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[REVIEW]: DynaMo: Dynamic Body Shape and Motion Capture with Intel RealSense Cameras #1466
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Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @melund, it looks like you're currently assigned as the reviewer for this paper 🎉. ⭐ Important ⭐ If you haven't already, you should seriously consider unsubscribing from GitHub notifications for this (https://github.com/openjournals/joss-reviews) repository. As a reviewer, you're probably currently watching this repository which means for GitHub's default behaviour you will receive notifications (emails) for all reviews 😿 To fix this do the following two things:
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@ixjlyons — I see that you haven't checked off any items in your review checklist. Have you been able to get a start on this? Let me know if you have any questions! |
Sorry I haven't gotten to this yet. I will try to get started this week and complete a review over the weekend. |
Hi @ixjlyons — I think you meant to work on this review over the past weekend. Can you give us a status update? We can also set an automatic reminder, if you have a new ETA. |
Apologies for the delay. Here is my review: PaperThe paper is written clearly and offers insight into the functionality of the library. A few minor points:
DocsThe documentation is distributed into the README, a couple other markdown documents, and a Jupyter notebook. These work together to cover much of the library's functionality and usage, but you could benefit from a dedicated documentation site with API documentation generated from the docstrings. Every function appears to have docstrings and those files are browsable through GitHub, so I will defer to @labarba on whether or not that satisfies the functionality documentation check. A few other minor issues:
Code/FunctionalityUnfortunately, I wasn't able to do much with Dynamo being stuck with Linux (no pyrealsense2) and lacking D4XX cameras, so I'm leaving the installation, functionality, and performance checks un-checked. I notice that some of the modules (e.g. Just out of curiosity, have you considered additional storage formats aside from pickle? HDF5 or other formats might work well and could provide better portability. OtherThe tests are not automated, but as far as I know the instructions for running the tests manually suffices for the "automated tests" check. This library poses some challenges for automated testing (with dependence on hardware), though some of the computational aspects of the software could be automatically tested. OverallOverall I think Dynamo would benefit from a dedicated documentation page with API documentation and perhaps automated testing of functionality that doesn't depend on presence of specific hardware. The documentation seems fairly complete, but a more cohesive presentation of it could help newcomers to the library. |
@labarba. I am also done with my review. Specific feedback has been handled on the issue tracker: Since I haven't got access to the cameras I couldn't review all part of the functionality. But what I could check and review does comply with the requirements of JOSS. I agree with @ixjlyons about the lack of API documentation, but it is not blocking in my view. I think the most important comment is the lack of a conda-forge package. It would help guarantee that this package continues to work in the future. However, the current state is in accordance with the requirements of JOSS. |
@whedon generate pdf |
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Hi all, Thank you for the insightful comments and help with getting DynaMo up to JOSS standards so far. I've fixed the errors in the paper and tutorial Jupyter Notebook. Is there anything else needed from me? I am a little unclear if I need to add to the documentation to proceed with the paper. Would a new section on the github which shows how to call each function of the package meet this requirement? If so I'm happy to get that done soon. I will also work on getting this package onto conda-forge. It took me a while to catch up on reading how conda-forge recipes work but I think once we have pyrealsense2 on conda-forge, I can easily create a package for DynaMo. Thanks again for all you contributions so far! |
That is great, but I think you will have to initiate the work with a |
@labarba Is there anything specific that I need to do for us to proceed with the review? I believe I addressed all the reviewer's comments (please let me know if I didn't). I am a bit confused from the reviews if I need to improve the documentation to meet the JOSS standards (since @melund mentioned it was non-blocking), so please let me know what is needed from me. |
Hi @abhishektha — neither of the two reviewers have been able to check the functionality of the software, due to the hardware dependency (cameras) and lack of access. Accepting the paper under those conditions is awkward enough, so I would request that you make every effort at improvements that you can, given the reviewer comments. Since you already have docstrings throughout, it should not be too hard to deploy API documentation using Sphinx? Please have a look at that and let me know what you think. In the meantime, would you be able to suggest someone who may have access to the cameras to provide a check of functionality through a partial & supplementary review? |
