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[REVIEW]: ENZO: An Adaptive Mesh Refinement Code for Astrophysics (Version 2.6) #1636

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whedon opened this issue Aug 9, 2019 · 74 comments
Closed
36 tasks done

[REVIEW]: ENZO: An Adaptive Mesh Refinement Code for Astrophysics (Version 2.6) #1636

whedon opened this issue Aug 9, 2019 · 74 comments
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@danielskatz @zingale @rtfisher
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accepted published Papers published in JOSS recommend-accept Papers recommended for acceptance in JOSS. review

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@whedon
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whedon commented Aug 9, 2019 •
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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

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/ee73bb825d396e5ddf95b96d9300f295"><img src="https://joss.theoj.org/papers/ee73bb825d396e5ddf95b96d9300f295/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/ee73bb825d396e5ddf95b96d9300f295/status.svg)](https://joss.theoj.org/papers/ee73bb825d396e5ddf95b96d9300f295)

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:

  1. Make sure you're logged in to your GitHub account
  2. Be sure to accept the invite at this URL: https://github.com/openjournals/joss-reviews/invitations

The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. Any questions/concerns please let @danielskatz know.

✨ Please try and complete your review in the next two weeks ✨

Review checklist for @zingale

Conflict of interest

Code of Conduct

General checks

  • Repository: Is the source code for this software available at the repository url?
  • License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
  • Version: v2.6.1
  • Authorship: Has the submitting author (@bwoshea) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

Functionality

  • Installation: Does installation proceed as outlined in the documentation?
  • Functionality: Have the functional claims of the software been confirmed?
  • Performance: If there are any performance claims of the software, have they been confirmed? (If there are no claims, please check off this item.)

Documentation

  • A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
  • Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
  • Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
  • Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
  • Automated tests: Are there automated tests or manual steps described so that the function of the software can be verified?
  • Community guidelines: Are there clear guidelines for third parties wishing to 1) Contribute to the software 2) Report issues or problems with the software 3) Seek support

Software paper

  • Authors: Does the paper.md file include a list of authors with their affiliations?
  • A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
  • References: Do all archival references that should have a DOI list one (e.g., papers, datasets, software)?

Review checklist for @rtfisher

Conflict of interest

Code of Conduct

General checks

  • Repository: Is the source code for this software available at the repository url?
  • License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
  • Version: v2.6.1
  • Authorship: Has the submitting author (@bwoshea) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

Functionality

  • Installation: Does installation proceed as outlined in the documentation?
  • Functionality: Have the functional claims of the software been confirmed?
  • Performance: If there are any performance claims of the software, have they been confirmed? (If there are no claims, please check off this item.)

Documentation

  • A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
  • Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
  • Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
  • Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
  • Automated tests: Are there automated tests or manual steps described so that the function of the software can be verified?
  • Community guidelines: Are there clear guidelines for third parties wishing to 1) Contribute to the software 2) Report issues or problems with the software 3) Seek support

Software paper

  • Authors: Does the paper.md file include a list of authors with their affiliations?
  • A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
  • References: Do all archival references that should have a DOI list one (e.g., papers, datasets, software)?
@whedon whedon added the review label Aug 9, 2019
@whedon whedon mentioned this issue Aug 9, 2019
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@whedon
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whedon commented Aug 9, 2019

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 🎉.

⭐ Important ⭐

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:

  1. Set yourself as 'Not watching' https://github.com/openjournals/joss-reviews:

watching

  1. You may also like to change your default settings for this watching repositories in your GitHub profile here: https://github.com/settings/notifications

notifications

For a list of things I can do to help you, just type:

@whedon commands

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

@whedon generate pdf

@whedon
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whedon commented Aug 9, 2019 

Attempting PDF compilation. Reticulating splines etc...

@whedon
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whedon commented Aug 9, 2019

👉 Check article proof 📄 👈

@danielskatz
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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.)

