Makefile for generating a preview of a JOSS journal paper

Makefile (updated 2018-02-09)

# =============================================================================
# @file    Makefile
# @brief   Makefile for generating previews of the paper
# @author  Michael Hucka <[email protected]>
# @license Please see the file named LICENSE in the project directory
# @website https://github.com/casics/dassie
# =============================================================================

# Change the following values to match your configuration.
# .............................................................................

input	:= paper.md
output	:= paper.pdf
bib	:= paper.bib

# Main code -- no more customization variables after this point
# .............................................................................

title	:= $(shell grep title: $(input) | sed 's/title: *//' | tr -d "'")
authors := $(shell sed -n '/authors:/,/affiliations:/p' $(input) | grep name: | sed 's/- name: *//' | paste -d, -s - | sed 's/,/, /g')
repo	:= $(shell git remote get-url origin | sed 's|[email protected]:|https://github.com/|' | sed 's/\.git//')

$(output): $(input) $(bib) Makefile
	pandoc \
	-V paper_title="$(title)" \
	-V citation_author="$(authors)" \
	-V repository="$(repo)" \
	-V archive_doi="http://dx.doi.org/00.00000/zenodo.0000000" \
	-V formatted_doi="00.00000/joss.00000" \
	-V paper_url="http://joss.theoj.org/papers/" \
	-V review_issue_url="http://joss.theoj.org/papers/" \
	-V issue="0" \
	-V volume="00" \
	-V year="2018" \
	-V submitted="00 January 0000" \
	-V published="00 January 0000" \
	-V page="00" \
	-V graphics="true" \
	-V joss_logo_path="whedon/resources/joss-logo.png" \
	-V geometry:margin=1in \
	-o $(output) \
	--pdf-engine=xelatex \
	--filter pandoc-citeproc $(input) \
	--from markdown+autolink_bare_uris \
	--template "whedon/resources/latex.template"

autorefresh:;
	((ls $(input) $(bib) | entr make $(output)) &)

@mhucka Note that the current version (with the aforementioned fixes applied) is unable to generate citations properly, I'm not sure if this was always a limitation or just something that's been broken by updates in the whedon latex template. I'll see if I can figure out what's going wrong, but have limited time to hunt this down at the moment.

Update for anyone who comes across this: I put a newer version of this Makefile in a separate gist at https://gist.github.com/mhucka/c0b82778417f38f7ae6ee7d051cec90a The new version incorporates changes from @steven-murray above and hopefully fixes a few issues like the one noted by @pmundt.

Update 2022-03-29: Discovered JOSS has changed to a different scheme for generating papers, and no longer uses Whedon. The updated makefile in the new gist doesn't account for that. I'm deleting the gist to avoid confusion.