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[REVIEW]: BayesEoR: Bayesian 21-cm Power Spectrum Estimation from Interferometric Visibilities #6667

Open editorialbot opened 2 months ago

editorialbot commented 2 months ago

Submitting author: !--author-handle-->@jburba<!--end-author-handle-- (Jacob Burba) Repository: https://github.com/PSims/BayesEoR Branch with paper.md (empty if default branch): Version: v1.0.0 Editor: !--editor-->@dfm<!--end-editor-- Reviewers: @musoke, @zonca Archive: Pending

Status

status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/e5972aa5021ae9492a44d55574119747"><img src="https://joss.theoj.org/papers/e5972aa5021ae9492a44d55574119747/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/e5972aa5021ae9492a44d55574119747/status.svg)](https://joss.theoj.org/papers/e5972aa5021ae9492a44d55574119747)

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

@musoke & @zonca, your review will be checklist based. Each of you will have a separate checklist that you should update when carrying out your review. First of all you need to run this command in a separate comment to create the checklist:

@editorialbot generate my checklist

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

✨ Please start on your review when you are able, and be sure to complete your review in the next six weeks, at the very latest ✨

Checklists

📝 Checklist for @musoke

📝 Checklist for @zonca

editorialbot commented 2 months ago

Hello humans, I'm @editorialbot, a robot that can help you with some common editorial tasks.

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

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

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editorialbot commented 2 months ago 
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1093/mnras/stw1768 is OK
- 10.1093/mnras/stz153 is OK
- 10.1093/mnras/stz1888 is OK
- 10.1093/mnras/stad401 is OK
- 10.1093/mnras/staa327 is OK
- 10.1093/mnras/staa414 is OK
- 10.3847/1538-4357/ac1c78 is OK

MISSING DOIs

- None

INVALID DOIs

- None
editorialbot commented 2 months ago

Software report:

github.com/AlDanial/cloc v 1.90  T=0.06 s (628.5 files/s, 162597.6 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          25            916           3160           5451
reStructuredText                 5            126             61            128
TeX                              1              6              0            117
Markdown                         2             41              0            114
YAML                             4              6             24             73
TOML                             1              4              0             35
C                                1             15             23             28
make                             1              4              7              9
-------------------------------------------------------------------------------
SUM:                            40           1118           3275           5955
-------------------------------------------------------------------------------

Commit count by author:

   333  jburba
    25  Jacob Burba
    19  PSims
editorialbot commented 2 months ago

Paper file info:

📄 Wordcount for paper.md is 589

✅ The paper includes a Statement of need section

editorialbot commented 2 months ago

License info:

🔴 Failed to discover a valid open source license

dfm commented 2 months ago

@musoke, @zonca — This is the review thread for the paper. All of our correspondence will happen here from now on. Thanks again for agreeing to participate!

👉 Please read the "Reviewer instructions & questions" in the first comment above, and generate your checklists by commenting @editorialbot generate my checklist on this issue ASAP. As you go over the submission, please check any items that you feel have been satisfied. There are also links to the JOSS reviewer guidelines.

The JOSS review is different from most other journals. Our goal is to work with the authors to help them meet our criteria instead of merely passing judgment on the submission. As such, the reviewers are encouraged to submit issues and pull requests on the software repository. When doing so, please mention openjournals/joss-reviews#6667 so that a link is created to this thread (and I can keep an eye on what is happening). Please also feel free to comment and ask questions on this thread. In my experience, it is better to post comments/questions/suggestions as you come across them instead of waiting until you've reviewed the entire package.

We aim for the review process to be completed within about 4-6 weeks but please try to make a start ahead of this as JOSS reviews are by their nature iterative and any early feedback you may be able to provide to the author will be very helpful in meeting this schedule. Please get your review started as soon as possible!

editorialbot commented 2 months ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

dfm commented 2 months ago

@jburba — I should have caught this before, but it looks like your code is not licensed. You'll need to add an appropriate open source license before we can proceed. https://choosealicense.com can be a useful resource.

jburba commented 2 months ago

Thanks @dfm , we forgot to add that. I've added a license to the repo.

musoke commented 2 months ago

Review checklist for @musoke

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

zonca commented 2 months ago

Review checklist for @zonca

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

https://github.com/PSims/BayesEoR/issues/25

zonca commented 2 months ago

@jburba I opened issues on the repository with some feedback, the only one which is blocking is https://github.com/PSims/BayesEoR/issues/20, if you focus first on this issue, I can continue trying to run the example config. I was able to build the matrix stack, but cannot run sampling.

zonca commented 2 months ago

@jburba @dfm finished my review and opened issues for follow-up on what I found, all linked in the review checklist. Once the issues are addressed (which doesn't necessarily mean we implement what I suggest, we could also agree something is a longer term goal), I think this is good for publication. Thanks!

musoke commented 2 months ago

@jburba, would you like to respond to some of @zonca's requests before I finish my review? As is, I expect that many of my comments will be agreement that installation should be simplified/clarified.

(@dfm, let me know if this would be procedurally problematic 😃)

jburba commented 2 months ago

@musoke yes, I can respond to @zonca's requests first, that's fine. I will note in my current job I only have ~1 day a week for independent research (which this falls under). Apologies in advance if I'm a bit slow to respond at times!

dfm commented 2 months ago

Thanks all!

@musoke — I'd probably recommend that you see how far you can get with your review, as long as @zonca's issues aren't full blockers (it does seem like the installation one might be?). That way @jburba could work on addressing all the comments in parallel. Otherwise this could end up dragging on longer than we want. But you are all welcome to proceed as you feel is best for everyone involved!

zonca commented 2 months ago

Good job @jburba, my review is finished, there are 3 open issues that I think would be good to address, but I do not think they are blocking.

@musoke I think you can get started, you might want to check the 3 issues I left open in the repo to see if you feel those should be addressed before publication or not: https://github.com/PSims/BayesEoR/issues/created_by/zonca

dfm commented 1 month ago

@musoke — Just a ping to make sure this is on your radar. Please revisit ASAP. Thank you!

musoke commented 1 month ago

I have finished my review.

Summary: it's a nice package but there are some outstanding issues to address.

dfm commented 3 weeks ago

@musoke, @zonca — It looks like @jburba has responded to the issues that you opened on the BayesEoR repo. Can you take a look soon and update your checklists / respond to those comments accordingly soon? Thanks!!

zonca commented 3 weeks ago

Thank you. I completed my checklist