 entry.max$ substring$
+ 'sort.key$ :=
+}
+
+ITERATE {bib.sort.order}
+
+SORT % by sort.label, year, title---giving final bibliography order
+
+FUNCTION {begin.bib}
+{
+ preamble$ empty$ % no \etalchar in apalike
+ 'skip$
+ { preamble$ write$ newline$ }
+ if$
+ "\begin{thebibliography}{}" write$ newline$ % no labels in apalike
+ "\makeatletter" write$ newline$
+ % The following is the contents of mnras-insert.sty, minus comments and whitespace.
+ % DO NOT EDIT THIS TEXT,
+ % but instead make mnras-insert.txt, and paste the results in here.
+"\relax" write$ newline$
+"\def\mn@urlcharsother{\let\do\@makeother \do\$\do\&\do\#\do\^\do\_\do\%\do\~}" write$ newline$
+"\def\mn@doi{\begingroup\mn@urlcharsother \@ifnextchar [ {\mn@doi@} {\mn@doi@[]}}" write$ newline$
+"\def\mn@doi@[#1]#2{\def\@tempa{#1}\ifx\@tempa\@empty \href {http://dx.doi.org/#2} {doi:#2}\else \href {http://dx.doi.org/#2} {#1}\fi \endgroup}" write$ newline$
+"\def\mn@eprint#1#2{\mn@eprint@#1:#2::\@nil}" write$ newline$
+"\def\mn@eprint@arXiv#1{\href {http://arxiv.org/abs/#1} {{\tt arXiv:#1}}}" write$ newline$
+"\def\mn@eprint@dblp#1{\href {http://dblp.uni-trier.de/rec/bibtex/#1.xml} {dblp:#1}}" write$ newline$
+"\def\mn@eprint@#1:#2:#3:#4\@nil{\def\@tempa {#1}\def\@tempb {#2}\def\@tempc {#3}\ifx \@tempc \@empty \let \@tempc \@tempb \let \@tempb \@tempa \fi \ifx \@tempb \@empty \def\@tempb {arXiv}\fi \@ifundefined {mn@eprint@\@tempb}{\@tempb:\@tempc}{\expandafter \expandafter \csname mn@eprint@\@tempb\endcsname \expandafter{\@tempc}}}" write$ newline$
+}
+
+EXECUTE {begin.bib}
+
+EXECUTE {init.state.consts}
+
+ITERATE {call.type$}
+
+FUNCTION {end.bib}
+{ newline$
+ "\makeatother" write$ newline$
+ "\end{thebibliography}" write$ newline$
+}
+
+EXECUTE {end.bib}
diff --git a/papers/joss_paper/paper_tex/paper.aux b/papers/joss_paper/paper_tex/paper.aux
new file mode 100644
index 0000000000000000000000000000000000000000..40bf76d53e72f39adb911b3b1559f7932738a74d
--- /dev/null
+++ b/papers/joss_paper/paper_tex/paper.aux
@@ -0,0 +1,43 @@
+\relax
+\providecommand\hyper@newdestlabel[2]{}
+\providecommand\zref@newlabel[2]{}
+\providecommand\HyperFirstAtBeginDocument{\AtBeginDocument}
+\HyperFirstAtBeginDocument{\ifx\hyper@anchor\@undefined
+\global\let\oldcontentsline\contentsline
+\gdef\contentsline#1#2#3#4{\oldcontentsline{#1}{#2}{#3}}
+\global\let\oldnewlabel\newlabel
+\gdef\newlabel#1#2{\newlabelxx{#1}#2}
+\gdef\newlabelxx#1#2#3#4#5#6{\oldnewlabel{#1}{{#2}{#3}}}
+\AtEndDocument{\ifx\hyper@anchor\@undefined
+\let\contentsline\oldcontentsline
+\let\newlabel\oldnewlabel
+\fi}
+\fi}
+\global\let\hyper@last\relax
+\gdef\HyperFirstAtBeginDocument#1{#1}
+\providecommand\HyField@AuxAddToFields[1]{}
+\providecommand\HyField@AuxAddToCoFields[2]{}
+\citation{izzardNewSyntheticModel2004,izzardPopulationNucleosynthesisSingle2006,izzardPopulationSynthesisBinary2009,izzardBinaryStarsGalactic2018}
+\citation{astropycollaborationAstropyCommunityPython2013,foreman-mackeyEmceeMCMCHammer2013,astropycollaborationAstropyProjectBuilding2018,speagleDynestyDynamicNested2020}
+\citation{mirouh_etal22}
+\citation{foreman-mackeyEmceeMCMCHammer2013}
+\@writefile{toc}{\contentsline {section}{\numberline {1}Summary}{1}{section.1}\protected@file@percent }
+\newlabel{sec:summary}{{1}{1}{Summary}{section.1}{}}
+\@writefile{toc}{\contentsline {section}{\numberline {2}Statement of need}{1}{section.2}\protected@file@percent }
+\newlabel{sec:statement}{{2}{1}{Statement of need}{section.2}{}}
+\@writefile{toc}{\contentsline {section}{\numberline {3}Projects that use \textsc {binary\_c-python}}{1}{section.3}\protected@file@percent }
+\newlabel{sec:projects}{{3}{1}{Projects that use \binarycpython }{section.3}{}}
+\bibstyle{mnras-custom.bst}
+\bibdata{references.bib}
+\bibcite{astropycollaborationAstropyCommunityPython2013}{{1}{2013}{{{Astropy Collaboration} et~al.}}{{{Astropy Collaboration} et~al.,}}}
+\bibcite{astropycollaborationAstropyProjectBuilding2018}{{2}{2018}{{{Astropy Collaboration} et~al.}}{{{Astropy Collaboration} et~al.,}}}
+\bibcite{foreman-mackeyEmceeMCMCHammer2013}{{3}{2013}{{{Foreman-Mackey} et~al.}}{{{Foreman-Mackey}, Hogg, Lang \& Goodman}}}
+\bibcite{izzardNewSyntheticModel2004}{{4}{2004}{{Izzard et~al.}}{{Izzard, Tout, Karakas \& Pols}}}
+\bibcite{izzardPopulationNucleosynthesisSingle2006}{{5}{2006}{{Izzard et~al.}}{{Izzard, Dray, Karakas, Lugaro \& Tout}}}
+\bibcite{izzardPopulationSynthesisBinary2009}{{6}{2009}{{Izzard et~al.}}{{Izzard, Glebbeek, Stancliffe \& Pols}}}
+\bibcite{izzardBinaryStarsGalactic2018}{{7}{2018}{{Izzard et~al.}}{{Izzard, Preece, Jofre, Halabi, Masseron \& Tout}}}
+\bibcite{mirouh_etal22}{{8}{submitted}{{{Mirouh} et~al.}}{{{Mirouh}, {Hendriks}, {Dykes}, {Moe} \& {Izzard}}}}
+\bibcite{speagleDynestyDynamicNested2020}{{9}{2020}{{Speagle}}{{Speagle}}}
+\@writefile{toc}{\contentsline {section}{\numberline {4}Acknowledgements}{2}{section.4}\protected@file@percent }
+\newlabel{sec:orgf6f5520}{{4}{2}{Acknowledgements}{section.4}{}}
+\ulp@afterend
diff --git a/papers/joss_paper/paper_tex/paper.bbl b/papers/joss_paper/paper_tex/paper.bbl
new file mode 100644
index 0000000000000000000000000000000000000000..9716251dfa5faa32601ccbaf812f90213089cccf
--- /dev/null
+++ b/papers/joss_paper/paper_tex/paper.bbl
@@ -0,0 +1,68 @@
+\begin{thebibliography}{}
+\makeatletter
+\relax
+\def\mn@urlcharsother{\let\do\@makeother \do\$\do\&\do\#\do\^\do\_\do\%\do\~}
+\def\mn@doi{\begingroup\mn@urlcharsother \@ifnextchar [ {\mn@doi@}
+ {\mn@doi@[]}}
+\def\mn@doi@[#1]#2{\def\@tempa{#1}\ifx\@tempa\@empty \href
+ {http://dx.doi.org/#2} {doi:#2}\else \href {http://dx.doi.org/#2} {#1}\fi
+ \endgroup}
+\def\mn@eprint#1#2{\mn@eprint@#1:#2::\@nil}
+\def\mn@eprint@arXiv#1{\href {http://arxiv.org/abs/#1} {{\tt arXiv:#1}}}
+\def\mn@eprint@dblp#1{\href {http://dblp.uni-trier.de/rec/bibtex/#1.xml}
+ {dblp:#1}}
+\def\mn@eprint@#1:#2:#3:#4\@nil{\def\@tempa {#1}\def\@tempb {#2}\def\@tempc
+ {#3}\ifx \@tempc \@empty \let \@tempc \@tempb \let \@tempb \@tempa \fi \ifx
+ \@tempb \@empty \def\@tempb {arXiv}\fi \@ifundefined
+ {mn@eprint@\@tempb}{\@tempb:\@tempc}{\expandafter \expandafter \csname
+ mn@eprint@\@tempb\endcsname \expandafter{\@tempc}}}
+
+\bibitem[\protect\citeauthoryear{{Astropy Collaboration} et~al.,}{{Astropy
+ Collaboration} et~al.}{2013}]{astropycollaborationAstropyCommunityPython2013}
+{Astropy Collaboration} et~al., 2013, \mn@doi [Astronomy and Astrophysics]
+ {10.1051/0004-6361/201322068}, 558, A33
+
+\bibitem[\protect\citeauthoryear{{Astropy Collaboration} et~al.,}{{Astropy
+ Collaboration} et~al.}{2018}]{astropycollaborationAstropyProjectBuilding2018}
+{Astropy Collaboration} et~al., 2018, \mn@doi [The Astronomical Journal]
+ {10.3847/1538-3881/aabc4f}, 156, 123
+
+\bibitem[\protect\citeauthoryear{{Foreman-Mackey}, Hogg, Lang \&
+ Goodman}{{Foreman-Mackey} et~al.}{2013}]{foreman-mackeyEmceeMCMCHammer2013}
