[REVIEW]: UltraDark.jl: A Julia package for simulation of cosmological scalar fields

[editorialbot]

Submitting author: @musoke (Nathan Musoke)
Repository: https://github.com/musoke/UltraDark.jl
Branch with paper.md (empty if default branch): joss
Version: v0.9.7
Editor: @xuanxu
Reviewers: @szabo137, @kiranshila
Archive: 10.5281/zenodo.10978864

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/7d8edc313bc8b81908b23c94d2f6adf5"><img src="https://joss.theoj.org/papers/7d8edc313bc8b81908b23c94d2f6adf5/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/7d8edc313bc8b81908b23c94d2f6adf5/status.svg)](https://joss.theoj.org/papers/7d8edc313bc8b81908b23c94d2f6adf5)

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

@szabo137 & @kiranshila, 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 @xuanxu 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 @kiranshila

📝 Checklist for @szabo137

[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]

Software report:

github.com/AlDanial/cloc v 1.88  T=0.05 s (1171.6 files/s, 132615.4 lines/s)
--------------------------------------------------------------------------------
Language                      files          blank        comment           code
--------------------------------------------------------------------------------
Julia                            29            794             70           2738
TOML                              7            136              1            625
TeX                               1             34              0            405
Jupyter Notebook                  2              0            912            220
YAML                              8              3             10            206
Markdown                          7             56              0            160
Bourne Again Shell                3             23             17             61
Bourne Shell                      1             13             27             54
--------------------------------------------------------------------------------
SUM:                             58           1059           1037           4469
--------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

[editorialbot]

Wordcount for paper.md is 902

[editorialbot]

Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1088/1475-7516/2018/10/027 is OK
- 10.1103/physrevd.105.123540 is OK
- 10.1103/physrevd.107.063520 is OK
- 10.48550/ARXIV.2301.13220 is OK
- 10.1137/141000671 is OK
- 10.1109/JPROC.2004.840301 is OK
- 10.21105/joss.03349 is OK
- 10.1007/s10670-020-00260-1 is OK
- 10.1007/s11229-008-9434-3 is OK
- 10.1086/716542 is OK
- 10.1086/715031 is OK
- 10.5281/zenodo.7675830 is OK
- 10.5281/zenodo.7675775 is OK
- 10.1103/PhysRevLett.124.061301 is OK
- 10.5281/zenodo.5148035 is OK
- 10.5281/zenodo.3618781 is OK
- 10.1103/PhysRevD.102.083518 is OK
- 10.48550/ARXIV.2109.09973 is OK
- 10.1103/PhysRevD.23.347 is OK
- 10.1016/0370-2693(82)91219-9 is OK
- 10.1103/PhysRevLett.48.1220 is OK
- 10.1103/PhysRevLett.108.241302 is OK
- 10.1051/0004-6361/201525830 is OK
- 10.1103/PhysRevLett.85.1158 is OK
- 10.1103/PhysRevD.81.123530 is OK
- 10.48550/ARXIV.2203.14923 is OK
- 10.1088/1475-7516/2023/04/053 is OK
- 10.1088/0264-9381/17/7/309 is OK
- 10.3389/fspas.2018.00048 is OK
- 10.1051/0004-6361/201936272 is OK

MISSING DOIs

- 10.1109/ipdpsw50202.2020.00120 may be a valid DOI for title: Simulating ultralight dark matter in Chapel

INVALID DOIs

- None

[editorialbot]

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

[musoke]

@editorialbot commands

[editorialbot]

Hello @musoke, here are the things you can ask me to do:

# List all available commands
@editorialbot commands

# Get a list of all editors's GitHub handles
@editorialbot list editors

# Check the references of the paper for missing DOIs
@editorialbot check references

# Perform checks on the repository
@editorialbot check repository

# Adds a checklist for the reviewer using this command
@editorialbot generate my checklist

# Set a value for branch
@editorialbot set joss-paper as branch

# Generates the pdf paper
@editorialbot generate pdf

# Generates a LaTeX preprint file
@editorialbot generate preprint

# Get a link to the complete list of reviewers
@editorialbot list reviewers

[musoke]

