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

[editorialbot]

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

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]

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:

@editorialbot commands

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

@editorialbot generate pdf

[editorialbot]

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]

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]

Paper file info:

📄 Wordcount for paper.md is 589

✅ The paper includes a Statement of need section

[editorialbot]

License info:

🔴 Failed to discover a valid open source license

[dfm]

@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]

👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

[dfm]

@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]

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

[musoke]

Review checklist for @musoke

Conflict of interest

• I confirm that I have read the JOSS conflict of interest (COI) policy and that: I have no COIs with reviewing this work or that any perceived COIs have been waived by JOSS for the purpose of this review.

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 https://github.com/PSims/BayesEoR?
• License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
• Contribution and authorship: Has the submitting author (@jburba) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
• Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines
• Data sharing: If the paper contains original data, data are accessible to the reviewers. If the paper contains no original data, please check this item.
• Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
• Human and animal research: If the paper contains original data research on humans subjects or animals, does it comply with JOSS's human participants research policy and/or animal research policy? If the paper contains no such data, please check this item.

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.
  • Names of dependencies are given in environment.yaml. It wouldn't hurt to specify version numbers.
• 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 functionality of the software can be verified?
  • [joss-review] Error when running tests PSims/BayesEoR#31 There are tests that should produce plots like those in the paper but I was unable to run them.
• 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

• Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
• A statement of need: Does the paper have a section titled 'Statement of need' that clearly states what problems the software is designed to solve, who the target audience is, and its relation to other work?
• State of the field: Do the authors describe how this software compares to other commonly-used packages?
  • see [joss-review] Feedback on draft PSims/BayesEoR#30
• Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
  • see [joss-review] Feedback on draft PSims/BayesEoR#30
• References: Is the list of references complete, and is everything cited appropriately that should be cited (e.g., papers, datasets, software)? Do references in the text use the proper citation syntax?
  • see [joss-review] Feedback on draft PSims/BayesEoR#30

[zonca]

Review checklist for @zonca

Conflict of interest

• I confirm that I have read the JOSS conflict of interest (COI) policy and that: I have no COIs with reviewing this work or that any perceived COIs have been waived by JOSS for the purpose of this review.

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 https://github.com/PSims/BayesEoR?
• License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
• Contribution and authorship: Has the submitting author (@jburba) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
• Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines
• Data sharing: If the paper contains original data, data are accessible to the reviewers. If the paper contains no original data, please check this item.
• Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
• Human and animal research: If the paper contains original data research on humans subjects or animals, does it comply with JOSS's human participants research policy and/or animal research policy? If the paper contains no such data, please check this item.

Functionality

• Installation: Does installation proceed as outlined in the documentation? [joss-review] do not install pymultinest to avoid installing mpi4py via conda PSims/BayesEoR#16 [joss-review] Install magma with conda? PSims/BayesEoR#18
• 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? [joss-review] Improve statement of need in docs PSims/BayesEoR#17
• Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution. [joss-review] how to create wrapmzpotrf.so PSims/BayesEoR#20 Makefile for wrapmzpotrf.so PSims/BayesEoR#23 feat: install magma and cuda with conda PSims/BayesEoR#24
• Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems). [joss-review] specify need for array-storage in example run PSims/BayesEoR#19 [joss-review] memory requirement of example run PSims/BayesEoR#22 [joss-review] reduce sampling time for example run PSims/BayesEoR#26
• 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 functionality of the software can be verified? [joss-review] Add testing PSims/BayesEoR#21
• 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

PSims/BayesEoR#25

• Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
• A statement of need: Does the paper have a section titled 'Statement of need' that clearly states what problems the software is designed to solve, who the target audience is, and its relation to other work?
• State of the field: Do the authors describe how this software compares to other commonly-used packages?
• Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
• References: Is the list of references complete, and is everything cited appropriately that should be cited (e.g., papers, datasets, software)? Do references in the text use the proper citation syntax?

[zonca]

@jburba I opened issues on the repository with some feedback, the only one which is blocking is PSims/BayesEoR#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]

@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]

@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]

@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]

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]

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]

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

[musoke]

I have finished my review.

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

• [joss-review] Feedback on draft PSims/BayesEoR#30
• [joss-review] Error when running tests PSims/BayesEoR#31 I don't doubt that the package does what it claims, but this issue prevented me from verifying the functionality.

[dfm]

@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]

Thank you. I completed my checklist