[REVIEW]: BoxKit: A Python library to manage analysis of block-structured simulation datasets #5649

editorialbot · 2023-07-11T16:44:54Z

Submitting author: @akashdhruv (Akash Dhruv)
Repository: https://github.com/akashdhruv/BoxKit
Branch with paper.md (empty if default branch): development
Version: 2023.12
Editor: @kellyrowland
Reviewers: @rvg296, @Abinashbunty
Archive: 10.5281/zenodo.10257565

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/2a882634c46d2b00f41b8184463c2d84"><img src="https://joss.theoj.org/papers/2a882634c46d2b00f41b8184463c2d84/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/2a882634c46d2b00f41b8184463c2d84/status.svg)](https://joss.theoj.org/papers/2a882634c46d2b00f41b8184463c2d84)

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

@rvg296 & @AnnikaStein, 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 @kellyrowland 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 @rvg296

📝 Checklist for @Abinashbunty

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

editorialbot · 2023-07-11T16:44:56Z

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:

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editorialbot · 2023-07-11T16:44:58Z

Software report:

github.com/AlDanial/cloc v 1.88  T=0.18 s (903.6 files/s, 177908.3 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
JavaScript                      13           2405           2470           9222
HTML                            31            605             93           4863
C/C++ Header                    18            478            257           2719
Python                          51            930            846           2699
SVG                              3              0              0           2673
CSS                              4            191             35            759
YAML                             7             22             29            227
reStructuredText                28            213            380            225
C++                              6             28             50            180
Markdown                         1             22              0            106
TeX                              1              5              0             68
DOS Batch                        1              8              1             26
make                             3             10             10             26
-------------------------------------------------------------------------------
SUM:                           167           4917           4171          23793
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

editorialbot · 2023-07-11T16:45:00Z

Wordcount for paper.md is 840

editorialbot · 2023-07-11T16:45:02Z

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

OK DOIs

- 10.1016/j.softx.2022.101168 is OK
- 10.5281/zenodo.8039787 is OK
- 10.1088/0067-0049/192/1/9 is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot · 2023-07-11T16:46:22Z

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

AnnikaStein · 2023-07-11T17:07:42Z

Review checklist for @AnnikaStein

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/akashdhruv/BoxKit?
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 (@akashdhruv) 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?

akashdhruv · 2023-07-12T01:45:22Z

@editorialbot check references

editorialbot · 2023-07-12T01:45:29Z

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

OK DOIs

- 10.1016/j.softx.2022.101168 is OK
- 10.5281/zenodo.8039787 is OK
- 10.1088/0067-0049/192/1/9 is OK

MISSING DOIs

- None

INVALID DOIs

- None

akashdhruv · 2023-07-12T01:45:48Z

@editorialbot generate pdf

editorialbot · 2023-07-12T01:47:19Z

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

rvg296 · 2023-07-12T01:53:24Z

@editorialbot generate my checklist

editorialbot · 2023-07-12T01:53:25Z

I'm sorry human, I don't understand that. You can see what commands I support by typing:

@editorialbot commands

akashdhruv · 2023-07-12T01:54:24Z

@editorialbot generate pdf

editorialbot · 2023-07-12T01:55:36Z

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

akashdhruv · 2023-07-12T01:55:38Z

@rvg296 I believe the command is:

@editorialbot generate my checklist

rvg296 · 2023-07-12T01:56:40Z

@rvg296 I believe the command is:

@editorialbot generate my checklist

Yes I have corrected it

akashdhruv · 2023-07-12T02:02:56Z

@editorialbot check references

editorialbot · 2023-07-12T02:03:08Z

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

OK DOIs

- 10.1016/j.softx.2022.101168 is OK
- 10.5281/zenodo.8039787 is OK
- 10.1088/0067-0049/192/1/9 is OK

MISSING DOIs

- None

INVALID DOIs

- None

akashdhruv · 2023-07-12T02:03:18Z

@editorialbot generate pdf

@rvg296 @AnnikaStein Please use this version here for review: I have included reference to performance data repository.

