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[REVIEW]: IMPPY3D: Image Processing in Python for 3D Image Stacks #7405

Open editorialbot opened 1 month ago

editorialbot commented 1 month ago

Submitting author: !--author-handle-->@NM0ser<!--end-author-handle-- (Newell Moser) Repository: https://github.com/usnistgov/imppy3d Branch with paper.md (empty if default branch): Version: v1.1.0 Editor: !--editor-->@danielskatz<!--end-editor-- Reviewers: @sitic, @gknapp1 Archive: Pending

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status

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HTML: <a href="https://joss.theoj.org/papers/8971a1c83405db498ceda13cb4a39ee1"><img src="https://joss.theoj.org/papers/8971a1c83405db498ceda13cb4a39ee1/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/8971a1c83405db498ceda13cb4a39ee1/status.svg)](https://joss.theoj.org/papers/8971a1c83405db498ceda13cb4a39ee1)

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

@sitic & @gknapp1, 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 @danielskatz 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 @sitic

📝 Checklist for @gknapp1

editorialbot commented 1 month 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 month ago 
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

✅ OK DOIs

- 10.7717/peerj.453 is OK
- 10.21105/joss.01450 is OK
- 10.1107/S1600577514013939 is OK
- 10.1038/nmeth.2019 is OK
- 10.1186/2193-9772-3-5 is OK
- 10.21105/joss.02286 is OK
- 10.1016/j.softx.2021.100775 is OK
- 10.1007/s40799-024-00715-y is OK
- 10.1007/s40192-023-00333-3 is OK
- 10.1016/j.matdes.2023.112381 is OK
- 10.1038/s41597-023-02092-4 is OK
- 10.1016/j.ijfatigue.2022.106810 is OK
- 10.1016/j.icarus.2024.116166 is OK

🟡 SKIP DOIs

- No DOI given, and none found for title: IMPPY3D
- No DOI given, and none found for title: Dragonfly 3D World
- No DOI given, and none found for title: Avizo
- No DOI given, and none found for title: The OpenCV Library
- No DOI given, and none found for title: The ParaView guide: updated for ParaView version 4...
- No DOI given, and none found for title: Tomviz
- No DOI given, and none found for title: 3D Slicer
- No DOI given, and none found for title: Miniforge

❌ MISSING DOIs

- None

❌ INVALID DOIs

- None
editorialbot commented 1 month ago

Software report:

github.com/AlDanial/cloc v 1.90  T=0.13 s (332.3 files/s, 248850.7 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
C                                1            695           3287          12337
Python                          28           3072           5447           5421
YAML                            10              0              0           1049
Cython                           1             76             79            276
TeX                              1             23              0            252
Markdown                         2             46              0            143
-------------------------------------------------------------------------------
SUM:                            43           3912           8813          19478
-------------------------------------------------------------------------------

Commit count by author:

    25  NM0ser
     8  Moser
     1  Karen Price
editorialbot commented 1 month ago

Paper file info:

📄 Wordcount for paper.md is 1256

✅ The paper includes a Statement of need section

editorialbot commented 1 month ago

License info:

🟡 License found: Other (Check here for OSI approval)

editorialbot commented 1 month ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

danielskatz commented 1 month ago

@sitic & @gknapp1 - Thanks for agreeing to review this submission. This is the review thread for the paper. All of our communications will happen here from now on.

As you can see above, you each should use the command @editorialbot generate my checklist to create your review checklist. @editorialbot commands need to be the first thing in a new comment.

As you go over the submission, please check any items that you feel have been satisfied. There are also links to the JOSS reviewer guidelines.

The JOSS review is different from most other journals. Our goal is to work with the authors to help them meet our criteria instead of merely passing judgment on the submission. As such, reviewers are encouraged to submit issues and pull requests on the software repository. When doing so, please mention openjournals/joss-reviews#7405 so that a link is created to this thread (and I can keep an eye on what is happening). Please also feel free to comment and ask questions on this thread. In my experience, it is better to post comments/questions/suggestions as you come across them instead of waiting until you've reviewed the entire package.

We aim for reviews to be completed within about 2-4 weeks. Please let me know if either of you require some more time. We can also use editorialbot (our bot) to set automatic reminders if you know you'll be away for a known period of time.

Please feel free to ping me (@danielskatz) if you have any questions/concerns.

sitic commented 1 month ago

Review checklist for @sitic

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

gknapp1 commented 1 month ago

Review checklist for @gknapp1

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

sitic commented 3 weeks ago

JOSS has some strict requirements for the LICENSE file:

Acceptable: A plain-text LICENSE or COPYING file with the contents of an OSI approved license https://joss.readthedocs.io/en/latest/review_criteria.html#software-license

The current LICENSE.txt however contains the MIT text with an additional "NIST Disclaimer" added to the end about government work being the public domain. The two other from NIST which went through JOSS review appear to have been using standard MIT licenses:

@NM0ser it is possible to change the LICENSE file to be only the MIT part? Perhaps have the NIST Disclaimer somewhere else?

NM0ser commented 2 weeks ago

Thank you for your comments and effort! We'll work on the official LICENSE.txt file to be in line with the MIT license exactly, and place the NIST disclaimer elsewhere. The paper proofreading fixes are simple enough as well, thanks for pointing those out.

I'm a bit new to the developer's side of packaging Python, so I appreciate the scaffolding you offered. I'll work to make it pip-installable and once proven successful, publish it to PyPI (this one might take a bit longer as I go through this process for the first time).

danielskatz commented 1 day ago

@NM0ser - how are your changes coming along?

danielskatz commented 1 day ago

@sitic & @gknapp1 - Are you able to make more progress in your reviews at this point? Or are you stuck waiting for changes from @NM0ser?

gknapp1 commented 1 day ago

@sitic & @gknapp1 - Are you able to make more progress in your reviews at this point? Or are you stuck waiting for changes from @NM0ser?

I'm waiting on some changes to address automated testing and community guidelines, but they should be relatively minor. The installation comments have been addressed.

@danielskatz, one question about data availability. Do the authors need to provide data to exactly reproduce the example figure in their paper? They have examples for individual parts of the analysis, but it doesn't appear they have a singular example to generate the exact analysis in the paper. Feels okay to me as-is, but I'm not clear on JOSS's stance on data for examples like that.

danielskatz commented 1 day ago

@gknapp1 - JOSS focuses on the software, not reproducibility of the paper. It's important that the software can be installed and checked.

However, if you think it's essential that this figure be reproducible, you should say so.

NM0ser commented 1 day ago

@danielskatz Thanks for checking in! I got a bit tied up with some projects that needed to be completed before the Thanksgiving holiday. But in general, the changes are coming along pretty well. Thanks to the feedback of the reviewers, I fixed the official license, updated the syntax of figure labels in the paper, and made IMPPY3D pip-installable (with Python 3.10). IMPPY3D is now available on PyPi as well. As @gknapp1 mentioned above, there are a couple of things left to do regarding the community guidelines on the ReadMe documentation, and a way to perform automated testing. I've been brainstorming on a what specific features are essential for such testing, and plan to start creating a test suite maybe this coming week, but with the holiday, it may get delayed until the week after.