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 🎉.

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Attempting PDF compilation. Reticulating splines etc...

👉 Check article proof 📄 👈

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.)

@whedon generate pdf

Attempting PDF compilation. Reticulating splines etc...

👉 Check article proof 📄 👈

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

👋 @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.

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.

@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)

@whedon generate pdf

Attempting PDF compilation. Reticulating splines etc...

👉 Check article proof 📄 👈

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 Should these be changed to an archived version of the code with a DOI?

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.

@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.

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

👋 @bwoshea - note that we're waiting for you to respond to a bunch of open issues - listed above...

Just to clarify, I am still in the process of completing my review. @bwoshea indicates that the ENZO team is awaiting this completion prior to starting their responses.

That's ok, but JOSS reviews typically are more interactive. Maybe with a complex team like this, it makes sense to wait.

@danielskatz Sorry about that. Given the vigor of @zingale 's review and the distributed nature of the Enzo team, we would prefer to wait until the reviews are completed (or at least the first wave of feedback) until we proceed. If you insist on doing it otherwise I'm sure we can make that happen, though.

It’s fine to wait, as I said previously

Ok, I've completed my initial review. It looks like I also identified some of the same issues as @zingale, though our final assessments of the JOSS requirements differ slightly.

Thanks @rtfisher! Now over to @bwoshea and the Enzo team...

@danielskatz We're on it! @rtfisher and @zingale , thank you for all of your feedback!

@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!

@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.

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.

@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.

@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!

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

I am fine with accepting after merger as well.

@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?

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.

The next steps will be

1. 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.
2. 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.