[REVIEW]: ParticleTracking: A GUI and library for particle tracking on stereo camera images

[editorialbot]

Submitting author: @a-niem (Adrian Niemann)
Repository: https://github.com/ANP-Granular/ParticleTracking
Branch with paper.md (empty if default branch): joss_paper
Version: v0.6.0
Editor: @jgostick
Reviewers: @mhubii, @aquilesC
Archive: Pending

Status

Status badge code:

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Markdown: [![status](https://joss.theoj.org/papers/41caf0076b48061c1efcc2810b85543f/status.svg)](https://joss.theoj.org/papers/41caf0076b48061c1efcc2810b85543f)

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

@mhubii, 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 @jgostick 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 @mhubii

📝 Checklist for @aquilesC

[editorialbot]

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

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[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.88  T=0.21 s (739.1 files/s, 133487.4 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          76           3005           7317          12987
Qt                               1              0              0           2348
Markdown                        19            296              0           1091
JSON                             7              0              0            508
TeX                              1             10              0            193
TOML                             2             13              0            155
reStructuredText                45             66            245             94
YAML                             3              8             14             69
DOS Batch                        2             14              1             49
Bourne Shell                     1              3              6             24
make                             1              4              7              9
-------------------------------------------------------------------------------
SUM:                           158           3419           7590          17527
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

[editorialbot]

Wordcount for paper.md is 1030

[editorialbot]

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

OK DOIs

- 10.1038/s41592-019-0686-2 is OK
- 10.1038/s41586-020-2649-2 is OK
- 10.5281/zenodo.7344967 is OK
- 10.1103/physrevlett.83.440 is OK
- 10.1209/epl/i2005-10589-8 is OK
- 10.1209/0295-5075/123/14003 is OK
- 10.1103/PhysRevLett.110.144102 is OK
- 10.1103/PhysRevLett.120.214301 is OK
- 10.1103/PhysRevLett.124.208007 is OK
- 10.1038/s41526-022-00196-6 is OK
- 10.1007/s12217-020-09800-4 is OK
- 10.1051/epjconf/202124904003 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[editorialbot]

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

[jgostick]

@editorialbot add @aquilesC as reviewer

[editorialbot]

@aquilesC added to the reviewers list!

[jgostick]

Hi @mhubii and @aquilesC, the review is now underway. Thanks to you both for donating your time and expertise to this endeavor. (I often wonder how much the peer review system would cost if journals actually paid reviewers as consultants...)

The JOSS review process, if you're not familiar, is based around filling out a checklist (the instructions for generating your own are given at the top of this thread). If you have changes to ask of the author(s) you can use the issue tracker on their repo, which is on github and is public.

Hopefully you can complete your reviewers in 2-3 week time frame, as this this submission has been sitting for a while already.

Happy coding!

[mhubii]

Review checklist for @mhubii

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/ANP-Granular/ParticleTracking?
• 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 (@a-niem) 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?

[aquilesC]

Review checklist for @aquilesC

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/ANP-Granular/ParticleTracking?
• 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 (@a-niem) 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?

[aquilesC]

Some issues along the way:

• The install misses some dependencies (link)
• Missing trained model to analyze example data (link)

[jgostick]

Hi @mhubii, how are things progressing with your review? You created the checklist, so I assume you're trying out the package still?

[mhubii]

hi @jgostick , I am in the process of writing up a Phd and will likely have time for a proper review beginning of January. Would that be too late?

I can begin with an initial review earlier.

[jgostick]

Hmmm, one one had it's a bit late since the authors have been waiting a while already. But on the other hand the authors have not responded to @aquilesC comments yet, so they may not be in a hurry?

@a-niem, do have any specific timeline in mind?

[aquilesC]

@jgostick, there was a comment on one of the issues I opened, with some proposed timeline, which also made me drop a bit my focus. I'm aiming to wrapping up my review by the end of this week, or mid-next week. Especially considering the end-of-year break, I will try not to delay it much, but not sure whether the authors have time to invest on the manuscript before the end of the year.

[jgostick]

Shutting down for the northern hemisphere winter solstice to hibernate with friends and family is my favorite time of the year, I don't blame them. Let's see if they drop in here with a response to my question about timeline.

[a-niem]

@jgostick, @aquilesC Unfortunately, I've been on vacation which continues until the end of the year. Therefore, I'm not able to properly respond to any reviews that are done right now and will only continue working on it thoroughly from the beginning of next year.

[jgostick]

Then that is perfect, as one of our reviewers is only able to get started on it in the new year as well.
@mhubii, you have your extension :-) Thanks all for the quick response.

[jgostick]

Hi Everyone...things are very quiet here, and I am at least partly to blame. @a-niem, I was waiting for you to respond to the comments of @aquilesC which I why I let things drag on so long. @mhubii, I hope you had a good vacation and are still able to review this package?

[mhubii]

hi, yes I'll start working on this @jgostick. Sorry, busy times!

[aquilesC]

I think @a-niem addressed the comments on the code repository. My bad for not checking earlier. I'll re-start the review process early next week.

[mhubii]

I have added some initial suggestions to the authors and will continue further in-depth reviews shortly. I think we can iterate from here so we reach a software standard necessary for JOSS

[jgostick]

Great stuff, thanks @mhubii! @a-niem, have you and your team been working on this? Do you think this list is do-able in a reasonable timeframe? Skimming the list of open issues above, these all seem to be valid requests.

[a-niem]

@jgostick I agree that all the opened issues are necessary improvements. I’ve already been loosely working on them and intend to have them finished within the next two weeks.
Thanks a lot to @mhubii for his review.

[jgostick]

Hi @a-niem, how are your updates coming along? It's been a while, and I would like to get this review off my desk soon :-)

[a-niem]

Hi @jgostick. I'm extremely sorry for the delay I'm causing at the moment.
Right after my last post I had to abandon this project for some time, due to health issues.
I'm currently working my way back, but I cannot promise any deadlines.

[jgostick]

I hope it was nothing serious! When the delay is by the author it's not such a problem, since the author is the only one that minds the delay :-)

[jgostick]

@a-niem, how are things going? This has been several months without any progress. Are you still interested in proceeding, or should we cancel this submission?

[a-niem]

@jgostick Unfortunately, my situation has not changed much. Nevertheless, I'm still interested in proceeding with my submission.

However, to spare everybody else involved here unnecessary work/waiting time, I suggest that we cancel the submission IF my former colleagues and I fail to provide significant progress here until the end of this week.

I hope this suggestion works for you.

[mhubii]

hi @jgostick , @a-niem , personally not in a hurry

[aquilesC]

Dear @jgostick , since this dragged for a bit too long, I would prefer to pass the reviewing duties to someone else. I do not have time available anymore.