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[REVIEW]: ENZO: An Adaptive Mesh Refinement Code for Astrophysics (Version 2.6) #1636
Comments
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. @zingale, @rtfisher it looks like you're currently assigned to review this paper If you haven't already, you should seriously consider unsubscribing from GitHub notifications for this (https://github.com/openjournals/joss-reviews) repository. As a reviewer, you're probably currently watching this repository which means for GitHub's default behaviour you will receive notifications (emails) for all reviews To fix this do the following two things:
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:
|
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.
danielskatz
commented
Aug 9, 2019
I had to update the repository URL on the top comment of this issue. (note to @arfon - whedon didn't use the URL in the pre-report issue, and this may also lead to a problem when we do the final acceptance.) |
This comment has been minimized.
This comment has been minimized.
danielskatz
commented
Aug 9, 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.
danielskatz
commented
Aug 9, 2019
@bwoshea - merging enzo-project/enzo-dev#93 will fix 2 small bib entries |
This comment has been minimized.
This comment has been minimized.
danielskatz
commented
Aug 9, 2019
If you have any questions or problems, please let me know. |
This comment has been minimized.
This comment has been minimized.
rtfisher
commented
Aug 10, 2019
I am just beginning the review process. I find the documentation link (https://enzo-project.org/docs/2.6/) under https://github.com/enzo-project/enzo-dev returns a 404. |
This comment has been minimized.
This comment has been minimized.
danielskatz
commented
Aug 11, 2019
Now that this has been done, I will recompile - @bwoshea, you can do this too, just the way I am, with an instruction in whedon in a new comment (letting you know in case more changes are needed) |
This comment has been minimized.
This comment has been minimized.
danielskatz
commented
Aug 11, 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.
zingale
commented
Aug 11, 2019
regarding
There are 2 references to Enzo itself, referring to github. Should these be changed to an archived version of the code with a DOI? |
This comment has been minimized.
This comment has been minimized.
zingale
commented
Aug 14, 2019
I'm done with my pass through the docs and have filed a number of issues, some which I would like to see addressed for the review (marked with I will try running some standard test problems next. |
This comment has been minimized.
This comment has been minimized.
danielskatz
commented
Aug 15, 2019
@zingale - thanks for all your comments so far. If possible, when you open an issue in https://github.com/enzo-project/enzo-dev, just mention this review thread (#1636) in that issue rather than posted that issue in this thread. This will insert a note here that will show if the issue is open or closed. |
This comment has been minimized.
This comment has been minimized.
zingale
commented
Aug 16, 2019
oh, I see, I did it backwards. I'll fix that. |
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.
danielskatz
commented
Sep 22, 2019
deposit the repository in an archive (e.g. zenodo) and report the DOI here |
This comment has been minimized.
This comment has been minimized.
danielskatz
commented
Sep 29, 2019
|
This comment has been minimized.
This comment has been minimized.
bwoshea
commented
Oct 2, 2019
•
@danielskatz sorry for the delay. We now have a DOI: 10.5281/zenodo.3469922: The lates version number is Enzo v2.6.1. We are verifying the paper text and references right now. The one issue I can see with the paper is the overlapping text in the bottom-left corner of the first page, where the 'LICENSE' block overlaps the footer: I anticipate that I will get back to you by no later than tomorrow finalizing the paper text and references. |
This comment has been minimized.
This comment has been minimized.
@bwoshea @danielskatz - this is an issue with our LaTeX template not handling long author lists very well. @danielskatz - feel free to accept this paper with Whedon here but I'll need to manually update the PDF afterwards to fix the layout issues. |
This comment has been minimized.
This comment has been minimized.
danielskatz
commented
Oct 2, 2019
@whedon set 10.5281/zenodo.3469922 as archive |
This comment has been minimized.
This comment has been minimized.
OK. 10.5281/zenodo.3469922 is the archive. |
This comment has been minimized.
This comment has been minimized.
danielskatz
commented
Oct 2, 2019
@whedon set v2.6.1 as version |
This comment has been minimized.
This comment has been minimized.
OK. v2.6.1 is the version. |
This comment has been minimized.
This comment has been minimized.
bwoshea
commented
Oct 3, 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
Oct 3, 2019
@danielskatz We've proofread the paper and pushed a small change. The revised PDF looks good to me. I think we're good to go! |
This comment has been minimized.
This comment has been minimized.
danielskatz
commented
Oct 3, 2019
@whedon accept |
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.
PDF failed to compile for issue #1636 with the following error: sh: 158: Syntax error: newline unexpected |
This comment has been minimized.
This comment has been minimized.
danielskatz
commented
Oct 3, 2019
@whedon accept |
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.
PDF failed to compile for issue #1636 with the following error: sh: 158: Syntax error: newline unexpected |
This comment has been minimized.
This comment has been minimized.
danielskatz
commented
Oct 3, 2019
|
This comment has been minimized.
This comment has been minimized.
danielskatz
commented
Oct 3, 2019
Actually, if you want to take over given that you have to generate the PDF manually for the spacing issue, please go ahead - this is fully ready to publish |
This comment has been minimized.
This comment has been minimized.
@zingale, @rtfisher - many thanks for your reviews here and to @danielskatz for editing this submission @bwoshea - your paper is now accepted into JOSS |
This comment has been minimized.
This comment has been minimized.
If you would like to include a link to your paper from your README use the following code snippets:
This is how it will look in your documentation: We need your help! Journal of Open Source Software is a community-run journal and relies upon volunteer effort. If you'd like to support us please consider doing either one (or both) of the the following:
|
This comment has been minimized.
This comment has been minimized.
danielskatz
commented
Oct 3, 2019
@arfon - can you generate a tweet for this? |
whedon commentedAug 9, 2019
•
edited
Submitting author: @bwoshea (Brian O'Shea)
Repository: https://github.com/enzo-project/enzo-dev
Version: v2.6.1
Editor: @danielskatz
Reviewer: @zingale, @rtfisher
Archive: 10.5281/zenodo.3469922
Status
Status badge code:
Reviewers and authors:
Please avoid lengthy details of difficulties in the review thread. Instead, please create a new issue in the target repository and link to those issues (especially acceptance-blockers) by leaving comments in the review thread below. (For completists: if the target issue tracker is also on GitHub, linking the review thread in the issue or vice versa will create corresponding breadcrumb trails in the link target.)
Reviewer instructions & questions
@zingale & @rtfisher, please carry out your review in this issue by updating the checklist below. If you cannot edit the checklist please:
The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. Any questions/concerns please let @danielskatz know.
Review checklist for @zingale
Conflict of interest
Code of Conduct
General checks
Functionality
Documentation
Software paper
paper.md
file include a list of authors with their affiliations?Review checklist for @rtfisher
Conflict of interest
Code of Conduct
General checks
Functionality
Documentation
Software paper
paper.md
file include a list of authors with their affiliations?