@danielskatz
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@whedon generate pdf

@whedon
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whedon commented Aug 9, 2019 

Attempting PDF compilation. Reticulating splines etc...

@whedon
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whedon commented Aug 9, 2019

👉 Check article proof 📄 👈

@danielskatz
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@bwoshea - merging enzo-project/enzo-dev#93 will fix 2 small bib entries

@danielskatz
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👋 @zingale, @rtfisher - we are ready for you to review this now. Please read the first 2 comments in this issue carefully. Your job now is to go through the paper (the latest "check article proof" in this issue) and the repository, and check off items in your checklist until you are done, and if you find problems, either report them here or create an issue in the repo and mention this issue in that one.

If you have any questions or problems, please let me know.

@rtfisher
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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.

@danielskatz
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@bwoshea - merging enzo-project/enzo-dev#93 will fix 2 small bib entries

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)

@danielskatz
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@whedon generate pdf

@whedon
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whedon commented Aug 11, 2019 

Attempting PDF compilation. Reticulating splines etc...

@whedon
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whedon commented Aug 11, 2019

👉 Check article proof 📄 👈

@zingale
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zingale commented Aug 11, 2019

regarding

References: Do all archival references that should have a DOI list one (e.g., papers, datasets, software)

There are 2 references to Enzo itself, referring to github. Should these be changed to an archived version of the code with a DOI?

@zingale
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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 [JOSS REVIEW]) and others that are suggestions to take into consideration.

I will try running some standard test problems next.

@danielskatz
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@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.

@zingale
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zingale commented Aug 16, 2019

oh, I see, I did it backwards. I'll fix that.

This was referenced Aug 16, 2019
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@danielskatz
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👋 @bwoshea - to finish up now, I need you to

  1. deposit the repository in an archive (e.g. zenodo) and report the DOI here
  2. tell me the latest version number here
  3. confirm that the paper text and references are final

@bwoshea
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bwoshea commented Oct 2, 2019 •
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@danielskatz sorry for the delay. We now have a DOI: 10.5281/zenodo.3469922:

DOI

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:

JOSS_paper_issue

I anticipate that I will get back to you by no later than tomorrow finalizing the paper text and references.

@arfon
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arfon commented Oct 2, 2019

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:

@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.

@danielskatz
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@whedon set 10.5281/zenodo.3469922 as archive

@whedon
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whedon commented Oct 2, 2019

OK. 10.5281/zenodo.3469922 is the archive.

@danielskatz
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@whedon set v2.6.1 as version

@whedon
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whedon commented Oct 2, 2019

OK. v2.6.1 is the version.

@bwoshea
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bwoshea commented Oct 3, 2019

@whedon generate pdf

@whedon
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whedon commented Oct 3, 2019 

Attempting PDF compilation. Reticulating splines etc...

@whedon
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whedon commented Oct 3, 2019

👉 Check article proof 📄 👈

@bwoshea
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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!

@danielskatz
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@whedon accept

@whedon
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whedon commented Oct 3, 2019 

Attempting dry run of processing paper acceptance...

@whedon
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whedon commented Oct 3, 2019 


OK DOIs

- 10.1088/0067-0049/211/2/19 is OK
- 10.1038/s41586-019-0873-4 is OK
- 10.1093/mnras/stv1509 is OK
- 10.1088/2041-8205/807/1/L12 is OK
- 10.3847/1538-4357/ab0654 is OK
- 10.3847/1538-4357/aa6fb1 is OK
- 10.1093/mnras/stv2641 is OK
- 10.3847/1538-4357/aa88c1 is OK
- 10.1103/PhysRevE.95.033206 is OK
- 10.1103/PhysRevLett.121.021104 is OK
- 10.3847/2041-8213/834/1/L1 is OK
- 10.1126/science.1173540 is OK
- 10.1093/mnras/sty2984 is OK
- 10.3847/1538-4357/aae30b is OK
- 10.1093/mnras/stw3291 is OK
- 10.1093/mnras/stt2121 is OK
- 10.1088/0004-637X/809/1/69 is OK
- 10.3847/1538-4357/aa799f is OK
- 10.1103/PhysRevD.99.063509 is OK
- 10.1051/0004-6361:200809967 is OK
- 10.1093/mnras/sty1289 is OK
- 10.3847/1538-4357/aa7263 is OK
- 10.3847/0004-637X/827/1/28 is OK
- 10.1093/mnras/stw1461 is OK
- 10.3847/1538-4357/aab7f2 is OK

