editorialbot commented 1 year ago

Submitting author: !--author-handle-->@PieterjanRobbe@jbytecode<!--end-editor-- Reviewers: @ziyiyin97, @shahmoradi Archive: 10.5281/zenodo.8306255

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/cbc743d5c3f81a96d846b5b4a3c865b1"><img src="https://joss.theoj.org/papers/cbc743d5c3f81a96d846b5b4a3c865b1/status.svg"></a>
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 commented 1 year 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:

@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 commented 1 year ago

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 commented 1 year ago

Wordcount for paper.md is 469

editorialbot commented 1 year ago

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 commented 1 year ago

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

jbytecode commented 1 year ago

@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 commented 1 year ago

Review checklist for @ziyiyin97

Conflict of interest

[x] 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

[x] I confirm that I read and will adhere to the JOSS code of conduct.

General checks

[x] Repository: Is the source code for this software available at the https://github.com/PieterjanRobbe/GaussianRandomFields.jl?
[x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
[x] 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?
[x] Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines
[x] 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.
[x] Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
[x] 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

[x] Installation: Does installation proceed as outlined in the documentation?
[x] Functionality: Have the functional claims of the software been confirmed?
[x] 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

[x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
[x] Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
[x] Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
[x] Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
[x] Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
[x] 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

[x] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
[x] 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?
[x] State of the field: Do the authors describe how this software compares to other commonly-used packages?
[x] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
[x] 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 commented 1 year ago

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

shahmoradi commented 1 year ago

Review checklist for @shahmoradi

Conflict of interest

[x] 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

[x] I confirm that I read and will adhere to the JOSS code of conduct.

General checks

[x] Repository: Is the source code for this software available at the https://github.com/PieterjanRobbe/GaussianRandomFields.jl?
[x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
[x] 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?
[x] Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines
[x] 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.
[x] Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
[x] 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

[x] Installation: Does installation proceed as outlined in the documentation?
[x] Functionality: Have the functional claims of the software been confirmed?
[x] 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

[x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
[x] Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
[x] Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
[x] Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
[x] Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
[x] 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

[x] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
[x] 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?
[x] State of the field: Do the authors describe how this software compares to other commonly-used packages?
[x] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
[x] 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 commented 12 months ago

Dear @ziyiyin97, @shahmoradi

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

Thank you in advance!

ziyiyin97 commented 11 months ago

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

jbytecode commented 11 months ago

@ziyiyin97 - thank you for the status update

ziyiyin97 commented 11 months ago

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

jbytecode commented 11 months ago

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

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

PieterjanRobbe commented 11 months ago

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

ziyiyin97 commented 11 months ago

LGTM!

jbytecode commented 11 months ago

@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 commented 11 months ago

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 commented 11 months ago

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

shahmoradi commented 11 months ago

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

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.
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.
Instructions for running the tests would also be helpful. Except Performance, I have marked all other checklist items as complete.

jbytecode commented 11 months ago

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

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

PieterjanRobbe commented 11 months ago

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

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.
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.
I've added instructions for testing to the README.

Thanks again!

PieterjanRobbe commented 11 months ago

@editorialbot generate pdf

editorialbot commented 11 months ago

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

jbytecode commented 10 months ago

@shahmoradi - could you please review the latest changes? thank you in advance!

shahmoradi commented 10 months ago

I will try to finalize this review tonight. Thanks for your patience.

On Mon, Aug 14, 2023 at 3:20 PM Mehmet Hakan Satman < @.***> wrote:

@shahmoradi https://github.com/shahmoradi - could you please review the latest changes? thank you in advance!

— Reply to this email directly, view it on GitHub https://github.com/openjournals/joss-reviews/issues/5595#issuecomment-1678001942, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABDXNCNWLLCXL2ZK6O2TN3LXVKB7HANCNFSM6AAAAAAZVJWIYM . You are receiving this because you were mentioned.Message ID: @.***>

PieterjanRobbe commented 10 months ago

Hi @shahmoradi, thanks again for your comments! Please let me know if there's anything I can do to help finalize your review.

jbytecode commented 10 months ago

Dear @shahmoradi

It seems there is a single unchecked item in your task list. Please review it and tell us your latest decisions.

