add JOSS paper template

paper/compile

@@ -0,0 +1,181 @@
+#!/usr/bin/env bash
+
+# Help text
+
+description="A bash script for compiling JOSS and JOSE papers locally";
+
+doc="compile [-j <journal>] [-d <doi>] [-v <volume>] [-i <issue>] [-p <page>]
+        [-s <submitted>] [-u <published>] [-r <review>] [-g <repository>] [-a <archive>] FILE
+
+Compile a markdown FILE to a JOSS or JOSE paper.
+
+Options:
+  -j JOURNAL      The journal the paper is being compiled for, either joss or jose, defaults to joss.
+  -d DOI          The DOI of the submitted paper, defaults to an empty string.
+  -v VOLUME       The journal volume the paper was published in, defaults to an empty string.
+  -i ISSUE        The journal issue the paper was published in, defaults to an empty string.
+  -p PAGE         The journal issue page the paper was published in, defaults to an empty string.
+  -s SUBMITTED    The date the paper was submitted, defaults to an empty string.
+  -u PUBLISHED    The date the paper was published, defaults to an empty string.
+  -r REVIEW       The review issue URL, defaults to an empty string.
+  -g REPOSITORY   The URL of the code repository, defaults to an empty string.
+  -a ARCHIVE      The DOI of the code archive, defaults to an empty string.
+  -h              Displays this help text and exit."
+
+# Default arguments
+
+journal="joss"
+doi="10.5281/zenodo.2587158"
+volume=""
+issue=""
+page=""
+submitted=""
+published=""
+review=""
+repository="https://github.com/GeoStat-Framework/pentapy"
+
+# Get command line arguments
+
+while getopts ":j:d:v:i:p:s:u:r:g:a:h" opt; do
+	case $opt in
+		j)
+			journal=$OPTARG;;
+		d)
+			doi=$OPTARG;;
+		v)
+			volume=$OPTARG;;
+		i)
+			issue=$OPTARG;;
+		p)
+			page=$OPTARG;;
+		s)
+			submitted=$OPTARG;;
+		u)
+			published=$OPTARG;;
+		r)
+			review=$OPTARG;;
+		g)
+			repository=$OPTARG;;
+		a)
+			archive=$OPTARG;;
+		h)
+			echo $description;
+			echo;
+			echo "$doc";
+			exit 0;;
+		\?)
+			echo "Invalid option: -$OPTARG.";
+			echo;
+			echo "$doc";
+			exit 1;;
+		:)
+			echo "Option -$OPTARG requires an argument.";
+			echo;
+			echo "$doc";
+			exit 1;;
+	esac;
+done;
+
+paper=${@:$OPTIND:1}
+
+if [ ! "$paper" ]; then
+	echo "FILE not specified."
+	echo;
+	echo "$doc"
+	exit 1;
+fi;
+
+# Check if pandoc and pandoc-citeproc are installed
+
+missing=""
+
+if [ ! "$(which pandoc)" ]; then
+	missing="$missing pandoc";
+fi;
+
+if [ ! "$(which pandoc-citeproc)" ]; then
+	missing="$missing pandoc-citeproc";
+fi;
+
+if [ ! "$(which xelatex)" ]; then
+	missing="$missing xelatex";
+fi;
+
+if [ "$missing" ]; then
+	if [ $(echo "$missing" | wc -w) -eq 2 ]; then
+		echo "Please install $(echo $missing | sed 's/ / and /').";
+	else
+		echo "Please install $(echo $missing | sed 's/ /, /g' | sed 's/\(.*\) /\1 and /').";
+	fi;
+	exit 1;
+fi;
+
+# Set journal specific variables
+
+outfile="${paper%.md}.pdf"
+logo="${journal}-logo.png"
+templateurl="https://raw.githubusercontent.com/openjournals/whedon/master/resources/latex.template"
+cslurl="https://raw.githubusercontent.com/openjournals/whedon/master/resources/apa.csl"
+logourl="https://github.com/openjournals/whedon/raw/master/resources/${journal}-logo.png"
+
+# Set journal full name
+
+if [ $journal == "joss" ]; then
+	journalname="Journal of Open Source Software";
+else
+	journalname="Journal of Open Source Education";
+fi;
+
+# Download logo and latex template files
+
+if [ ! -f latex.template ]; then
+	wget "$templateurl";
+fi;
+
+if [ ! -f apa.csl ]; then
+	wget "$cslurl";
+fi;
+
+if [ ! -f $logo ]; then
+	wget "$logourl";
+fi;
+
+# Collect necessary paper metadata
+
+year=$(grep "date: " $paper | cut -d " " -f 4 -)
+bib=$(grep "bibliography: " $paper | cut -d " " -f 2 -)
+
+title=$( \
+	grep "title: " $paper | \
+	cut -d " " -f 2- - | \
+	sed 's/^"\(.*\)"$/\1/' | \
+	sed "s/^'\(.*\)'$/\1/")
+
+name=$(grep -m 1 "name: " $paper | rev | cut -d " " -f 1 - | rev)
+
+# Compile the paper
+
+pandoc \
+	--filter pandoc-citeproc \
+	--bibliography=$bib \
+	--template=latex.template \
+	-V logo_path=$logo \
+	-V citation_author=$name \
+	-V year=$year \
+	-V footnote_paper_title="$title" \
+	-V journal_name="$journalname" \
+	-V formatted_doi="$doi" \
+	-V archive_doi="https://doi.org/$archive" \
+	-V review_issue_url=$review \
+	-V repository=$repository \
+	-V submitted=$submitted \
+	-V published=$published \
+	-V issue=$issue \
+	-V volume=$volume \
+	-V page=$page \
+	-V graphics=true \
+	--latex-engine=xelatex \
+	--from markdown+autolink_bare_uris \
+	--csl=apa.csl \
+	-s $paper \
+	-o $outfile

paper/paper.bib

@@ -0,0 +1,8 @@
+@misc{zenodo,
+  author       = {Sebastian Müller},
+  title        = {ogs5py},
+  month        = aug,
+  year         = 2019,
+  doi          = {10.5281/zenodo.2546767},
+  url          = {https://doi.org/10.5281/zenodo.2546767}
+}

paper/paper.md

@@ -0,0 +1,41 @@
+---
+title: 'ogs5py: A Python-API for the OpenGeoSys 5 scientific modeling package'
+tags:
+  - Python
+  - numerics
+  - linear equation systems
+  - pentadiagonal matrices
+  - pentadiagonal systems
+authors:
+  - name: Sebastian Müller
+    orcid: 0000-0001-9060-4008
+    affiliation: "1, 2"
+  - name: Falk Heße
+    orcid: 0000-0002-2547-8102
+    affiliation: "1, 2"
+affiliations:
+ - name: Department of Computational Hydrosystems, UFZ -- Helmholtz Centre for Environmental Research, Leipzig, Germany
+   index: 1
+ - name: Institute of Earth and Environmental Sciences, University Potsdam, Potsdam, Germany
+   index: 2
+date: 28 June 2019
+bibliography: paper.bib
+---
+
+# Summary
+
+The source code for ``ogs5py`` has been archived to Zenodo with the linked DOI: [@zenodo]
+
+# Acknowledgements
+
+Sebastian Müller:
+I acknowledge the supervision by Prof. Sabine Attinger, Prof. Alraune Zech,
+Prof. Peter Dietrich and Dr. Falk Heße and herewith want to thank them for
+their trust and support.
+I also want to thank Dr. Lennart Schüler for his constant help and the
+pleasant partnership during the work on the GeoStat Framwork.
+This research was funded by the German Federal Environmental Foundation.
+
+Falk Heße:
+
+# References