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

whedon · 2019-08-09T16:14:25Z

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:

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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:

Make sure you're logged in to your GitHub account
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

As the reviewer I confirm that I have read the JOSS conflict of interest policy and that there are no conflicts of interest for me to review this work.

Code of Conduct

I confirm that I read and will adhere to the JOSS 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

As the reviewer I confirm that I have read the JOSS conflict of interest policy and that there are no conflicts of interest for me to review this work.

Code of Conduct

I confirm that I read and will adhere to the JOSS 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 · 2019-08-09T16:14:28Z

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:

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

You may also like to change your default settings for this watching repositories in your GitHub profile here: https://github.com/settings/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 · 2019-08-09T16:14:29Z

Attempting PDF compilation. Reticulating splines etc...

whedon · 2019-08-09T16:14:50Z

👉 Check article proof 📄 👈

danielskatz · 2019-08-09T16:16:48Z

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 · 2019-08-09T16:16:55Z

@whedon generate pdf

whedon · 2019-08-09T16:16:58Z

Attempting PDF compilation. Reticulating splines etc...

whedon · 2019-08-09T16:17:38Z

👉 Check article proof 📄 👈

danielskatz · 2019-08-09T16:20:12Z

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

danielskatz · 2019-08-09T16:23:07Z

👋 @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 · 2019-08-10T14:28:29Z

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 · 2019-08-11T14:14:37Z

@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 · 2019-08-11T14:14:44Z

@whedon generate pdf

whedon · 2019-08-11T14:14:46Z

Attempting PDF compilation. Reticulating splines etc...

whedon · 2019-08-11T14:15:32Z

👉 Check article proof 📄 👈

zingale · 2019-08-11T17:26:23Z

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 · 2019-08-14T15:21:59Z

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 · 2019-08-15T20:40:22Z

@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 · 2019-08-16T00:14:42Z

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

bwoshea · 2019-09-12T10:01:21Z

@danielskatz @rtfisher @zingale The Enzo developers have been working on the issues you raised (at https://github.com/enzo-project/enzo-dev/issues), and we currently have a bunch of open pull requests to address them (at https://github.com/enzo-project/enzo-dev/pulls). Some of the issues have comments on them that directly address reviewer comments without a PR (e.g., enzo-project/enzo-dev#108), but mostly the changes in the PRs themselves should address your comments.

Please let us know how you'd like to proceed at this point!

danielskatz · 2019-09-12T12:44:56Z

@bwoshea - it's up to you, with the goal of getting the reviewers to agree that the submission meets the criteria. You could make all the changes, then ask the reviewers to check them, or ask reviewers for specific opinions on possible changes first.

zingale · 2019-09-12T14:10:02Z

I would suggest that you refer to the PRs in the issues we raised and when we are satisfied, we will close the issues that we opened for the review, and that will be reflected here automatically.

bwoshea · 2019-09-12T14:34:17Z

@danielskatz -- duly noted, thank you! We'll engage the reviewers on the open PRs rather than waiting. That way we'll be able to respond more quickly.

@zingale -- Great suggestion, thanks. I've done that now! We have a couple of outstanding issues that still need developer attention, but the bulk have been addressed.

bwoshea · 2019-09-13T20:48:21Z

@zingale @rtfisher just to give you a heads-up, we've addressed all of the issues you have raised but one, and that should be done in the next day or so. We've left all off the PRs open so that you can see what has been changed, and all PRs and issues are cross-referenced. We're ready for your feedback whenever you are available.

Edit: we now (as of 2019-09-15) have PRs that address all issues raised!

zingale · 2019-09-16T19:30:47Z

It looks like all of my issues have been addressed via PRs. Once those PRs are merged, I am happy with accepting.

rtfisher · 2019-09-16T23:00:12Z

I am fine with accepting after merger as well.

bwoshea · 2019-09-16T23:03:03Z

@zingale @rtfisher thanks!

@rtfisher to clarify, there are two open issues that you raised (enzo-project/enzo-dev#108 and enzo-project/enzo-dev#109 ) - would you mind making a quick note saying you're OK with what we've done for those?

rtfisher · 2019-09-17T22:34:55Z

Thank you, @bwoshea. Sorry for the delayed response -- I was serving on a panel today.

I concur that the issues are now resolved, and have closed both.

danielskatz · 2019-09-18T06:06:02Z

The next steps will be

The authors (@bwoshea) to make any remaining changes (sorry, I can't easily tell if there's more to do or if you've already done this because the PRs didn't reference this review thread) and saying that they are done here.
The reviewers (@zingale and @rtfisher) to confirm that they are satisfied by checking off the remaining items in their review checklists above and by saying so in this thread.

bwoshea · 2019-09-19T10:38:10Z

@danielskatz we have made the remaining changes!

danielskatz · 2019-09-19T10:41:52Z

👋 @zingale and @rtfisher: please confirm that you are satisfied by checking off the remaining items in your review checklists above and by saying so in this thread. If not, please say what you think any current issues are.

zingale · 2019-09-19T12:08:48Z

I'm happy to accept. I've check all my boxes. Nice job @bwoshea and the Enzo team.

rtfisher · 2019-09-19T13:41:32Z

I accept as well, and second Michael's congratulations to @bwoshea and all of the many Enzo developers!

danielskatz · 2019-09-19T14:11:12Z

Great - thanks @zingale and @rtfisher!

danielskatz · 2019-09-19T14:12:19Z

👋 @bwoshea - to finish up now, I need you to

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

danielskatz · 2019-09-19T14:12:24Z

@whedon generate pdf

whedon · 2019-09-19T14:12:26Z

Attempting PDF compilation. Reticulating splines etc...

whedon · 2019-09-19T14:13:12Z

👉 Check article proof 📄 👈

danielskatz · 2019-09-19T14:28:21Z

@whedon check references

whedon · 2019-09-19T14:28:23Z

Attempting to check references...

whedon · 2019-09-19T14:28:41Z


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

danielskatz · 2019-09-22T21:04:37Z

👋 @bwoshea - to finish up now, I need you to

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

danielskatz · 2019-09-29T13:42:37Z

👋 @bwoshea - to finish up now, I need you to

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

bwoshea · 2019-10-02T13:54:23Z

@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.

arfon · 2019-10-02T13:57:58Z

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 · 2019-10-02T13:58:19Z

@whedon set 10.5281/zenodo.3469922 as archive

whedon · 2019-10-02T13:58:23Z

OK. 10.5281/zenodo.3469922 is the archive.

danielskatz · 2019-10-02T13:58:34Z

@whedon set v2.6.1 as version

whedon · 2019-10-02T13:58:38Z

OK. v2.6.1 is the version.

whedon assigned danielskatz Aug 9, 2019

whedon added the review label Aug 9, 2019

whedon referenced this issue Aug 9, 2019

[PRE REVIEW]: ENZO: An Adaptive Mesh Refinement Code for Astrophysics (Version 2.6) #1624

Closed

whedon assigned rtfisher and zingale Aug 10, 2019

openjournals/joss-reviews

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

Comments

whedon commented Aug 9, 2019 • edited

Status

Reviewer instructions & questions

Review checklist for @zingale

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

Review checklist for @rtfisher

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

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