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@bjmorgan
Forked from CameronDevine/compile
Last active January 2, 2019 21:09
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A bash script for compiling JOSS and JOSE papers locally
#!/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=""
volume=""
issue=""
page=""
submitted=""
published=""
review=""
repository=""
# 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 \
--pdf-engine=xelatex \
--from markdown+autolink_bare_uris \
--csl=apa.csl \
-s $paper \
-o $outfile
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