search

openjournals / joss-reviews

Reviews for the Journal of Open Source Software
Creative Commons Zero v1.0 Universal
694 stars 36 forks source link

[REVIEW]: VisualTorch: Streamlining Visualization for PyTorch Neural Network Architectures #6678

Open editorialbot opened 2 months ago

editorialbot commented 2 months ago

Submitting author: !--author-handle-->@willyfh<!--end-author-handle-- (Willy Fitra Hendria) Repository: https://github.com/willyfh/visualtorch Branch with paper.md (empty if default branch): joss-review Version: v0.2.2 Editor: !--editor-->@jromanowska<!--end-editor-- Reviewers: @Asieh-A-Mofrad, @dgrell Archive: Pending

Status

status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/766c23fd3c7d174aab5443e7ac073043"><img src="https://joss.theoj.org/papers/766c23fd3c7d174aab5443e7ac073043/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/766c23fd3c7d174aab5443e7ac073043/status.svg)](https://joss.theoj.org/papers/766c23fd3c7d174aab5443e7ac073043)

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

@Asieh-A-Mofrad & @dgrell, 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 @jromanowska 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 @Asieh-A-Mofrad

📝 Checklist for @dgrell

editorialbot commented 2 months 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 2 months ago 
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1109/MCSE.2007.55 is OK
- 10.1109/5.726791 is OK

MISSING DOIs

- No DOI given, and none found for title: An Empirical Study of Library Usage and Dependency...
- No DOI given, and none found for title: visualkeras
- 10.1163/2214-8647_dnp_e612900 may be a valid DOI for title: Keras
- No DOI given, and none found for title: PyTorch: An Imperative Style, High-Performance Dee...
- No DOI given, and none found for title:  TensorFlow: Large-Scale Machine Learning on Heter...

INVALID DOIs

- None
editorialbot commented 2 months ago

Software report:

github.com/AlDanial/cloc v 1.90  T=0.03 s (1743.2 files/s, 123510.9 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          26            472            376           1625
Markdown                        16            177              0            368
XML                              1              0              0            328
YAML                             6             34             23            126
TOML                             1             24             25            118
TeX                              1              7              0             65
DOS Batch                        1              8              1             26
make                             1              4              7              9
CSS                              1              0              0              3
-------------------------------------------------------------------------------
SUM:                            54            726            432           2668
-------------------------------------------------------------------------------

Commit count by author:

    43  Willy Fitra Hendria
editorialbot commented 2 months ago

Paper file info:

📄 Wordcount for paper.md is 769

✅ The paper includes a Statement of need section

editorialbot commented 2 months ago

License info:

✅ License found: MIT License (Valid open source OSI approved license)

editorialbot commented 2 months ago

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

jromanowska commented 2 months ago

👋🏼 @willyfh @Asieh-A-Mofrad @dgrell this is the review thread for the paper. All of our communications will happen here from now on.

As a reviewer, the first step is to create a checklist for your review by entering

@editorialbot generate my checklist

as the top of a new comment in this thread.

These checklists contain the JOSS requirements. As you go over the submission, please check any items that you feel have been satisfied. The first comment in this thread also contains 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, the reviewers are encouraged to submit issues and pull requests on the software repository. When doing so, please mention openjournals/joss-reviews#6678 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 any 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 (@jromanowska) if you have any questions/concerns.

jromanowska commented 2 months ago

@willyfh - could you address the missing DOI issue first and re-generate the paper?

Asieh-A-Mofrad commented 2 months ago

Review checklist for @Asieh-A-Mofrad

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

willyfh commented 2 months ago

@editorialbot generate pdf

editorialbot commented 2 months ago

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

willyfh commented 2 months ago

@willyfh - could you address the missing DOI issue first and re-generate the paper?

👋🏼 @jromanowska, I have addressed the missing DOIs first. As far as I found, for VisualKeras and Keras, there are no DOIs for the GitHub repositories. Thank you.

willyfh commented 2 months ago

@editorialbot generate pdf

editorialbot commented 2 months ago

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

willyfh commented 2 months ago

@willyfh - could you address the missing DOI issue first and re-generate the paper?

👋🏼 @jromanowska, I have addressed the missing DOIs first. As far as I found, for VisualKeras and Keras, there are no DOIs for the GitHub repositories. Thank you.

In addition, I have also updated the paper by including the code in the examples as code instead of presenting them as figure. Thank you for your comments

jromanowska commented 1 month ago

Hi, @dgrell - are you still up to review this submission? Could you generate your checklist so that we see the progress?

dgrell commented 1 month ago

Review checklist for @dgrell

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

jromanowska commented 1 month ago

@willyfh - FYI, I've contacted the reviewers and asked them to update us on their progress.

Asieh-A-Mofrad commented 1 month ago

Hi, Sorry for not showing up for a while. I'm still on the task and try to do some progress during this week. @willyfh could you please check the hyperlink on the MIT licence? The link (https://github.com/willyfh/visualtorch/blob/update-readme/LICENSE) ends up to '404 - page not found' message.

Asieh-A-Mofrad commented 1 month ago

@willyfh This is the correct link: https://github.com/willyfh/visualtorch/blob/main/LICENSE Please update the hyperlink.