+{Foreman-Mackey} D., Hogg D.~W., Lang D., Goodman J., 2013, \mn@doi
+ [Publications of the Astronomical Society of the Pacific] {10.1086/670067},
+ 125, 306
+
+\bibitem[\protect\citeauthoryear{Izzard, Tout, Karakas \& Pols}{Izzard
+ et~al.}{2004}]{izzardNewSyntheticModel2004}
+Izzard R.~G., Tout C.~A., Karakas A.~I., Pols O.~R., 2004, \mn@doi
+ [Monthly Notices of the Royal Astronomical Society]
+ {10.1111/j.1365-2966.2004.07446.x}, 350, 407
+
+\bibitem[\protect\citeauthoryear{Izzard, Dray, Karakas, Lugaro \& Tout}{Izzard
+ et~al.}{2006}]{izzardPopulationNucleosynthesisSingle2006}
+Izzard R.~G., Dray L.~M., Karakas A.~I., Lugaro M., Tout C.~A., 2006,
+ \mn@doi [Astronomy \& Astrophysics] {10.1051/0004-6361:20066129}, 460, 565
+
+\bibitem[\protect\citeauthoryear{Izzard, Glebbeek, Stancliffe \& Pols}{Izzard
+ et~al.}{2009}]{izzardPopulationSynthesisBinary2009}
+Izzard R.~G., Glebbeek E., Stancliffe R.~J., Pols O.~R., 2009, \mn@doi
+ [Astronomy and Astrophysics] {10.1051/0004-6361/200912827}, 508, 1359
+
+\bibitem[\protect\citeauthoryear{Izzard, Preece, Jofre, Halabi, Masseron \&
+ Tout}{Izzard et~al.}{2018}]{izzardBinaryStarsGalactic2018}
+Izzard R.~G., Preece H., Jofre P., Halabi G.~M., Masseron T., Tout C.~A.,
+ 2018, \mn@doi [Monthly Notices of the Royal Astronomical Society]
+ {10.1093/mnras/stx2355}, 473, 2984
+
+\bibitem[\protect\citeauthoryear{{Mirouh}, {Hendriks}, {Dykes}, {Moe} \&
+ {Izzard}}{{Mirouh} et~al.}{submitted}]{mirouh_etal22}
+{Mirouh} G.~M., {Hendriks} D.~D., {Dykes} S., {Moe} M., {Izzard} R.~G.,
+ submitted, \mnras
+
+\bibitem[\protect\citeauthoryear{Speagle}{Speagle}{2020}]{speagleDynestyDynamicNested2020}
+Speagle J.~S., 2020, \mn@doi [Monthly Notices of the Royal Astronomical
+ Society] {10.1093/mnras/staa278}, 493, 3132
+
+\makeatother
+\end{thebibliography}
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diff --git a/papers/joss_paper/paper_tex/paper.md b/papers/joss_paper/paper_tex/paper.md
new file mode 100644
index 0000000000000000000000000000000000000000..a4dc41770c8a0142773903ecc304ce2a41bcfe83
--- /dev/null
+++ b/papers/joss_paper/paper_tex/paper.md
@@ -0,0 +1,135 @@
+---
+title: '[binary\_c-python]{.smallcaps}: A python-based stellar population synthesis tool and interface to [binary\_c]{.smallcaps}'
+tags:
+ - Python
+ - astronomy
+authors:
+ - name: D. D. Hendriks[^1]
+ orcid: 0000-0002-8717-6046
+ affiliation: 1
+ - name: R. G. Izzard
+ orcid: 0000-0003-0378-4843
+ affiliation: 1
+affiliations:
+ - name: Department of Physics, University of Surrey, Guildford, GU2 7XH, Surrey, UK
+ index: 1
+date: 18 June 2022
+bibliography: paper.bib
+---
+
+Summary {#sec:summary}
+=======
+
+We present our package
+[[binary\_c-python]{.smallcaps}](https://ri0005.pages.surrey.ac.uk/binary_c-python/),
+which is aimed to provide a convenient and easy-to-use interface to the
+[[binary\_c]{.smallcaps}](http://personal.ph.surrey.ac.uk/~ri0005/doc/binary_c/binary_c.html)Â [@izzardNewSyntheticModel2004; @izzardPopulationNucleosynthesisSingle2006; @izzardPopulationSynthesisBinary2009; @izzardBinaryStarsGalactic2018]
+framework, allowing the user to rapidly evolve individual systems and
+populations of stars. [binary\_c-python]{.smallcaps}Â is available on
+[Pip](https://pypi.org/project/binarycpython/) and on
+[Gitlab](https://gitlab.com/binary_c/binary_c-python).
+
+The user can control output from [binary\_c]{.smallcaps}by providing
+[binary\_c-python]{.smallcaps}Â with logging statements that are
+dynamically compiled and loaded into [binary\_c]{.smallcaps}.
+[binary\_c-python]{.smallcaps}Â uses multiprocessing to utilise all the
+cores on a particular machine, and can run populations with HPC cluster
+workload managers like [HTCondor]{.smallcaps} and [Slurm]{.smallcaps},
+allowing the user to run simulations on very large computing clusters.
+
+[binary\_c-python]{.smallcaps}Â is easily interfaced or integrated with
+other Python-based codes, e.g. sampling codes like [Emcee]{.smallcaps}
+or [Dynesty]{.smallcaps}, or the astrophysics oriented package
+[Astropy]{.smallcaps}Â [@astropycollaborationAstropyCommunityPython2013; @foreman-mackeyEmceeMCMCHammer2013; @astropycollaborationAstropyProjectBuilding2018; @speagleDynestyDynamicNested2020].
+Moreover, it is possible to provide custom system-generating functions
+through our function hooks, allowing third-party packages to control the
+populations of stars and evolve them through
+[binary\_c-python]{.smallcaps}.
+
+Recent developments in [binary\_c]{.smallcaps}Â include standardised
+output datasets called *ensembles*.
+[binary\_c-python]{.smallcaps}Â easily processes these datasets and
+provides a suite of utility functions to handle them. Furthermore,
+[binary\_c]{.smallcaps}Â now includes the *ensemble-manager* class, which
+makes use of the core functions and classes of
+[binary\_c-python]{.smallcaps}Â to evolve a grid of stellar populations
+of stars with varying input physics, allowing for huge, automated
+parameter studies through a single interface.
+
+We provide
+[documentation](https://ri0005.pages.surrey.ac.uk/binary_c-python/index.html)
+that is automatically generated based on docstrings and a suite of
+[Jupyter]{.smallcaps}
+[notebooks](https://ri0005.pages.surrey.ac.uk/binary_c-python/example_notebooks.html).
+These notebooks consist of technical tutorials on how to use
+[binary\_c-python]{.smallcaps}, and use-case scenarios aimed at doing
+science. Much of [binary\_c-python]{.smallcaps}Â is covered by unit tests
+to ensure reliability and correctness, and the test coverage is
+continually increased as the package is being improved.
+
+Statement of need {#sec:statement}
+=================
+
+In the current scientific climate [Python]{.smallcaps} is ubiquitous,
+and while lower-level codes written in e.g. [Fortran]{.smallcaps} or
+[C]{.smallcaps} are still widely used, much of the newer software is
+written in [Python]{.smallcaps}, either entirely or as a wrapper around
+other codes. Education in programming also often includes
+[Python]{.smallcaps} courses because of its ease of use and its
+flexibility. Moreover, [Python]{.smallcaps} has a large community with
+many resources and tutorials. We have created
+[binary\_c-python]{.smallcaps}Â to allow students and scientists alike to
+explore current scientific issues while enjoying the familiar syntax,
+and at the same time make use of the plentiful scientific and
+astrophysical packages like [Numpy]{.smallcaps}, [Scipy]{.smallcaps},
+[Pandas]{.smallcaps}, [Astropy]{.smallcaps}Â and platforms like
+[Jupyter]{.smallcaps}.
+
+Earlier versions of [binary\_c-python]{.smallcaps}Â were written in Perl,
+where much of the debugging and the logic and structure developments
+were done. This greatly made porting to [Python]{.smallcaps} relatively
+easy.
