# HG changeset patch
# User paugier <pierre.augier@ens-lyon.org>
# Date 1469532284 -7200
#      Tue Jul 26 13:24:44 2016 +0200
# Node ID 035bda199138f5c81dd49a8eb7f882dee34fa3e9
# Parent  0000000000000000000000000000000000000000
First commit.

diff --git a/.hgignore b/.hgignore
new file mode 100644
--- /dev/null
+++ b/.hgignore
@@ -0,0 +1,16 @@
+syntax: glob
+
+*.pyd*
+*.pyc
+*~
+*tmp
+
+\#*\#
+
+*.log
+*.aux
+*.out
+*.dvi
+*.pdf
+
+auto/*
\ No newline at end of file
diff --git a/README.rst b/README.rst
new file mode 100644
--- /dev/null
+++ b/README.rst
@@ -0,0 +1,4 @@
+FluidDyn paper
+==============
+
+To be submitted to http://openresearchsoftware.metajnl.com
diff --git a/fluiddyn_paper.tex b/fluiddyn_paper.tex
new file mode 100644
--- /dev/null
+++ b/fluiddyn_paper.tex
@@ -0,0 +1,207 @@
+%% Journal of Open Research Software Latex template -- Created By Stephen Bonner and John Brennan, Durham Universtiy, UK.
+%% see http://openresearchsoftware.metajnl.com
+
+\documentclass{jors}
+
+%% Set the header information
+\pagestyle{fancy}
+\definecolor{mygray}{gray}{0.6}
+\renewcommand\headrule{}
+\rhead{\footnotesize 3}
+\rhead{\textcolor{gray}{UP JORS software Latex paper template version 0.1}}
+
+\begin{document}
+
+{\bf Software paper for submission to the Journal of Open Research Software} \\
+
+To complete this template, please replace the blue text with your own. The
+paper has three main sections: (1) Overview; (2) Availability; (3) Reuse
+potential.
+
+Please submit the completed paper to: editor.jors@ubiquitypress.com
+
+\rule{\textwidth}{1pt}
+
+\section*{(1) Overview}
+
+\vspace{0.5cm}
+
+\section*{Title}
+
+\textcolor{blue}{The title of the software paper should focus on the software,
+e.g. “Text mining software from the X project”. If the software is closely
+linked to a specific research paper, then “Software from Paper Title” is
+appropriate. The title should be factual, relating to the functionality of the
+software and the area it relates to rather than making claims about the
+software, e.g. “Easy-to-use”.}
+
+\section*{Paper Authors}
+
+\textcolor{blue}{1. Last name, first name; (Lead/corresponding author first) \\
+2. Last name, first name; etc.}
+
+\section*{Paper Author Roles and Affiliations}
+\textcolor{blue}{1. First author role and affiliation \\
+2. Second author role and affiliation etc.}
+
+\section*{Abstract}
+
+\textcolor{blue}{A short (ca. 100 word) summary of the software being
+described: what problem the software addresses, how it was implemented and
+architected, where it is stored, and its reuse potential.}
+
+\section*{Keywords}
+
+\textcolor{blue}{keyword 1; keyword 2; etc. \\
+Keywords should make it easy to identify who and what the software will be
+useful for.}
+
+\section*{Introduction}
+
+\textcolor{blue}{An overview of the software, how it was produced, and the
+research for which it has been used, including references to relevant research
+articles. A short comparison with software which implements similar
+functionality should be included in this section. }
+
+\section*{Implementation and architecture}
+
+\textcolor{blue}{How the software was implemented, with details of the
+architecture where relevant. Use of relevant diagrams is appropriate. Please
+also describe any variants and associated implementation differences.}
+
+
+\section*{Quality control}
+
+\textcolor{blue}{Detail the level of testing that has been carried out on the
+code (e.g. unit, functional, load etc.), and in which environments. If not
+already included in the software documentation, provide details of how a user
+could quickly understand if the software is working (e.g. providing examples of
+running the software with sample input and output data). }
+
+\section*{(2) Availability}
+\vspace{0.5cm}
+\section*{Operating system}
+
+\textcolor{blue}{Please include minimum version compatibility.}
+
+\section*{Programming language}
+
+\textcolor{blue}{Please include minimum version compatibility.}
+
+\section*{Additional system requirements}
+
+\textcolor{blue}{E.g. memory, disk space, processor, input devices, output devices.}
+
+\section*{Dependencies}
+
+\textcolor{blue}{E.g. libraries, frameworks, incl. minimum version compatibility.}