@editorialbot check references

[editorialbot]

Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1088/1475-7516/2018/10/027 is OK
- 10.1103/physrevd.105.123540 is OK
- 10.1103/physrevd.107.063520 is OK
- 10.48550/ARXIV.2301.13220 is OK
- 10.1137/141000671 is OK
- 10.1109/JPROC.2004.840301 is OK
- 10.21105/joss.03349 is OK
- 10.1007/s10670-020-00260-1 is OK
- 10.1007/s11229-008-9434-3 is OK
- 10.1086/716542 is OK
- 10.1086/715031 is OK
- 10.5281/zenodo.7675830 is OK
- 10.5281/zenodo.7675775 is OK
- 10.1103/PhysRevLett.124.061301 is OK
- 10.1109/ipdpsw50202.2020.00120 is OK
- 10.5281/zenodo.5148035 is OK
- 10.5281/zenodo.3618781 is OK
- 10.1103/PhysRevD.102.083518 is OK
- 10.48550/ARXIV.2109.09973 is OK
- 10.1103/PhysRevD.23.347 is OK
- 10.1016/0370-2693(82)91219-9 is OK
- 10.1103/PhysRevLett.48.1220 is OK
- 10.1103/PhysRevLett.108.241302 is OK
- 10.1051/0004-6361/201525830 is OK
- 10.1103/PhysRevLett.85.1158 is OK
- 10.1103/PhysRevD.81.123530 is OK
- 10.48550/ARXIV.2203.14923 is OK
- 10.1088/1475-7516/2023/04/053 is OK
- 10.1088/0264-9381/17/7/309 is OK
- 10.3389/fspas.2018.00048 is OK
- 10.1051/0004-6361/201936272 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[musoke]

I just pushed a small update to add the missing DOI flagged by the bot.

[musoke]

@editorialbot generate pdf

[editorialbot]

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

[xuanxu]

@szabo137, @kiranshila – This is the review thread for the paper. All of our communications will happen here from now on.

Please read the "Reviewer instructions & questions" in the first comment above. Please create your checklist typing:

@editorialbot generate my checklist

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 https://github.com/openjournals/joss-reviews/issues/6035 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 make a start well 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.

[kiranshila]

Review checklist for @kiranshila

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/musoke/UltraDark.jl?
• License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
• Contribution and authorship: Has the submitting author (@musoke) 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.
• 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?
• 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?
• 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?

[szabo137]

Review checklist for @szabo137

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/musoke/UltraDark.jl?
• License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
• Contribution and authorship: Has the submitting author (@musoke) 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.
• 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?
• 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?
• 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?

[kiranshila]

Review

Great work @musoke, nice to see more Julia work in astronomy! The fact that you have published science results using your package is really awesome!

I have just a few comments,

Critical

1. Please add something like a CONTRIBUTING file to the repository to satisfy the "Community Guidelines" documentation requirement.

General Comments / Feedback

1. I think the API docs are a little on the light side, most of the "how do I use this package" stuff seems to be contained in the notebooks. Maybe another page or so on general use would be nice. Still seems like more than PyUltraLight though :) I'm not in this domain, so it's hard for me to say if some of the use is obvious, but I thought I'd mention it anyway.
2. It might be nice to have a result figure or so for eye candy

[musoke]

Thank you for the review @kiranshila! I'll wait for the other review before addressing them so I don't confuse things.

[xuanxu]

@szabo137 please update us on the current status of your review

[szabo137]

@xuanxu Sorry for the late reply, I plan to submit the review till Sunday. I apologize for any inconvenience.

[szabo137]

Review

First of all, very nice work @musoke, I also love to see more of Julia in astronomy!

