[REVIEW]: DRDMannTurb: A python package for scalable, data-driven synthetic turbulence #6838

editorialbot · 2024-06-04T17:09:38Z

Submitting author: @alizma (Alexey Izmailov)
Repository: https://github.com/METHODS-Group/DRDMannTurb
Branch with paper.md (empty if default branch): main
Version: v1.0.3
Editor: @HaoZeke
Reviewers: @paroomk, @olivecha
Archive: https://dx.doi.org/10.5281/zenodo.13922330

Status

Status badge code:

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Markdown: [![status](https://joss.theoj.org/papers/4c1af9b22a5861f5be343ba20133d24c/status.svg)](https://joss.theoj.org/papers/4c1af9b22a5861f5be343ba20133d24c)

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

@paroomk & @olivecha, 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:

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

📝 Checklist for @olivecha

The text was updated successfully, but these errors were encountered:

editorialbot · 2024-06-04T17:09:41Z

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

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editorialbot · 2024-06-04T17:10:02Z

Software report:

github.com/AlDanial/cloc v 1.90  T=0.06 s (1355.5 files/s, 140389.2 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          41           1360           2102           3712
reStructuredText                23            295            392            158
CSV                              4              0              0            128
YAML                             6             11              9             99
Markdown                         2             36              0             72
TeX                              1             13              0             41
DOS Batch                        1              8              1             26
make                             1              4              7              9
JavaScript                       2              0              0              7
JSON                             1              0              0              3
-------------------------------------------------------------------------------
SUM:                            82           1727           2511           4255
-------------------------------------------------------------------------------

Commit count by author:

   200	Alexey Izmailov
    56	mjachi
    32	gdeskos
    27	Matthew Meeker
    10	Brendan Keith
     1	Georgios (Yorgos) Deskos
     1	dependabot[bot]

editorialbot · 2024-06-04T17:10:04Z

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

OK DOIs

- 10.1063/5.0064394 is OK
- 10.5281/zenodo.7254149 is OK
- 10.1017/S0022112094001886 is OK

MISSING DOIs

- None

INVALID DOIs

- https://doi.org/10.1016/S0266-8920(97)00036-2 is INVALID because of 'https://doi.org/' prefix

editorialbot · 2024-06-04T17:10:09Z

Paper file info:

📄 Wordcount for paper.md is 886

✅ The paper includes a Statement of need section

editorialbot · 2024-06-04T17:10:10Z

License info:

✅ License found: BSD 3-Clause "New" or "Revised" License (Valid open source OSI approved license)

editorialbot · 2024-06-04T17:10:58Z

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

paroomk · 2024-06-06T16:48:30Z

Review checklist for @paroomk

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/METHODS-Group/DRDMannTurb?
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 (@alizma) 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?

HaoZeke · 2024-07-03T06:01:32Z

@paroomk @olivecha could you update me on the progress please?

HaoZeke · 2024-07-03T06:25:19Z

@editorialbot remind @paroomk and @olivecha in three days

editorialbot · 2024-07-03T06:25:21Z

@paroomk and @olivecha doesn't seem to be a reviewer or author for this submission.

HaoZeke · 2024-07-03T06:26:27Z

@editorialbot add @paroomk as reviewer

editorialbot · 2024-07-03T06:26:30Z

@paroomk is already included in the reviewers list

HaoZeke · 2024-07-03T06:26:35Z

@editorialbot add @olivecha as reviewer

editorialbot · 2024-07-03T06:26:37Z

@olivecha is already included in the reviewers list

paroomk · 2024-07-04T16:44:05Z

@paroomk @olivecha could you update me on the progress please?

Hi @HaoZeke, I am working on verifying the functionality now. I am hoping to finish this by next weekend (July 14).

I have also submitted an issue regarding the inclusion of examples and documentation in the pre-compiled wheels.

alizma · 2024-07-12T18:28:29Z

@editorialbot generate pdf

editorialbot · 2024-07-12T18:29:32Z

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

paroomk · 2024-07-18T03:13:33Z

@HaoZeke Everything looks good to me now and I recommend this for publication in JOSS. Kudos to @alizma and co-authors!

HaoZeke · 2024-07-18T13:41:17Z

Thanks @paroomk!

@olivecha could you provide an update please?

olivecha · 2024-07-26T13:25:32Z

Review checklist for @olivecha

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/METHODS-Group/DRDMannTurb?
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 (@alizma) 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?

olivecha · 2024-07-29T17:28:28Z

I've submitted three small issues about installation requirements, tests and missing community guidelines.

HaoZeke · 2024-10-15T15:23:18Z

@editorialbot generate pdf

HaoZeke · 2024-10-15T15:23:25Z

@editorialbot check references

editorialbot · 2024-10-15T15:23:46Z

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

✅ OK DOIs

- 10.1063/5.0064394 is OK
- 10.5281/zenodo.7254149 is OK
- 10.5194/wes-5-1-2020 is OK
- 10.1017/S0022112094001886 is OK
- 10.1016/S0266-8920(97)00036-2 is OK

🟡 SKIP DOIs

- None

❌ MISSING DOIs

- None

❌ INVALID DOIs

- None

editorialbot · 2024-10-15T15:24:33Z

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

HaoZeke · 2024-10-15T15:26:56Z

@editorialbot recommend-accept

editorialbot · 2024-10-15T15:26:58Z

Attempting dry run of processing paper acceptance...

editorialbot · 2024-10-15T15:27:12Z

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

✅ OK DOIs

- 10.1063/5.0064394 is OK
- 10.5281/zenodo.7254149 is OK
- 10.5194/wes-5-1-2020 is OK
- 10.1017/S0022112094001886 is OK
- 10.1016/S0266-8920(97)00036-2 is OK

🟡 SKIP DOIs

- None

❌ MISSING DOIs

- None

❌ INVALID DOIs

- None

editorialbot · 2024-10-15T15:28:23Z

👋 @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#6001, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

crvernon · 2024-10-15T15:51:20Z

editorialbot · 2024-10-15T15:52:33Z

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

crvernon · 2024-10-18T14:00:50Z

👋 @alizma - I need you to address the following before I accept this submission for publication:

In your archive:

The archive name (including capitalization) and author list (including order) in your Zenodo archive should match what is in your paper exactly. Also, please ensure that the license you list in your Zenodo archive matches the one you use in your GitHub repository. Please edit the metadata in your Zenodo archive to fix these things. A new release is not required.