+
+Projects that use [binary\_c-python]{.smallcaps} {#sec:projects}
+================================================
+
+[binary\_c-python]{.smallcaps}Â has already been used in a variety of
+situations, ranging from pure research to educational purposes, as well
+as in outreach events. In the summer of 2021 we used
+[binary\_c-python]{.smallcaps}Â as the basis for the interactive classes
+on stellar ecosystems during the [International Max-Planck Research
+School summer school 2021 in
+Heidelberg](https://www2.mpia-hd.mpg.de/imprs-hd/SummerSchools/2021/),
+where students were introduced to the topic of population synthesis and
+were able to use our notebooks to perform their own calculations.
+[binary\_c-python]{.smallcaps}Â has been used in @mirouh_etal22, where
+improvements to tidal interactions between stars were implemented, and
+initial birth parameter distributions were varied to match to observed
+binary systems in star clusters. A Master's thesis project, aimed at
+finding the birth system parameters of the V106 stellar system,
+comparing observations to results of [binary\_c]{.smallcaps}Â and
+calculating the maximum likelihood with Bayesian inference through
+Markov chain Monte Carlo sampling. The project made use of
+[binary\_c-python]{.smallcaps}Â and the [Emcee]{.smallcaps} package.
+
+Currently [binary\_c-python]{.smallcaps}Â is used in several ongoing
+projects that study the effect of birth distributions on the occurrence
+of carbon-enhanced metal-poor (CEMP) stars, the occurrence and
+properties of accretion disks in main-sequence stars and the predicted
+observable black hole distribution by combining star formation and
+metallicity distributions with the output of [binary\_c]{.smallcaps}.
+Moreover, we use the *ensemble* output structure to generate datasets
+for galactic chemical evolution on cosmological timescales, where we
+rely heavily on the utilities of [binary\_c-python]{.smallcaps}.
+
+Acknowledgements {#sec:orgf6f5520}
+================
+
+We acknowledge the helpful discussions and early testing efforts from M.
+Delorme, G. Mirouh, and D. Tracey, and the early work of J. Andrews
+which inspired our Python-C interface code. DDH thanks the UKRI/UoS for
+the funding grant H120341A. RGI thanks STFC for funding grants
+[ST/R000603/1](https://gtr.ukri.org/projects?ref=ST%2FR000603%2F1) and
+[ST/L003910/2](https://gtr.ukri.org/projects?ref=ST/L003910/2).
+
+[^1]: E-mail: <dh00601@surrey.ac.uk>Â (DDH)
diff --git a/papers/joss_paper/paper_tex/paper.org b/papers/joss_paper/paper_tex/paper.org
new file mode 100644
index 0000000000000000000000000000000000000000..0b54cdd3ef60cbd6c2f780f6d87036efb745b40b
--- /dev/null
+++ b/papers/joss_paper/paper_tex/paper.org
@@ -0,0 +1,68 @@
+#+AUTHOR: David Hendriks
+#+EMAIL: davidhendriks93@gmail.com
+#+OPTIONS: ':nil *:t -:t ::t <:t H:3 ^:nil arch:headline
+#+OPTIONS: author:t c:nil creator:comment d:(not "LOGBOOK") date:t
+#+OPTIONS: e:t email:nil f:t inline:t num:t p:nil pri:nil stat:t
+#+OPTIONS: tasks:t tex:t timestamp:t toc:nil todo:nil |:t
+#+DESCRIPTION:
+#+EXCLUDE_TAGS: noexport
+#+KEYWORDS:
+#+LANGUAGE: en
+#+SELECT_TAGS: export
+#+BIBLIOGRAPHY:
+#+OPTIONS: \n:t tags:nil
+#+LATEX: \setlength\parindent{0pt}
+#+TITLE: JOSS article
+#+DATE:
+
+* Summary
+# [comment]: <> What is binary_c-python
+binary_c-python is a population synthesis code python package that wraps the rapid stellar synthesis code binary_c. It is developed to provide an easy interface between python and the binary_c code (CITE: binary_c) and allows for evolving both single systems and populations of stars. The user can control the output via the python interface by providing logging statements that are dynamically loaded into binary_c. The package uses multiprocessing to run on many cores, and can run populations via HPC cluster workload managers like Condor and Slurm.
+# - [x] Python package wrapping binary-c code
+# - [x] HPC functionality
+# - [x] Logging can be configured from python
+
+It can easily be interfaced with other python based codes like Emcee, STROOPWAFEL and Dynesty through API endpoints that are provided by binary_c-python.
+# - [x] Easy interface
+# - [x] Interfacing with Emcee
+# - [x] Interfacing with STROOPWAFEL
+# - [x] Interfacing with other codes
+
+# [comment]: <> New functionality in binary_c and binary_c-python
+Recent developments in binary_c include the design of standardised output datasets called ensembles, which binary_c-python is designed to easily process, and a suite of utility functions to handle these datasets is present in the code.
+# - [X] Ensemble functionality
+
+# [comment]: <> Documentation
+The [[https://ri0005.pages.surrey.ac.uk/binary_c-python/index.html][documentation]] is generated automatically, based on docstrings and accompanying notebooks. The [[https://ri0005.pages.surrey.ac.uk/binary_c-python/example_notebooks.html][notebooks]] consist of example notebooks explaining how to use the code, as use-case notebooks showing practical usage of the code, which were used in the Heidelberg summer school 2021. Moreover, much of the code is covered by unit tests to ensure reliability.
+# - [x] Documentation built automatically, based on docstrings
+# - [x] Example notebooks to explain how to use the code
+# - [x] Use-case notebooks to instruct and provide exercises on usecases
+
+* Statement of need
+In the current scientific climate the use of Python is
+# - [ ] Python part of basic toolkit for many students and scientists
+# - [ ] Python-based package can interface with other astro/science based packages that are available (e.g. Astropy, Scipy, Emcee)
+
+* Projects using our code
+# [comment]: <> Heidelberg
+Binarycpython has been used in interactive classes during the [[https://www2.mpia-hd.mpg.de/imprs-hd/SummerSchools/2021/][Heidelberg Summer School]],
+
+It has been used in [paper Gio](paper Gio) where improvements to tidal interactions between binaries were implemented, and initial birth parameter distribution were varied to match to observed systems in clusters.
+# [comment]: <> Paper on tides
+
+# [comment]: <> Paper V106
+A master thesis project, studying the birth system parameters of the V106 system, was done by using binary_c-python and interfacing it with the Emcee (CITE) package.
+
+# [comment]: <> Paper on CEMP,
+Currently it is used in a several ongoing projects that study the effect of birth distributions on the occurrence of carbon-enhanced metal-poor (CEMP) stars, the occurrence and properties of accretion disks in main-sequence stars and the predicted observable black hole distribution by combining star formation and metallicity distributions with the output of binary_c.
+
+# * Citations
+# - [ ] Astropy
+# - [ ] emcee
+# - [ ] binary_c citations
+
+# ** Figures
+
+* Acknowledgements
+DDH acknowledges UKRI/SURREY funding (FIXME)
+We acknowledge the helpful discussions and early testing efforts from G. Mirouh and D. Tracey
diff --git a/papers/joss_paper/paper_tex/paper.out b/papers/joss_paper/paper_tex/paper.out
new file mode 100644
index 0000000000000000000000000000000000000000..22057aecb240128e478e9f80118de7b4acb46eab
--- /dev/null
+++ b/papers/joss_paper/paper_tex/paper.out
@@ -0,0 +1,4 @@
+\BOOKMARK [1][-]{section.1}{Summary}{}% 1
+\BOOKMARK [1][-]{section.2}{Statement of need}{}% 2
+\BOOKMARK [1][-]{section.3}{Projects that use binary\137c-python}{}% 3
+\BOOKMARK [1][-]{section.4}{Acknowledgements}{}% 4
diff --git a/papers/joss_paper/paper_tex/paper.synctex.gz b/papers/joss_paper/paper_tex/paper.synctex.gz
new file mode 100644
index 0000000000000000000000000000000000000000..0d8095a1c5afbdbe243b740f1a9a6ce631a959f6
Binary files /dev/null and b/papers/joss_paper/paper_tex/paper.synctex.gz differ
diff --git a/papers/joss_paper/paper_tex/paper.tex b/papers/joss_paper/paper_tex/paper.tex
new file mode 100644
index 0000000000000000000000000000000000000000..b0455ced56351db6f9974b886ff722a8b84fa086
--- /dev/null
+++ b/papers/joss_paper/paper_tex/paper.tex
@@ -0,0 +1,127 @@
+%%% reftex-default-bibliography: ("references.bib")
+%%% Local Variables:
+%%% mode: latex
+%%% TeX-master: t
+%%% End:
+
+% Created 2021-11-18 Thu 14:24
+\documentclass[fleqn,usenatbib]{mnras}
+
+% Allow "Thomas van Noord" and "Simon de Laguarde" and alike to be sorted by "N" and "L" etc. in the bibliography.