Thanks for the reply @labarba! I can definitely deploy API documentation through Sphinx, and will let you and the reviewers know when that is done. Would it be okay if we had someone independently review functionality of the code using our own camera setup in our lab? We have a few colleagues in the field who have not worked with us on this project but may be able to provide a check of functionality. We would simply provide them access to our set of cameras and allow them to hook up their own computer to check functionality. |
hey @abhishektha ... do you have updates with regards to the documentation? As to your question, if you could get someone to contribute some functionality checks to this review, that would good, give the restrictions we face. |
@labarba Sorry for the delay, I had some trouble using Sphinx with the numpydoc style of tooltips I had been using, but its all fixed now and we finally have API documentation hosted on Github Pages and linked from the readme. @ixjlyons, @melund, please let me know if this new API documentation meets the standards. I would like to suggest @alcantarar to contribute functionality checks to the review. He has access to our cameras but has not worked on the development of this project. |
👋 @alcantarar — would you be willing to contribute a partial review of this JOSS submission, given that the assigned reviewers both lack access to the needed hardware to confirm functionality? |
I would be willing to assist with the review. |
@whedon add @alcantarar as reviewer |
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@labarba I think the DOIs are okay now. I did fix a missing reference for the OpenCV library, which was not provided with a DOI. |
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@whedon accept |
No archive DOI set. Exiting... |
@abhishekbajpayee — We need the following pre-publication steps:
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@labarba All done: zenodo DOI: zenodo link: https://zenodo.org/record/3464497 Thanks! |
@whedon set v1.1 as version |
OK. v1.1 is the version. |
@whedon set 10.5281/zenodo.3464497 as archive |
OK. 10.5281/zenodo.3464497 is the archive. |
@whedon accept |
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Check final proof 👉 openjournals/joss-papers#986 If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#986, then you can now move forward with accepting the submission by compiling again with the flag
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@whedon accept deposit=true |
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🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦 |
🚨🚨🚨 THIS IS NOT A DRILL, YOU HAVE JUST ACCEPTED A PAPER INTO JOSS! 🚨🚨🚨 Here's what you must now do:
Any issues? notify your editorial technical team... |
Congratulations, @abhishekbajpayee, your JOSS paper is published! 🚀 Thank you and hats off to our reviewers: @melund, @ixjlyons, @alcantarar — JOSS depends on you! 🙏 |
🎉🎉🎉 Congratulations on your paper acceptance! 🎉🎉🎉 If you would like to include a link to your paper from your README use the following code snippets:
This is how it will look in your documentation: We need your help! Journal of Open Source Software is a community-run journal and relies upon volunteer effort. If you'd like to support us please consider doing either one (or both) of the the following:
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@labarba I think you mean "Congrats @abhishektha!" |
Thank you so much everyone! |
Yikes. Auto-complete fail. |
Submitting author: @abhishektha (Abhishektha Boppana)
Repository: https://github.com/anderson-cu-bioastronautics/dynamo_realsense-capture
Version: v1.1
Editor: @labarba
Reviewers: @melund, @ixjlyons, @alcantarar
Archive: 10.5281/zenodo.3464497
Status
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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
@melund & @ixjlyons, please carry out your review in this issue by updating the checklist below. If you cannot edit the checklist please:
The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. Any questions/concerns please let @labarba know.
✨ Please try and complete your review in the next two weeks ✨
Review checklist for @melund
Conflict of interest
Code of Conduct
General checks
Functionality
Documentation
Software paper
paper.md
file include a list of authors with their affiliations?Review checklist for @ixjlyons
Conflict of interest
Code of Conduct
General checks
Functionality
Documentation
Software paper
paper.md
file include a list of authors with their affiliations?Review checklist for @alcantarar
Conflict of interest
Code of Conduct
General checks
Functionality
Documentation
Software paper
paper.md
file include a list of authors with their affiliations?The text was updated successfully, but these errors were encountered: