[REVIEW]: MyPTV: A Python Package for 3D Particle Tracking

[editorialbot]

Submitting author: @ronshnapp (Ron Shnapp)
Repository: https://github.com/ronshnapp/MyPTV
Branch with paper.md (empty if default branch): JOSS_paper
Version: V0.4.3
Editor: @jgostick
Reviewers: @leahmendelson, @jgostick
Archive: 10.5281/zenodo.6846969

Status

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Markdown: [![status](https://joss.theoj.org/papers/b19c0c3a7d02bfa0686ab4021dfb1692/status.svg)](https://joss.theoj.org/papers/b19c0c3a7d02bfa0686ab4021dfb1692)

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

@leahmendelson, your review will be checklist based. Each of you will have a separate checklist that you should update when carrying out your review.
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@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 @leahmendelson

📝 Checklist for @jgostick

[editorialbot]

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[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.88  T=0.06 s (505.5 files/s, 122065.9 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          18           1136           1082           1990
TeX                              4            521             26            952
Jupyter Notebook                 2              0           1046            232
YAML                             4              7              4            104
Markdown                         2             52              0             92
-------------------------------------------------------------------------------
SUM:                            30           1716           2158           3370
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

[editorialbot]

Wordcount for paper.md is 1185

[editorialbot]

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

OK DOIs

- 10.1088/0957-0233/8/12/017 is OK
- 10.1007/BF00190953 is OK
- 10.1063/5.0009357 is OK
- 10.1007/s00348-005-0068-7 is OK
- 10.1038/s41598-019-43555-2 is OK
- 10.1017/S0022112004003283 is OK
- 10.1146/annurev.fluid.010908.165210 is OK
- 10.1017/S0022112000001658 is OK
- 10.1017/S0022112008000141 is OK
- 10.1103/PhysRevLett.100.254504 is OK
- 10.1103/PhysRevX.11.031060 is OK
- 10.1088/0957-0233/19/7/075105 is OK
- 10.1007/s10494-015-9616-2 is OK
- 10.1007/s00348-005-0031-7 is OK
- 10.1098/rspb.2017.0235 is OK
- 10.1109/TPAMI.2015.2414427 is OK
- 10.1073/pnas.1708888114 is OK
- 10.3354/meps300105 is OK
- 10.1038/sdata.2019.36 is OK
- 10.1371/journal.pone.0240963 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[editorialbot]

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

[jgostick]

@editorialbot add @quynhneo as reviewer

[editorialbot]

@quynhneo added to the reviewers list!

[jgostick]

Hi @leahmendelson and @quynhneo. Thank you very much for agreeing to review this submission. You can ask the "editorialbot" to generate your checklist by typing @editorialbot generate my checklist in new comment on this thread. Your task is to help the author of the package refine the submission until all the checkboxes are satisfied. This package looks to be in good shape so I'm hopefully for a smooth review process.

[leahmendelson]

Review checklist for @leahmendelson

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/ronshnapp/MyPTV?
• 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 (@ronshnapp) 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

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 and who the target audience is?
• 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?

[leahmendelson]

@ronshnapp I'll use this comment as a checklist for issues I've added in the MyPTV repository

• DOC - typos ronshnapp/MyPTV#16
• Legacy calibration example ronshnapp/MyPTV#17
• example folder .ipynb_checkpoints ronshnapp/MyPTV#18
• Installation (Conda directions) ronshnapp/MyPTV#19
• DOC - Calibration Section ronshnapp/MyPTV#20
• Bug - Changing segmentation method to 'dilation' missing 'particle_size' ronshnapp/MyPTV#21
• example_cal folder ronshnapp/MyPTV#22
• Please add community guidelines ronshnapp/MyPTV#23
• JOSS paper feedback ronshnapp/MyPTV#24

[ronshnapp]

@leahmendelson Thank you very much for the comments! I'll wait for comments from the other reviewer before starting the revision.

[jgostick]

I have just emailed the other review to ask for a time frame for their review.

[jgostick]

Hi @ronshnapp I am thinking you should start addressing @leahmendelson's comments. The other reviewer has just informed me that they may not have time after all.

[ronshnapp]

Hi @jgostick, thanks for the update. I'll start working on the revision.

[ronshnapp]

Hi @jgostick and @leahmendelson.
I went through the detailed comments and issues raised in the review and addressed them all (@leahmendelson, thank you very much, I truly appreciate your effort and value your comments). The revision to the code, manual, and readme can be found in the master branch. The revision to the paper can be found in the JOSS_paper branch. The changes I made are listed as comments in the issues raised.
Kindly let me know what I should do in order to proceed.

[leahmendelson]

@ronshnapp has done a great job addressing my comments and my review checklist is now complete. I'm happy to recommend MyPTV. @jgostick, any other steps for me?