+% Write the name in the bibliography as "\VAN{Noord}{Van}{van} Noord, Thomas"
+\DeclareRobustCommand{\VAN}[3]{#2}
+\let\VANthebibliography\thebibliography
+\def\thebibliography{\DeclareRobustCommand{\VAN}[3]{##3}\VANthebibliography}
+
+\usepackage[utf8]{inputenc}
+\usepackage[T1]{fontenc}
+\usepackage{graphicx}
+\usepackage{grffile}
+\usepackage{longtable}
+\usepackage{wrapfig}
+\usepackage{rotating}
+\usepackage[normalem]{ulem}
+\usepackage{amsmath}
+\usepackage{textcomp}
+\usepackage{amssymb}
+\usepackage{capt-of}
+\usepackage{hyperref}
+\usepackage{color}
+\usepackage{listings}
+\usepackage{natbib}
+\usepackage{hypernat}
+
+% Custom packages
+\usepackage{/home/david/projects/latex_todo_upgrade/tex_todo}
+\usepackage{/home/david/projects/latex_editing_colors/editing_colors}
+
+% Custom commands
+\newcommand{\binaryc}{\textsc{binary\_c}}
+\newcommand{\binarycpython}{\textsc{binary\_c-python}}
+
+% Title
+\newcommand{\mytitle}{\binarycpython: A python-based stellar population synthesis tool and interface to \binaryc}
+
+%%%%%%%%%%%%%%%%%%%%%
+% The list of authors, and the short list which is used in the headers.
+% If you need two or more lines of authors, add an extra line using \newauthor
+\author[D.D. Hendriks. et al.]{
+ D. D. Hendriks $^{1}$\thanks{E-mail: \href{mailto:dh00601@surrey.ac.uk}{dh00601@surrey.ac.uk}\ (DDH)},
+ R. G. Izzard $^{1}$
+\\
+% List of institutions
+ $^{1}$Department of Physics, University of Surrey, Guildford, GU2 7XH, Surrey, UK\\
+}
+
+\title[]{\mytitle}
+\hypersetup{
+ pdfauthor={David Hendriks},
+ pdftitle={\mytitle},
+ pdfkeywords={},
+ pdfsubject={},
+ pdflang={English}
+}
+%%%
+\begin{document}
+
+\maketitle
+
+\section{Summary}
+\label{sec:summary}
+% general astrophysics
+%Calculating the evolution of populations of stars, and investigating how certain physical assumptions affect this evolution, requires methods to rapidly simulate stellar systems.
+
+% Intro sentence
+We present our package \href{https://ri0005.pages.surrey.ac.uk/binary_c-python/}{\binarycpython}, which is aimed to provide a convenient and easy-to-use interface to the \href{http://personal.ph.surrey.ac.uk/~ri0005/doc/binary_c/binary_c.html}{\binaryc}~\citep{izzardNewSyntheticModel2004, izzardPopulationNucleosynthesisSingle2006, izzardPopulationSynthesisBinary2009, izzardBinaryStarsGalactic2018} framework, allowing the user to rapidly evolve individual systems and populations of stars. \binarycpython\ is available on \href{https://pypi.org/project/binarycpython/}{Pip} and on \href{https://gitlab.com/binary_c/binary_c-python}{Gitlab}.
+
+% A bit more about what we can do
+The user can control output from \binaryc by providing \binarycpython\ with logging statements that are dynamically compiled and loaded into \binaryc. \binarycpython\ uses multiprocessing to utilise all the cores on a particular machine, and can run populations with HPC cluster workload managers like \textsc{HTCondor} and \textsc{Slurm}, allowing the user to run simulations on very large computing clusters.
+
+% Interfacing
+\binarycpython\ is easily interfaced or integrated with other Python-based codes, e.g.\ sampling codes like \textsc{Emcee} or \textsc{Dynesty}, or the astrophysics oriented package \textsc{Astropy}~\citep{astropycollaborationAstropyCommunityPython2013,foreman-mackeyEmceeMCMCHammer2013,astropycollaborationAstropyProjectBuilding2018,speagleDynestyDynamicNested2020}. Moreover, it is possible to provide custom system-generating functions through our function hooks, allowing third-party packages to control the populations of stars and evolve them through \binarycpython.
+
+% Recent developments
+Recent developments in \binaryc\ include standardised output datasets called \textit{ensembles}. \binarycpython\ easily processes these datasets and provides a suite of utility functions to handle them. Furthermore, \binaryc\ now includes the \textit{ensemble-manager} class, which makes use of the core functions and classes of \binarycpython\ to evolve a grid of stellar populations of stars with varying input physics, allowing for huge, automated parameter studies through a single interface.
+
+% Documentation
+We provide \href{https://ri0005.pages.surrey.ac.uk/binary\_c-python/index.html}{documentation} that is automatically generated based on docstrings and a suite of \textsc{Jupyter} \href{https://ri0005.pages.surrey.ac.uk/binary\_c-python/example\_notebooks.html}{notebooks}. These notebooks consist of technical tutorials on how to use \binarycpython, and use-case scenarios aimed at doing science. Much of \binarycpython\ is covered by unit tests to ensure reliability and correctness, and the test coverage is continually increased as the package is being improved.
+
+\section{Statement of need}
+\label{sec:statement}
+% Current climate
+In the current scientific climate \textsc{Python} is ubiquitous, and while lower-level codes written in e.g. \textsc{Fortran} or \textsc{C} are still widely used, much of the newer software is written in \textsc{Python}, either entirely or as a wrapper around other codes. Education in programming also often includes \textsc{Python} courses because of its ease of use and its flexibility. Moreover, \textsc{Python} has a large community with many resources and tutorials.
+% Why
+We have created \binarycpython\ to allow students and scientists alike to explore current scientific issues while enjoying the familiar syntax, and at the same time make use of the plentiful scientific and astrophysical packages like \textsc{Numpy}, \textsc{Scipy}, \textsc{Pandas}, \textsc{Astropy}\ and platforms like \textsc{Jupyter}.
+
+% Earlier versions
+Earlier versions of \binarycpython\ were written in Perl, where much of the debugging and the logic and structure developments were done. This greatly made porting to \textsc{Python} relatively easy.
+
+\section{Projects that use \binarycpython}
+\label{sec:projects}
+% Intro to projects
+\binarycpython\ has already been used in a variety of situations, ranging from pure research to educational purposes, as well as in outreach events.
+% Educational
+In the summer of 2021 we used \binarycpython\ as the basis for the interactive classes on stellar ecosystems during the \href{https://www2.mpia-hd.mpg.de/imprs-hd/SummerSchools/2021/}{International Max-Planck Research School summer school 2021 in Heidelberg}, where students were introduced to the topic of population synthesis and were able to use our notebooks to perform their own calculations.
+%% Past Research
+%
+\binarycpython\ has been used in \citet{mirouh_etal22}, where improvements to tidal interactions between stars were implemented, and initial birth parameter distributions were varied to match to observed binary systems in star clusters.
+%
+A Master’s thesis project, aimed at finding the birth system parameters of the V106 stellar system, comparing observations to results of \binaryc\ and calculating the maximum likelihood with Bayesian inference through Markov chain Monte Carlo sampling. The project made use of \binarycpython\ and the \textsc{Emcee} package.
+
+%
+Currently \binarycpython\ is used in several ongoing projects that study the effect of birth distributions on the occurrence of carbon-enhanced metal-poor (CEMP) stars, the occurrence and properties of accretion disks in main-sequence stars and the predicted observable black hole distribution by combining star formation and metallicity distributions with the output of \binaryc. Moreover, we use the \textit{ensemble} output structure to generate datasets for galactic chemical evolution on cosmological timescales, where we rely heavily on the utilities of \binarycpython.
+
+\section{Acknowledgements}
+\label{sec:orgf6f5520}
+We acknowledge the helpful discussions and early testing efforts from M. Delorme, G. Mirouh, and D. Tracey, and the early work of J. Andrews which inspired our Python-C interface code. DDH thanks the UKRI/UoS for the funding grant H120341A. RGI thanks STFC for funding grants \href{https://gtr.ukri.org/projects?ref=ST%2FR000603%2F1}{ST/R000603/1} and \href{https://gtr.ukri.org/projects?ref=ST/L003910/2}{ST/L003910/2}.
