editorialbot commented 11 months ago

Submitting author: !--author-handle-->@mroavi@osorensen<!--end-editor-- Reviewers: @emstoudenmire, @gdalle Archive: 10.5281/zenodo.8399580

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/a6792845b2522b07898cd35e246ec4d2"><img src="https://joss.theoj.org/papers/a6792845b2522b07898cd35e246ec4d2/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/a6792845b2522b07898cd35e246ec4d2/status.svg)](https://joss.theoj.org/papers/a6792845b2522b07898cd35e246ec4d2)

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

@emstoudenmire & @gdalle, 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 @osorensen 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 @gdalle

📝 Checklist for @emstoudenmire

editorialbot commented 11 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 11 months ago

Software report:

github.com/AlDanial/cloc v 1.88  T=0.05 s (1147.4 files/s, 126190.2 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
SVG                              2              1              1           2299
Julia                           23            275            245           1281
Markdown                         9            192              0            744
TeX                              4             38              9            413
YAML                             5              4              9            110
TOML                             7             12              0             98
Lisp                             1             13              0             49
Bourne Shell                     2              4             23              9
-------------------------------------------------------------------------------
SUM:                            53            539            287           5003
-------------------------------------------------------------------------------

gitinspector failed to run statistical information for the repository

editorialbot commented 11 months ago

Wordcount for paper.md is 1363

editorialbot commented 11 months ago

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

OK DOIs

- 10.1137/141000671 is OK
- 10.48550/arXiv.1209.5145 is OK
- 10.48550/arXiv.2108.05665 is OK
- 10.22331/q-2021-03-15-410 is OK
- 10.1103/PhysRevLett.128.030501 is OK
- 10.48550/ARXIV.2205.03718 is OK
- 10.1093/imaiai/iay009 is OK
- 10.1137/050644756 is OK
- 10.1016/j.aop.2014.06.013 is OK
- 10.1038/s42254-019-0086-7 is OK
- 10.1109/DSD57027.2022.00064 is OK
- 10.1145/567806.567807 is OK
- 10.1103/PhysRevB.99.155131 is OK
- 10.1103/PhysRevX.8.031012 is OK
- 10.48550/arXiv.2112.01657 is OK
- 10.1103/physrevlett.126.090506 is OK
- 10.1103/PhysRevX.9.031041 is OK
- 10.21468/SciPostPhysCodeb.4 is OK
- 10.5281/zenodo.8166121 is OK

MISSING DOIs

- 10.1111/j.2517-6161.1988.tb01721.x may be a valid DOI for title: Local computations with probabilities on graphical structures and their application to expert systems

INVALID DOIs

- None

editorialbot commented 11 months ago

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

gdalle commented 11 months ago

Review checklist for @gdalle

Conflict of interest

[x] 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

[x] I confirm that I read and will adhere to the JOSS code of conduct.

General checks

[x] Repository: Is the source code for this software available at the https://github.com/TensorBFS/TensorInference.jl?
[x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
[x] Contribution and authorship: Has the submitting author (@mroavi) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
[x] Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines
[x] Data sharing: If the paper contains original data, data are accessible to the reviewers. If the paper contains no original data, please check this item.
[x] Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
[x] Human and animal research: If the paper contains original data research on humans subjects or animals, does it comply with JOSS's human participants research policy and/or animal research policy? If the paper contains no such data, please check this item.

Functionality

[x] Installation: Does installation proceed as outlined in the documentation?
[x] Functionality: Have the functional claims of the software been confirmed?
[x] 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

[x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
[x] Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
[x] Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
[x] Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
[x] Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
[x] 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

[x] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
[x] 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, who the target audience is, and its relation to other work?
[x] State of the field: Do the authors describe how this software compares to other commonly-used packages?
[x] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
[x] 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?

osorensen commented 11 months ago

@editorialbot remind @emstoudenmire in 2 weeks

editorialbot commented 11 months ago

Reminder set for @emstoudenmire in 2 weeks

osorensen commented 11 months ago

@editorialbot remind @gdalle in 2 weeks

editorialbot commented 11 months ago

Reminder set for @gdalle in 2 weeks

gdalle commented 11 months ago

This is still on my radar, no worries ☺️ thanks for the reminder

editorialbot commented 10 months ago

:wave: @emstoudenmire, please update us on how your review is going (this is an automated reminder).

editorialbot commented 10 months ago

:wave: @gdalle, please update us on how your review is going (this is an automated reminder).

osorensen commented 10 months ago

@emstoudenmire and @gdalle, could you please update us on how it's going with your reviews? I'll also send you a gentle reminder by e-mail.

gdalle commented 10 months ago

I haven't forgotten, just completed my previous JOSS review so I'll get to it sometime next week

emstoudenmire commented 10 months ago

Review checklist for @emstoudenmire

Conflict of interest

[x] 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

[x] I confirm that I read and will adhere to the JOSS code of conduct.