In your paper:

LINE 26: The citation format for this should be changed from "...described in (Keith et al., 2021)." to "...described in Keith et al. (2021)."
LINE 29: Same as the above comment about the citation format.
LINE 40: "numpy" should be written in this case as "NumPy"
LINE 70: Is there something missing in this statement? "The U.S. Government retains and the publisher, by accepting the article..."

Once you adderss the above let me know and I'll accept this for publication. Thanks!

crvernon · 2024-10-23T15:09:33Z

👋 This is just a reminder of my last steps post above @alizma

mdmeeker · 2024-10-23T16:28:27Z

@editorialbot generate pdf

editorialbot · 2024-10-23T16:29:54Z

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

mdmeeker · 2024-10-23T16:35:07Z

Hi @crvernon

I've addressed the issues with the draft that you pointed out. RE Line 70, I believe it is complete although somewhat unclearly written.

alizma · 2024-10-23T17:16:12Z

Hi @crvernon please see the updated metadata on the Zenodo archive here. I updated the title, description and license. Please let us know if there is anything else. Thank you!

crvernon · 2024-10-23T20:06:35Z

@alizma one last thing in the Zenodo archive name: the "p" in "python" should be capitalized.

alizma · 2024-10-24T18:55:24Z

@crvernon Fixed, please see here.

crvernon · 2024-10-24T20:16:32Z

@editorialbot accept

editorialbot · 2024-10-24T20:16:34Z

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

editorialbot · 2024-10-24T20:23:06Z

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: Izmailov
  given-names: Alexey
- family-names: Meeker
  given-names: Matthew
- family-names: Deskos
  given-names: Georgios
- family-names: Keith
  given-names: Brendan
doi: "https://dx.doi.org/10.5281/zenodo.13922330"
message: If you use this software, please cite our article in the
  Journal of Open Source Software.
preferred-citation:
  authors:
  - family-names: Izmailov
    given-names: Alexey
  - family-names: Meeker
    given-names: Matthew
  - family-names: Deskos
    given-names: Georgios
  - family-names: Keith
    given-names: Brendan
  date-published: 2024-10-24
  doi: 10.21105/joss.06838
  issn: 2475-9066
  issue: 102
  journal: Journal of Open Source Software
  publisher:
    name: Open Journals
  start: 6838
  title: "DRDMannTurb: A Python package for scalable, data-driven
    synthetic turbulence"
  type: article
  url: "https://joss.theoj.org/papers/10.21105/joss.06838"
  volume: 9
title: "DRDMannTurb: A Python package for scalable, data-driven
  synthetic turbulence"

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 · 2024-10-24T20:23:10Z

🐘🐘🐘 👉 Toot for this paper 👈 🐘🐘🐘

editorialbot · 2024-10-24T20:23:10Z

🦋🦋🦋 👉 Bluesky post for this paper 👈 🦋🦋🦋

editorialbot · 2024-10-24T20:23:11Z

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

Here's what you must now do:

Check final PDF and Crossref metadata that was deposited 👉 Creating pull request for 10.21105.joss.06838 joss-papers#6052
Wait five minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.06838
If everything looks good, then close this review issue.
Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

crvernon · 2024-10-24T20:24:22Z

🥳 Congratulations on your new publication @alizma! Many thanks to @HaoZeke for editing and @paroomk and @olivecha for your time, hard work, and expertise!! JOSS wouldn't be able to function nor succeed without your efforts.

Please consider becoming a reviewer for JOSS if you are not already: https://reviewers.joss.theoj.org/join

editorialbot · 2024-10-24T20:24:23Z

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

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</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.06838/status.svg
   :target: https://doi.org/10.21105/joss.06838

This is how it will look in your documentation:

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editorialbot added Python review TeX Track: 5 (DSAIS) Data Science, Artificial Intelligence, and Machine Learning labels Jun 4, 2024

editorialbot assigned HaoZeke Jun 4, 2024

editorialbot mentioned this issue Jun 4, 2024

[PRE REVIEW]: DRDMannTurb: A python package for scalable, data-driven synthetic turbulence #6506

Closed

openjournals deleted a comment from editorialbot Jul 3, 2024

paroomk mentioned this issue Jul 4, 2024

Include examples and documentation in the pre-compiled wheels for the package METHODS-Group/DRDMannTurb#97

Closed

paroomk mentioned this issue Jul 11, 2024

[JOSS Review] Typo in references METHODS-Group/DRDMannTurb#98

Closed

editorialbot added the recommend-accept Papers recommended for acceptance in JOSS. label Oct 15, 2024

editorialbot added accepted published Papers published in JOSS labels Oct 24, 2024

crvernon closed this as completed Oct 24, 2024

[REVIEW]: DRDMannTurb: A python package for scalable, data-driven synthetic turbulence #6838

[REVIEW]: DRDMannTurb: A python package for scalable, data-driven synthetic turbulence #6838

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Software paper

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