+
+%%%%%%%%%%%%%%%%%%%% REFERENCES %%%%%%%%%%%%%%%%%%
+% The best way to enter references is to use BibTeX:
+\bibliographystyle{mnras-custom.bst}
+\bibliography{references.bib} % if your bibtex file is called example.bib
+
+\end{document}
+%%% Local Variables:
+%%% mode: latex
+%%% TeX-master: t
+%%% End:
diff --git a/papers/joss_paper/paper_tex/paper.upa b/papers/joss_paper/paper_tex/paper.upa
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/papers/joss_paper/paper_tex/paper.upb b/papers/joss_paper/paper_tex/paper.upb
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/papers/joss_paper/paper_tex/references.bib b/papers/joss_paper/paper_tex/references.bib
new file mode 100644
index 0000000000000000000000000000000000000000..a4ab8faaa9b869b7bbeaf633f9d24b6f6bd690c7
--- /dev/null
+++ b/papers/joss_paper/paper_tex/references.bib
@@ -0,0 +1,144 @@
+@article{izzardNewSyntheticModel2004,
+ title = {A New Synthetic Model for Asymptotic Giant Branch Stars},
+ author = {Izzard, Robert G. and Tout, Christopher A. and Karakas, Amanda I. and Pols, Onno R.},
+ year = {2004},
+ month = may,
+ journal = {Monthly Notices of the Royal Astronomical Society},
+ volume = {350},
+ number = {2},
+ pages = {407--426},
+ issn = {0035-8711},
+ doi = {10.1111/j.1365-2966.2004.07446.x},
+ abstract = {Abstract. We present a synthetic model for thermally pulsing asymptotic giant branch (TPAGB) evolution constructed by fitting expressions to full evolutionary},
+ langid = {english},
+ keywords = {masterthesis},
+ file = {/home/david/pdfs/Zotero/Izzard et al_2004_A new synthetic model for asymptotic giant branch stars.pdf;/home/david/Zotero/storage/DNNTAJQF/1113239.html}
+}
+
+@article{izzardPopulationNucleosynthesisSingle2006,
+ title = {Population Nucleosynthesis in Single and Binary Stars - {{I}}. {{Model}}},
+ author = {Izzard, R. G. and Dray, L. M. and Karakas, A. I. and Lugaro, M. and Tout, C. A.},
+ year = {2006},
+ month = dec,
+ journal = {Astronomy \& Astrophysics},
+ volume = {460},
+ number = {2},
+ pages = {565--572},
+ issn = {0004-6361, 1432-0746},
+ doi = {10.1051/0004-6361:20066129},
+ abstract = {We present a synthetic algorithm to rapidly calculate nucleosynthetic yields from populations of single and binary stars for use in population synthesis, globular cluster and Galactic chemical evolution simulations. Single star nucleosynthesis is fitted directly to full evolution models and our model includes first, second and third dredge-ups with \emph{s{$<$}i/{$>$}-process enhancements, an analytic calculation for hot-bottom burning of CNO, NeNa and MgAl isotopes, surface enhancements due to wind loss in massive stars and core-collapse supernova yields. Even though this algorithm operates about 10\textsuperscript{7{$<$}sup/{$>$} times faster than full evolution and nucleosynthesis calculations, agreement with such models is good. We extend the single star model to include prescriptions of binary star interactions, notably mass loss and gain by stellar winds and Roche-lobe overflow, novae and type Ia supernovae. As examples of the application of our algorithm we present models of some interesting systems containing chemically peculiar stars that may occur in binaries.}}},
+ copyright = {\textcopyright{} ESO, 2006},
+ langid = {english},
+ keywords = {masterthesis},
+ file = {/home/david/pdfs/Zotero/Izzard et al_2006_Population nucleosynthesis in single and binary stars - I.pdf;/home/david/Zotero/storage/8EB73LN9/aa6129-06.html}
+}
+
+@article{izzardPopulationSynthesisBinary2009,
+ ids = {izzardPopulationSynthesisBinary2009a},
+ title = {Population Synthesis of Binary Carbon-Enhanced Metal-Poor Stars},
+ author = {Izzard, R. G. and Glebbeek, E. and Stancliffe, R. J. and Pols, O. R.},
+ year = {2009},
+ month = dec,
+ journal = {Astronomy and Astrophysics},
+ volume = {508},
+ number = {3},
+ pages = {1359--1374},
+ publisher = {{EDP Sciences}},
+ issn = {0004-6361},
+ doi = {10.1051/0004-6361/200912827},
+ abstract = {The carbon-enhanced metal-poor (CEMP) stars constitute approximately one fifth of the metal-poor ([Fe/H] {$\lnapprox$} -2) population but their origin is not well understood. The most widely accepted formation scenario, at least for the majority of CEMP stars which are also enriched in s-process elements, invokes mass-transfer of carbon-rich material from a thermally-pulsing asymptotic giant branch (TPAGB) primary star to a less massive main-sequence companion which is seen today. Recent studies explore the possibility that an initial mass function biased toward intermediate-mass stars is required to reproduce the observed CEMP fraction in stars with metallicity [Fe/H]{$<$}-2.5. These models also implicitly predict a large number of nitrogen-enhanced metal-poor (NEMP) stars which is not seen. In this paper we investigate whether the observed CEMP and NEMP to extremely metal-poor (EMP) ratios can be explained without invoking a change in the initial mass function. We construct binary-star populations in an attempt to reproduce the observed number and chemical abundance patterns of CEMP stars at a metallicity [Fe/H]\texttildelow -2.3. Our binary-population models include synthetic nucleosynthesis in TPAGB stars and account for mass transfer and other forms of binary interaction. This approach allows us to explore uncertainties in the CEMP-star formation scenario by parameterization of uncertain input physics. In particular, we consider the uncertainty in the physics of third dredge up in the TPAGB primary, binary mass transfer and mixing in the secondary star. We confirm earlier findings that with current detailed TPAGB models, in which third dredge up is limited to stars more massive than about 1.25\textasciitilde M{$\odot$}, the large observed CEMP fraction cannot be accounted for. We find that efficient third dredge up in low-mass (less than 1.25\textasciitilde M{$\odot$}), low-metallicity stars may offer at least a partial explanation for the large observed CEMP fraction while remaining consistent with the small observed NEMP fraction. Appendices A-E are only available in electronic form at http://www.aanda.org},
+ keywords = {abundances,binaries: close,Galaxy: halo,Galaxy: stellar content,masterthesis,nuclear reactions,nucleosynthesis,project_core,stars: carbon,stars: chemically peculiar,to_read},
+ file = {/home/david/pdfs/Zotero/Izzard et al_2009_Population synthesis of binary carbon-enhanced metal-poor stars.pdf;/home/david/Zotero/storage/BAXNURKG/aa12827-09.html}
+}
+
+@article{izzardBinaryStarsGalactic2018,
+ title = {Binary Stars in the {{Galactic}} Thick Disc},
+ author = {Izzard, Robert G. and Preece, Holly and Jofre, Paula and Halabi, Ghina M. and Masseron, Thomas and Tout, Christopher A.},
+ year = {2018},
+ month = jan,
+ journal = {Monthly Notices of the Royal Astronomical Society},
+ volume = {473},
+ pages = {2984--2999},
+ issn = {0035-8711},
+ doi = {10.1093/mnras/stx2355},
+ abstract = {The combination of asteroseismologically measured masses with abundances from detailed analyses of stellar atmospheres challenges our fundamental knowledge of stars and our ability to model them. Ancient red-giant stars in the Galactic thick disc are proving to be most troublesome in this regard. They are older than 5 Gyr, a lifetime corresponding to an initial stellar mass of about 1.2 M{$\odot$}. So why do the masses of a sizeable fraction of thick-disc stars exceed 1.3 M{$\odot$}, with some as massive as 2.3 M{$\odot$}? We answer this question by considering duplicity in the thick-disc stellar population using a binary population-nucleosynthesis model. We examine how mass transfer and merging affect the stellar mass distribution and surface abundances of carbon and nitrogen. We show that a few per cent of thick-disc stars can interact in binary star systems and become more massive than 1.3 M{$\odot$}. Of these stars, most are single because they are merged binaries. Some stars more massive than 1.3 M{$\odot$} form in binaries by wind mass transfer. We compare our results to a sample of the APOKASC data set and find reasonable agreement except in the number of these thick-disc stars more massive than 1.3 M{$\odot$}. This problem is resolved by the use of a logarithmically flat orbital-period distribution and a large binary fraction.},
+ keywords = {binaries: general,binary,Galaxy: disc,Galaxy: stellar content,masterthesis,surrey,to_Read},
+ file = {/home/david/pdfs/Zotero/Izzard et al_2018_Binary stars in the Galactic thick disc2.pdf}
+}
+
+@article{foreman-mackeyEmceeMCMCHammer2013,
+ title = {Emcee: {{The MCMC Hammer}}},
+ shorttitle = {Emcee},
+ author = {{Foreman-Mackey}, Daniel and Hogg, David W. and Lang, Dustin and Goodman, Jonathan},
+ year = {2013},
+ month = mar,
+ journal = {Publications of the Astronomical Society of the Pacific},
+ volume = {125},
+ number = {925},
+ eprint = {1202.3665},
+ eprinttype = {arxiv},
+ pages = {306--312},
+ issn = {00046280, 15383873},
+ doi = {10.1086/670067},
+ abstract = {We introduce a stable, well tested Python implementation of the affine-invariant ensemble sampler for Markov chain Monte Carlo (MCMC) proposed by Goodman \& Weare (2010). The code is open source and has already been used in several published projects in the astrophysics literature. The algorithm behind emcee has several advantages over traditional MCMC sampling methods and it has excellent performance as measured by the autocorrelation time (or function calls per independent sample). One major advantage of the algorithm is that it requires hand-tuning of only 1 or 2 parameters compared to \$\textbackslash sim N\^2\$ for a traditional algorithm in an N-dimensional parameter space. In this document, we describe the algorithm and the details of our implementation and API. Exploiting the parallelism of the ensemble method, emcee permits any user to take advantage of multiple CPU cores without extra effort. The code is available online at http://dan.iel.fm/emcee under the MIT License.},
