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 <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)) &)

While writing and submitting a new JOSS paper, I updated the Makefile to grab the title and authors automatically from the .md file. The updated version is shown above.

I forgot to mention: for this to work, one needs to clone the whedon repo into the current directory. (It wouldn't be hard to put that location in a variable in the makefile, or even have the makefile do a git clone if it can't find a copy of whedon...)

Thanks for this! I found it very useful. In my case, I wanted to post my paper on arXiv, which will not accept pdf submissions (you have to submit the latex source). I did have to modify a few things from this Makefile, as seen below:

# =============================================================================
# @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

vol     := 0
issue   := 00
gh_issue  := 000
year    := 2018
submitted := 23 July $(year)
accepted  := 21 August $(year)

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

title   := $(shell grep title: $(input).md | sed 's/title: *//' | tr -d "'")
authors := $(shell sed -n '/authors:/,/affiliations:/p' $(input).d | 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//')

$(input).tex: $(input).md $(input).bib Makefile
        /usr/bin/pandoc \
        -V paper_title="$(title)" \
        -V footnote_paper_title="$(title)" \
        -V citation_author="$(authors)" \
        -V repository="$(repo)" \
        -V archive_doi="http://dx.doi.org/10.21105/zenodo.1400822" \
        -V formatted_doi="10.21105/joss.00850" \
        -V paper_url="http://joss.theoj.org/papers/" \
        -V review_issue_url="https://github.com/openjournals/joss-reviews/issues/$(issue)" \
        -V issue="$(issue)" \
        -V volume="$(vol)" \
        -V year="$(year)" \
        -V submitted="$(submitted)" \
        -V published="$(accepted)" \
        -V page="$(issue)" \
        -V graphics="true" \
        -V logo_path="joss-logo.png" \
        -V geometry:margin=1in \
        --verbose \
        -o $(input).tex \
        --pdf-engine=xelatex \
        --filter /usr/bin/pandoc-citeproc $(input).md \
        --from markdown+autolink_bare_uris \
        --template "latex.template"

$(input).pdf: $(input).tex
        xelatex $(input).tex

autorefresh:;
        ((ls $(input).md $(input).bib | entr make $(input).tex) &)

Note that I copied the whedon/resources/latex.template and whedon/resources/joss-logo.png into the same directory as the paper.md (this enabled me to zip it all up for submission). I also needed to comment out the line in the latex.template that set the bibliography (not quite sure why). It should be easy enough to auto-download those two files to the current directory in the Makefile, but I couldn't be bothered. Also, this keeps the actual tex file.

Note that this apparently requires pandoc > 2.0. And beware that your Anaconda installation may be providing < 2.0 (as I just discovered).

There have a few changes in the whedon repository since this was written. The logo path and variable must now be changed to:

        -V logo_path="whedon/resources/joss/logo.png" \

or you will end up with a not very helpful error:

Error producing PDF.
! LaTeX Error: File `' not found.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
                                                  
l.315 \end{document}

make: *** [Makefile:24: paper.pdf] Error 43

This is due to an update in the latex.template that now looks for logo_path. The logo has also been shifted and now lives in whedon/resources/joss/logo.png.

@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.

@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.

@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.