+
+\section*{List of contributors}
+
+\textcolor{blue}{Please list anyone who helped to create the software (who may
+also not be an author of this paper), including their roles and affiliations.}
+
+\section*{Software location:}
+
+{\bf Archive} \textcolor{blue}{(e.g. institutional repository, general
+repository) (required – please see instructions on journal website for
+depositing archive copy of software in a suitable repository)}
+
+\begin{description}[noitemsep,topsep=0pt]
+\item[Name:] \textcolor{blue}{The name of the archive.}
+\item[Persistent identifier:] \textcolor{blue}{e.g. DOI, handle, PURL, etc.}
+\item[Licence:] \textcolor{blue}{Open license under which the software is licensed.}
+\item[Publisher:]  \textcolor{blue}{Name of the person who deposited the software.}
+\item[Version published:] \textcolor{blue}{The version number of the software archived.}
+\item[Date published:] \textcolor{blue}{dd/mm/yy}
+\end{description}
+
+
+
+{\bf Code repository} \textcolor{blue}{(e.g. SourceForge, GitHub etc.) (required)}
+
+\begin{description}[noitemsep,topsep=0pt]
+\item[Name:] \textcolor{blue}{The name of the archive.}
+\item[Persistent identifier:] \textcolor{blue}{e.g. DOI, handle, PURL, etc.}
+\item[Licence:] \textcolor{blue}{Open license under which the software is licensed.}
+\item[Date published:] \textcolor{blue}{dd/mm/yy}
+\end{description}
+
+{\bf Emulation environment} \textcolor{blue}{(if appropriate)}
+
+\begin{description}[noitemsep,topsep=0pt]
+\item[Name:] \textcolor{blue}{The name of the archive.}
+\item[Persistent identifier:] \textcolor{blue}{e.g. DOI, handle, PURL, etc.}
+\item[Licence:] \textcolor{blue}{Open license under which the software is licensed.}
+\item[Date published:] \textcolor{blue}{dd/mm/yy}
+\end{description}
+
+\section*{Language}
+
+\textcolor{blue}{Language of repository, software and supporting files.}
+
+\section*{(3) Reuse potential}
+
+\textcolor{blue}{Please describe in as much detail as possible the ways in
+which the software could be reused by other researchers both within and outside
+of your field. This should include the use cases for the software, and also
+details of how the software might be modified or extended (including how
+contributors should contact you) if appropriate. Also you must include details
+of what support mechanisms are in place for this software (even if there is no
+support).}
+
+\section*{Acknowledgements}
+
+\textcolor{blue}{Please add any relevant acknowledgements to anyone else who
+supported the project in which the software was created, but did not work
+directly on the software itself.}
+
+\section*{Funding statement}
+
+\textcolor{blue}{If the software resulted from funded research please give the
+funder and grant number.}
+
+\section*{Competing interests}
+
+\textcolor{blue}{If any of the authors have any competing interests then these
+must be declared. The authors’ initials should be used to denote differing
+competing interests. For example: “BH has minority shares in [company name],
+which part funded the research grant for this project. All other authors have
+no competing interests."
+%
+If there are no competing interests, please add the statement: “The authors
+declare that they have no competing interests.” }
+
+\section*{References}
+
+\textcolor{blue}{Please enter references in the Harvard style and include a DOI
+where available, citing them in the text with a number in square brackets,
+e.g.}
+
+\textcolor{blue}{[1] Piwowar, H A 2011 Who Shares? Who Doesn't? Factors
+Associated with Openly Archiving Raw Research Data. PLoS ONE 6(7): e18657. DOI:
+\\ http://dx.doi.org/10.1371/journal.pone.0018657.}
+
+\vspace{2cm}
+
+\rule{\textwidth}{1pt}
+
+{ \bf Copyright Notice} \\
+Authors who publish with this journal agree to the following terms: \\
+
+Authors retain copyright and grant the journal right of first publication with
+the work simultaneously licensed under a
+\href{http://creativecommons.org/licenses/by/3.0/}{Creative Commons Attribution
+License} that allows others to share the work with an acknowledgement of the
+work's authorship and initial publication in this journal.
