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

editorialbot commented 1 year ago

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

Status

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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

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

- None

INVALID DOIs

- https://doi.org/10.1111/j.2517-6161.1988.tb01721.x is INVALID because of 'https://doi.org/' prefix

mroavi commented 11 months ago

@editorialbot check references

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
- 10.1111/j.2517-6161.1988.tb01721.x 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

- None

INVALID DOIs

- None

mroavi commented 11 months ago

@editorialbot generate pdf

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:

osorensen commented 11 months ago

Thanks for fixing everything so quickly @mroavi!

osorensen commented 11 months ago

@mroavi, at this point could you:

[x] Make a tagged release of your software, and list the version tag of the archived version here.
[x] Archive the reviewed software in Zenodo or a similar service (e.g., figshare, an institutional repository)
[x] Check the archival deposit (e.g., in Zenodo) has the correct metadata. This includes the title (should match the paper title) and author list (make sure the list is correct and people who only made a small fix are not on it). You may also add the authors' ORCID.
[x] Please list the DOI of the archived version here.

I can then move forward with recommending acceptance of the submission.

mroavi commented 11 months ago

Version tag of the archived version: v0.4.1 DOI of the archived version: 10.5281/zenodo.8399580

osorensen commented 11 months ago

Thanks @mroavi. Could you please change the title of the Zenodo archive so it exactly matches that of the paper: "TensorInference: A Julia package for tensor-based probabilistic inference". This may result in a new DOI, if so, please post it here.

mroavi commented 11 months ago

Oh, I thought I had done that already. Hmm, I see. I clicked on "save" instead of "publish". After publishing the change made to the metadata, The DOI did not change:

Version tag of the archived version: v0.4.1 DOI of the archived version: 10.5281/zenodo.8399580

osorensen commented 11 months ago

@editorialbot set 10.5281/zenodo.8399580 as archive

editorialbot commented 11 months ago

Done! archive is now 10.5281/zenodo.8399580

osorensen commented 11 months ago

@editorialbot set v0.4.1 as version

editorialbot commented 11 months ago

Done! version is now v0.4.1

osorensen commented 11 months ago

@editorialbot recommend-accept

editorialbot commented 11 months ago

Attempting dry run of processing paper acceptance...

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
- 10.1111/j.2517-6161.1988.tb01721.x 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

- None

INVALID DOIs

- None

editorialbot commented 11 months ago

:wave: @openjournals/dsais-eics, this paper is ready to be accepted and published.

Check final proof :point_right::page_facing_up: Download article

If the paper PDF and the deposit XML files look good in https://github.com/openjournals/joss-papers/pull/4644, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

arfon commented 10 months ago

@editorialbot accept

editorialbot commented 10 months ago

Doing it live! Attempting automated processing of paper acceptance...

editorialbot commented 10 months ago

Ensure proper citation by uploading a plain text CITATION.cff file to the default branch of your repository.

If using GitHub, a Cite this repository menu will appear in the About section, containing both APA and BibTeX formats. When exported to Zotero using a browser plugin, Zotero will automatically create an entry using the information contained in the .cff file.

You can copy the contents for your CITATION.cff file here:

CITATION.cff

``` cff-version: "1.2.0" authors: - family-names: Roa-Villescas given-names: Martin orcid: "https://orcid.org/0009-0009-0291-503X" - family-names: Liu given-names: Jin-Guo orcid: "https://orcid.org/0000-0003-1635-2679" doi: 10.5281/zenodo.8399580 message: If you use this software, please cite our article in the Journal of Open Source Software. preferred-citation: authors: - family-names: Roa-Villescas given-names: Martin orcid: "https://orcid.org/0009-0009-0291-503X" - family-names: Liu given-names: Jin-Guo orcid: "https://orcid.org/0000-0003-1635-2679" date-published: 2023-10-03 doi: 10.21105/joss.05700 issn: 2475-9066 issue: 90 journal: Journal of Open Source Software publisher: name: Open Journals start: 5700 title: "TensorInference: A Julia package for tensor-based probabilistic inference" type: article url: "https://joss.theoj.org/papers/10.21105/joss.05700" volume: 8 title: "TensorInference: A Julia package for tensor-based probabilistic inference" ```

If the repository is not hosted on GitHub, a .cff file can still be uploaded to set your preferred citation. Users will be able to manually copy and paste the citation.

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editorialbot commented 10 months ago

🐘🐘🐘 👉 Toot for this paper 👈 🐘🐘🐘

editorialbot commented 10 months ago

🚨🚨🚨 THIS IS NOT A DRILL, YOU HAVE JUST ACCEPTED A PAPER INTO JOSS! 🚨🚨🚨

Here's what you must now do:

Check final PDF and Crossref metadata that was deposited :point_right: https://github.com/openjournals/joss-papers/pull/4646
Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.05700
If everything looks good, then close this review issue.
Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

arfon commented 10 months ago

@emstoudenmire, @gdalle – many thanks for your reviews here and to @osorensen for editing this submission! JOSS relies upon the volunteer effort of people like you and we simply wouldn't be able to do this without you ✨

@mroavi – your paper is now accepted and published in JOSS :zap::rocket::boom:

editorialbot commented 10 months ago

:tada::tada::tada: Congratulations on your paper acceptance! :tada::tada::tada:

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  <img src="https://joss.theoj.org/papers/10.21105/joss.05700/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.05700/status.svg
   :target: https://doi.org/10.21105/joss.05700

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mroavi commented 10 months ago

Paper accepted 🥳! A huge thanks to our editor @osorensen and to our reviewers @emstoudenmire and @gdalle. Your feedback helped improve our submission quite considerably. We appreciate the time and effort you've put into this. You've made this process not only constructive but also very enjoyable. We are grateful for your support for open-source projects and science in general.

OriolAbril commented 10 months ago

Is it still possible to update the pdf?

It looks like there are some commas missing in https://github.com/TensorBFS/TensorInference.jl/blob/paper/paper/paper.bib#L325 and the reference is rendered using our full names and abbreviated surnames instead of the standard way

osorensen commented 10 months ago

Sorry @OriolAbril, I doubt that is possible, but I'll ask the track editor @openjournals/dsais-eics just to be sure.

mroavi commented 10 months ago

@osorensen I'd also like to make a small update if possible. Realized I forgot to mention the NWO project number that's been funding part of our research. Eager to hear what the track editor decides!

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