[REVIEW]: elsa: an elegant framework for tomographic reconstruction

editorialbot commented 9 months ago

Submitting author: !--author-handle-->@ner0-m@jbytecode<!--end-editor-- Reviewers: @uellue, @DanNixon Archive: 10.5281/zenodo.10609174

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Markdown: [![status](https://joss.theoj.org/papers/cd26f77e40404f0403c91531e61b07e9/status.svg)](https://joss.theoj.org/papers/cd26f77e40404f0403c91531e61b07e9)

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

@uellue & @DanNixon, 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:

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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 @DanNixon

📝 Checklist for @uellue

jbytecode commented 7 months ago

@editorialbot generate pdf

editorialbot commented 7 months ago

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

jbytecode commented 7 months ago

@ner0-m - What do you mean by locally? Do we have a chance to see the changes publicly? The rendered pdf still lacks the orcid.

ner0-m commented 7 months ago

@editorialbot generate pdf

editorialbot commented 7 months ago

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

ner0-m commented 7 months ago

@jbytecode Now it works! I forgot to push to my upstream :see_no_evil: Sorry for the back and forth!

jbytecode commented 7 months ago

@ner0-m - The both manuscript and bibtex look fine to me. Please have a full read of the paper. Fix and correct any issue if exists. Please ping me when you've done with them. Thank you in advance.

ner0-m commented 7 months ago

@editorialbot generate pdf

editorialbot commented 7 months ago

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

ner0-m commented 7 months ago

@editorialbot generate pdf

editorialbot commented 7 months ago

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

ner0-m commented 7 months ago

@jbytecode I've changed a sentence in the last paragraph; otherwise, I'm pleased with it!

jbytecode commented 7 months ago

@editorialbot check references

editorialbot commented 7 months ago

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

OK DOIs

- 10.21105/joss.04722 is OK
- 10.1098/rsta.2020.0192 is OK
- 10.1098/rsta.2020.0193 is OK
- 10.1364/oe.24.025129 is OK
- 10.1117/12.2534833 is OK
- 10.1088/2631-8695/ac8224 is OK
- 10.1117/12.2646492 is OK
- 10.1088/2631-8695/ad08fd is OK
- 10.1109/tci.2023.3240078 is OK
- 10.48550/ARXIV.2304.14505 is OK
- 10.48550/arXiv.2310.16846 is OK
- 10.5281/zenodo.6986012 is OK
- 10.5281/zenodo.6983008 is OK
- 10.1103/PhysRevLett.117.158101 is OK
- 10.1038/nphys265 is OK

MISSING DOIs

- None

INVALID DOIs

- None

jbytecode commented 7 months ago

@editorialbot generate pdf

editorialbot commented 7 months ago

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

jbytecode commented 7 months ago

@editorialbot recommend-accept

editorialbot commented 7 months ago

Attempting dry run of processing paper acceptance...

editorialbot commented 7 months ago

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

OK DOIs

- 10.21105/joss.04722 is OK
- 10.1098/rsta.2020.0192 is OK
- 10.1098/rsta.2020.0193 is OK
- 10.1364/oe.24.025129 is OK
- 10.1117/12.2534833 is OK
- 10.1088/2631-8695/ac8224 is OK
- 10.1117/12.2646492 is OK
- 10.1088/2631-8695/ad08fd is OK
- 10.1109/tci.2023.3240078 is OK
- 10.48550/ARXIV.2304.14505 is OK
- 10.48550/arXiv.2310.16846 is OK
- 10.5281/zenodo.6986012 is OK
- 10.5281/zenodo.6983008 is OK
- 10.1103/PhysRevLett.117.158101 is OK
- 10.1038/nphys265 is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot commented 7 months ago

:wave: @openjournals/csism-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/4986, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

danielskatz commented 7 months ago

👋 @ner0-m - As the track editor, I'll next proofread this and otherwise check it, and get back to you shortly if anything else is needed from you.

danielskatz commented 7 months ago

@ner0-m - I've suggested a few minor changes in https://gitlab.com/tum-ciip/elsa/-/merge_requests/466 - please merge this, or let me know what you disagree with.

There's also an odd issue in the references where I don't understand exactly why we've generated something the way we have, which I'm investigating.

ner0-m commented 7 months ago

@danielskatz I've added your suggestions. Thank you!

