editorialbot commented 2 years ago

Submitting author: !--author-handle-->@jessdtate@kellyrowland<!--end-editor-- Reviewers: @shahmoradi, @RichardClayton, @kellyrowland Archive: 10.5281/zenodo.8226383

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/660d2fe53fbf67dd2714e9546251bd33"><img src="https://joss.theoj.org/papers/660d2fe53fbf67dd2714e9546251bd33/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/660d2fe53fbf67dd2714e9546251bd33/status.svg)](https://joss.theoj.org/papers/660d2fe53fbf67dd2714e9546251bd33)

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

@shahmoradi & @RichardClayton, 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 @kellyrowland 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 @shahmoradi

📝 Checklist for @RichardClayton

📝 Checklist for @kellyrowland

kellyrowland commented 10 months ago

@editorialbot set 10.5281/zenodo.8226383 as archive

editorialbot commented 10 months ago

Done! archive is now 10.5281/zenodo.8226383

kellyrowland commented 10 months ago

@editorialbot set v1.0 as version

editorialbot commented 10 months ago

Done! version is now v1.0

kellyrowland commented 10 months ago

Post-Review Checklist for Editor and Authors

Additional Author Tasks After Review is Complete

[ ] Double check authors and affiliations (including ORCIDs)
[x] 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.
[x] 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.
[x] Make sure that the license listed for the archive is the same as the software license.

Editor Tasks Prior to Acceptance

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

kellyrowland 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:

kellyrowland commented 10 months ago

@editorialbot check references

kellyrowland commented 10 months ago

@jessdtate thanks - it looks like the title and author list differ between the archive and what's in the paper. I think you'll want to update the archive to include all of the authors listed and change the title to match the paper title as well.

editorialbot commented 10 months ago

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

OK DOIs

- 10.1002/cnm.3395 is OK
- 10.1007/s10439-011-0391-5 is OK
- 10.1109/iembs.2005.1615736 is OK
- 10.1007/978-3-030-78710-3_49 is OK
- 10.22489/CinC.2020.275 is OK
- 10.23919/cinc53138.2021.9662950 is OK
- 10.23919/cinc53138.2021.9662837 is OK
- 10.1109/TMI.2015.2464315 is OK
- 10.1016/j.brs.2021.10.226 is OK
- 10.1007/978-3-540-28650-9_4 is OK
- 10.1137/17M1140960 is OK
- 10.5802/smai-jcm.24 is OK
- 10.1553/etna_vol50s71 is OK

MISSING DOIs

- 10.1007/978-3-319-10470-6_66 may be a valid DOI for title: Variational Bayesian electrophysiological imaging of myocardial infarction.

INVALID DOIs

- None

kellyrowland commented 10 months ago

Looks like the JDT:Xu2014 bibliography entry could use an addition of doi = "10.1007/978-3-319-10470-6_66", as well.

arfon commented 9 months ago

@kellyrowland – it looks like this paper is pretty much ready to accept. Do you agree?

kellyrowland commented 9 months ago

@arfon I would agree that this paper is just about ready to accept. I am mildly concerned about the discrepancies between the paper and the archive entry that I mentioned above, but if the EiCs don't see that as a blocker for acceptance then we can move forward.

arfon commented 9 months ago

👍 In an effort to keep things moving, I proposed we move on.

kellyrowland commented 9 months ago

@editorialbot recommend-accept

editorialbot commented 9 months ago

Attempting dry run of processing paper acceptance...

editorialbot commented 9 months ago

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

OK DOIs

- 10.1002/cnm.3395 is OK
- 10.1007/s10439-011-0391-5 is OK
- 10.1109/iembs.2005.1615736 is OK
- 10.1007/978-3-030-78710-3_49 is OK
- 10.22489/CinC.2020.275 is OK
- 10.23919/cinc53138.2021.9662950 is OK
- 10.23919/cinc53138.2021.9662837 is OK
- 10.1109/TMI.2015.2464315 is OK
- 10.1016/j.brs.2021.10.226 is OK
- 10.1007/978-3-540-28650-9_4 is OK
- 10.1137/17M1140960 is OK
- 10.5802/smai-jcm.24 is OK
- 10.1553/etna_vol50s71 is OK

MISSING DOIs

- 10.1007/978-3-319-10470-6_66 may be a valid DOI for title: Variational Bayesian electrophysiological imaging of myocardial infarction.

INVALID DOIs

- None

editorialbot commented 9 months ago

:warning: Error preparing paper acceptance. The generated XML metadata file is invalid.