Asieh-A-Mofrad commented 1 month ago

@editorialbot pre-review

editorialbot commented 1 month ago

I'm sorry human, I don't understand that. You can see what commands I support by typing:

@editorialbot commands

Asieh-A-Mofrad commented 1 month ago

@editorialbot commands

editorialbot commented 1 month ago

Hello @Asieh-A-Mofrad, here are the things you can ask me to do:


# List all available commands
@editorialbot commands

# Get a list of all editors's GitHub handles
@editorialbot list editors

# Adds a checklist for the reviewer using this command
@editorialbot generate my checklist

# Set a value for branch
@editorialbot set joss-paper as branch

# Run checks and provide information on the repository and the paper file
@editorialbot check repository

# Check the references of the paper for missing DOIs
@editorialbot check references

# Generates the pdf paper
@editorialbot generate pdf

# Generates a LaTeX preprint file
@editorialbot generate preprint

# Get a link to the complete list of reviewers
@editorialbot list reviewers
Asieh-A-Mofrad commented 4 weeks ago

@editorialbot check repository

editorialbot commented 4 weeks ago

Software report:

github.com/AlDanial/cloc v 1.90  T=0.03 s (1742.6 files/s, 128465.2 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          26            472            376           1625
Markdown                        16            197              0            439
XML                              1             14              0            377
YAML                             6             34             23            126
TOML                             1             24             25            118
TeX                              1              7              0             66
DOS Batch                        1              8              1             26
make                             1              4              7              9
CSS                              1              0              0              3
-------------------------------------------------------------------------------
SUM:                            54            760            432           2789
-------------------------------------------------------------------------------

Commit count by author:

    45  Willy Fitra Hendria
editorialbot commented 4 weeks ago

Paper file info:

📄 Wordcount for paper.md is 931

✅ The paper includes a Statement of need section

editorialbot commented 4 weeks ago

License info:

✅ License found: MIT License (Valid open source OSI approved license)

willyfh commented 3 weeks ago

@willyfh - FYI, I've contacted the reviewers and asked them to update us on their progress.

@jromanowska Thank you for your assistance. I will monitor for their updates and revise my submission accordingly. :+1:

@willyfh This is the correct link: https://github.com/willyfh/visualtorch/blob/main/LICENSE Please update the hyperlink.

@Asieh-A-Mofrad Thank you for your feedback. I have fixed the hyperlink as requested :+1:

jromanowska commented 3 weeks ago

@dgrell - we are waiting patiently for your comments - when can we expect the review to be ready?

dgrell commented 3 weeks ago

https://github.com/willyfh/visualtorch/issues/48 is substantial. Also, looking at the code for visualkeras, a clearer statement of which parts are new/modified in visualtorch would be helpful for the review process.

dgrell commented 3 weeks ago

@jromanowska Question about the bullet points listed under "Documentation". Is it OK for them to be somewhere in the codebase, or is the idea that all these points should be mentioned on the documentation website https://visualtorch.readthedocs.io/ ?

I don't know what's common practice here, I personally prefer the latter.

jromanowska commented 3 weeks ago

@jromanowska Question about the bullet points listed under "Documentation". Is it OK for them to be somewhere in the codebase, or is the idea that all these points should be mentioned on the documentation website visualtorch.readthedocs.io ?

I don't know what's common practice here, I personally prefer the latter.

All these should be easily accessible - in case of python, these should be on the documentation website :+1:

jromanowska commented 3 weeks ago

willyfh/visualtorch#48 is substantial. Also, looking at the code for visualkeras, a clearer statement of which parts are new/modified in visualtorch would be helpful for the review process.

Thank you for checking! We'll wait for @willyfh to explain in details which parts are new or modified - this is an important issue, as you noticed. As long as your code provides new functionality, which is useful for researchers, using code from another software is fine, however, it needs to be clearly stated and properly cited, using correct licences, etc.

jromanowska commented 3 weeks ago

@Asieh-A-Mofrad - how is checking functionality going?

Asieh-A-Mofrad commented 2 weeks ago

@jromanowska I'm almost done with the review process. The paper appears to be well written and situate VisualTorch within the field of neural network visualization tools. There are some repetitions but it is structured logically, with sections for the summary, statement of need, introduction, usage examples, and acknowledgements. @willyfh Please check the reference to TensorFlow (Abadi:2015?) and edit it.

jromanowska commented 2 weeks ago

FYI, @willyfh, I will be on holidays the entire July.

jromanowska commented 2 days ago

@willyfh , I hope you're doing well. Could you provide some answers to the reviewers? The best would be during this week as I am on holidays entire July.

willyfh commented 2 days ago

@willyfh , I hope you're doing well. Could you provide some answers to the reviewers? The best would be during this week as I am on holidays entire July.

👋🏼 @jromanowska, I am sorry I was busy with my notice period as I will be changing my company soon. I will provide my responses and revise the papers based on the reviewers' comments as soon as possible within this week. Sorry for any inconvenience caused. 🙏

cc: @Asieh-A-Mofrad @dgrell

willyfh commented 1 day ago

@editorialbot generate pdf

editorialbot commented 1 day ago

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