+
+Authors are able to enter into separate, additional contractual arrangements
+for the non-exclusive distribution of the journal's published version of the
+work (e.g., post it to an institutional repository or publish it in a book),
+with an acknowledgement of its initial publication in this journal.
+
+By submitting this paper you agree to the terms of this Copyright Notice, which
+will apply to this submission if and when it is published by this journal.
+
+
+\end{document}
diff --git a/jors.cls b/jors.cls
new file mode 100644
--- /dev/null
+++ b/jors.cls
@@ -0,0 +1,63 @@
+%% Journal of Open Research Software Latex template -- Created By Stephen Bonner and John Brennan, Durham Universtiy, UK.
+
+\NeedsTeXFormat{LaTeX2e}
+\ProvidesClass{josr}[2016/03/08 Journal Of Open Software Research]
+
+%% Article options
+\DeclareOption{12pt}{
+  \PassOptionsToClass{\CurrentOption}{article}
+}
+
+
+\DeclareOption{sansserif}{
+  \PassOptionsToPackage{\CurrentOption}{paxcommands}
+}
+\DeclareOption{neverindent}{
+  \PassOptionsToPackage{\CurrentOption}{paxcommands}
+}
+
+%% Fallback
+\DeclareOption*{
+  \ClassWarning{josr}{Unknown option '\CurrentOption'}
+}
+
+
+\ExecuteOptions{12pt}
+
+
+\ProcessOptions\relax
+
+\LoadClass[a4paper]{article}
+
+%% Load additional packages and commands.
+\RequirePackage{xcolor}
+\RequirePackage{sectsty}
+\RequirePackage{enumitem}
+\RequirePackage{hyperref}
+\RequirePackage{fancyhdr}
+\RequirePackage{titlesec}
+
+%% Additional TeX/LaTeX code...
+
+%% Remove the indentation
+\newlength\tindent
+\setlength{\tindent}{\parindent}
+\setlength{\parindent}{0pt}
+\renewcommand{\indent}{\hspace*{\tindent}}
+
+%% Remove the page numbers
+\pagenumbering{gobble}
+
+%% Set the font too 13 for the titles 
+\sectionfont{\fontsize{13}{15}\selectfont}
+
+%% Set indentation for the lists
+\setlist[description]{leftmargin=1cm,labelindent=1cm}
+
+%% Set spacing for the section headings
+\titlespacing\section{0pt}{12pt plus 4pt minus 2pt}{0pt plus 2pt minus 2pt}
+
+%% Set margins
+\usepackage[margin=1.2in,footskip=0.25in]{geometry}
+
+\endinput
\ No newline at end of file
diff --git a/template/jors.cls b/template/jors.cls
new file mode 100644
--- /dev/null
+++ b/template/jors.cls
@@ -0,0 +1,63 @@
+%% Journal of Open Research Software Latex template -- Created By Stephen Bonner and John Brennan, Durham Universtiy, UK.
+
+\NeedsTeXFormat{LaTeX2e}
+\ProvidesClass{josr}[2016/03/08 Journal Of Open Software Research]
+
+%% Article options
+\DeclareOption{12pt}{
+  \PassOptionsToClass{\CurrentOption}{article}
+}
+
+
+\DeclareOption{sansserif}{
+  \PassOptionsToPackage{\CurrentOption}{paxcommands}
+}
+\DeclareOption{neverindent}{
+  \PassOptionsToPackage{\CurrentOption}{paxcommands}
+}
+
+%% Fallback
+\DeclareOption*{
+  \ClassWarning{josr}{Unknown option '\CurrentOption'}
+}
+
+
+\ExecuteOptions{12pt}
+
+
+\ProcessOptions\relax
+
+\LoadClass[a4paper]{article}
+
+%% Load additional packages and commands.
+\RequirePackage{xcolor}
+\RequirePackage{sectsty}
+\RequirePackage{enumitem}
+\RequirePackage{hyperref}
+\RequirePackage{fancyhdr}
+\RequirePackage{titlesec}
+
+%% Additional TeX/LaTeX code...