+ archiveprefix = {arXiv},
+ keywords = {Astrophysics - Instrumentation and Methods for Astrophysics,Physics - Computational Physics,Statistics - Computation},
+ file = {/home/david/pdfs/Zotero/Foreman-Mackey et al_2013_emcee.pdf;/home/david/Zotero/storage/SSM96UY2/1202.html}
+}
+
+@article{speagleDynestyDynamicNested2020,
+ title = {Dynesty: A Dynamic Nested Sampling Package for Estimating {{Bayesian}} Posteriors and Evidences},
+ shorttitle = {Dynesty},
+ author = {Speagle, Joshua S},
+ year = {2020},
+ month = apr,
+ journal = {Monthly Notices of the Royal Astronomical Society},
+ volume = {493},
+ number = {3},
+ pages = {3132--3158},
+ issn = {0035-8711},
+ doi = {10.1093/mnras/staa278},
+ abstract = {We present dynesty, a public, open-source, python package to estimate Bayesian posteriors and evidences (marginal likelihoods) using the dynamic nested sampling methods developed by Higson et~al. By adaptively allocating samples based on posterior structure, dynamic nested sampling has the benefits of Markov chain Monte Carlo (MCMC) algorithms that focus exclusively on posterior estimation while retaining nested sampling's ability to estimate evidences and sample from complex, multimodal distributions. We provide an overview of nested sampling, its extension to dynamic nested sampling, the algorithmic challenges involved, and the various approaches taken to solve them in this and previous work. We then examine dynesty's performance on a variety of toy problems along with several astronomical applications. We find in particular problems dynesty can provide substantial improvements in sampling efficiency compared to popular MCMC approaches in the astronomical literature. More detailed statistical results related to nested sampling are also included in the appendix.},
+ file = {/home/david/pdfs/Zotero/Speagle_2020_dynesty.pdf;/home/david/Zotero/storage/PZBMLD2H/5721521.html}
+}
+
+@article{astropycollaborationAstropyCommunityPython2013,
+ title = {Astropy: {{A}} Community {{Python}} Package for Astronomy},
+ shorttitle = {Astropy},
+ author = {{Astropy Collaboration} and Robitaille, Thomas P. and Tollerud, Erik J. and Greenfield, Perry and Droettboom, Michael and Bray, Erik and Aldcroft, Tom and Davis, Matt and Ginsburg, Adam and {Price-Whelan}, Adrian M. and Kerzendorf, Wolfgang E. and Conley, Alexander and Crighton, Neil and Barbary, Kyle and Muna, Demitri and Ferguson, Henry and Grollier, Fr{\'e}d{\'e}ric and Parikh, Madhura M. and Nair, Prasanth H. and Unther, Hans M. and Deil, Christoph and Woillez, Julien and Conseil, Simon and Kramer, Roban and Turner, James E. H. and Singer, Leo and Fox, Ryan and Weaver, Benjamin A. and Zabalza, Victor and Edwards, Zachary I. and Azalee Bostroem, K. and Burke, D. J. and Casey, Andrew R. and Crawford, Steven M. and Dencheva, Nadia and Ely, Justin and Jenness, Tim and Labrie, Kathleen and Lim, Pey Lian and Pierfederici, Francesco and Pontzen, Andrew and Ptak, Andy and Refsdal, Brian and Servillat, Mathieu and Streicher, Ole},
+ year = {2013},
+ month = oct,
+ journal = {Astronomy and Astrophysics},
+ volume = {558},
+ pages = {A33},
+ issn = {0004-6361},
+ doi = {10.1051/0004-6361/201322068},
+ abstract = {We present the first public version (v0.2) of the open-source and community-developed Python package, Astropy. This package provides core astronomy-related functionality to the community, including support for domain-specific file formats such as flexible image transport system (FITS) files, Virtual Observatory (VO) tables, and common ASCII table formats, unit and physical quantity conversions, physical constants specific to astronomy, celestial coordinate and time transformations, world coordinate system (WCS) support, generalized containers for representing gridded as well as tabular data, and a framework for cosmological transformations and conversions. Significant functionality is under activedevelopment, such as a model fitting framework, VO client and server tools, and aperture and point spread function (PSF) photometry tools. The core development team is actively making additions and enhancements to the current code base, and we encourage anyone interested to participate in the development of future Astropy versions.},
+ langid = {english},
+ file = {/home/david/pdfs/Zotero/Collaboration et al_2013_Astropy.pdf;/home/david/Zotero/storage/VXZP754H/abstract.html}
+}
+
+@article{astropycollaborationAstropyProjectBuilding2018,
+ title = {The {{Astropy Project}}: {{Building}} an {{Open-science Project}} and {{Status}} of the v2.0 {{Core Package}}},
+ shorttitle = {The {{Astropy Project}}},
+ author = {{Astropy Collaboration} and {Price-Whelan}, A. M. and Sip{\H 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 Bach, Y. P. 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 Corrales, L. and Crichton, D. and D'Avella, 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. and {Astropy Contributors}},
+ year = {2018},
+ month = sep,
+ journal = {The Astronomical Journal},
+ volume = {156},
+ pages = {123},
+ issn = {0004-6256},
+ doi = {10.3847/1538-3881/aabc4f},
+ abstract = {The Astropy Project supports and fosters the development of open-source and openly developed Python packages that provide commonly needed functionality to the astronomical community. A key element of the Astropy Project is the core package astropy, which serves as the foundation for more specialized projects and packages. In this article, we provide an overview of the organization of the Astropy project and summarize key features in the core package, as of the recent major release, version 2.0. We then describe the project infrastructure designed to facilitate and support development for a broader ecosystem of interoperable packages. We conclude with a future outlook of planned new features and directions for the broader Astropy Project. .},
+ keywords = {Astrophysics - Instrumentation and Methods for Astrophysics,methods: data analysis,methods: miscellaneous,methods: statistical,reference systems},
+ annotation = {ADS Bibcode: 2018AJ....156..123A},
+ file = {/home/david/pdfs/Zotero/Astropy Collaboration et al_2018_The Astropy Project2.pdf}
+}
+
+
+@article{mirouh_etal22,
+ author = {{Mirouh}, Giovanni M. and {Hendriks}, David D. and {Dykes}, Sophie and {Moe}, Maxwell and {Izzard}, Robert G.},
+ title = "{Detailed equilibrium and dynamical tides: impact on circularization and synchronization in open clusters}",
+ journal = {\mnras},
+ year = "submitted",
+}
\ No newline at end of file
diff --git a/papers/joss_paper/paper_tex/run_pandoc.sh b/papers/joss_paper/paper_tex/run_pandoc.sh
new file mode 100755
index 0000000000000000000000000000000000000000..871de4c540da252efd9b13619ac54afe0874bdd1
--- /dev/null
+++ b/papers/joss_paper/paper_tex/run_pandoc.sh
@@ -0,0 +1,3 @@
+#!/bin/bash
+
+pandoc -s paper.tex -o paper.md
diff --git a/papers/joss_paper/paper_tex/title_and_affiliation.md b/papers/joss_paper/paper_tex/title_and_affiliation.md
new file mode 100644
index 0000000000000000000000000000000000000000..4b28669ece8764436810b923197b652a0f4a356a
--- /dev/null
+++ b/papers/joss_paper/paper_tex/title_and_affiliation.md
@@ -0,0 +1,18 @@
+---
+title: '[binary\_c-python]{.smallcaps}: A python-based stellar population synthesis tool and interface to [binary\_c]{.smallcaps}'
+tags:
+ - Python
+ - astronomy
+authors:
+ - name: D. D. Hendriks[^1]
+ orcid: 0000-0002-8717-6046
+ affiliation: 1
+ - name: R. G. Izzard
+ orcid: 0000-0003-0378-4843
+ affiliation: 1
+affiliations:
+ - name: Department of Physics, University of Surrey, Guildford, GU2 7XH, Surrey, UK
+ index: 1
+date: 18 June 2022
+bibliography: paper.bib
+---
\ No newline at end of file
diff --git a/papers/joss_paper/publishing_in_JOSS/requirements.org b/papers/joss_paper/publishing_in_JOSS/requirements.org
new file mode 100644
index 0000000000000000000000000000000000000000..1295e98fefa9f9f29074803b14023527040b43f0
--- /dev/null
+++ b/papers/joss_paper/publishing_in_JOSS/requirements.org
@@ -0,0 +1,99 @@
+#+AUTHOR: David Hendriks
+#+EMAIL: davidhendriks93@gmail.com
+#+OPTIONS: ':nil *:t -:t ::t <:t H:2 ^:t arch:headline
+#+OPTIONS: author:t c:nil creator:comment d:(not "LOGBOOK") date:t
+#+OPTIONS: e:t email:nil f:t inline:t num:t p:nil pri:nil stat:t
+#+OPTIONS: tasks:t tex:t timestamp:t toc:t todo:t |:t
+#+DESCRIPTION:
+#+EXCLUDE_TAGS: noexport
+#+KEYWORDS:
+#+LANGUAGE: en
+#+SELECT_TAGS: export
+#+BIBLIOGRAPHY:
+#+OPTIONS: \n:nil tags:nil
+#+LATEX: \setlength\parindent{0pt}
+#+TITLE:
+#+DATE:
+
+* Requirements for submission:
+** DONE Requirements for the project
+*** DONE The software must be open source as per the OSI definition.
+
+ Yes.
+*** DONE The software must have an obvious research application.
+
+ Yes: main tool used to operate binary-c and generate populations of stars through various mtehods
+*** DONE You must be a major contributor to the software you are submitting, and have a GitHub account to participate in the review process.
+
+ Yes. https://github.com/ddhendriks
+*** DONE Your paper must not focus on new research results accomplished with the software.
+
+ It does not.
+*** DONE Your paper (paper.md and BibTeX files, plus any figures) must be hosted in a Git-based repository together with your software (although they may be in a short-lived branch which is never merged with the default).