General checks

[x] Repository: Is the source code for this software available at the https://github.com/TensorBFS/TensorInference.jl?
[x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
[x] Contribution and authorship: Has the submitting author (@mroavi) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
[x] Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines
[x] Data sharing: If the paper contains original data, data are accessible to the reviewers. If the paper contains no original data, please check this item.
[x] Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
[x] Human and animal research: If the paper contains original data research on humans subjects or animals, does it comply with JOSS's human participants research policy and/or animal research policy? If the paper contains no such data, please check this item.

Functionality

[x] Installation: Does installation proceed as outlined in the documentation?
[x] Functionality: Have the functional claims of the software been confirmed?
[x] 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

[x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
[x] Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
[x] Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
[x] Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
[x] Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
[x] 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

[x] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
[x] 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, who the target audience is, and its relation to other work?
[x] State of the field: Do the authors describe how this software compares to other commonly-used packages?
[x] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
[x] 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?

osorensen commented 10 months ago

I haven't forgotten, just completed my previous JOSS review so I'll get to it sometime next week

Thanks a lot @gdalle.

emstoudenmire commented 10 months ago

To the authors: @mroavi @GiggleLiu

Overall this is an excellent submission. The need for the software is made clear in the writing, and the software is easy to install and appears to work as claimed. (I ran both of the example codes and the unit tests.)

Here are some points the authors should address before I approve of it:

Would it be helpful to show typical example output of the code demo in the JOSS paper? Or is that not customary? I did note that the output is shown in the documentation.
The documentation does not appear to give any Community Guidelines about how people can get involved in the project. I need to approve that these exists to finish the checklist above.
One detail I noticed about the documentation is that the marginals function returns a set of 2-element arrays, but the docstring does not mention this or explain that aspect of the output. Is there a simple explanation? Could the docstring for marginals be expanded to explain this behavior?

mroavi commented 10 months ago

@editorialbot generate pdf

editorialbot commented 10 months ago

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

mroavi commented 10 months ago

Hi @emstoudenmire,

Thanks for your time and insightful feedback on our submission. We've incorporated your suggestions and added the missing parts. The paper is being regenerated to reflect these changes. You can check out the updated documentation on our dev URL.

emstoudenmire commented 10 months ago

Great – the above changes to the documentation and paper draft completely address all of the issues I raised.

I've also completed my checklist.

osorensen commented 10 months ago

@editorialbot generate pdf

osorensen commented 10 months ago

@editorialbot check references

editorialbot commented 10 months ago

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

OK DOIs

- 10.1137/141000671 is OK
- 10.48550/arXiv.1209.5145 is OK
- 10.48550/arXiv.2108.05665 is OK
- 10.22331/q-2021-03-15-410 is OK
- 10.1103/PhysRevLett.128.030501 is OK
- 10.48550/ARXIV.2205.03718 is OK
- 10.1093/imaiai/iay009 is OK
- 10.1137/050644756 is OK
- 10.1016/j.aop.2014.06.013 is OK
- 10.1038/s42254-019-0086-7 is OK
- 10.1109/DSD57027.2022.00064 is OK
- 10.1145/567806.567807 is OK
- 10.1103/PhysRevB.99.155131 is OK
- 10.1103/PhysRevX.8.031012 is OK
- 10.48550/arXiv.2112.01657 is OK
- 10.1103/physrevlett.126.090506 is OK
- 10.1103/PhysRevX.9.031041 is OK
- 10.21468/SciPostPhysCodeb.4 is OK
- 10.5281/zenodo.8166121 is OK

MISSING DOIs

- 10.1111/j.2517-6161.1988.tb01721.x may be a valid DOI for title: Local computations with probabilities on graphical structures and their application to expert systems

INVALID DOIs

- None

editorialbot commented 10 months ago

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

gdalle commented 10 months ago

Congrats on this cool submission! As is customary, I opened a few issues on the repo, which I hope the authors can address. Most of them are minor, but 66, 67 and 68 are pretty important to me.

osorensen commented 10 months ago

Thanks a lot for your review @gdalle!

mroavi commented 10 months ago

Hi @gdalle. Thank you very much for your thorough review of our submission! We will try to address each of the concerns you raised. If we need to discuss any of them, we will do so under the issues you created.

mroavi commented 10 months ago

@editorialbot generate pdf

editorialbot commented 10 months ago

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

mroavi commented 10 months ago

Hi @gdalle. We've made some changes and hope we've addressed most, if not all, of the issues you raised. We're feeling positive that the submission has improved. Could you take a look and let us know what you think?

gdalle commented 10 months ago

I'll take a look this week, thanks!

gdalle commented 9 months ago

As far as I'm concerned this is a significant improvement in clarity and accessibility, and we're nearly there!

I suggest to merge the summary and statement of need in the paper, because at present they are better understood in reverse order (when reading first the statement of need and then the summary).
I would like to see https://github.com/TensorBFS/TensorInference.jl/issues/65 addressed or at least explained

mroavi commented 9 months ago

Hi @gdalle. Again, thanks for the suggestions to further improve the submission and the package itself.