Thank you in advance.

shahmoradi commented 10 months ago

Thanks, Mehmet, for your reminder. I am traveling at the moment. Please allow me to respond by Thursday. Thanks for your patience, Amir

On Tue, Aug 29, 2023 at 11:32 AM Mehmet Hakan Satman < @.***> wrote:

Dear @shahmoradi https://github.com/shahmoradi

It seems there is a single unchecked item in your task list. Please review it and tell us your latest decisions.

Thank you in advance.

— Reply to this email directly, view it on GitHub https://github.com/openjournals/joss-reviews/issues/5595#issuecomment-1697786368, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABDXNCIURXTSZMSXUTEEFL3XXYKRBANCNFSM6AAAAAAZVJWIYM . You are receiving this because you were mentioned.Message ID: @.***>

jbytecode commented 10 months ago

@shahmoradi - Thank you for the response, sorry for bothering and being verbose in your vacation season. We are looking forward to hearing from you.

shahmoradi commented 10 months ago

Thank you for your response @PieterjanRobbe. My checklist is now complete.

jbytecode commented 10 months ago

@editorialbot check references

editorialbot commented 10 months ago

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

- 10.1016/s0098-3004(00)00063-7 may be a valid DOI for title: Geostatistics: modeling spatial uncertainty

INVALID DOIs

- None

jbytecode commented 10 months ago

@editorialbot generate pdf

editorialbot commented 10 months ago

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

jbytecode commented 10 months ago

Post-Review Checklist for Editor and Authors

Additional Author Tasks After Review is Complete

[ ] 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.
[ ] Archive the release on Zenodo/figshare/etc and post the DOI here.
[ ] 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.

Editor Tasks Prior to Acceptance

[x] Read the text of the paper and offer comments/corrections (as either a list or a PR)
[x] Check the references in the paper for corrections (e.g. capitalization)
[x] Check that the archive title, author list, version tag, and the license are correct
[x] Set archive DOI with @editorialbot set <DOI here> as archive
[x] Set version with @editorialbot set <version here> as version
[x] Double check rendering of paper with @editorialbot generate pdf
[x] Specifically check the references with @editorialbot check references and ask author(s) to update as needed
[x] Recommend acceptance with @editorialbot recommend-accept

jbytecode commented 10 months ago

@PieterjanRobbe - I've just sent a pull request that contains minor changes in your bibtex. Could you please review the changes and apply them if they are okay?

PR: https://github.com/PieterjanRobbe/GaussianRandomFields.jl/pull/51

Thank you in advance.

jbytecode commented 10 months ago

@editorialbot check references

editorialbot commented 10 months ago

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 commented 10 months ago

@editorialbot generate pdf

editorialbot commented 10 months ago

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

jbytecode commented 10 months ago

@PieterjanRobbe - One more PR about bibtex

PR: https://github.com/PieterjanRobbe/GaussianRandomFields.jl/pull/52

jbytecode commented 10 months ago

@PieterjanRobbe - Meanwhile checking out the references and the manuscript, you can follow the instructions given in the https://github.com/openjournals/joss-reviews/issues/5595#issuecomment-1701418760. We need a tagged release created in the repository and then a related Zenodo archive DOI which is linked to this tagged release. The Zenodo archive should match the exact title of the paper, the author list and their information including ORCIDs.

jbytecode commented 10 months ago

@editorialbot check references

editorialbot commented 10 months ago

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 commented 10 months ago

@editorialbot generate pdf

editorialbot commented 10 months ago

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

jbytecode commented 10 months ago

@PieterjanRobbe - The manuscript and the bibtex look good to me.

jbytecode commented 10 months ago

@editorialbot set v2.2.3 as version

editorialbot commented 10 months ago

Done! version is now v2.2.3

openjournals / joss-reviews

[REVIEW]: GaussianRandomFields.jl: A Julia package to generate and sample from Gaussian random fields #5595

Status

Reviewer instructions & questions

Checklists

Review checklist for @ziyiyin97

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

Review checklist for @shahmoradi

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

Post-Review Checklist for Editor and Authors

Additional Author Tasks After Review is Complete

Editor Tasks Prior to Acceptance