Joss-reviews: [PRE REVIEW]: CoreBreakout: Subsurface Core Images to Depth-Registered Datasets

[whedon]

Submitting author: @rgmyr (Ross Meyer)
Repository: https://github.com/rgmyr/corebreakout
Version: v0.2
Editor: @kbarnhart
Reviewers: @brendonhall, @JesperDramsch, @jessepisel

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Thanks for submitting your paper to JOSS @rgmyr. Currently, there isn't an JOSS editor assigned to your paper.

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For example, to regenerate the paper pdf after making changes in the paper's md or bib files, type:

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[whedon]

Attempting to check references...

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

PDF failed to compile for issue #1946 with the following error:

/app/vendor/ruby-2.4.4/lib/ruby/2.4.0/find.rb:43:in block in find': No such file or directory - tmp/1946 (Errno::ENOENT) from /app/vendor/ruby-2.4.4/lib/ruby/2.4.0/find.rb:43:incollect!'
from /app/vendor/ruby-2.4.4/lib/ruby/2.4.0/find.rb:43:in find' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-cd7dadefdab3/lib/whedon/processor.rb:61:infind_paper_paths'
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-cd7dadefdab3/bin/whedon:50:in prepare' from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor/command.rb:27:inrun'
from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor/invocation.rb:126:in invoke_command' from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor.rb:387:indispatch'
from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor/base.rb:466:in start' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-cd7dadefdab3/bin/whedon:116:in from /app/vendor/bundle/ruby/2.4.0/bin/whedon:23:in load' from /app/vendor/bundle/ruby/2.4.0/bin/whedon:23:in

'

[kyleniemeyer]

@kbarnhart could you edit this submission?

[kyleniemeyer]

@openjournals/dev any ideas why the paper won't compile? The error message is not too helpful for me.

[danielskatz]

could be a problem with a file - is the bib file correctly named and does it exist? or any images?

[kyleniemeyer]

The bib file looks ok, but there is an image in the article: ![Figure 1](JOSS_figure_workflow.png)

I do see a JOSS_figure_workflow.png in the repo, in the same location as the paper.md, so I'm not sure why that would cause an error.

[arfon]

A couple of issues here:

• Whedon is likely timing out here as the repository is _very_ large (2.3GB!) even though there's only ~104MB of files present in the repository.
• Also, the bibtex has errors that I've fixed in https://github.com/rgmyr/corebreakout/pull/3

Finally, here's a copy of the paper I compiled locally: 10.21105.joss.01946.pdf

[kyleniemeyer]

@arfon @rgmyr wow! That is a huge repository... is the large size due to files that were removed but are in the history?

If you know the files, you can remove them from the history using this: https://help.github.com/en/github/authenticating-to-github/removing-sensitive-data-from-a-repository#purging-a-file-from-your-repositorys-history

This is likely going to continue to be an issue, not only for whedon but for others looking to clone the repo, and so worth addressing.

[rgmyr]

Sounds good, thanks for the help guys. I wasn't sure what the problem was with paper compilation -- it seemed to be working via the preview service for awhile, and then it just stopped being able to compile all of the sudden.

I've merged @arfon's PR, and will look through the history to see where that extra size is coming from... I'm not sure off the top of my head, but I wouldn't be surprised if there were a few model files or data folders hiding in there accidentally.

[rgmyr]

I was having a hard time tracking down and removing the offending files/folders individually, so I tried a couple of things:

• Created a new --orphan branch, set that as master, and removed some old temporary branches that aren't relevant anymore. (Following this stackoverflow answer.)
• That didn't seem to actually change the size much, if at all, so I also tried cleaning things up BFG Repo-Cleaner.

I ended up having to be pretty aggressive with the latter. I think a lot of files were deleted from the history, but I made a local backup incase I need to restore for some reason, and I don't foresee it being a big problem for code management going forward.

In any case, the repo size is now 182MB, and the paper compiles pretty quickly on the preview service.

[rgmyr]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

:point_right: Check article proof :page_facing_up: :point_left:

[rgmyr]

Just made a couple of small fixes (multiple reference separator, figure text)...

[rgmyr]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

:point_right: Check article proof :page_facing_up: :point_left:

[whedon]

```Reference check summary:

OK DOIs

• 10.1007/s11263-007-0090-8 is OK
• 10.6084/m9.figshare.8023835.v2 is OK
• 10.1002/2016JF003903 is OK

MISSING DOIs

• None

INVALID DOIs

• None
  ```

[kbarnhart]

@kyleniemeyer I can also handle this one.

[kbarnhart]

@whedon assign @kbarnhart as editor

[whedon]

OK, the editor is @kbarnhart

[kyleniemeyer]

@kbarnhart thanks!