I suggest to merge the summary and statement of need in the paper, because at present they are better understood in reverse order (when reading first the statement of need and then the summary).

We did the exercise and found that it reads better in reverse order. We swapped the sections but kept them separate. This is because we want to keep these concerns separated and avoid having one very long section.

I would like to see https://github.com/TensorBFS/TensorInference.jl/issues/65 addressed or at least explained

We finally had time to delve into this one. Please see our complete response under the issue you opened. Here is a summary: The tests for both the MAR and PR tasks are now consistent with the reference solutions. We fixed an arithmetic overflow here, which was affecting our PR solutions. As for the MAP and MMAP tasks, we explain why we can't produce solutions for certain problems and why some of our results differ from those of other reference tools.

mroavi commented 9 months ago

@editorialbot generate pdf

editorialbot commented 9 months ago

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

gdalle commented 9 months ago

I'm satisfied with this answer! And after checking the JOSS guidelines, the actual presence of a section named "statement of need" is a requirement, so it is better not to merge

mroavi commented 9 months ago

👋 @gdalle, I noticed that the check mark for the automated tests item is still missing from your list. I'm not sure if this is unintentional or if something is still expected from our side.

gdalle commented 9 months ago

Just checked it, had forgotten to update after you explained the roots of the test failures

osorensen commented 9 months ago

@editorialbot generate post-review checklist

editorialbot commented 9 months ago

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

@editorialbot commands

osorensen commented 9 months ago

Post-Review Checklist for Editor and Authors

Additional Author Tasks After Review is Complete

[ ] Double check authors and affiliations (including ORCIDs)
[ ] Make a release of the software with the latest changes from the review and post the version number here. This is the version that will be used in the JOSS paper.
[ ] Archive the release on Zenodo/figshare/etc and post the DOI here.
[ ] Make sure that the title and author list (including ORCIDs) in the archive match those in the JOSS paper.
[ ] Make sure that the license listed for the archive is the same as the software license.

Editor Tasks Prior to Acceptance

[ ] Read the text of the paper and offer comments/corrections (as either a list or a PR)
[ ] Check the references in the paper for corrections (e.g. capitalization)
[ ] Check that the archive title, author list, version tag, and the license are correct
[ ] Set archive DOI with @editorialbot set <DOI here> as archive
[ ] Set version with @editorialbot set <version here> as version
[ ] Double check rendering of paper with @editorialbot generate pdf
[ ] Specifically check the references with @editorialbot check references and ask author(s) to update as needed
[ ] Recommend acceptance with @editorialbot recommend-accept

osorensen commented 9 months ago

@editorialbot check references

osorensen commented 9 months ago

@editorialbot generate pdf

editorialbot commented 9 months ago

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

OK DOIs

- 10.1137/141000671 is OK
- 10.48550/arXiv.1209.5145 is OK
- 10.48550/arXiv.2108.05665 is OK
- 10.22331/q-2021-03-15-410 is OK
- 10.1103/PhysRevLett.128.030501 is OK
- 10.48550/ARXIV.2205.03718 is OK
- 10.1093/imaiai/iay009 is OK
- 10.1137/050644756 is OK
- 10.1016/j.aop.2014.06.013 is OK
- 10.1038/s42254-019-0086-7 is OK
- 10.1109/DSD57027.2022.00064 is OK
- 10.1145/567806.567807 is OK
- 10.1103/PhysRevB.99.155131 is OK
- 10.1103/PhysRevX.8.031012 is OK
- 10.48550/arXiv.2112.01657 is OK
- 10.1103/physrevlett.126.090506 is OK
- 10.1103/PhysRevX.9.031041 is OK
- 10.21468/SciPostPhysCodeb.4 is OK
- 10.5281/zenodo.8166121 is OK
- 10.7717/peerj-cs.1516 is OK
- 10.21105/joss.05161 is OK
- 10.1007/s10601-016-9245-y is OK

MISSING DOIs

- 10.1111/j.2517-6161.1988.tb01721.x may be a valid DOI for title: Local computations with probabilities on graphical structures and their application to expert systems

INVALID DOIs

- None

editorialbot commented 9 months ago

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

osorensen commented 9 months ago

@mroavi, I'm reading through the paper now and will post suggested edits as issues in your source repository, and add a link to here.

mroavi commented 9 months ago

Hi, @osorensen . Thanks for your remarks. We believe they all should be addressed now. I will regenerate the paper for you to verify.

mroavi commented 9 months ago

@editorialbot check references

openjournals / joss-reviews

[REVIEW]: TensorInference: A Julia package for tensor-based probabilistic inference #5700

Status

Reviewer instructions & questions

Checklists

Review checklist for @gdalle

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

Review checklist for @emstoudenmire

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

Post-Review Checklist for Editor and Authors

Additional Author Tasks After Review is Complete

Editor Tasks Prior to Acceptance