Join GitHub today
GitHub is home to over 40 million developers working together to host and review code, manage projects, and build software together.
Sign up[PRE REVIEW]: ENZO: An Adaptive Mesh Refinement Code for Astrophysics (Version 2.6) #1624
Comments
whedon
added
the
pre-review
label
Aug 2, 2019
This comment has been minimized.
This comment has been minimized.
Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. For a list of things I can do to help you, just type:
For example, to regenerate the paper pdf after making changes in the paper's md or bib files, type:
What happens now? This submission is currently in a You can help the editor by looking at this list of potential reviewers to identify individuals who might be able to review your submission (please start at the bottom of the list). Also, feel free to suggest individuals who are not on this list by mentioning their GitHub handles here. |
This comment has been minimized.
This comment has been minimized.
|
whedon
added
the
TeX
label
Aug 2, 2019
This comment has been minimized.
This comment has been minimized.
PDF failed to compile for issue #1624 with the following error: /app/vendor/ruby-2.4.4/lib/ruby/2.4.0/psych.rb:377:in |
This comment has been minimized.
This comment has been minimized.
Also, JOSS papers usually reside in the software repository (a different branch is OK), but here you've created a separate repo for just the paper. Is this the software repo? Note that in the JOSS workflow the software repository gets added to the decorators on the first-page margin of the published paper, so it kind of breaks things if you put the paper in another repo. |
This comment has been minimized.
This comment has been minimized.
@xuanxu — the submitting author suggested you as handling editor. Could you take this one? ENZO: An Adaptive Mesh Refinement Code for Astrophysics |
This comment has been minimized.
This comment has been minimized.
@bwoshea — if you make changes to the paper, you can run |
This comment has been minimized.
This comment has been minimized.
@labarba I can’t take this right now, sorry. I’ll be mostly offline next week. I’d prefer you find another editor for this one. |
This comment has been minimized.
This comment has been minimized.
danielskatz
commented
Aug 2, 2019
@whedon assign @danielskatz as editor |
whedon
assigned
danielskatz
Aug 2, 2019
This comment has been minimized.
This comment has been minimized.
OK, the editor is @danielskatz |
This comment has been minimized.
This comment has been minimized.
danielskatz
commented
Aug 2, 2019
This comment has been minimized.
This comment has been minimized.
danielskatz
commented
Aug 2, 2019
@bwoshea - part of the problem with the paper compiling is (or will be) blank ORCIDs - for authors without ORCIDS, remove the blank ORCID line from the .md file |
This comment has been minimized.
This comment has been minimized.
This comment has been minimized.
This comment has been minimized.
yes, I can do this, but as it is quite a big code, it would be useful to have additional reviewer(s). |
This comment has been minimized.
This comment has been minimized.
Oh, yes, absolutely! We've defaulted to a minimum of two reviewers in JOSS now. But maybe here we need three? Do you know anyone you might recommend? |
This comment has been minimized.
This comment has been minimized.
whedon
assigned
danielskatz and
zingale and unassigned
danielskatz
Aug 3, 2019
This comment has been minimized.
This comment has been minimized.
OK, the reviewer is @zingale |
This comment has been minimized.
This comment has been minimized.
danielskatz
commented
Aug 3, 2019
Hey @labarba - do you want to take over editing this one? |
This comment has been minimized.
This comment has been minimized.
|
This comment has been minimized.
This comment has been minimized.
@danielskatz — here's a lead for you for another potential reviewer |
This comment has been minimized.
This comment has been minimized.
Maybe @rtfisher would be interested in reviewing. |
This comment has been minimized.
This comment has been minimized.
danielskatz
commented
Aug 3, 2019
|
This comment has been minimized.
This comment has been minimized.
danielskatz
commented
Aug 3, 2019
@zingale - thanks - you were actually suggested to me by some else as well, so it's great to have you on board. We'll need to wait for some changes to the paper so that it compiles, and a second reviewer, then we'll start the reviews |
This comment has been minimized.
This comment has been minimized.
I'm happy to pitch in the reviewing. |
This comment has been minimized.
This comment has been minimized.
r-j-arnold
commented
Aug 3, 2019
Hi @danielskatz I'm afraid I'm submitting my thesis and moving to america in the next few weeks so I wouldn't be able to do this in a timely fashion. Since Robert and Michael have now said yes, it may be best to proceed with them. |
This comment has been minimized.
