JOSS manuscript

[tsalo]

Closes #669.

To do:

• Review references. Some are wrong or outdated. Please comment in the references file at the relevant lines.
• Check rendering. You can use this link. Just put in https://github.com/tsalo/tedana for the repo and joss for the branch.
• Figure out how to denote co-first authorship for myself and @emdupre.
  • Figured out from "These authors contributed equally to this work" openjournals/joss#337.

Changes proposed in this pull request:

• Add JOSS manuscript, in markdown format.
• Add figure.
• Add bibliography in BibLaTeX format.

[tsalo]

I don't want to run the CI, but including [skip-ci] in my commit message didn't do anything ☹️. Anyone have a solution?

[jbteves]

I think you want space instead of -

[codecov]

Codecov Report

Merging #693 (9c52f3f) into joss (009ccc5) will not change coverage.
The diff coverage is n/a.

@@           Coverage Diff           @@
##             joss     #693   +/-   ##
=======================================
  Coverage   93.64%   93.64%           
=======================================
  Files          26       26           
  Lines        2029     2029           
=======================================
  Hits         1900     1900           
  Misses        129      129           

---

Continue to review full report at Codecov.

Legend - Click here to learn more
Δ = absolute <relative> (impact), ø = not affected, ? = missing data
Powered by Codecov. Last update 009ccc5...9c52f3f. Read the comment docs.

[tsalo]

That seems to have worked. Thanks @jbteves!

[handwerkerd]

In the rendered version of the paper, the first author & title is on the bottom of each page. The title is correct, but the author is Mickey Mouse. I suspect that, wherever the render is pulling that info from is getting confused by the two first authors.

[emdupre]

In the rendered version of the paper, the first author & title is on the bottom of each page. The title is correct, but the author is Mickey Mouse. I suspect that, wherever the render is pulling that info from is getting confused by the two first authors.

Ah no sorry, this is just the JOSS preview template ! It's also not filling in the year, for example :) You can confirm this by building a preview for PyBIDS, which includes a previously accepted paper.

It will be updated when built by Whedon in the proper submission pipeline.

[notZaki]

The sub/sup scripts don't look like they're being rendered in the pdf. Maybe because the current syntax is html-specific?

If JOSS uses pandoc, then the following change might work

- T<sub>2</sub><sup>\*</sup>
+ T~2~^\*^

Edit: Or switch to math mode? But that often changes the font and I find that distracting.

[emdupre]

From my reading, the JOSS submission guidelines ask for non-abbreviated references:

Also note that the references include full names of venues, e.g., journals and conferences, not abbreviations only understood in the context of a specific discipline.

I've made suggestions to that effect ! I've also gone through and changed the UNPUBLISHED biblatex classes to MISC so that we can add and display a DOI, which will almost definitely be requested by Whedon on submission !

[tsalo]

The sub/sup scripts don't look like they're being rendered in the pdf. Maybe because the current syntax is html-specific?

If JOSS uses pandoc, then the following change might work

- T<sub>2</sub><sup>\*</sup>
+ T~2~^\*^

Edit: Or switch to math mode? But that often changes the font and I find that distracting.

@notZaki Your recommendation worked! Thanks!

[tsalo]

@smoia @CesarCaballeroGaudes you noted issues with some of the references, but PaperPile autogenerated them. We can change them now though! Would you mind adding comments about any incorrect references?

[CesarCaballeroGaudes]

Where is the link to the paper? I mean the final version with the references?

[emdupre]

Where is the link to the paper? I mean the final version with the references?

You can use: http://whedon.theoj.org
Just put in https://github.com/tsalo/tedana for the repo and joss for the branch.

But it's building automatically from the files in this PR !

[CesarCaballeroGaudes]

Ok, I've checked the current version. I assume @tsalo is referring to my comment about the fact that @smoia paper (Moia, Termenon) has been accepted in Neuroimage, but we don't have DOI number yet (at least at this time of the day). But the biorxiv website will indicate that the paper is accepted. Somehow similar with @jsheunis paper which is under review too.

[CesarCaballeroGaudes]

One suggestion/question: Why are the DOI numbers only included in the biorxiv papers, and not in the others?

[smoia]

The preview looks good to me! The only thing I find strange (besides the inconsistency of DOIs that César was pointing out) is the inconsistency of the author lists in the bibliography, in which you have fMRI prep list most of its authors and the paper after using "& others". But that's more OCP spasms than anything else, probably.

[emdupre]

Adding DOIs to all article types

[emdupre]

Why are the DOI numbers only included in the biorxiv papers, and not in the others?

I had previously only added them under the preprints since I know that they'll be required for cross-checking any unpublished references, but I've made suggestions now to add them for all article classes !

[emdupre]

The only thing I find strange (besides the inconsistency of DOIs that César was pointing out) is the inconsistency of the author lists in the bibliography, in which you have fMRI prep list most of its authors and the paper after using "& others". But that's more OCP spasms than anything else, probably.

Thanks for catching that, @smoia ! Some how that reference only imported the first handful of authors. I've made a suggestion to add the rest.

[KirstieJane]

READ IT! Finally.

Held back a temptation to put 🎉 emojis after all the tedanas 😉

A few updates to my affiliation and added my funding - I hope that's ok?

All approved from my side. Many many apologies and great sadness for not being able to contribute more over the last year.

[tsalo]

Thank you so much @KirstieJane!

[tsalo]

I believe we have approval from all authors now, so @emdupre and I are planning to submit later today. @ME-ICA/tedana-devs if anyone has any final thoughts, please comment soon!

We're currently planning to merge the PR at 1pm EST, and then submit to JOSS at 2pm.

[smoia]

@tsalo would it be a problem to update the reference to my paper to the "in press" Neuroimage version, rather than the bioRxiv one? I made the changes already, I hope it's ok.