MISSING DOIs

- None

INVALID DOIs

- None

@whedon
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whedon commented Oct 3, 2019

PDF failed to compile for issue #1636 with the following error:

sh: 158: Syntax error: newline unexpected
Looks like we failed to compile the Crossref XML

@danielskatz
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@whedon accept

@whedon
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whedon commented Oct 3, 2019 

Attempting dry run of processing paper acceptance...

@whedon
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whedon commented Oct 3, 2019 


OK DOIs

- 10.1088/0067-0049/211/2/19 is OK
- 10.1038/s41586-019-0873-4 is OK
- 10.1093/mnras/stv1509 is OK
- 10.1088/2041-8205/807/1/L12 is OK
- 10.3847/1538-4357/ab0654 is OK
- 10.3847/1538-4357/aa6fb1 is OK
- 10.1093/mnras/stv2641 is OK
- 10.3847/1538-4357/aa88c1 is OK
- 10.1103/PhysRevE.95.033206 is OK
- 10.1103/PhysRevLett.121.021104 is OK
- 10.3847/2041-8213/834/1/L1 is OK
- 10.1126/science.1173540 is OK
- 10.1093/mnras/sty2984 is OK
- 10.3847/1538-4357/aae30b is OK
- 10.1093/mnras/stw3291 is OK
- 10.1093/mnras/stt2121 is OK
- 10.1088/0004-637X/809/1/69 is OK
- 10.3847/1538-4357/aa799f is OK
- 10.1103/PhysRevD.99.063509 is OK
- 10.1051/0004-6361:200809967 is OK
- 10.1093/mnras/sty1289 is OK
- 10.3847/1538-4357/aa7263 is OK
- 10.3847/0004-637X/827/1/28 is OK
- 10.1093/mnras/stw1461 is OK
- 10.3847/1538-4357/aab7f2 is OK

MISSING DOIs

- None

INVALID DOIs

- None

@whedon
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whedon commented Oct 3, 2019

PDF failed to compile for issue #1636 with the following error:

sh: 158: Syntax error: newline unexpected
Looks like we failed to compile the Crossref XML

@danielskatz
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👋 @arfon - can you debug this?

@danielskatz
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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

@arfon arfon added the accepted label Oct 3, 2019
@arfon
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arfon commented Oct 3, 2019

@zingale, @rtfisher - many thanks for your reviews here and to @danielskatz for editing this submission ✨

@bwoshea - your paper is now accepted into JOSS ⚡🚀💥

@arfon arfon closed this as completed Oct 3, 2019
@whedon
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whedon commented Oct 3, 2019

🎉🎉🎉 Congratulations on your paper acceptance! 🎉🎉🎉

If you would like to include a link to your paper from your README use the following code snippets:

Markdown:
[![DOI](https://joss.theoj.org/papers/10.21105/joss.01636/status.svg)](https://doi.org/10.21105/joss.01636)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.01636">
  <img src="https://joss.theoj.org/papers/10.21105/joss.01636/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.01636/status.svg
   :target: https://doi.org/10.21105/joss.01636

This is how it will look in your documentation:

DOI

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:

@danielskatz
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@arfon - can you generate a tweet for this?

@arfon
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arfon commented Oct 3, 2019

Sure thing: https://twitter.com/JOSS_TheOJ/status/1179768071877214208?s=20

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@whedon whedon added published Papers published in JOSS recommend-accept Papers recommended for acceptance in JOSS. labels Mar 2, 2020
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