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@mhucka
Last active March 29, 2022 20:34
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Makefile for generating a preview of a JOSS journal paper
# =============================================================================
# @file Makefile
# @brief Makefile for generating previews of the paper
# @author Michael Hucka <mhucka@caltech.edu>
# @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|git@github.com:|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
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mhucka commented Jun 18, 2021

@pmundt thank you very much for that information. I am about to start writing another JOSS paper and will have a chance to test it and update this gist.

@mhucka
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mhucka commented Jun 18, 2021

@steven-murray thank you very much for your work as well!
@rheiland thanks for your note. You made me realize this makefile should check the versions of things too.

@pmundt
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pmundt commented Jun 24, 2021

@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.

@mhucka
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mhucka commented Mar 28, 2022

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.

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