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[REVIEW]: ParticleTracking: A GUI and library for particle tracking on stereo camera images #5986

Open editorialbot opened 1 year ago

editorialbot commented 1 year ago

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

Status

status

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HTML: <a href="https://joss.theoj.org/papers/41caf0076b48061c1efcc2810b85543f"><img src="https://joss.theoj.org/papers/41caf0076b48061c1efcc2810b85543f/status.svg"></a>
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

📝 Checklist for @merrygoat

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=0.21 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 commented 1 year ago

Wordcount for paper.md is 1030

editorialbot commented 1 year ago 
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 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:

jgostick commented 1 year ago

@editorialbot add @aquilesC as reviewer

editorialbot commented 1 year ago

@aquilesC added to the reviewers list!

jgostick commented 1 year ago

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 commented 1 year ago

Review checklist for @mhubii

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

aquilesC commented 1 year ago

Review checklist for @aquilesC

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

aquilesC commented 1 year ago

Some issues along the way:

jgostick commented 11 months ago

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

mhubii commented 11 months ago

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 commented 11 months ago

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 commented 11 months ago

@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 commented 11 months ago

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 commented 11 months ago

@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 commented 11 months ago

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 commented 10 months ago

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 commented 10 months ago

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

aquilesC commented 10 months ago

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 commented 10 months ago

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 commented 9 months ago

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 commented 9 months ago

@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 commented 8 months ago

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 commented 8 months ago

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 commented 8 months ago

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 commented 7 months ago

@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 commented 6 months ago

@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 commented 6 months ago

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

aquilesC commented 6 months ago

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.

Kevin-Mattheus-Moerman commented 6 months ago

@a-niem given that no updates were provided here within the time frame you indicated, we'll follow your suggestion and withdraw this submission.

Kevin-Mattheus-Moerman commented 6 months ago

@editorialbot withdraw

editorialbot commented 6 months ago

Paper withdrawn.

a-niem commented 6 months ago

@Kevin-Mattheus-Moerman I had provided updates, by fixing and closing the issues mentioned in this thread. Specifically #83, #80, and #79. Since yesterday, all issues are fixed, with the exception of #84 not being closed yet.

I have put all my currently available strength in bringing this to a positive end since my last post here. And I thought that my work mentioned above would justify to continue this here.

I completely understand, if that's not the case for you given my poor availability. But would nevertheless kindly ask to keep the submission running and finish it.

Kind regards Adrian

Kevin-Mattheus-Moerman commented 6 months ago

@a-niem okay given you've made those changes we've reopened this issue, so the review can resume.

Kevin-Mattheus-Moerman commented 6 months ago

@jgostick we've decided to resume this review. It looks like we need to replace one reviewer.

a-niem commented 6 months ago

Thanks a lot.

dmitrypuzyrev commented 5 months ago

Dear @Kevin-Mattheus-Moerman, dear @jgostick,

thank you a lot for resuming the review. We have talked with @a-niem around 10 days ago and agreed that as soon as he resolves the pending issues, he would contact you about going forward with the review and re-assignment of one reviewer. You were a little bit faster with the withdrawal notification, but I am thankful it is resolved now and the process is back on track.

In any case, I want to ensure you that we commit to the review. I am extremely grateful to @a-niem that he is still working on the project where he was a main developer, given his current limited availability. But even in case if he will not be available for the future required edits, I will do my best to resolve it.

Sincerely yours, Dr. Dmitry Puzyrev

mhubii commented 5 months ago

thanks for closing the pending issues. I will start a second round of reviews shortly and delve deeper into functionality.

jgostick commented 5 months ago

Hi @dmitrypuzyrev, please update us on the progress here? 10 months is much longer than a normal JOSS review so this is getting into uncharted territory.

a-niem commented 5 months ago

Hi @jgostick. With @dmitrypuzyrev apparently being busy, I'll attempt to answer here. As mentioned to Kevin-Mattheus-Moerman above, I've fixed the issues opened during the review process. The changed version is available in the joss_paper branch. I thought that now @mhubii was going to finish his review, and I'd fix any additional comments he has. With that ongoing, I thought another reviewer had to be appointed (please let me know if I'm supposed to make suggestions again). Fortunately, I have improved significantly in the meantime and there should be no periods of me being unavailable in the foreseeable future anymore. I'm committed to get this process finished as soon as possible. Please let me know about any tasks that I have overlooked that I'm supposed to finish here.

dmitrypuzyrev commented 5 months ago

Dear @jgostick,

I confirm that I have been busy last week and could not reply. With @a-niem, we were expecting the second reviewer to be reappointed as @Kevin-Mattheus-Moerman mentioned and also waiting for further comments from @mhubii. I am sorry that the review is taking so long, mainly due to temporary absense of the main developer. However, @a-niem has already fixed multiple issues, the package is actively used at the moment and a paper was recently published in npj Microgravity Journal based on the result which were obtained with its help. I believe that now when the main developer @a-niem is available, the review can be finished smoothly. Please let us know what is required from our side.

Sincerely yours Dr. Dmitry Puzyrev

mhubii commented 5 months ago

Hi all, I reviewed already quite a bit in my spare time, hope this can be acknowledged by all authors. I also read up on this thread with and without tag.

From my understanding we are currently short a reviewer. Think that issue is more relevant than more reviews from my end. From my perspective, it is currently the author's task to find a new reviewer.

Let me know once that is sorted. Thank you for the understanding :)

mhubii commented 5 months ago

I would really like to express that I don't understand the tone towards me :D, my reviews have already improved the quality of the software significantly, and I believe I am not at fault here.

mhubii commented 5 months ago

waiting for further comments from @mhubii. I am sorry that the review is taking so long, mainly due to temporary absense of the main developer. However, @a-niem has already fixed multiple issues

this should really read: I am dearly sorry that due to absence of the main developer we could not address pending issues in time. We will now find a new reviewer and would like to thank the current reviewer for their extended commitment and time.

a-niem commented 5 months ago

Hi @mhubii. I'm sorry that you feel this way, and I'd like to apologize for any misunderstanding that I caused here. I thought I made it clear, that my absence was the reason for the delay. Furthermore, I'd like you to know that I value your comments/issues you posted, especially as I had mentioned some of those months/years ago in the development process, but that got dismissed by my colleagues as 'unnecessary'. I'll be looking through the list of potential reviewers and make suggestions here as asap so that the time you've sunken in this already does not go to waste in the end. For any further comments, I'll try to be more mindful with my wording to not have any unwanted passive-aggressive undertone, as I believe was the case in my last comment.

dmitrypuzyrev commented 5 months ago

Dear @mhubii,

I think this was my comment, not @a-niem, which had an improper tone. I am very sorry for that. I really just meant that we were expecting the second reviewer to be reappointed (which we should propose ourselves as we understand now) and waiting for (possible) additional comments from the first reviewer. Of cause we are extremely thankful for your time and effort, this goes without question.

mhubii commented 5 months ago

no worries. The process goes as follows: If you don't have a reviewer, you suggest new reviewers without tagging them. The editor then reaches out to them and asks for help

dmitrypuzyrev commented 5 months ago

@editorialbot list reviewers