# 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 projectâ€. 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-useâ€.} + +\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 projectâ€. 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-useâ€.} + +\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}