+
+%% Remove the indentation
+\newlength\tindent
+\setlength{\tindent}{\parindent}
+\setlength{\parindent}{0pt}
+\renewcommand{\indent}{\hspace*{\tindent}}
+
+%% Remove the page numbers
+\pagenumbering{gobble}
+
+%% Set the font too 13 for the titles 
+\sectionfont{\fontsize{13}{15}\selectfont}
+
+%% Set indentation for the lists
+\setlist[description]{leftmargin=1cm,labelindent=1cm}
+
+%% Set spacing for the section headings
+\titlespacing\section{0pt}{12pt plus 4pt minus 2pt}{0pt plus 2pt minus 2pt}
+
+%% Set margins
+\usepackage[margin=1.2in,footskip=0.25in]{geometry}
+
+\endinput
\ No newline at end of file
diff --git a/template/jors_template.tex b/template/jors_template.tex
new file mode 100644
--- /dev/null
+++ b/template/jors_template.tex
@@ -0,0 +1,206 @@
+%% Journal of Open Research Software Latex template -- Created By Stephen Bonner and John Brennan, Durham Universtiy, UK.
+
+\documentclass{jors}
+
+%% Set the header information
+\pagestyle{fancy}
+\definecolor{mygray}{gray}{0.6}
+\renewcommand\headrule{}
+\rhead{\footnotesize 3}
+\rhead{\textcolor{gray}{UP JORS software Latex paper template version 0.1}}
+
+\begin{document}
+
+{\bf Software paper for submission to the Journal of Open Research Software} \\
+
+To complete this template, please replace the blue text with your own. The
+paper has three main sections: (1) Overview; (2) Availability; (3) Reuse
+potential.
+
+Please submit the completed paper to: editor.jors@ubiquitypress.com
+
+\rule{\textwidth}{1pt}
+
+\section*{(1) Overview}
+
+\vspace{0.5cm}
+
+\section*{Title}
+
+\textcolor{blue}{The title of the software paper should focus on the software,
+e.g. “Text mining software from the X project”. If the software is closely
+linked to a specific research paper, then “Software from Paper Title” is
+appropriate. The title should be factual, relating to the functionality of the
+software and the area it relates to rather than making claims about the
+software, e.g. “Easy-to-use”.}
+
+\section*{Paper Authors}
+
+\textcolor{blue}{1. Last name, first name; (Lead/corresponding author first) \\
+2. Last name, first name; etc.}
+
+\section*{Paper Author Roles and Affiliations}
+\textcolor{blue}{1. First author role and affiliation \\
+2. Second author role and affiliation etc.}
+
+\section*{Abstract}
+
+\textcolor{blue}{A short (ca. 100 word) summary of the software being
+described: what problem the software addresses, how it was implemented and
+architected, where it is stored, and its reuse potential.}
+
+\section*{Keywords}
+
+\textcolor{blue}{keyword 1; keyword 2; etc. \\
+Keywords should make it easy to identify who and what the software will be
+useful for.}
+
+\section*{Introduction}
+
+\textcolor{blue}{An overview of the software, how it was produced, and the
+research for which it has been used, including references to relevant research
+articles. A short comparison with software which implements similar
+functionality should be included in this section. }
+
+\section*{Implementation and architecture}
+
+\textcolor{blue}{How the software was implemented, with details of the
+architecture where relevant. Use of relevant diagrams is appropriate. Please
+also describe any variants and associated implementation differences.}
+
+
+\section*{Quality control}
+
+\textcolor{blue}{Detail the level of testing that has been carried out on the
+code (e.g. unit, functional, load etc.), and in which environments. If not
+already included in the software documentation, provide details of how a user
+could quickly understand if the software is working (e.g. providing examples of
+running the software with sample input and output data). }
+
+\section*{(2) Availability}
+\vspace{0.5cm}
+\section*{Operating system}
+
+\textcolor{blue}{Please include minimum version compatibility.}
+
+\section*{Programming language}
+
+\textcolor{blue}{Please include minimum version compatibility.}
+
+\section*{Additional system requirements}
+
+\textcolor{blue}{E.g. memory, disk space, processor, input devices, output devices.}
+
+\section*{Dependencies}
+
+\textcolor{blue}{E.g. libraries, frameworks, incl. minimum version compatibility.}
+
+\section*{List of contributors}
+
+\textcolor{blue}{Please list anyone who helped to create the software (who may
+also not be an author of this paper), including their roles and affiliations.}
+
+\section*{Software location:}
+
+{\bf Archive} \textcolor{blue}{(e.g. institutional repository, general
+repository) (required – please see instructions on journal website for
+depositing archive copy of software in a suitable repository)}
+
+\begin{description}[noitemsep,topsep=0pt]
+\item[Name:] \textcolor{blue}{The name of the archive.}
+\item[Persistent identifier:] \textcolor{blue}{e.g. DOI, handle, PURL, etc.}
+\item[Licence:] \textcolor{blue}{Open license under which the software is licensed.}
+\item[Publisher:]  \textcolor{blue}{Name of the person who deposited the software.}
+\item[Version published:] \textcolor{blue}{The version number of the software archived.}
+\item[Date published:] \textcolor{blue}{dd/mm/yy}
+\end{description}
+
+
+
+{\bf Code repository} \textcolor{blue}{(e.g. SourceForge, GitHub etc.) (required)}
+
+\begin{description}[noitemsep,topsep=0pt]
+\item[Name:] \textcolor{blue}{The name of the archive.}
+\item[Persistent identifier:] \textcolor{blue}{e.g. DOI, handle, PURL, etc.}
+\item[Licence:] \textcolor{blue}{Open license under which the software is licensed.}
+\item[Date published:] \textcolor{blue}{dd/mm/yy}
+\end{description}
+
+{\bf Emulation environment} \textcolor{blue}{(if appropriate)}
+
+\begin{description}[noitemsep,topsep=0pt]
+\item[Name:] \textcolor{blue}{The name of the archive.}
+\item[Persistent identifier:] \textcolor{blue}{e.g. DOI, handle, PURL, etc.}
+\item[Licence:] \textcolor{blue}{Open license under which the software is licensed.}
+\item[Date published:] \textcolor{blue}{dd/mm/yy}
+\end{description}
+
+\section*{Language}
+
+\textcolor{blue}{Language of repository, software and supporting files.}
+
+\section*{(3) Reuse potential}
+
+\textcolor{blue}{Please describe in as much detail as possible the ways in
+which the software could be reused by other researchers both within and outside
+of your field. This should include the use cases for the software, and also
+details of how the software might be modified or extended (including how
+contributors should contact you) if appropriate. Also you must include details
+of what support mechanisms are in place for this software (even if there is no
+support).}
+
+\section*{Acknowledgements}
+
+\textcolor{blue}{Please add any relevant acknowledgements to anyone else who
+supported the project in which the software was created, but did not work
+directly on the software itself.}
+
+\section*{Funding statement}
+
+\textcolor{blue}{If the software resulted from funded research please give the
+funder and grant number.}
+
+\section*{Competing interests}
+
+\textcolor{blue}{If any of the authors have any competing interests then these
+must be declared. The authors’ initials should be used to denote differing
+competing interests. For example: “BH has minority shares in [company name],
+which part funded the research grant for this project. All other authors have
+no competing interests."
+%
+If there are no competing interests, please add the statement: “The authors
+declare that they have no competing interests.” }
+
+\section*{References}
+
+\textcolor{blue}{Please enter references in the Harvard style and include a DOI
+where available, citing them in the text with a number in square brackets,
+e.g.}
+
+\textcolor{blue}{[1] Piwowar, H A 2011 Who Shares? Who Doesn't? Factors
+Associated with Openly Archiving Raw Research Data. PLoS ONE 6(7): e18657. DOI:
+\\ http://dx.doi.org/10.1371/journal.pone.0018657.}
+
+\vspace{2cm}
+
+\rule{\textwidth}{1pt}
+
+{ \bf Copyright Notice} \\
+Authors who publish with this journal agree to the following terms: \\
+
+Authors retain copyright and grant the journal right of first publication with
+the work simultaneously licensed under a
+\href{http://creativecommons.org/licenses/by/3.0/}{Creative Commons Attribution
+License} that allows others to share the work with an acknowledgement of the
+work's authorship and initial publication in this journal.
+
+Authors are able to enter into separate, additional contractual arrangements
+for the non-exclusive distribution of the journal's published version of the
+work (e.g., post it to an institutional repository or publish it in a book),
+with an acknowledgement of its initial publication in this journal.
+
+By submitting this paper you agree to the terms of this Copyright Notice, which
+will apply to this submission if and when it is published by this journal.
+
+
+\end{document}