Closed editorialbot closed 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:
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For example, to regenerate the paper pdf after making changes in the paper's md or bib files, type:
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Software report:
github.com/AlDanial/cloc v 1.88 T=0.05 s (1147.4 files/s, 126190.2 lines/s)
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Language files blank comment code
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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
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SUM: 53 539 287 5003
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gitinspector failed to run statistical information for the repository
Wordcount for paper.md
is 1363
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
:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:
@editorialbot remind @emstoudenmire in 2 weeks
Reminder set for @emstoudenmire in 2 weeks
@editorialbot remind @gdalle in 2 weeks
Reminder set for @gdalle in 2 weeks
This is still on my radar, no worries βΊοΈ thanks for the reminder
:wave: @emstoudenmire, please update us on how your review is going (this is an automated reminder).
:wave: @gdalle, please update us on how your review is going (this is an automated reminder).
@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.
I haven't forgotten, just completed my previous JOSS review so I'll get to it sometime next week
I haven't forgotten, just completed my previous JOSS review so I'll get to it sometime next week
Thanks a lot @gdalle.
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:
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?@editorialbot generate pdf
:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:
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.
Great β the above changes to the documentation and paper draft completely address all of the issues I raised.
I've also completed my checklist.
@editorialbot generate pdf
@editorialbot check references
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
:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:
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.
Thanks a lot for your review @gdalle!
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.
@editorialbot generate pdf
:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:
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?
I'll take a look this week, thanks!
As far as I'm concerned this is a significant improvement in clarity and accessibility, and we're nearly there!
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.
@editorialbot generate pdf
:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:
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
π @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.
Just checked it, had forgotten to update after you explained the roots of the test failures
@editorialbot generate post-review checklist
I'm sorry human, I don't understand that. You can see what commands I support by typing:
@editorialbot commands
@editorialbot set <DOI here> as archive
@editorialbot set <version here> as version
@editorialbot generate pdf
@editorialbot check references
and ask author(s) to update as needed@editorialbot recommend-accept
@editorialbot check references
@editorialbot generate pdf
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
:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:
@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.
Hi, @osorensen . Thanks for your remarks. We believe they all should be addressed now. I will regenerate the paper for you to verify.
@editorialbot check references
Submitting author: !--author-handle-->@mroavi<!--end-author-handle-- (Martin Roa-Villescas) Repository: https://github.com/TensorBFS/TensorInference.jl Branch with paper.md (empty if default branch): paper Version: v0.4.1 Editor: !--editor-->@osorensen<!--end-editor-- Reviewers: @emstoudenmire, @gdalle Archive: 10.5281/zenodo.8399580
Status
Status badge code:
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:
The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. Any questions/concerns please let @osorensen know.
β¨ 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 β¨
Checklists
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π Checklist for @emstoudenmire