# HG changeset patch
# User paugier <pierre.augier@ens-lyon.org>
# Date 1514826227 -3600
#      Mon Jan 01 18:03:47 2018 +0100
# Node ID 975e38cecc50c892acee6d58fa7496e4ba1c4bfd
# Parent  79bee7c3294c92f61360b78f59a1cccda971ff9e
Reorganize files

diff --git a/fluiddyn/fluiddyn_paper.tex b/fluiddyn/fluiddyn_paper.tex
--- a/fluiddyn/fluiddyn_paper.tex
+++ b/fluiddyn/fluiddyn_paper.tex
@@ -1,14 +1,8 @@
-%% Journal of Open Research Software Latex template -- Created By Stephen Bonner and John Brennan, Durham Universtiy, UK.
+%% 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}}
+\documentclass{../jors}
 
 \begin{document}
 
@@ -57,8 +51,10 @@
 % \textcolor{blue}{1. First author role and affiliation \\
 % 2. Second author role and affiliation etc.}
 
-1. \\
-2.
+1. Researcher, LEGI, Universit\'e Grenoble Alpes, CNRS, France
+2. Ph.D. student, Linn\'e Flow Center, KTH Royal Institute of Technology,
+Sweden; \\
+3. Research Engineer, LEGI, Universit\'e Grenoble Alpes, CNRS, France; \\
 
 
 \section*{Abstract}
@@ -483,10 +479,14 @@
 
 \textcolor{blue}{Please include minimum version compatibility.}
 
+Windows and any POSIX based OS, such as GNU/Linux and Mac OS X 
+
 \section*{Programming language}
 
 \textcolor{blue}{Please include minimum version compatibility.}
 
+Python 2.7, 3.4 or above
+
 \section*{Additional system requirements}
 
 \textcolor{blue}{E.g. memory, disk space, processor, input devices, output devices.}
@@ -495,11 +495,24 @@
 
 \textcolor{blue}{E.g. libraries, frameworks, incl. minimum version compatibility.}
 
+numpy
+
 \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.}
 
+\begin{itemize}
+\item Pierre Augier (LEGI): Creator of the FluidDyn project, developer
+of majority of the modules and solvers, future-proofing with Python 3
+compatibility and documentation
+\item Ashwin Vishnu Mohanan (KTH): Development of the shallow water equations
+solver, \texttt{fluidsim.solvers.sw1l} testing, code coverage and documentation
+\item Cyrille Bonamy (LEGI): Extending the sub-package
+\texttt{fluidsim.operators.fft} (currently pending deprecation) into a
+dedicated package, FluidFFT used by FluidSim solvers
+\end{itemize}
+
 \section*{Software location:}
 
 {\bf Archive} \textcolor{blue}{(e.g. institutional repository, general
@@ -507,23 +520,21 @@
 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}
+\item[Name:] PyPI
+\item[Persistent identifier:] https://pypi.org/project/fluiddyn
+\item[Licence:] CeCILL-B, a BSD compatible French licence. 
+\item[Publisher:] Pierre Augier
+\item[Version published:] ?
+\item[Date published:] ?
 \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}
+\item[Name:] Bitbucket
+\item[Persistent identifier:] https://bitbucket.org/fluiddyn/fluiddyn
+\item[Licence:] CeCILL-B, a BSD compatible French licence. 
+\item[Date published:] ?
 \end{description}
 
 % {\bf Emulation environment} \textcolor{blue}{(if appropriate)}
@@ -539,6 +550,8 @@
 
 \textcolor{blue}{Language of repository, software and supporting files.}
 
+English
+
 \section*{(3) Reuse potential}
 
 \textcolor{blue}{Please describe in as much detail as possible the ways in
@@ -549,8 +562,6 @@
 of what support mechanisms are in place for this software (even if there is no
 support).}
 
-
-
 \subsection*{Conclusions}
 
 Possibly another usage of open-source in science and fluid dynamics.
diff --git a/fluiddyn/jors.cls b/fluiddyn/jors.cls
deleted file mode 100644
--- a/fluiddyn/jors.cls
+++ /dev/null
@@ -1,75 +0,0 @@
-%% Journal of Open Research Software Latex template -- Created By Stephen Bonner and John Brennan, Durham Universtiy, UK.
-
-\NeedsTeXFormat{LaTeX2e}
-\ProvidesClass{jors}[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}
-% http://tex.stackexchange.com/questions/301669
-\RequirePackage[pageanchor=false]{hyperref}
-
-\hypersetup{
-    colorlinks,
-    linkcolor={red!50!black},
-    citecolor={blue!50!black},
-    urlcolor={blue!99!black}
-}
-
-\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}
-% pa: this is not possible...
-% http://tex.stackexchange.com/questions/58087/
-
-
-%% 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/fluidsim/fluidsim_paper.tex b/fluidsim/fluidsim_paper.tex
--- a/fluidsim/fluidsim_paper.tex
+++ b/fluidsim/fluidsim_paper.tex
@@ -1,22 +1,8 @@
-%% Journal of Open Research Software Latex template -- Created By Stephen Bonner and John Brennan, Durham Universtiy, UK.
-
-\documentclass{jors}
-
-\usepackage{amsmath}
-\usepackage{graphicx}
-\usepackage{epstopdf}
-\usepackage{listings}
-\usepackage{fancyref}
+%% Journal of Open Research Software Latex template -- Created By Stephen
+%% Bonner and John Brennan, Durham Universtiy, UK.
+%% see http://openresearchsoftware.metajnl.com
 
-%% Set source code listings style
-\lstset{basicstyle=\ttfamily, language=Python}
-
-%% 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}}
+\documentclass{../jors}
 
 \begin{document}
 
@@ -34,9 +20,15 @@
 
 \section*{Paper Authors}
 
-1. Mohanan, Ashwin Vishnu; \\
-2. Bonamy, Cyrille; \\
-3. Augier, Pierre
+1. Mohanan, Ashwin Vishnu$^a$ \\
+2. Bonamy, Cyrille$^b$ \\
+3. Augier, Pierre$^b$
+
+\smallskip
+
+$^a$ Linn\'e Flow Centre, Department of Mechanics, KTH, 10044 Stockholm, Sweden.\\
+$^b$ Univ. Grenoble Alpes, CNRS, Grenoble INP\footnote{Institute of Engineering
+Univ. Grenoble Alpes}, LEGI, 38000 Grenoble, France.
 
 \section*{Paper Author Roles and Affiliations}
 1. Ph.D. student, Linn\'e Flow Center, KTH Royal Institute of Technology,
@@ -396,10 +388,16 @@
 \section*{List of contributors}
 
 \begin{itemize}
- \item Ashwin Vishnu Mohanan (KTH): Development of the shallow water equations solver, \texttt{fluidsim.solvers.sw1l} testing, code coverage and documentation
- \item Cyrille Bonamy (LEGI): Porting sub-package \texttt{fluidsim.operators.fft} (currently pending deprecation) and extending it into a dedicated package, FluidFFT used by FluidSim solvers
- \item Miguel Calpe (LEGI): Development of the 2D Boussinesq equation solver, \texttt{fluidsim.solvers.ns2d.strat}
- \item Pierre Augier (LEGI): Creator of FluidSim and FluidDyn project, developer of majority of the modules and solvers, future-proofing with Python 3 compatibility and documentation
+\item Ashwin Vishnu Mohanan (KTH): Development of the shallow water equations
+solver, \texttt{fluidsim.solvers.sw1l} testing, code coverage and documentation
+\item Cyrille Bonamy (LEGI): Extending the sub-package
+\texttt{fluidsim.operators.fft} (currently pending deprecation) into a
+dedicated package, FluidFFT used by FluidSim solvers
+\item Miguel Calpe (LEGI): Development of the 2D Boussinesq equation solver,
+\texttt{fluidsim.solvers.ns2d.strat}
+\item Pierre Augier (LEGI): Creator of FluidSim and FluidDyn project, developer
+of majority of the modules and solvers, future-proofing with Python 3
+compatibility and documentation
 \end{itemize}
 
 
diff --git a/template/jors.cls b/jors.cls
rename from template/jors.cls
rename to jors.cls
--- a/template/jors.cls
+++ b/jors.cls
@@ -33,7 +33,16 @@
 \RequirePackage{xcolor}
 \RequirePackage{sectsty}
 \RequirePackage{enumitem}
-\RequirePackage{hyperref}
+% http://tex.stackexchange.com/questions/301669
+\RequirePackage[pageanchor=false]{hyperref}
+
+\hypersetup{
+    colorlinks,
+    linkcolor={red!50!black},
+    citecolor={blue!50!black},
+    urlcolor={blue!99!black}
+}
+
 \RequirePackage{fancyhdr}
 \RequirePackage{titlesec}
 
@@ -49,7 +58,10 @@
 \pagenumbering{gobble}
 
 %% Set the font too 13 for the titles 
-\sectionfont{\fontsize{13}{15}\selectfont}
+% \sectionfont{\fontsize{13}{15}\selectfont}
+% pa: this is not possible...
+% http://tex.stackexchange.com/questions/58087/
+
 
 %% Set indentation for the lists
 \setlist[description]{leftmargin=1cm,labelindent=1cm}
@@ -60,4 +72,20 @@
 %% Set margins
 \usepackage[margin=1.2in,footskip=0.25in]{geometry}
 
+\usepackage{amsmath}
+\usepackage{graphicx}
+\usepackage{epstopdf}
+\usepackage{listings}
+\usepackage{fancyref}
+
+%% Set source code listings style
+\lstset{basicstyle=\ttfamily, language=Python}
+
+%% 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}}
+
 \endinput
\ No newline at end of file