+*** DONE Be stored in a repository that can be cloned without registration.
+
+ Yes, it does. https://gitlab.com/binary_c/binary_c-python
+*** DONE Be stored in a repository that is browsable online without registration.
+
+ Yes, it does. https://gitlab.com/binary_c/binary_c-python
+*** DONE Have an issue tracker that is readable without registration.
+
+ Yes, it does. https://gitlab.com/binary_c/binary_c-python/-/issues
+*** DONE Permit individuals to create issues/file tickets against your repository.
+
+ Yes. It does. https://gitlab.com/binary_c/binary_c-python/-/issues
+*** DONE Your software should be a significant contribution to the available open source software that either enables some new research challenges to be addressed or makes addressing research challenges significantly better (e.g., faster, easier, simpler).
+*** DONE should represent not less than three months of work for an individual.
+
+ It represents work done throughout my PhD
+
+** DONE submission workflow
+*** DONE Make your software available in an open repository (GitHub, Bitbucket, etc.) and include an OSI approved open source license.
+
+ Available on https://gitlab.com/binary_c/binary_c-python licenced under GPL3
+
+*** DONE Make sure that the software complies with the JOSS review criteria. In particular, your software should be full-featured, well-documented, and contain procedures (such as automated tests) for checking correctness.
+
+*** DONE Write a short paper in Markdown format using paper.md as file name, including a title, summary, author names, affiliations, and key references. See our example paper to follow the correct format.
+
+ Working on it
+
+*** DONE (Optional) create a metadata file describing your software and include it in your repository. We provide a script that automates the generation of this metadata.
+
+ Yes, is included in https://gitlab.surrey.ac.uk/ri0005/binary_c-python/-/blob/papers/JOSS_release/papers/joss_paper/codemeta.json
+** DONE Paper should include
+*** DONE A list of the authors of the software and their affiliations, using the correct format (see the example below).
+*** DONE A summary describing the high-level functionality and purpose of the software for a diverse, non-specialist audience.
+*** DONE A Statement of Need section that clearly illustrates the research purpose of the software.
+*** DONE A list of key references, including to other software addressing related needs. Note that the references should include full names of venues, e.g., journals and conferences, not abbreviations only understood in the context of a specific discipline.
+*** DONE Mention (if applicable) a representative set of past or ongoing research projects using the software and recent scholarly publications enabled by it.
+*** DONE Acknowledgement of any financial support.
+* Review checklist
+https://joss.readthedocs.io/en/latest/review_checklist.html
+** General checks
+*** DONE Repository: Is the source code for this software available at the repository url?
+*** DONE License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
+*** DONE Contribution and authorship: Has the submitting author made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
+** DONE Functionality
+*** DONE Installation: Does installation proceed as outlined in the documentation?
+*** ANSWERED Functionality: Have the functional claims of the software been confirmed?
+*** DONE Performance: If there are any performance claims of the software, have they been confirmed? (If there are no claims, please check off this item.)
+** DONE Documentation
+*** DONE A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
+*** DONE Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
+*** DONE Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
+*** DONE Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
+*** DONE Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
+*** DONE Community guidelines: Are there clear guidelines for third parties wishing to 1) Contribute to the software 2) Report issues or problems with the software 3) Seek support
+** TODO Software paper
+*** DONE Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
+*** DONE A statement of need: Does the paper have a section titled ‘Statement of Need’ that clearly states what problems the software is designed to solve and who the target audience is?
+*** TODO State of the field: Do the authors describe how this software compares to other commonly-used packages?
+
+Well, not sure if i want to do that. If they ask about it then i will add more text i think
+
+*** TODO Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
+
+That is to the reviewer
+
+*** DONE References: Is the list of references complete, and is everything cited appropriately that should be cited (e.g., papers, datasets, software)? Do references in the text use the proper citation syntax?
diff --git a/papers/joss_paper/publishing_in_JOSS/requirements.org_archive b/papers/joss_paper/publishing_in_JOSS/requirements.org_archive
new file mode 100644
index 0000000000000000000000000000000000000000..57587774691153a30315e6f816a142e27eb712b5
--- /dev/null
+++ b/papers/joss_paper/publishing_in_JOSS/requirements.org_archive
@@ -0,0 +1,38 @@
+# -*- mode: org -*-
+
+
+Archived entries from file /home/david/papers/paper_joss_binarycpython/requirements.org
+
+
+* Requirements for submission:
+:PROPERTIES:
+:ARCHIVE_TIME: 2022-06-02 Thu 14:40
+:ARCHIVE_FILE: ~/papers/paper_joss_binarycpython/requirements.org
+:ARCHIVE_CATEGORY: requirements
+:END:
+- [X] The software must be open source as per the OSI definition.
+- [ ] The software must have an obvious research application.
+- [X] You must be a major contributor to the software you are submitting, and have a GitHub account to participate in the review process.
+- [X] Your paper must not focus on new research results accomplished with the software.
+- [ ] Your paper (paper.md and BibTeX files, plus any figures) must be hosted in a Git-based repository together with your software (although they may be in a short-lived branch which is never merged with the default).
+- [ ] Be stored in a repository that can be cloned without registration.
+- [ ] Be stored in a repository that is browsable online without registration.
+- [X] Have an issue tracker that is readable without registration.
+- [X] Permit individuals to create issues/file tickets against your repository.
+- [ ] Your software should be a significant contribution to the available open source software that either enables some new research challenges to be addressed or makes addressing research challenges significantly better (e.g., faster, easier, simpler).
+- [X] should represent not less than three months of work for an individual.
+
+submission workflow
+- [ ] Make your software available in an open repository (GitHub, Bitbucket, etc.) and include an OSI approved open source license.
+- [ ] Make sure that the software complies with the JOSS review criteria. In particular, your software should be full-featured, well-documented, and contain procedures (such as automated tests) for checking correctness.
+- [ ] Write a short paper in Markdown format using paper.md as file name, including a title, summary, author names, affiliations, and key references. See our example paper to follow the correct format.
+- [ ] (Optional) create a metadata file describing your software and include it in your repository. We provide a script that automates the generation of this metadata.
+
+Paper should include
+- [ ] A list of the authors of the software and their affiliations, using the correct format (see the example below).
+- [ ] A summary describing the high-level functionality and purpose of the software for a diverse, non-specialist audience.
+- [ ] A Statement of Need section that clearly illustrates the research purpose of the software.
+- [ ] A list of key references, including to other software addressing related needs. Note that the references should include full names of venues, e.g., journals and conferences, not abbreviations only understood in the context of a specific discipline.
+- [X] Mention (if applicable) a representative set of past or ongoing research projects using the software and recent scholarly publications enabled by it.
+- [ ] Acknowledgement of any financial support.
+
diff --git a/papers/joss_paper/publishing_in_JOSS/requirements.tex b/papers/joss_paper/publishing_in_JOSS/requirements.tex
new file mode 100644
index 0000000000000000000000000000000000000000..534da52fbe24e6e2bc6b4f6df1d346f934e67d2a
--- /dev/null
+++ b/papers/joss_paper/publishing_in_JOSS/requirements.tex
@@ -0,0 +1,177 @@
+% Created 2022-06-07 Tue 18:52
+% Intended LaTeX compiler: pdflatex
+\documentclass[11pt]{article}
+\usepackage[utf8]{inputenc}
+\usepackage[T1]{fontenc}
+\usepackage{graphicx}
+\usepackage{longtable}
+\usepackage{wrapfig}
+\usepackage{rotating}
+\usepackage[normalem]{ulem}
+\usepackage{amsmath}
+\usepackage{amssymb}
+\usepackage{capt-of}
+\usepackage{hyperref}
+\usepackage{color}
+\usepackage{listings}
+\author{David Hendriks}
+\date{}
+\title{}
+\hypersetup{
+ pdfauthor={David Hendriks},
+ pdftitle={},
+ pdfkeywords={},
+ pdfsubject={},
+ pdfcreator={Emacs 27.2 (Org mode 9.5.1)},
+ pdflang={English}}
+\begin{document}
+
+\tableofcontents
+
+\setlength\parindent{0pt}
+
+\section{Requirements for submission:}
+\label{sec:org578d1a3}
+\subsection{{\bfseries\sffamily DONE} Requirements for the project}
+\label{sec:orgc5371a8}
+\begin{enumerate}
+\item {\bfseries\sffamily DONE} The software must be open source as per the OSI definition.
+\label{sec:orgd2bd136}
+
+Yes.
+\item {\bfseries\sffamily DONE} The software must have an obvious research application.
+\label{sec:org0963730}
+
+Yes: main tool used to operate binary-c and generate populations of stars through various mtehods
+\item {\bfseries\sffamily DONE} You must be a major contributor to the software you are submitting, and have a GitHub account to participate in the review process.
+\label{sec:org7d5a126}
+
+Yes. \url{https://github.com/ddhendriks}
+\item {\bfseries\sffamily DONE} Your paper must not focus on new research results accomplished with the software.
+\label{sec:org1bebc12}
+
+It does not.
+\item {\bfseries\sffamily DONE} Your paper (paper.md and BibTeX files, plus any figures) must be hosted in a Git-based repository together with your software (although they may be in a short-lived branch which is never merged with the default).