Element isbn: [facet 'minLength'] The value has a length of '9'; this underruns the allowed minimum length of '10'.

kellyrowland commented 9 months ago

@jessdtate I've opened https://github.com/SCIInstitute/UncertainSCI/pull/113 to address the issue above; please take a look when you're able to.

kellyrowland commented 9 months ago

@editorialbot recommend-accept

editorialbot commented 9 months ago

Attempting dry run of processing paper acceptance...

editorialbot commented 9 months ago

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

OK DOIs

- 10.1002/cnm.3395 is OK
- 10.1007/s10439-011-0391-5 is OK
- 10.1109/iembs.2005.1615736 is OK
- 10.1007/978-3-030-78710-3_49 is OK
- 10.22489/CinC.2020.275 is OK
- 10.23919/cinc53138.2021.9662950 is OK
- 10.23919/cinc53138.2021.9662837 is OK
- 10.1109/TMI.2015.2464315 is OK
- 10.1016/j.brs.2021.10.226 is OK
- 10.1007/978-3-540-28650-9_4 is OK
- 10.1137/17M1140960 is OK
- 10.5802/smai-jcm.24 is OK
- 10.1553/etna_vol50s71 is OK

MISSING DOIs

- 10.1007/978-3-319-10470-6_66 may be a valid DOI for title: Variational Bayesian electrophysiological imaging of myocardial infarction.

INVALID DOIs

- None

editorialbot commented 9 months ago

:wave: @openjournals/sbcs-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/4681, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

oliviaguest commented 9 months ago

@editorialbot recommend-accept

editorialbot commented 9 months ago

Attempting dry run of processing paper acceptance...

editorialbot commented 9 months ago

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

OK DOIs

- 10.1002/cnm.3395 is OK
- 10.1007/s10439-011-0391-5 is OK
- 10.1109/iembs.2005.1615736 is OK
- 10.1007/978-3-030-78710-3_49 is OK
- 10.22489/CinC.2020.275 is OK
- 10.23919/cinc53138.2021.9662950 is OK
- 10.23919/cinc53138.2021.9662837 is OK
- 10.1109/TMI.2015.2464315 is OK
- 10.1016/j.brs.2021.10.226 is OK
- 10.1007/978-3-540-28650-9_4 is OK
- 10.1137/17M1140960 is OK
- 10.5802/smai-jcm.24 is OK
- 10.1553/etna_vol50s71 is OK

MISSING DOIs

- 10.1007/978-3-319-10470-6_66 may be a valid DOI for title: Variational Bayesian electrophysiological imaging of myocardial infarction.

INVALID DOIs

- None

oliviaguest commented 9 months ago

@jessdtate I think this is the correct DOI for the article?

Xu, J., Sapp, J.L., Rahimi Dehaghani, A., Gao, F., Wang, L. (2014). Variational Bayesian Electrophysiological Imaging of Myocardial Infarction. In: Golland, P., Hata, N., Barillot, C., Hornegger, J., Howe, R. (eds) Medical Image Computing and Computer-Assisted Intervention – MICCAI 2014. MICCAI 2014. Lecture Notes in Computer Science, vol 8674. Springer, Cham. https://doi.org/10.1007/978-3-319-10470-6_66

editorialbot commented 9 months ago

:wave: @openjournals/sbcs-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/4697, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

jessdtate commented 9 months ago

@oliviaguest I've made a tag of a branch with the suggested changes, v1.0.1.1. It should be merged into master soon.

oliviaguest commented 9 months ago

@kellyrowland have you used the checklist for this? 😊 see below...

Edit: I see one from August! Sorry!

oliviaguest commented 9 months ago

@jessdtate can you run check citations command when it's done, please? ☺️

jessdtate commented 8 months ago

@editorialbot check references

editorialbot commented 8 months ago

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

OK DOIs

- 10.1002/cnm.3395 is OK
- 10.1007/s10439-011-0391-5 is OK
- 10.1109/iembs.2005.1615736 is OK
- 10.1007/978-3-030-78710-3_49 is OK
- 10.22489/CinC.2020.275 is OK
- 10.23919/cinc53138.2021.9662950 is OK
- 10.23919/cinc53138.2021.9662837 is OK
- 10.1109/TMI.2015.2464315 is OK
- 10.1016/j.brs.2021.10.226 is OK
- 10.1007/978-3-319-10470-6_66 is OK
- 10.1007/978-3-319-10470-6_66 is OK
- 10.1007/978-3-540-28650-9_4 is OK
- 10.1137/17M1140960 is OK
- 10.5802/smai-jcm.24 is OK
- 10.1553/etna_vol50s71 is OK

MISSING DOIs

- None

INVALID DOIs

- None

oliviaguest commented 8 months ago

Thank you!!!

oliviaguest commented 8 months ago

@editorialbot recommend-accept

editorialbot commented 8 months ago

Attempting dry run of processing paper acceptance...