Regarding the package, I also want to add some comments:

Critical

• IMHO the package's documentation deserves a bit more content to highlight its functionality and context. Maybe you could consider adding a bit more explanation on what your package does, and maybe a little quickstart section would help to get in touch with the code
• I also suggest adding some guide (either as a file or in the docs, or both) on how to interact with the repository, if one wants to contribute, i.e. following the community guideline requirements.

General feedback

I like the simplistic API design and tight interconnection of this package with the scientific use case. Especially, the addition of the example folder helps a lot to understand the package and the science behind it.

[musoke]

Thank you @szabo137! I will address these over the next couple weeks.

[musoke]

@xuanxu, one question: should I merge the JOSS branch into the main branch before or after I make the release that gets archived?

[xuanxu]

You can merge the JOSS branch into main before making the release, that way the new release based in main will include all the changes made during the review.

[musoke]

@xuanxu, I have completed my checklist. The details to report here are bolded:

• Double check authors and affiliations (including ORCIDs)
• Make a release of the software with the latest changes from the review and post the version number here. This is the version that will be used in the JOSS paper.
  I have released v0.9.7
  • Julia General registry release: JuliaRegistries/General@1701c16, https://juliahub.com/ui/Packages/General/UltraDark/0.9.7
  • GitHub release: https://github.com/musoke/UltraDark.jl/releases/tag/v0.9.7
• Archive the release on Zenodo/figshare/etc and post the DOI here.
  I have archived the release on Zenodo with doi https://doi.org/10.5281/zenodo.10978864
• Make sure that the title and author list (including ORCIDs) in the archive match those in the JOSS paper.
• Make sure that the license listed for the archive is the same as the software license.

@editorialbot reported a missing DOI for Folds.jl. The authors didn't provide a DOI or preferred citation in the original repo. I have inquired again in what seems to be the current repo. This probably isn't a blocker (?).

The branch joss is currently identical to tag v0.9.7, the version archived at zenodo. I will keep that branch around until this is done.

[xuanxu]

Thanks @musoke

[xuanxu]

@editorialbot set v0.9.7 as version

[editorialbot]

Done! version is now v0.9.7

[xuanxu]

@editorialbot set 10.5281/zenodo.10978864 as archive

[editorialbot]

Done! archive is now 10.5281/zenodo.10978864

[xuanxu]

Looking good!

[xuanxu]

@editorialbot recommend-accept

[editorialbot]

Attempting dry run of processing paper acceptance...

[editorialbot]

Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1088/1475-7516/2018/10/027 is OK
- 10.1103/PhysRevD.109.063501 is OK
- 10.1103/physrevd.105.123540 is OK
- 10.1103/physrevd.107.063520 is OK
- 10.1088/1475-7516/2023/07/004 is OK
- 10.1137/141000671 is OK
- 10.1109/JPROC.2004.840301 is OK
- 10.21105/joss.03349 is OK
- 10.1007/s10670-020-00260-1 is OK
- 10.1007/s11229-008-9434-3 is OK
- 10.1086/716542 is OK
- 10.1086/715031 is OK
- 10.1007/s41781-023-00104-x is OK
- 10.5281/zenodo.7675830 is OK
- 10.5281/zenodo.7675775 is OK
- 10.5281/zenodo.7927474 is OK
- 10.1103/PhysRevLett.124.061301 is OK
- 10.1109/ipdpsw50202.2020.00120 is OK
- 10.5281/zenodo.5148035 is OK
- 10.5281/zenodo.3618781 is OK
- 10.1103/PhysRevD.102.083518 is OK
- 10.48550/ARXIV.2109.09973 is OK
- 10.1103/PhysRevD.23.347 is OK
- 10.1016/0370-2693(82)91219-9 is OK
- 10.1103/PhysRevLett.48.1220 is OK
- 10.1103/PhysRevLett.108.241302 is OK
- 10.1051/0004-6361/201525830 is OK
- 10.1103/PhysRevLett.85.1158 is OK
- 10.1103/PhysRevD.81.123530 is OK
- 10.48550/ARXIV.2203.14923 is OK
- 10.1088/1475-7516/2023/04/053 is OK
- 10.1103/physreve.108.055305 is OK
- 10.1088/0264-9381/17/7/309 is OK
- 10.3389/fspas.2018.00048 is OK
- 10.1051/0004-6361/201936272 is OK

MISSING DOIs

- No DOI given, and none found for title: Folds: sequential, threaded, and distributed fold ...

INVALID DOIs

- None

[editorialbot]

👋 @openjournals/aass-eics, this paper is ready to be accepted and published.

Check final proof 👉📄 Download article

If the paper PDF and the deposit XML files look good in openjournals/joss-papers#5245, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

[musoke]

The proof looks good to me!

[dfm]

@editorialbot accept

[editorialbot]

Doing it live! Attempting automated processing of paper acceptance...

[editorialbot]

Ensure proper citation by uploading a plain text CITATION.cff file to the default branch of your repository.

If using GitHub, a Cite this repository menu will appear in the About section, containing both APA and BibTeX formats. When exported to Zotero using a browser plugin, Zotero will automatically create an entry using the information contained in the .cff file.

You can copy the contents for your CITATION.cff file here:

CITATION.cff

cff-version: "1.2.0"
authors:
- family-names: Musoke
  given-names: Nathan
  orcid: "https://orcid.org/0000-0001-9839-9256"
doi: 10.5281/zenodo.10978864
message: If you use this software, please cite our article in the
  Journal of Open Source Software.
preferred-citation:
  authors:
  - family-names: Musoke
    given-names: Nathan
    orcid: "https://orcid.org/0000-0001-9839-9256"
  date-published: 2024-04-17
  doi: 10.21105/joss.06035
  issn: 2475-9066
  issue: 96
  journal: Journal of Open Source Software
  publisher:
    name: Open Journals
  start: 6035
  title: "UltraDark.jl: A Julia package for simulation of cosmological
    scalar fields"
  type: article
  url: "https://joss.theoj.org/papers/10.21105/joss.06035"
  volume: 9
title: "UltraDark.jl: A Julia package for simulation of cosmological
  scalar fields"

If the repository is not hosted on GitHub, a .cff file can still be uploaded to set your preferred citation. Users will be able to manually copy and paste the citation.

Find more information on .cff files here and here.

[editorialbot]

🐘🐘🐘 👉 Toot for this paper 👈 🐘🐘🐘

[editorialbot]

🚨🚨🚨 THIS IS NOT A DRILL, YOU HAVE JUST ACCEPTED A PAPER INTO JOSS! 🚨🚨🚨

Here's what you must now do:

0. Check final PDF and Crossref metadata that was deposited 👉 Creating pull request for 10.21105.joss.06035 joss-papers#5247
1. Wait five minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.06035
2. If everything looks good, then close this review issue.
3. Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

[dfm]

Many thanks to @szabo137 and @kiranshila for reviewing and to @xuanxu for editing! JOSS relies upon the volunteer effort of people like you and we simply wouldn't be able to do this without you!!

@musoke — Your paper is now accepted and published in JOSS! ⚡🚀💥

[editorialbot]

🎉🎉🎉 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.06035/status.svg)](https://doi.org/10.21105/joss.06035)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.06035">
  <img src="https://joss.theoj.org/papers/10.21105/joss.06035/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.06035/status.svg
   :target: https://doi.org/10.21105/joss.06035

This is how it will look in your documentation:

We need your help!

The 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:

• Volunteering to review for us sometime in the future. You can add your name to the reviewer list here: https://reviewers.joss.theoj.org/join
• Making a small donation to support our running costs here: https://numfocus.org/donate-to-joss

[musoke]

Thank you to @szabo13, @kiranshila and @xuanxu for your helpful feedback and patience!

[musoke]

@editorialbot generate preprint

[editorialbot]

📄 Preprint file created: Find it here in the Artifacts list 📄