[ronshnapp]

Hi @jgostick, I wanted to ask if there is any status update on the paper?

[jgostick]

Other reviewer's gone awol and have not been able to find a replacement.

[jgostick]

@leahmendelson, great work and thanks so much for your time. You're all done.

[jgostick]

@editorialbot remove @quynhneo as reviewer

[editorialbot]

@quynhneo removed from the reviewers list!

[jgostick]

@editorialbot add @jgostick as reviewer

[jgostick]

@editorialbot set 10.5281/zenodo.6846969 as archive

[editorialbot]

Done! Archive is now 10.5281/zenodo.6846969

[jgostick]

@editorialbot set V0.4.3 as version

[editorialbot]

Done! version is now V0.4.3

[jgostick]

@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

- 10.1088/0957-0233/8/12/017 is OK
- 10.1007/BF00190953 is OK
- 10.1063/5.0009357 is OK
- 10.1007/s00348-005-0068-7 is OK
- 10.1038/s41598-019-43555-2 is OK
- 10.1017/S0022112004003283 is OK
- 10.1146/annurev.fluid.010908.165210 is OK
- 10.1017/S0022112000001658 is OK
- 10.1017/S0022112008000141 is OK
- 10.1103/PhysRevLett.100.254504 is OK
- 10.1103/PhysRevX.11.031060 is OK
- 10.1088/0957-0233/19/7/075105 is OK
- 10.1007/s10494-015-9616-2 is OK
- 10.1007/s00348-005-0031-7 is OK
- 10.1098/rspb.2017.0235 is OK
- 10.1109/TPAMI.2015.2414427 is OK
- 10.1073/pnas.1708888114 is OK
- 10.3354/meps300105 is OK
- 10.1038/sdata.2019.36 is OK
- 10.1371/journal.pone.0240963 is OK
- 10.1007/s00348-019-2875-2 is OK
- 10.1007/s00348-016-2157-1 is OK
- 10.1088/0957-0233/24/2/024008 is OK
- 10.1016/j.jsb.2005.06.002 is OK
- 10.1016/j.cageo.2019.03.007 is OK
- 10.5281/zenodo.4682814 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[editorialbot]

👋 @openjournals/joss-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#3401, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

[jgostick]

@ronshnapp very sorry for the delays on this review. Please don't let it reflect badly on JOSS, we jsut had a reviewer drop out, and I have had full teaching load this summer, plus several conferences, etc, so it's been hectic. Anyway, congrats, this looks like a great package. An editor-in-chief will be by soon to make it official.

[ronshnapp]

@jgostick There's nothing to be sorry about. I think JOSS is a great project and the fact people such a you do so much to keep it going is incredible. I will definitely consider chipping in as a reviewer despite a slight impostor syndrome. Thank you very much for managing this process!

[Kevin-Mattheus-Moerman]

@ronshnapp

I am an AEiC for JOSS and here to help process the final steps for acceptance. I have studied this review issue, your repository, and the paper, and have some issues below that require your attention.

• Please manually edit the ZENODO archive such that the title matches that of the paper.
• The ZENODO archive currently lists "Other (open)" as the license. I believe you can manually edit it to refer to your MIT license.

I have read your paper and have the following comments:

• Please add the city and country to your affiliation.
• Can you check if Applications of 3D-PTV abound..., should read Applications of 3D-PTV are abound....
• Check the effort the programming which should probably be the effort of programming.
• When you say building on the foundation of a previous project, can you mention/cite/refer to that project? Sorry if I missed it.
• Check leverage it’s high speed, which should be leverage its high speed
• The paper says MyPTV, currently in version 0.2, contains..., yet the review here is for version V0.4.3. Should the text in the paper be amended?
• It looks like it would be better if MyPTV had been tested in a series.. is written MyPTV has been tested in a series....
• It looks like MyPTV includes several helpful tools to ensure the software user friendly... should be rewritten e.g. as MyPTV includes several helpful tools to ensure the software's user friendliness... or use something like to ensure the user friendliness of the software.

Please work on the above and we can proceed with the next steps. Thanks.

[ronshnapp]

Hello @Kevin-Mattheus-Moerman

Thanks for your review and comments!
I fixed the ZENODO archive as you suggested and made the corrections needed to the paper.

[Kevin-Mattheus-Moerman]

@editorialbot generate pdf

[editorialbot]

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

[Kevin-Mattheus-Moerman]

@ronshnapp great thanks, I just reviewed those changes, and it looks like we are all set to proceed.

[Kevin-Mattheus-Moerman]

@editorialbot accept

[editorialbot]

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

[editorialbot]

🐦🐦🐦 👉 Tweet 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.04398 joss-papers#3403
1. Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.04398
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]

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