editorialbot commented 8 months ago

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

OK DOIs

- 10.1002/cnm.3395 is OK
- 10.1007/s10439-011-0391-5 is OK
- 10.1109/iembs.2005.1615736 is OK
- 10.1007/978-3-030-78710-3_49 is OK
- 10.22489/CinC.2020.275 is OK
- 10.23919/cinc53138.2021.9662950 is OK
- 10.23919/cinc53138.2021.9662837 is OK
- 10.1109/TMI.2015.2464315 is OK
- 10.1016/j.brs.2021.10.226 is OK
- 10.1007/978-3-319-10470-6_66 is OK
- 10.1007/978-3-319-10470-6_66 is OK
- 10.1007/978-3-540-28650-9_4 is OK
- 10.1137/17M1140960 is OK
- 10.5802/smai-jcm.24 is OK
- 10.1553/etna_vol50s71 is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot commented 8 months ago

:wave: @openjournals/sbcs-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/4729, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

oliviaguest commented 8 months ago

@editorialbot accept

editorialbot commented 8 months ago

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

editorialbot commented 8 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: Tate given-names: Jess orcid: "https://orcid.org/0000-0002-2934-1453" - family-names: Liu given-names: Zexin orcid: "https://orcid.org/0000-0003-3409-5709" - family-names: Bergquist given-names: Jake A orcid: "https://orcid.org/0000-0002-4586-6911" - family-names: Rampersad given-names: Sumientra orcid: "https://orcid.org/0000-0001-9860-4459" - family-names: White given-names: Dan - family-names: Charlebois given-names: Chantel orcid: "https://orcid.org/0000-0002-4139-3539" - family-names: Rupp given-names: Lindsay orcid: "https://orcid.org/0000-0002-2688-7688" - family-names: Brooks given-names: Dana H orcid: "https://orcid.org/0000-0003-3231-6715" - family-names: MacLeod given-names: Rob S orcid: "https://orcid.org/0000-0002-0000-0356" - family-names: Narayan given-names: Akil orcid: "https://orcid.org/0000-0002-5914-4207" doi: 10.5281/zenodo.8226383 message: If you use this software, please cite our article in the Journal of Open Source Software. preferred-citation: authors: - family-names: Tate given-names: Jess orcid: "https://orcid.org/0000-0002-2934-1453" - family-names: Liu given-names: Zexin orcid: "https://orcid.org/0000-0003-3409-5709" - family-names: Bergquist given-names: Jake A orcid: "https://orcid.org/0000-0002-4586-6911" - family-names: Rampersad given-names: Sumientra orcid: "https://orcid.org/0000-0001-9860-4459" - family-names: White given-names: Dan - family-names: Charlebois given-names: Chantel orcid: "https://orcid.org/0000-0002-4139-3539" - family-names: Rupp given-names: Lindsay orcid: "https://orcid.org/0000-0002-2688-7688" - family-names: Brooks given-names: Dana H orcid: "https://orcid.org/0000-0003-3231-6715" - family-names: MacLeod given-names: Rob S orcid: "https://orcid.org/0000-0002-0000-0356" - family-names: Narayan given-names: Akil orcid: "https://orcid.org/0000-0002-5914-4207" date-published: 2023-10-27 doi: 10.21105/joss.04249 issn: 2475-9066 issue: 90 journal: Journal of Open Source Software publisher: name: Open Journals start: 4249 title: "UncertainSCI: A Python Package for Noninvasive Parametric Uncertainty Quantification of Simulation Pipelines" type: article url: "https://joss.theoj.org/papers/10.21105/joss.04249" volume: 8 title: "UncertainSCI: A Python Package for Noninvasive Parametric Uncertainty Quantification of Simulation Pipelines" ```

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.

Find more information on .cff files here and here.

editorialbot commented 8 months ago

🐘🐘🐘 👉 Toot for this paper 👈 🐘🐘🐘

editorialbot commented 8 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/4732
Wait five minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.04249
If everything looks good, then close this review issue.
Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

oliviaguest commented 8 months ago

Huge thanks to the reviewers @shahmoradi, @RichardClayton, and also editor @kellyrowland! ✨ JOSS appreciates your work and effort. ✨ Also, big congratulations to the authors (@jessdtate)! 🥳 🍾

editorialbot commented 8 months ago

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

If you would like to include a link to your paper from your README use the following code snippets:

Markdown:
[![DOI](https://joss.theoj.org/papers/10.21105/joss.04249/status.svg)](https://doi.org/10.21105/joss.04249)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.04249">
  <img src="https://joss.theoj.org/papers/10.21105/joss.04249/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.04249/status.svg
   :target: https://doi.org/10.21105/joss.04249

This is how it will look in your documentation:

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openjournals / joss-reviews

[REVIEW]: UncertainSCI: A Python Package for Noninvasive Parametric Uncertainty Quantification of Simulation Pipelines #4249

Status

Reviewer instructions & questions

Checklists

Post-Review Checklist for Editor and Authors

Additional Author Tasks After Review is Complete

Editor Tasks Prior to Acceptance