[ThomasMGeo]

Maybe @brendonhall or @kwinkunks would be interested in reviewing?

[brendonhall]

@ThomasMGeo I'm happy to take a look. Are there instructions for reviewing?

[rgmyr]

Hi @brendonhall, here's the Reviewer Guidelines. Once a [Review] issue is opened, each reviewer gets a review checklist to work through (check out some of the review issues in this repo for examples).

[kbarnhart]

@rgmyr thank you for the recommendations. I'm now fully back online after a week at AGU.

@brendonhall thank you for agreeing to review this publication. In my next comment, I'll formally add you.

:wave: @kwinkunks would you be willing to review this submission for JOSS? We carry out our checklist-driven reviews here in GitHub issues and follow these guidelines: https://joss.readthedocs.io/en/latest/review_criteria.html

This is a pre-review issue that I use to coordinate reviewers. Once there are sufficient reviewers (usually 2-3), I will open a new issue where the review will take place.

If you are not able, please let me know if you have recommendations for other reviewers.

[kbarnhart]

@whedon assign @brendonhall as reviewer

[whedon]

OK, the reviewer is @brendonhall

[ThomasMGeo]

Jesper Dramsch @ JesperDramsch might also be a fantastic reviewer

[kbarnhart]

:wave: @JesperDramsch would you be willing to review this submission for JOSS? We carry out our checklist-driven reviews here in GitHub issues and follow these guidelines: https://joss.readthedocs.io/en/latest/review_criteria.html

This is a pre-review issue that I use to coordinate reviewers. Once there are sufficient reviewers (usually 2-3), I will open a new issue where the review will take place.

If you are not able, please let me know if you have recommendations for other reviewers.

[ThomasMGeo]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

:point_right: Check article proof :page_facing_up: :point_left:

[ThomasMGeo]

Jesse Pisel @jessepisel just reached out to me to be a reviewer! Thanks Jesse!

[JesperDramsch]

This seems awesome. I'd love to take a look and review this.

I'll probably be best on the python and ml bits and ok on the core.

[ThomasMGeo]

Luckily it's way more the python/ML bits, and just being able to say rock vs no rock! Thanks @JesperDramsch

[ThomasMGeo]

Dr. Chris Yeomans (@swgeoscience) also reached out to be a reviewer.

[kbarnhart]

Thanks for being willing to review @JesperDramsch

Thanks also @ThomasMGeo for your assistance in finding appropriate reviewers.

:wave: @swgeoscience @jessepisel can you confirm on this thread that would you be willing to review this submission for JOSS? We carry out our checklist-driven reviews here in GitHub issues and follow these guidelines: https://joss.readthedocs.io/en/latest/review_criteria.html

This is a pre-review issue that I use to coordinate reviewers. Once there are sufficient reviewers (usually 2-3, it looks like this submission may have 4), I will open a new issue where the review will take place.

[kbarnhart]

@whedon add @JesperDramsch as reviewer

[whedon]

OK, @JesperDramsch is now a reviewer

[jessepisel]

I am willing to review this submission. Excited to check it out.

[kbarnhart]

@whedon add @jessepisel as reviewer

[whedon]

OK, @jessepisel is now a reviewer

[kbarnhart]

@whedon start review

[whedon]

OK, I've started the review over in https://github.com/openjournals/joss-reviews/issues/1969. Feel free to close this issue now!

[kbarnhart]

Thanks all for your enthusiasm for finding reviewers and recommending reviewers. I've started the formal review over at #1969. @swgeoscience, if you are really excited to also be a reviewer, let me know and I can add you over on that issue.

For those of you who are interested in being listed on our list of potential reviewers for future submissions, please consider filling out the 1-minute form at this link. This helps editors and authors find appropriate reviewers.

[swgeoscience]

Hi Katy,

Apologies, I’ve just found this email – combination of being on leave and not having my github linked to the right account!

If you still require a review from me I am happy to complete it.

Again, apologies!

Best wishes,
Chris

From: Katy Barnhart [e-mail]
Sent: 18 December 2019 18:01
To: openjournals/joss-reviews [e-mail]
Cc: Chris Yeomans [e-mail]; Mention [e-mail]
Subject: Re: [openjournals/joss-reviews] [PRE REVIEW]: CoreBreakout: Subsurface Core Images to Depth-Registered Datasets (#1946)

Closed #1946 https://github.com/openjournals/joss-reviews/issues/1946 .

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[kbarnhart]

@swgeoscience no worries. I think that we are good with three reviewers. If you are interested in generally being considered as a JOSS reviewer 🎉, please consider filling out the 1-minute form at this link.