@khinsen Can you handle this submission (from me) ? I think @ThomasA can edit it but I'll let you decide. I'll now restrict myself to my author role for this submission.

Yes, I'll take over the EIC role for this submission!

@ThomasA can you supervise the reviewing process?

Yes 👍
Just a moment while I read up on the procedure as this is my first.

@rth and @soolijoo can you review this replication?

Hi, Sorry this is outside my expertise.

@soolijoo OK, I will try someone else.

@almarklein can you review this replication?

Sure! Is this ready for review at this point?

@rougier I am stuck trying to build the PDF. I cannot use the 'fontawesome' package on my system. XeLaTeX seems to try to call some font-generating stuff that fails. I have TeXlive 2016 installed in Ubuntu (installed directly from TexLive - not Ubuntu repositories). The fontawesome package is installed, but somehow not useable.

@rougier if I comment out \usepackage{fontawesome} from the template, make just seems to stall and never get further than this:

$ make all
[1/4] Processing Rougier-2017.tex (pass 1)

If you compile using directly the latex command, what is the output ?
The fontawesome package is needed only for putting the github glyph into the red box on the right.

For the fontawesome installation, what is the error in the font generating stuff ?

@rougier By the way, I just by mistake pushed some updates to your repo. Now I do not understand how I actually had the permission to do so? I guess this is not a major problem - the updates are supposed to go in the archive repo anyway.

Regarding fonawesome, making the paper says:

$ make Rougier-2017.pdf
 [1/4] Processing Rougier-2017.tex (pass 1)

kpathsea: Running mktextfm FontAwesome
/usr/local/texlive/2016/texmf-dist/web2c/mktexnam: Could not map source abbreviation F for FontAwesome.
/usr/local/texlive/2016/texmf-dist/web2c/mktexnam: Need to update /usr/local/texlive/2016/texmf-dist/fonts/map/fontname/special.map?
mktextfm: Running mf-nowin -progname=mf \mode:=ljfour; mag:=1; nonstopmode; input FontAwesome
This is METAFONT, Version 2.7182818 (TeX Live 2016) (preloaded base=mf)


kpathsea: Running mktexmf FontAwesome
! I can't find file `FontAwesome'.
<*> ...our; mag:=1; nonstopmode; input FontAwesome
                                                  
Please type another input file name
! Emergency stop.
<*> ...our; mag:=1; nonstopmode; input FontAwesome
                                                  
Transcript written on mfput.log.
grep: FontAwesome.log: Ingen sådan fil eller filkatalog
mktextfm: `mf-nowin -progname=mf \mode:=ljfour; mag:=1; nonstopmode; input FontAwesome' failed to make FontAwesome.tfm.
kpathsea: Appending font creation commands to missfont.log.

I am whining about it here as well: https://tex.stackexchange.com/questions/369068/how-can-i-use-the-fontawesome-package-with-xelatex

Yes, I can see your changes in my repo. That's totally weird.
In the meantime, once you've made all the changes, I'll be able to build the PDF and push it.

Just to be sure, you've also installed the FontAwesome.otf somewhere ?

Yes, it is in the Texlive tree

Oh, the font is bundled with the tex package ?
For the push permission, I'll ask github support how this is possible.

Yes, fontawesome is included in Texlive. I am getting some help here: https://tex.stackexchange.com/questions/369068/how-can-i-use-the-fontawesome-package-with-xelatex, but none of it seems to work...

OK, I finally made it work.
One remaining oddity is that xelatex does not seem to interpret `` '' correctly the way pdflatex does. Is that normal?

I have been looking at this: https://tex.stackexchange.com/questions/193412/what-is-happening-to-the-quotes and this: https://tex.stackexchange.com/questions/278251/ligatures-stopped-working-in-xelatex.
I can fix the quotes if I insert \defaultfontfeatures{Ligatures=TeX} after line 33 in 'rescience-template.tex', but only if I run \setmainfont{[some font]} afterwards to set a font. Without it it has no effect. If I attempt to insert the \defaultfontfeatures line before line 32 in 'rescience-template.tex', make stalls in the first processing of Rougier-2017.tex (doesn't err - just never finishes).
I suspect that fontawesome is somehow messing with this Ligatures feature...

Should we simply ignore that `` '' quotes look ugly with this compile workflow?

Could you make a PR for the main rescience-template and fix it on this repo then ?
I go the explanation for your commit in my branch, it's a new feature of the PR where you can allow edits from maintainers (there is a tickbox for allowing or not).

Sorry, I got stuck last week trying to compile the paper for publishing. This week I am swamped with a course I am giving. I hope to pick this back up tomorrow or during the weekend.

@ThomasA Any chance to publish it this week ?

@ThomasA a gentle reminder...

@rougier could you please rebuild the PDF on rougier/ReScience-submission on your rougier-2017 branch (including the changes it turned out I was able to push to your repo)? I have no XeTeX experience and seem unable to get the fonts set up correctly on my system to make it compile.
Then I will pull it from there and archive it.

Done.

EDITOR

This submission has been published and will soon appear at http://rescience.github.io/read/

This looks good! Thanks to @ThomasA for handling the review, to @rth and @almarklein for reviewing, and to @rougier for doing the replication work!