This comment has been minimized.
bwoshea
commented
Aug 4, 2019
@danielskatz Thank you! @rtfisher and @zingale would be great reviewers. |
This comment has been minimized.
This comment has been minimized.
bwoshea
commented
Aug 4, 2019
@whedon generate pdf |
This comment has been minimized.
This comment has been minimized.
|
This comment has been minimized.
This comment has been minimized.
This comment has been minimized.
This comment has been minimized.
You could do that. Our bot |
This comment has been minimized.
This comment has been minimized.
@arfon — have a look at this compiled article proof. With a very long author list, the margin decorators get pushed to the bottom of the page, colliding with the footer. This may require some change to the paper template. |
This comment has been minimized.
This comment has been minimized.
bwoshea
commented
Aug 4, 2019
@whedon generate pdf |
This comment has been minimized.
This comment has been minimized.
|
This comment has been minimized.
This comment has been minimized.
This comment has been minimized.
This comment has been minimized.
bwoshea
commented
Aug 4, 2019
@whedon generate pdf |
This comment has been minimized.
This comment has been minimized.
|
This comment has been minimized.
This comment has been minimized.
This comment has been minimized.
This comment has been minimized.
bwoshea
commented
Aug 4, 2019
This comment has been minimized.
This comment has been minimized.
bwoshea
commented
Aug 4, 2019
Understood. Let me check with the other Enzo developers regarding how they wish to do that. Would it be OK to proceed with the review using the current repository for the moment? |
This comment has been minimized.
This comment has been minimized.
I believe so. |
This comment has been minimized.
This comment has been minimized.
It does not but I can fix up the JOSS site so that it will. |
This comment has been minimized.
This comment has been minimized.
bwoshea
commented
Aug 4, 2019
Excellent, thanks! I just messaged all of the Enzo developers, and we'll move on the repository issue pretty quickly as soon as we reach consensus (meaning on the 2-3 day time frame, given the number of developers). |
This comment has been minimized.
This comment has been minimized.
Thanks for spotting this. This is something we'll have to fix at the end of the review as I'll have to manually override the margin formatting for this paper. |
This comment has been minimized.
This comment has been minimized.
danielskatz
commented
Aug 9, 2019
@bwoshea - any news on this? |
This comment has been minimized.
This comment has been minimized.
bwoshea
commented
Aug 9, 2019
@danielskatz - yes, I'm moving it over to the enzo-dev repository right now. As soon as the PR is approved you will be able to find it in the master branch of github.com/enzo-project/enzo-dev in the subdirectory "method-paper-joss-2019". I'm working to get our required number of approvals right now, and expect that will happen pretty soon. |
This comment has been minimized.
This comment has been minimized.
danielskatz
commented
Aug 9, 2019
Thanks - please be sure to let us know when this is done so that we can start the review |
This comment has been minimized.
This comment has been minimized.
bwoshea
commented
Aug 9, 2019
@danielskatz - the PR is now merged, and you can find the paper in the Enzo code repository (specifically, in https://github.com/enzo-project/enzo-dev/tree/master/method-paper-joss-2019) . Do you need anything else to start the review? |
This comment has been minimized.
This comment has been minimized.
@whedon generate pdf |
This comment has been minimized.
This comment has been minimized.
|
This comment has been minimized.
This comment has been minimized.
This comment has been minimized.
This comment has been minimized.
I changed the repository URL on the top comment of this issue, then compiled with |
This comment has been minimized.
This comment has been minimized.
danielskatz
commented
Aug 9, 2019
Ok, let's try it and see how the review issue looks |
This comment has been minimized.
This comment has been minimized.
danielskatz
commented
Aug 9, 2019
@whedon start review |
This comment has been minimized.
This comment has been minimized.
OK, I've started the review over in #1636. Feel free to close this issue now! |
whedon commentedAug 2, 2019
•
edited by labarba
Submitting author: @bwoshea (Brian O'Shea)
Repository: https://github.com/enzo-project/enzo-dev
Version: v2.6
Editor: @danielskatz
Reviewers: @zingale, @rtfisher
Author instructions
Thanks for submitting your paper to JOSS @bwoshea. Currently, there isn't an JOSS editor assigned to your paper.
@bwoshea if you have any suggestions for potential reviewers then please mention them here in this thread. In addition, this list of people have already agreed to review for JOSS and may be suitable for this submission.
Editor instructions
The JOSS submission bot @whedon is here to help you find and assign reviewers and start the main review. To find out what @whedon can do for you type: