[REVIEW]: GaussianRandomFields.jl: A Julia package to generate and sample from Gaussian random fields

[editorialbot]

Submitting author: @PieterjanRobbe (Pieterjan Robbe)
Repository: https://github.com/PieterjanRobbe/GaussianRandomFields.jl
Branch with paper.md (empty if default branch): joss
Version: v2.2.4
Editor: @jbytecode
Reviewers: @ziyiyin97, @shahmoradi
Archive: 10.5281/zenodo.8306255

Status

Status badge code:

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Markdown: [![status](https://joss.theoj.org/papers/cbc743d5c3f81a96d846b5b4a3c865b1/status.svg)](https://joss.theoj.org/papers/cbc743d5c3f81a96d846b5b4a3c865b1)

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

@ziyiyin97 & @shahmoradi, 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 @jbytecode 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 @ziyiyin97

📝 Checklist for @shahmoradi

[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:

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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]

Software report:

github.com/AlDanial/cloc v 1.88  T=0.05 s (1093.9 files/s, 202869.7 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Julia                           34            635            270           7218
Markdown                         6            200              0            532
YAML                             7              2             10            221
TeX                              1             14              0            132
TOML                             2              5              0             34
-------------------------------------------------------------------------------
SUM:                            50            856            280           8137
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

[editorialbot]

Wordcount for paper.md is 469

[editorialbot]

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

OK DOIs

- 10.1137/141000671 is OK
- 10.3390/a13050110 is OK
- 10.1046/j.1365-8711.2000.03086.x is OK
- 10.1145/3240765.3240860 is OK
- 10.5194/gmd-15-3161-2022 is OK
- 10.1016/j.jhydrol.2015.07.036 is OK
- 10.5334/jors.431 is OK
- 10.1002/nla.2281 is OK
- 10.1155/asp/2006/31062 is OK
- 10.1038/s41598-022-26898-1 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[editorialbot]

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

[jbytecode]

@ziyiyin97, @shahmoradi

This is the review thread. Firstly, type

@editorialbot generate my checklist

to generate your own checklist. In that checklist, there are many check items. Whenever you complete the corresponding task, you can check off them.

Please write your comments as separate posts and do not modify your checklist descriptions.

The review process is interactive so you can always interact with the authors, reviewers, and the editor. You can also create issues and pull requests in the target repository. Please do mention this thread's URL in the issues so we can keep tracking what is going on out of our world.

Please do not hesitate to ask me about anything, anytime.

Thank you in advance!

[ziyiyin97]

Review checklist for @ziyiyin97

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/PieterjanRobbe/GaussianRandomFields.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 (@PieterjanRobbe) 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?

[jbytecode]

@shahmoradi - Could you please generate your checklist before starting your review? Thank you in advance.

[shahmoradi]

Review checklist for @shahmoradi

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/PieterjanRobbe/GaussianRandomFields.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 (@PieterjanRobbe) 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?

[jbytecode]

Dear @ziyiyin97, @shahmoradi

Could you please update your status and inform us on how is your review going?

Thank you in advance!

[ziyiyin97]

Hi, sorry for the delay. I should be able to finish my reviews in a week if that works.

[jbytecode]

@ziyiyin97 - thank you for the status update

[ziyiyin97]

I just posted my reviews via an issue to the repository shown above.

[jbytecode]

@ziyiyin97 - thank you for opening the issues and minor suggestions.

@PieterjanRobbe - could you please perform the changes indicated in the issue?

[PieterjanRobbe]

Hi @ziyiyin97, thank you so much for your time reviewing the software and paper! I've addressed your comments with this commit.

[ziyiyin97]

LGTM!

[jbytecode]

@ziyiyin97 - Thank you, could you please take a look at your task list and complete filling boxes if they are okay.

@shahmoradi - Do we have a chance to get a status update? Could you please update your status and review? Thank you in advance

[shahmoradi]

I apologize for the late response. I have been dealing with multiple deadlines and trips over the past month. I am still on a trip, but I will try to complete this review within the next few days.

[jbytecode]

@shahmoradi - thank you for the response. We are looking forward to hear from you.

[shahmoradi]

Thank you for your work @PieterjanRobbe . I have reviewed this paper, and most look fine and justified.
Two minor issues:

1. Some of the code snippets in the tutorial are not functioning. They may have been meant to be templates for users to fill in with their parameter values, but if not, minor fixes may be required.
2. The performance benefit mentioned in the paper may need more elaboration. Obviously, the overall runtime of the package, including compilation time, makes it slower than Python/R equivalents for typical tasks. But I understand what you meant here was the runtime performance for larger, more demanding tasks (excluding compilation time and, even then, any performance benefits, if claimed, should be evidence-based). So either the text needs clarifications or benchmarks would be needed.
3. Instructions for running the tests would also be helpful.
   Except Performance, I have marked all other checklist items as complete.

[jbytecode]

@shahmoradi - thank you for your valuable review and suggestions.

@PieterjanRobbe - could you please apply the suggestions? thank you in advance.

[PieterjanRobbe]

Hi @shahmoradi, thank you so much for your time and effort! Here's an answer to your questions:

1. If you're referring to the code snippet under Package Overview, then yes, this is intentional. The goal of these lines is to illustrate the general workflow of the package, where Kernel() and Generator() are supposed to be replaced by a call to the appropriate methods, as mentioned below the code block. I've tested all other code blocks in the tutorial, and they seem to work fine for me.
2. Perhaps this was not clearly stated in the manuscript. The performance benefits mentioned in the paper refer to the performance increase of Julia over R/Python (see [1]): "As such, [the package] benefits from the performance advantage of Julia, [and ...]". I've added a reference for this performance claim, but I could also rephrase/remove that sentence if needed.
3. I've added instructions for testing to the README.

Thanks again!

[PieterjanRobbe]

@editorialbot generate pdf

[editorialbot]

Done! archive is now 10.5281/zenodo.8306255

[jbytecode]

@PieterjanRobbe - I will check references and generate pdf one more time. Please check the generated pdf and correct any typo if exists. We will not need to register a new version if we get a new change.

[jbytecode]

@editorialbot check references

[editorialbot]

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

OK DOIs

- 10.1137/141000671 is OK
- 10.3390/a13050110 is OK
- 10.1046/j.1365-8711.2000.03086.x is OK
- 10.1016/s0098-3004(00)00063-7 is OK
- 10.1145/3240765.3240860 is OK
- 10.5194/gmd-15-3161-2022 is OK
- 10.1016/j.jhydrol.2015.07.036 is OK
- 10.5334/jors.431 is OK
- 10.1002/nla.2281 is OK
- 10.1155/asp/2006/31062 is OK
- 10.1038/s41598-022-26898-1 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[jbytecode]

@editorialbot generate pdf

[editorialbot]

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

[PieterjanRobbe]

I double checked the pdf/references and all looks good to me 👍

[jbytecode]

@ziyiyin97, @shahmoradi - Many thanks for your efforts on reviewing this software and manuscript.

@PieterjanRobbe - Thank you for submitting your work to JOSS. Everyting looks good to me.

I am now recommending an acceptance. Our Editor-in-chief will make the final decision.

[jbytecode]

@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

- 10.1137/141000671 is OK
- 10.3390/a13050110 is OK
- 10.1046/j.1365-8711.2000.03086.x is OK
- 10.1016/s0098-3004(00)00063-7 is OK
- 10.1145/3240765.3240860 is OK
- 10.5194/gmd-15-3161-2022 is OK
- 10.1016/j.jhydrol.2015.07.036 is OK
- 10.5334/jors.431 is OK
- 10.1002/nla.2281 is OK
- 10.1155/asp/2006/31062 is OK
- 10.1038/s41598-022-26898-1 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[editorialbot]

👋 @openjournals/dsais-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#4522, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

[PieterjanRobbe]

Thanks a lot @ziyiyin97 and @shahmoradi for reviewing this submission, and thanks @jbytecode for serving as editor! 🥳

[gkthiruvathukal]

@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: Robbe
  given-names: Pieterjan
  orcid: "https://orcid.org/0000-0002-6254-8245"
doi: 10.5281/zenodo.8306255
message: If you use this software, please cite our article in the
  Journal of Open Source Software.
preferred-citation:
  authors:
  - family-names: Robbe
    given-names: Pieterjan
    orcid: "https://orcid.org/0000-0002-6254-8245"
  date-published: 2023-09-02
  doi: 10.21105/joss.05595
  issn: 2475-9066
  issue: 89
  journal: Journal of Open Source Software
  publisher:
    name: Open Journals
  start: 5595
  title: "GaussianRandomFields.jl: A Julia package to generate and
    sample from Gaussian random fields"
  type: article
  url: "https://joss.theoj.org/papers/10.21105/joss.05595"
  volume: 8
title: "GaussianRandomFields.jl: A Julia package to generate and sample
  from Gaussian random 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.05595 joss-papers#4525
1. Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.05595
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...

[editorialbot]

🎉🎉🎉 Congratulations on your paper acceptance! 🎉🎉🎉

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HTML:
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</a>

reStructuredText:
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