[PRE REVIEW]: Scientific Computational Imaging Code (SCICO)

[editorialbot]

Submitting author: !--author-handle-->@bwohlberg<!--end-author-handle-- (Brendt Wohlberg) Repository: https://github.com/lanl/scico Branch with paper.md (empty if default branch): joss-paper Version: v0.0.2 Editor: !--editor-->@danielskatz<!--end-editor-- Reviewers: @vitorsr, @DanNixon, @lucaferranti Managing EiC: Arfon Smith

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[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.88  T=0.39 s (468.8 files/s, 81283.3 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                         133           4946           6265          14317
reStructuredText                24           1028            450           1833
TeX                              2             67              0            789
Bourne Shell                     7             82             69            402
SVG                              1              0              0            396
YAML                            11             45             75            374
Markdown                         1            113              0            238
make                             2             29              6            151
CSS                              1             50             10            130
TOML                             1              3              1             31
INI                              1              0              0              5
-------------------------------------------------------------------------------
SUM:                           184           6363           6876          18666
-------------------------------------------------------------------------------

gitinspector failed to run statistical information for the repository

[editorialbot]

Wordcount for paper.md is 3328

[editorialbot]

:warning: An error happened when generating the pdf.

[arfon]

@bwohlberg – please fix the whitespace in your paper to match our example – YAML is whitespace sensitive.

Also, I'm not sure that adding those extra packages in the header-includes section will work here, but we can try :-)

[bwohlberg]

@bwohlberg – please fix the whitespace in your paper to match our example – YAML is whitespace sensitive.

Sorry about that. We fixed the header a while back, but somehow the bad indentation seems to have made its way back in. It's fixed now.

Also, I'm not sure that adding those extra packages in the header-includes section will work here, but we can try :-)

It worked when we built the paper in the joss github workflow or using the docker image.

[bwohlberg]

@editorialbot generate pdf

[editorialbot]

:warning: An error happened when generating the pdf.

[bwohlberg]

@arfon: As requested, a list of suggested reviewers:

jwbuurlage mh-skjelvareid alberto-battistel vitorsr DanNixon grlee77 lheagy

[bwohlberg]

@editorialbot generate pdf

[editorialbot]

:warning: An error happened when generating the pdf.

[bwohlberg]

@editorialbot generate pdf

[editorialbot]

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

[arfon]

@bwohlberg – thanks for fixing up the paper. While we look for an editor to pick up this submission could you please take a look at substantially reducing the size of your paper please? As a guideline, JOSS papers should be between 250 -- 1000 words (yours is upwards of 3000 currently).

[danielskatz]

@bwohlberg - I'll edit this submission. Please let me know when you have reduced the size of the paper, then we can get started

[danielskatz]

@editorialbot assign me as editor

[editorialbot]

Assigned! @danielskatz is now the editor

[bwohlberg]

@arfon: Would you please consider granting an exception on the word count guideline?

We've put considerable effort into writing what we believe is a coherent overview of the purpose and features of the package described by the paper. The "additional" detail addresses the high-level design and usage of the package, and does not involve the sort of API-level details that clearly belong in the project documentation. Cutting it by a factor of three would turn it into a completely different document, and involve removal of a great deal of valuable content.

[danielskatz]

We (I and @arfon) think this paper needs to be reduced in size. JOSS papers are meant to stand in for the software, not completely document it. Specifically, I suggest that the section "Solving Imaging Inverse Problems in SCICO" could be dramatically reduced, with most of the existing content of this section being moved to a webpage that the shortened section could point to for more details.

While I sympathize with the effort you've put into writing this, the JOSS guidance is quite clear about what a JOSS paper should (and should not) include, and has been in place for years, so I think moving this content to the software repo outside of the paper is the best way to not waste this effort and still meet the JOSS requirements.

We can be somewhat loose in terms of the 1000-word maximum for a paper, but this paper far exceeds that limit and does need to be reduced to get much closer to it.

[bwohlberg]

Understood. We'll cut it down to the brief abstract-like document that is expected. We had been thinking of JOSS as an alternative venue for the sort of papers that are published in the SciPy Proceedings.

[danielskatz]

If you want to publish a long paper about the software, you might want to consider options in https://www.software.ac.uk/which-journals-should-i-publish-my-software

[bwohlberg]

Thanks for the suggestion. We already looked there, but none of the other options are ideal. Some of the most promising looking ones seem to be defunct, and the remaining ones that might be suitable for the type of software presented in this paper are run by publishing companies with a poor reputation in terms of open science.

[danielskatz]

We are happy to have your submission, but I did want to offer alternatives. Did you consider JORS? That might meet your needs, though the review process can be somewhat slow

[bwohlberg]

JORS was one of the more promising ones I looked at, but my impression from their template for software description papers is that they also expect something much shorter than our paper. But if you think I'm being overly pessimistic, perhaps it's worth asking them for clarification.

As a matter of interest, why the strict length constraint for JOSS? I'm sure many other authors would also be interested in a venue for more SciPy-like papers.

[bwohlberg]

@editorialbot generate pdf

[editorialbot]

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

[bwohlberg]

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[bwohlberg]

@editorialbot generate pdf

[editorialbot]

:warning: An error happened when generating the pdf.

[bwohlberg]

@editorialbot generate pdf

[editorialbot]

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

[danielskatz]

You can certainly write to JORS. The reason for the length limit on JOSS papers is that we want to focus on the software, which ideally would be reviewed and published as is, along with documentation. However, the current scholarly publishing system basically requires papers, so we wanted to create a way that authors could do a little extra work on top of their software to get credit in the current system. See the developer friendly heading in https://joss.theoj.org/about and https://www.arfon.org/announcing-the-journal-of-open-source-software

[danielskatz]

Do you want to proceed with the review of the software and your shortened paper?

[bwohlberg]

Yes, please. We may consider publishing a much longer paper in the future, but that would be a completely independent document.

[danielskatz]

👋 @jwbuurlage - Are you able to review this JOSS submission?

[danielskatz]

👋 @mh-skjelvareid - Are you able to review this JOSS submission?

[danielskatz]

👋 @alberto-battistel - Are you able to review this JOSS submission?

[danielskatz]

👋 @vitorsr - Are you able to review this JOSS submission?

[mh-skjelvareid]

👋 @mh-skjelvareid - Are you able to review this JOSS submission?

@danielskatz I'm very sorry, but I don't currently have time to review this submission.

[vitorsr]

👋 @vitorsr - Are you able to review this JOSS submission?

I would be happy to.

[danielskatz]

Thanks @vitorsr - I'll assign you, but we won't start the review until we find one more reviewer.

[danielskatz]

@editorialbot add @vitorsr as reviewer

[editorialbot]

@vitorsr added to the reviewers list!

[danielskatz]

👋 @DanNixon - Are you able to review this JOSS submission?

[danielskatz]

👋 @grlee77 - Are you able to review this JOSS submission?

[danielskatz]

👋 @lheagy - Are you able to review this JOSS submission?

[vitorsr]

Thanks @vitorsr - I'll assign you, but we won't start the review until we find one more reviewer.

Thanks for assigning me. If you wouldn't mind my suggesting, I find it would be best if we had more than two reviewers for this submission given the size of the project.

[danielskatz]

We can try... Do you have any thoughts of any complementary reviewers we should ask?

[DanNixon]

wave @DanNixon - Are you able to review this JOSS submission?

I'm happy to.