[REVIEW]: Ciclope: micro Computed Tomography to Finite Elements

editorialbot commented 1 year ago

Submitting author: !--author-handle-->@gianthk@danasolav<!--end-editor-- Reviewers: @dankusanovic, @jacobmerson Archive: 10.5281/zenodo.7716943

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Markdown: [![status](https://joss.theoj.org/papers/8f9176ffe46a0ef54f93ad860ff7b731/status.svg)](https://joss.theoj.org/papers/8f9176ffe46a0ef54f93ad860ff7b731)

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

@dankusanovic & @jacobmerson, 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

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✨ 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 @jacobmerson

📝 Checklist for @dankusanovic

editorialbot commented 1 year ago

Done! Archive is now https://doi.org/10.5281/zenodo.7716943

danasolav commented 1 year ago

@editorialbot set v1.3.4 as version

editorialbot commented 1 year ago

Done! version is now v1.3.4

danasolav commented 1 year ago

@editorialbot recommend-accept

editorialbot commented 1 year ago

Attempting dry run of processing paper acceptance...

editorialbot commented 1 year ago

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

IDREFS attribute rid references an unknown ID "Examples"

editorialbot commented 1 year ago

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

OK DOIs

- 10.1016/S0021-9290(03)00257-4 is OK
- 10.1016/S8756-3282(02)00736-6 is OK
- 10.1016/j.jbiomech.2020.110205 is OK
- 10.1115/1.2746368 is OK
- 10.1016/j.jbiomech.2008.02.032 is OK
- 10.1115/1.2146001 is OK
- 10.1007/s10237-019-01254-x is OK
- 10.1371/journal.pone.0180151 is OK
- 10.1002/cnm.2941 is OK
- 10.1007/978-3-642-29843-1_56 is OK
- 10.1016/j.parco.2011.08.001 is OK
- 10.1016/j.jmbbm.2020.104190 is OK
- 10.1016/j.jmbbm.2018.06.022 is OK
- 10.1016/j.medntd.2021.100088 is OK
- 10.1115/1.4028968 is OK
- 10.1007/s10237-007-0109-7 is OK
- 10.1016/j.bonr.2022.101179 is OK
- 10.1016/j.jmbbm.2022.105303 is OK
- 10.1101/2021.11.30.470675 is OK
- 10.1016/j.cmpb.2022.106764 is OK
- 10.1016/j.jbiomech.2003.10.002 is OK
- 10.1109/tsmc.1979.4310076 is OK
- 10.1109/tsmc.1978.4310039 is OK
- 10.1007/s10237-008-0125-2 is OK
- 10.5281/zenodo.1173115 is OK
- 10.5281/zenodo.5564818 is OK
- 10.1107/S160057751401604X is OK
- 10.1002/adem.201900080 is OK
- 10.1016/j.jmbbm.2016.11.020 is OK
- 10.1080/10255840701848756 is OK
- 10.1080/10255840410001656408 is OK
- 10.1038/s41592-019-0686-2 is OK
- 10.7717/peerj.453 is OK

MISSING DOIs

- None

INVALID DOIs

- None

arfon commented 1 year ago

@danasolav @gianthk – it looks like the paper is referencing a figure that doesn't exist which is causing the JATS validation to fail (https://github.com/openjournals/joss-reviews/issues/4952#issuecomment-1465576720). Can you please see if you can resolve this?

gianthk commented 1 year ago

@arfon @danasolav the issue was not a missing figure, but a wrong internal ref to the Examples section. It should be fixed now, pointing to the readthedocs Examples page.

gianthk commented 1 year ago

@arfon @danasolav can you please check again if the paper can build? the previous issue should be solved

danasolav commented 1 year ago

@editorialbot recommend-accept

editorialbot commented 1 year ago

Attempting dry run of processing paper acceptance...

editorialbot commented 1 year ago

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

OK DOIs

- 10.1016/S0021-9290(03)00257-4 is OK
- 10.1016/S8756-3282(02)00736-6 is OK
- 10.1016/j.jbiomech.2020.110205 is OK
- 10.1115/1.2746368 is OK
- 10.1016/j.jbiomech.2008.02.032 is OK
- 10.1115/1.2146001 is OK
- 10.1007/s10237-019-01254-x is OK
- 10.1371/journal.pone.0180151 is OK
- 10.1002/cnm.2941 is OK
- 10.1007/978-3-642-29843-1_56 is OK
- 10.1016/j.parco.2011.08.001 is OK
- 10.1016/j.jmbbm.2020.104190 is OK
- 10.1016/j.jmbbm.2018.06.022 is OK
- 10.1016/j.medntd.2021.100088 is OK
- 10.1115/1.4028968 is OK
- 10.1007/s10237-007-0109-7 is OK
- 10.1016/j.bonr.2022.101179 is OK
- 10.1016/j.jmbbm.2022.105303 is OK
- 10.1101/2021.11.30.470675 is OK
- 10.1016/j.cmpb.2022.106764 is OK
- 10.1016/j.jbiomech.2003.10.002 is OK
- 10.1109/tsmc.1979.4310076 is OK
- 10.1109/tsmc.1978.4310039 is OK
- 10.1007/s10237-008-0125-2 is OK
- 10.5281/zenodo.1173115 is OK
- 10.5281/zenodo.5564818 is OK
- 10.1107/S160057751401604X is OK
- 10.1002/adem.201900080 is OK
- 10.1016/j.jmbbm.2016.11.020 is OK
- 10.1080/10255840701848756 is OK
- 10.1080/10255840410001656408 is OK
- 10.1038/s41592-019-0686-2 is OK
- 10.7717/peerj.453 is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot commented 1 year ago

:wave: @openjournals/bcm-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/4064, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

Kevin-Mattheus-Moerman commented 1 year ago

@editorialbot set 10.5281/zenodo.7716943 as archive

editorialbot commented 1 year ago

Done! Archive is now 10.5281/zenodo.7716943

Kevin-Mattheus-Moerman commented 1 year ago

@gianthk I am the AEiC for this track and here to help process the final steps. Below are some minor points which require your attention:

On the paper:

[x] Please add the town/city for affiliation 1
[x] Please write United Kingdom, instead of UK for affiliation 3.

On the archive:

[x] Please manually edit the archive listed license to match your open source license. It currently says "Creative Commons Attribution 4.0 International", but it should refer to the MIT license you use.
[x] You may also edit the archive title to have the same use of capitals as the paper title e.g. : "Ciclope: micro Computed Tomography to Finite Elements"
[x] The author Giulia Fraterrigo appears missing from the archived version
[x] You may want to update the "Publish in" field, which says: Journal of Open Source Software (JOSS):. but should perhaps say Journal of Open Source Software (JOSS). i.e. remove :..

Kevin-Mattheus-Moerman commented 1 year ago

@gianthk 👋

gianthk commented 1 year ago

@Kevin-Mattheus-Moerman thank you for doing a last check. I have done the following modifications:

On the paper:

[X] Please add the town/city for affiliation 1

[X] Please write United Kingdom, instead of UK for affiliation 3. On the archive:

[X] Please manually edit the archive listed license to match your open source license. It currently says "Creative Commons Attribution 4.0 International", but it should refer to the MIT license you use.

[x] You may also edit the archive title to have the same use of capitals as the paper title e.g. : "Ciclope: micro Computed Tomography to Finite Elements" I can't find the difference between paper and archive title..

[X] The author Giulia Fraterrigo appears missing from the archived version
[x] You may want to update the "Publish in" field, which says: Journal of Open Source Software (JOSS):. but should perhaps say Journal of Open Source Software (JOSS). i.e. remove :..

:. is there because journal volume and issue fields are empty. Once published, and if available, I can update the fields on the archive

Kevin-Mattheus-Moerman commented 1 year ago

@editorialbot generate pdf

editorialbot commented 1 year ago

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

Kevin-Mattheus-Moerman commented 1 year ago

@gianthk thanks for working on those points. All looks good now.

Kevin-Mattheus-Moerman commented 1 year ago

@editorialbot accept

editorialbot commented 1 year ago

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

editorialbot commented 1 year 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: Iori given-names: Gianluca orcid: "https://orcid.org/0000-0001-8611-3281" - family-names: Crimi given-names: Gianluigi - family-names: Schileo given-names: Enrico orcid: "https://orcid.org/0000-0003-3515-1231" - family-names: Taddei given-names: Fulvia orcid: "https://orcid.org/0000-0002-8342-7434" - family-names: Fraterrigo given-names: Giulia - family-names: Pani given-names: Martino orcid: "https://orcid.org/0000-0002-5786-4462" contact: - family-names: Iori given-names: Gianluca orcid: "https://orcid.org/0000-0001-8611-3281" doi: 10.5281/zenodo.7716943 message: If you use this software, please cite our article in the Journal of Open Source Software. preferred-citation: authors: - family-names: Iori given-names: Gianluca orcid: "https://orcid.org/0000-0001-8611-3281" - family-names: Crimi given-names: Gianluigi - family-names: Schileo given-names: Enrico orcid: "https://orcid.org/0000-0003-3515-1231" - family-names: Taddei given-names: Fulvia orcid: "https://orcid.org/0000-0002-8342-7434" - family-names: Fraterrigo given-names: Giulia - family-names: Pani given-names: Martino orcid: "https://orcid.org/0000-0002-5786-4462" date-published: 2023-04-02 doi: 10.21105/joss.04952 issn: 2475-9066 issue: 84 journal: Journal of Open Source Software publisher: name: Open Journals start: 4952 title: "Ciclope: micro Computed Tomography to Finite Elements" type: article url: "https://joss.theoj.org/papers/10.21105/joss.04952" volume: 8 title: "Ciclope: micro Computed Tomography to Finite Elements" ```

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 1 year ago

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

editorialbot commented 1 year ago

🐘🐘🐘 👉 Toot for this paper 👈 🐘🐘🐘

editorialbot commented 1 year 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/4094
Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.04952
If everything looks good, then close this review issue.
Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

Kevin-Mattheus-Moerman commented 1 year ago

@gianthk congratulations on your published paper!

@danasolav thanks for editing this one!

And a special thans to the reviewers @dankusanovic and @jacobmerson !!!

editorialbot commented 1 year ago

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gianthk commented 1 year ago

@danasolav @Kevin-Mattheus-Moerman @dankusanovic @jacobmerson thank you for the very nice review experience! We are really happy to see this work published.

danasolav commented 1 year ago

Congratulations @gianthk and many thanks to @jacobmerson and @dankusanovic for reviewing and @Kevin-Mattheus-Moerman for the final edit!

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