editorialbot · 2023-07-12T02:04:32Z

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

akashdhruv · 2023-07-12T04:38:04Z

@editorialbot generate pdf

editorialbot · 2023-07-12T04:39:20Z

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

AnnikaStein · 2023-07-12T07:18:57Z

Review checklist for @AnnikaStein

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/akashdhruv/BoxKit?
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 (@akashdhruv) 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?

editorialbot · 2023-12-04T18:09:47Z

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

akashdhruv · 2023-12-04T18:36:28Z

@kellyrowland

Release version number: 2023.12
Zenodo DOI: 10.5281/zenodo.10257565

editorialbot · 2023-12-04T18:37:09Z

@akashdhruv I can't do that because you are not a reviewer

akashdhruv · 2023-12-04T18:44:38Z

kellyrowland · 2023-12-04T19:32:53Z

@editorialbot set 2023.12 as version

editorialbot · 2023-12-04T19:32:55Z

Done! version is now 2023.12

kellyrowland · 2023-12-04T19:33:20Z

@editorialbot set 10.5281/zenodo.10257565 as archive

editorialbot · 2023-12-04T19:33:22Z

Done! archive is now 10.5281/zenodo.10257565

kellyrowland · 2023-12-04T19:33:52Z

@editorialbot generate pdf

editorialbot · 2023-12-04T19:35:05Z

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

kellyrowland · 2023-12-04T19:36:15Z

@editorialbot check references

editorialbot · 2023-12-04T19:36:26Z

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

OK DOIs

- 10.1016/j.softx.2022.101168 is OK
- 10.5281/zenodo.8039787 is OK
- 10.1088/0067-0049/192/1/9 is OK

MISSING DOIs

- None

INVALID DOIs

- None

kellyrowland · 2023-12-04T19:38:48Z

@akashdhruv would you be able to change the archive title from "Box-Tools/BoxKit: Peer reviewed release for JOSS" to "BoxKit: A Python library to manage analysis of block-structured simulation datasets" to match that of the submission?

akashdhruv · 2023-12-04T19:59:48Z

@akashdhruv would you be able to change the archive title from "Box-Tools/BoxKit: Peer reviewed release for JOSS" to "BoxKit: A Python library to manage analysis of block-structured simulation datasets" to match that of the submission?

Done

kellyrowland · 2023-12-04T20:01:17Z

@editorialbot recommend-accept

editorialbot · 2023-12-04T20:01:19Z

Attempting dry run of processing paper acceptance...

editorialbot · 2023-12-04T20:01:34Z

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

OK DOIs

- 10.1016/j.softx.2022.101168 is OK
- 10.5281/zenodo.8039787 is OK
- 10.1088/0067-0049/192/1/9 is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot · 2023-12-04T20:03:00Z

👋 @openjournals/csism-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#4814, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

danielskatz · 2023-12-05T13:39:45Z

👋 @akashdhruv - I'll proofread this in the next few hours, as the editor in charge of the rest of the process, then let you know if I need anything else from you.

danielskatz · 2023-12-05T14:32:47Z

@editorialbot accept

editorialbot · 2023-12-05T14:32:48Z

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

editorialbot · 2023-12-05T14:34:23Z

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: Dhruv
  given-names: Akash
  orcid: "https://orcid.org/0000-0003-4997-321X"
doi: 10.5281/zenodo.10257565
message: If you use this software, please cite our article in the
  Journal of Open Source Software.
preferred-citation:
  authors:
  - family-names: Dhruv
    given-names: Akash
    orcid: "https://orcid.org/0000-0003-4997-321X"
  date-published: 2023-12-05
  doi: 10.21105/joss.05649
  issn: 2475-9066
  issue: 92
  journal: Journal of Open Source Software
  publisher:
    name: Open Journals
  start: 5649
  title: "BoxKit: A Python library to manage analysis of
    block-structured simulation datasets"
  type: article
  url: "https://joss.theoj.org/papers/10.21105/joss.05649"
  volume: 8
title: "BoxKit: A Python library to manage analysis of block-structured
  simulation datasets"

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 · 2023-12-05T14:34:31Z

🐘🐘🐘 👉 Toot for this paper 👈 🐘🐘🐘

editorialbot · 2023-12-05T14:34:32Z

🚨🚨🚨 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.05649 joss-papers#4815
Wait five minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.05649
If everything looks good, then close this review issue.
Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

danielskatz · 2023-12-05T14:43:35Z

Congratulations to @akashdhruv (Akash Dhruv) on your publication!!