If I need to change anything regarding the references please let me know!

danielskatz commented 7 months ago

@editorialbot recommend-accept

editorialbot commented 7 months ago

Attempting dry run of processing paper acceptance...

editorialbot commented 7 months ago

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

OK DOIs

- 10.21105/joss.04722 is OK
- 10.1098/rsta.2020.0192 is OK
- 10.1098/rsta.2020.0193 is OK
- 10.1364/oe.24.025129 is OK
- 10.1117/12.2534833 is OK
- 10.1088/2631-8695/ac8224 is OK
- 10.1117/12.2646492 is OK
- 10.1088/2631-8695/ad08fd is OK
- 10.1109/tci.2023.3240078 is OK
- 10.48550/ARXIV.2304.14505 is OK
- 10.48550/arXiv.2310.16846 is OK
- 10.5281/zenodo.6986012 is OK
- 10.5281/zenodo.6983008 is OK
- 10.1103/PhysRevLett.117.158101 is OK
- 10.1038/nphys265 is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot commented 7 months ago

:wave: @openjournals/csism-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/4993, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

danielskatz commented 7 months ago

👋 @ner0-m - In your frank2023 bib entry, can you add an editor field, I think which should contain "Chuan Huang and Paul Vaska and Yongfeng Gao and Shaojie Chang and Thomas Wesley Holmes and Amir Pourmorteza and Jerome Liang" judging from the arxiv deposit. This should fix the inconsistency in the generated pdf that's technically correct but that is bothering me.

ner0-m commented 7 months ago

@danielskatz Done :-)

danielskatz commented 7 months ago

@editorialbot recommend-accept

editorialbot commented 7 months ago

Attempting dry run of processing paper acceptance...

editorialbot commented 7 months ago

Checking the BibTeX entries failed with the following error:

Failed to parse BibTeX on value "booktitle" (NAME) [#<BibTeX::Bibliography data=[11]>, "@", #<BibTeX::Entry >, {:title=>["An update to elsa - an elegant framework for tomographic reconstruction"], :author=>["Frank, David and Jelten, Jonas and Lasser, Tobias"], :editor=>["Chuan Huang and Paul Vaska and Yongfeng Gao and Shaojie Chang and Thomas Wesley Holmes and Amir Pourmorteza and Jerome Liang"]}]

editorialbot commented 7 months ago

:warning: Error preparing paper acceptance.

danielskatz commented 7 months ago

👋 @ner0-m - I think you left off the comma at the end of the new bib line.

ner0-m commented 7 months ago

@danielskatz Of course, I did... Now it should be fine!

danielskatz commented 7 months ago

@editorialbot recommend-accept

editorialbot commented 7 months ago

Attempting dry run of processing paper acceptance...

editorialbot commented 7 months ago

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

OK DOIs

- 10.21105/joss.04722 is OK
- 10.1098/rsta.2020.0192 is OK
- 10.1098/rsta.2020.0193 is OK
- 10.1364/oe.24.025129 is OK
- 10.1117/12.2534833 is OK
- 10.1088/2631-8695/ac8224 is OK
- 10.1117/12.2646492 is OK
- 10.1088/2631-8695/ad08fd is OK
- 10.1109/tci.2023.3240078 is OK
- 10.48550/ARXIV.2304.14505 is OK
- 10.48550/arXiv.2310.16846 is OK
- 10.5281/zenodo.6986012 is OK
- 10.5281/zenodo.6983008 is OK
- 10.1103/PhysRevLett.117.158101 is OK
- 10.1038/nphys265 is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot commented 7 months ago

:wave: @openjournals/csism-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/4995, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

danielskatz commented 7 months ago

@editorialbot accept

editorialbot commented 7 months ago

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

editorialbot commented 7 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: Frank given-names: David orcid: "https://orcid.org/0009-0006-4989-2144" - family-names: Jelten given-names: Jonas orcid: "https://orcid.org/0000-0002-5167-2419" - family-names: Lasser given-names: Tobias orcid: "https://orcid.org/0000-0001-5669-920X" doi: 10.5281/zenodo.10609174 message: If you use this software, please cite our article in the Journal of Open Source Software. preferred-citation: authors: - family-names: Frank given-names: David orcid: "https://orcid.org/0009-0006-4989-2144" - family-names: Jelten given-names: Jonas orcid: "https://orcid.org/0000-0002-5167-2419" - family-names: Lasser given-names: Tobias orcid: "https://orcid.org/0000-0001-5669-920X" date-published: 2024-02-09 doi: 10.21105/joss.06174 issn: 2475-9066 issue: 94 journal: Journal of Open Source Software publisher: name: Open Journals start: 6174 title: "elsa: an elegant framework for tomographic reconstruction" type: article url: "https://joss.theoj.org/papers/10.21105/joss.06174" volume: 9 title: "**elsa**: an elegant framework for tomographic reconstruction" ```

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 7 months ago

🐘🐘🐘 👉 Toot for this paper 👈 🐘🐘🐘

editorialbot commented 7 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/4996
Wait five minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.06174
If everything looks good, then close this review issue.
Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

danielskatz commented 7 months ago

Congratulations to @ner0-m (David Frank) and co-authors on your publication!!

And thanks to @uellue and @DanNixon for reviewing, and to @jbytecode for editing! JOSS depends on volunteers and we couldn't do this without you

editorialbot commented 7 months ago

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ner0-m commented 7 months ago

@danielskatz @jbytecode @DanNixon @uellue Thank you for your help, comments and suggestions! We are thrilled that our paper has been accepted :tada:

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