+\label{sec:orge3646ef}
+\item {\bfseries\sffamily DONE} Be stored in a repository that can be cloned without registration.
+\label{sec:orgf1ad9ad}
+
+Yes, it does. \url{https://gitlab.com/binary\_c/binary\_c-python}
+\item {\bfseries\sffamily DONE} Be stored in a repository that is browsable online without registration.
+\label{sec:orgb254b83}
+
+Yes, it does. \url{https://gitlab.com/binary\_c/binary\_c-python}
+\item {\bfseries\sffamily DONE} Have an issue tracker that is readable without registration.
+\label{sec:orge4c27bd}
+
+Yes, it does. \url{https://gitlab.com/binary\_c/binary\_c-python/-/issues}
+\item {\bfseries\sffamily DONE} Permit individuals to create issues/file tickets against your repository.
+\label{sec:org7af104d}
+
+Yes. It does. \url{https://gitlab.com/binary\_c/binary\_c-python/-/issues}
+\item {\bfseries\sffamily DONE} Your software should be a significant contribution to the available open source software that either enables some new research challenges to be addressed or makes addressing research challenges significantly better (e.g., faster, easier, simpler).
+\label{sec:orgce45c54}
+\item {\bfseries\sffamily DONE} should represent not less than three months of work for an individual.
+\label{sec:org2b28a10}
+
+It represents work done throughout my PhD
+\end{enumerate}
+
+\subsection{{\bfseries\sffamily DONE} submission workflow}
+\label{sec:org5ab3adc}
+\begin{enumerate}
+\item {\bfseries\sffamily DONE} Make your software available in an open repository (GitHub, Bitbucket, etc.) and include an OSI approved open source license.
+\label{sec:orgf955a73}
+
+Available on \url{https://gitlab.com/binary\_c/binary\_c-python} licenced under GPL3
+
+\item {\bfseries\sffamily DONE} Make sure that the software complies with the JOSS review criteria. In particular, your software should be full-featured, well-documented, and contain procedures (such as automated tests) for checking correctness.
+\label{sec:org523e384}
+
+\item {\bfseries\sffamily DONE} Write a short paper in Markdown format using paper.md as file name, including a title, summary, author names, affiliations, and key references. See our example paper to follow the correct format.
+\label{sec:orgace508c}
+
+Working on it
+
+\item {\bfseries\sffamily DONE} (Optional) create a metadata file describing your software and include it in your repository. We provide a script that automates the generation of this metadata.
+\label{sec:orgae02cfc}
+
+Yes, is included in \url{https://gitlab.surrey.ac.uk/ri0005/binary\_c-python/-/blob/papers/JOSS\_release/papers/joss\_paper/codemeta.json}
+\end{enumerate}
+\subsection{{\bfseries\sffamily DONE} Paper should include}
+\label{sec:orge12a2fc}
+\begin{enumerate}
+\item {\bfseries\sffamily DONE} A list of the authors of the software and their affiliations, using the correct format (see the example below).
+\label{sec:org7660499}
+\item {\bfseries\sffamily DONE} A summary describing the high-level functionality and purpose of the software for a diverse, non-specialist audience.
+\label{sec:org617ce83}
+\item {\bfseries\sffamily DONE} A Statement of Need section that clearly illustrates the research purpose of the software.
+\label{sec:org02782f6}
+\item {\bfseries\sffamily DONE} A list of key references, including to other software addressing related needs. Note that the references should include full names of venues, e.g., journals and conferences, not abbreviations only understood in the context of a specific discipline.
+\label{sec:org2a72310}
+\item {\bfseries\sffamily DONE} Mention (if applicable) a representative set of past or ongoing research projects using the software and recent scholarly publications enabled by it.
+\label{sec:org0d1fce7}
+\item {\bfseries\sffamily DONE} Acknowledgement of any financial support.
+\label{sec:org8ed51c7}
+\end{enumerate}
+\section{Review checklist}
+\label{sec:orga7c9485}
+\url{https://joss.readthedocs.io/en/latest/review\_checklist.html}
+\subsection{General checks}
+\label{sec:org97f909f}
+\begin{enumerate}
+\item {\bfseries\sffamily DONE} Repository: Is the source code for this software available at the repository url?
+\label{sec:orgc07689e}
+\item {\bfseries\sffamily DONE} License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
+\label{sec:orgb6f4e50}
+\item {\bfseries\sffamily DONE} Contribution and authorship: Has the submitting author made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
+\label{sec:orgdd40fe2}
+\end{enumerate}
+\subsection{{\bfseries\sffamily DONE} Functionality}
+\label{sec:org406418f}
+\begin{enumerate}
+\item {\bfseries\sffamily DONE} Installation: Does installation proceed as outlined in the documentation?
+\label{sec:org934689a}
+\item {\bfseries\sffamily ANSWERED} Functionality: Have the functional claims of the software been confirmed?
+\label{sec:org943260a}
+\item {\bfseries\sffamily DONE} Performance: If there are any performance claims of the software, have they been confirmed? (If there are no claims, please check off this item.)
+\label{sec:orgaa2e0bd}
+\end{enumerate}
+\subsection{{\bfseries\sffamily DONE} Documentation}
+\label{sec:orgd19b2e4}
+\begin{enumerate}
+\item {\bfseries\sffamily DONE} A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
+\label{sec:org346bd8c}
+\item {\bfseries\sffamily DONE} Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
+\label{sec:org0106b64}
+\item {\bfseries\sffamily DONE} Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
+\label{sec:org6cb08b7}
+\item {\bfseries\sffamily DONE} Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
+\label{sec:orga040125}
+\item {\bfseries\sffamily DONE} Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
+\label{sec:org6a350c4}
+\item {\bfseries\sffamily DONE} Community guidelines: Are there clear guidelines for third parties wishing to 1) Contribute to the software 2) Report issues or problems with the software 3) Seek support
+\label{sec:org0f7b40a}
+\end{enumerate}
+\subsection{{\bfseries\sffamily TODO} Software paper}
+\label{sec:orgab22051}
+\begin{enumerate}
+\item {\bfseries\sffamily DONE} Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
+\label{sec:org76c5768}
+\item {\bfseries\sffamily DONE} A statement of need: Does the paper have a section titled ‘Statement of Need’ that clearly states what problems the software is designed to solve and who the target audience is?
+\label{sec:org4d2cd77}
+\item {\bfseries\sffamily TODO} State of the field: Do the authors describe how this software compares to other commonly-used packages?
+\label{sec:org36e90fb}
+
+Well, not sure if i want to do that. If they ask about it then i will add more text i think
+
+\item {\bfseries\sffamily TODO} Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
+\label{sec:orgde5133b}
+
+That is to the reviewer
+
+\item {\bfseries\sffamily DONE} References: Is the list of references complete, and is everything cited appropriately that should be cited (e.g., papers, datasets, software)? Do references in the text use the proper citation syntax?
+\label{sec:orga593479}
+\end{enumerate}
+Emacs 27.2 (Org mode 9.5.1)
+\end{document}
\ No newline at end of file
diff --git a/papers/joss_paper/publishing_in_JOSS/steps.org b/papers/joss_paper/publishing_in_JOSS/steps.org
new file mode 100644
index 0000000000000000000000000000000000000000..3c7a1a3f13f348a412ab37c33c8855299377f74a
--- /dev/null
+++ b/papers/joss_paper/publishing_in_JOSS/steps.org
@@ -0,0 +1,10 @@
+* Steps for publishing in JOSS
+
+https://joss.readthedocs.io/en/latest/review_criteria.html
+
+
+1) make sure we fulfill the submission requirements: https://joss.readthedocs.io/en/latest/submitting.html#submission-requirements
+2) Follow sumbission flow: https://joss.readthedocs.io/en/latest/submitting.html#typical-paper-submission-flow
+3) Check that your paper compiles: https://joss.readthedocs.io/en/latest/submitting.html#checking-that-your-paper-compiles
+4) Submit the paper project by filling in a form and waiting
+ https://joss.readthedocs.io/en/latest/submitting.html#submitting-your-paper
diff --git a/papers/joss_paper/readme.org b/papers/joss_paper/readme.org
new file mode 100644
index 0000000000000000000000000000000000000000..f53dca034759153e6d508550cfd6d9877f8f2526
--- /dev/null
+++ b/papers/joss_paper/readme.org
@@ -0,0 +1,18 @@
+* Repo containing the JOSS contribution for binary_c-python
+** Steps to make the md
+in paper/tex:
+- change the paper.tex file for all the actual text changes
+- run `run_pandoc.sh` to turn it into md
+- replace the title and affiliation by the contents of `title_and_affiliation.md`
+- copy the md file to the main dir
+- run `sudo docker run --rm -it -v $PWD:/data -u $(id -u):$(id -g) openjournals/inara -o pdf,crossref paper.md`
+
+** Notes for JOSS
+- https://joss.readthedocs.io/en/latest/review_criteria.html
+- https://joss.readthedocs.io/en/latest/
+
+https://lucydot.github.io/slides/JOSS_0119/JOSS_0119.pdf
+
+*** Example papers relevant to our work
+https://joss.theoj.org/papers/10.21105/joss.03257
+https://joss.theoj.org/papers/10.21105/joss.01987