And thanks to @rvg296 and @Abinashbunty for reviewing, and to @kellyrowland for editing!
JOSS depends on volunteers and we couldn't do this without you

editorialbot · 2023-12-05T14:43:37Z

🎉🎉🎉 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.05649/status.svg)](https://doi.org/10.21105/joss.05649)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.05649">
  <img src="https://joss.theoj.org/papers/10.21105/joss.05649/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.05649/status.svg
   :target: https://doi.org/10.21105/joss.05649

This is how it will look in your documentation:

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editorialbot added Batchfile Makefile Python review Track: 7 (CSISM) Computer science, Information Science, and Mathematics labels Jul 11, 2023

editorialbot assigned kellyrowland Jul 11, 2023

editorialbot mentioned this issue Jul 11, 2023

[PRE REVIEW]: BoxKit: A Python library to manage analysis of block-structured simulation datasets #5632

Closed

editorialbot added the recommend-accept Papers recommended for acceptance in JOSS. label Dec 4, 2023

editorialbot added accepted published Papers published in JOSS labels Dec 5, 2023

danielskatz closed this as completed Dec 5, 2023

[REVIEW]: BoxKit: A Python library to manage analysis of block-structured simulation datasets #5649

[REVIEW]: BoxKit: A Python library to manage analysis of block-structured simulation datasets #5649

Comments

editorialbot commented Jul 11, 2023 • edited

Status

Reviewer instructions & questions

Checklists

editorialbot commented Jul 11, 2023

editorialbot commented Jul 11, 2023

editorialbot commented Jul 11, 2023

editorialbot commented Jul 11, 2023

editorialbot commented Jul 11, 2023

AnnikaStein commented Jul 11, 2023 • edited

Review checklist for @AnnikaStein

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

akashdhruv commented Jul 12, 2023

editorialbot commented Jul 12, 2023

akashdhruv commented Jul 12, 2023

editorialbot commented Jul 12, 2023

rvg296 commented Jul 12, 2023 • edited

editorialbot commented Jul 12, 2023

akashdhruv commented Jul 12, 2023

editorialbot commented Jul 12, 2023

akashdhruv commented Jul 12, 2023

rvg296 commented Jul 12, 2023

akashdhruv commented Jul 12, 2023

editorialbot commented Jul 12, 2023

akashdhruv commented Jul 12, 2023 • edited

editorialbot commented Jul 12, 2023

akashdhruv commented Jul 12, 2023

editorialbot commented Jul 12, 2023

AnnikaStein commented Jul 12, 2023 • edited by editorialbot

Review checklist for @AnnikaStein

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

editorialbot commented Dec 4, 2023

akashdhruv commented Dec 4, 2023

editorialbot commented Dec 4, 2023

akashdhruv commented Dec 4, 2023 • edited

Additional Author Tasks After Review is Complete

kellyrowland commented Dec 4, 2023

editorialbot commented Dec 4, 2023

kellyrowland commented Dec 4, 2023

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kellyrowland commented Dec 4, 2023

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kellyrowland commented Dec 4, 2023

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editorialbot commented Jul 11, 2023 •

edited

AnnikaStein commented Jul 11, 2023 •

edited

rvg296 commented Jul 12, 2023 •

edited

akashdhruv commented Jul 12, 2023 •

edited

AnnikaStein commented Jul 12, 2023 •

edited by editorialbot

akashdhruv commented Dec 4, 2023 •

edited