[REVIEW]: ComFiT: a Python library for computational field theory with topological defects

editorialbot commented 6 months ago

Submitting author: !--author-handle-->@vidarsko@lucydot<!--end-editor-- Reviewers: @flokno, @sharanroongta, @sbacchio Archive: 10.5281/zenodo.11395524

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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

@flokno & @sharanroongta & @sbacchio, 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 @lucydot 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 @sharanroongta

📝 Checklist for @sbacchio

📝 Checklist for @flokno

vidarsko commented 4 months ago

Thank you. I made some minor changes to the pull request before merging, split the sentence for readability and have written out the acronym.

The University of Oslo does not assign DOIs to doctoral theses. I do, however, have urls for where these are hosted on the Universitys research archive: Skogvoll Rønning. Do you want med to add these URLs to the bibliography?

vidarsko commented 4 months ago

Author check list:

Double check authors and affiliations (including ORCIDs)

Double checked. OK.

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.

Updated to version 1.5.0 which is released both on github and pypi.

Archive the release on Zenodo/figshare/etc and post the DOI here.

doi.org/10.5281/zenodo.11395524

Make sure that the title and author list (including ORCIDs) in the archive match those in the JOSS paper.

Done. I have also changed the date of the paper to today (30 May 2024).

Make sure that the license listed for the archive is the same as the software license.

Checked. Both are MIT.

vidarsko commented 4 months ago

@editorialbot generate pdf

editorialbot commented 4 months ago

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

vidarsko commented 4 months ago

@lucydot I forgot to tag you in my response. Are there any other items I need to take care of?

lucydot commented 4 months ago

Thanks @vidarsko: could you add a DOI for pyclaw citation, I can see one given here: https://epubs.siam.org/doi/abs/10.1137/110856976. I think adding URLs is a good idea, especially as they are associated with a "unique identifier" on the UiO repository.

All else looks good with the paper :)

lucydot commented 4 months ago

@editorialbot set 10.5281/zenodo.11395524 as archive

editorialbot commented 4 months ago

Done! archive is now 10.5281/zenodo.11395524

lucydot commented 4 months ago

@editorialbot set v1.5.0 as version

editorialbot commented 4 months ago

Done! version is now v1.5.0

lucydot commented 4 months ago

@vidarsko a couple of other points:

the title associated with the Zenodo archive does not look correct. It is currently vidarsko/ComFiT: ComFiT v1.5.0. It should exactly match that of the paper ComFiT: a Python library for computational field 2 theory with topological defects. You should be able to update this meta-data without having to create a new release, but let me know if you bump into any problems (the Zenodo interface seems to have changed recently).
the license is listed as Creative Commons on Zenodo, and MIT on Github. Please update so that they are the same.

vidarsko commented 4 months ago

@lucydot Thanks!

I have added links to the PhD theses, changed the name on Zenodo and the changed the license.

vidarsko commented 4 months ago

@editorialbot generate pdf

editorialbot commented 4 months ago

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

vidarsko commented 4 months ago

@lucydot Do you need anything more from me now?

lucydot commented 4 months ago

@editorialbot check references

editorialbot commented 4 months ago

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

OK DOIs

- 10.1103/PhysRevLett.78.401 is OK
- 10.1103/PhysRevE.59.1574 is OK
- 10.1103/PhysRevE.85.011153 is OK
- 10.1006/jcph.2002.6995 is OK
- 10.1103/PhysRevE.95.052144 is OK
- 10.1103/PhysRevLett.121.255501 is OK
- 10.1103/PhysRevE.93.042137 is OK
- 10.1103/PhysRevE.93.032106 is OK
- 10.1103/PhysRevB.103.014107 is OK
- 10.1103/PhysRevB.103.224107 is OK
- 10.1016/j.jmps.2022.104932 is OK
- 10.1088/1361-651X/ac9493 is OK
- 10.1038/s41524-023-01077-6 is OK
- 10.1039/D3SM00316G is OK
- 10.1088/1367-2630/ab95de is OK
- 10.1103/PhysRevResearch.5.023108 is OK
- 10.11588/ans.2015.100.20553 is OK
- 10.1137/110856976 is OK
- 10.25561/104839 is OK
- 10.1103/PhysRevResearch.2.023068 is OK

MISSING DOIs

- No DOI given, and none found for title: A Unified Perspective on Two-Dimensional Quantum T...
- No DOI given, and none found for title: Symmetry, Topology, and Crystal Deformations: A Ph...
- No DOI given, and none found for title: Topological Defects and Flows in BECs and Active M...

INVALID DOIs

- None

lucydot commented 4 months ago

@editorialbot recommend-accept

editorialbot commented 4 months ago

Attempting dry run of processing paper acceptance...

editorialbot commented 4 months ago

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

OK DOIs

- 10.1103/PhysRevLett.78.401 is OK
- 10.1103/PhysRevE.59.1574 is OK
- 10.1103/PhysRevE.85.011153 is OK
- 10.1006/jcph.2002.6995 is OK
- 10.1103/PhysRevE.95.052144 is OK
- 10.1103/PhysRevLett.121.255501 is OK
- 10.1103/PhysRevE.93.042137 is OK
- 10.1103/PhysRevE.93.032106 is OK
- 10.1103/PhysRevB.103.014107 is OK
- 10.1103/PhysRevB.103.224107 is OK
- 10.1016/j.jmps.2022.104932 is OK
- 10.1088/1361-651X/ac9493 is OK
- 10.1038/s41524-023-01077-6 is OK
- 10.1039/D3SM00316G is OK
- 10.1088/1367-2630/ab95de is OK
- 10.1103/PhysRevResearch.5.023108 is OK
- 10.11588/ans.2015.100.20553 is OK
- 10.1137/110856976 is OK
- 10.25561/104839 is OK
- 10.1103/PhysRevResearch.2.023068 is OK

MISSING DOIs

- No DOI given, and none found for title: A Unified Perspective on Two-Dimensional Quantum T...
- No DOI given, and none found for title: Symmetry, Topology, and Crystal Deformations: A Ph...
- No DOI given, and none found for title: Topological Defects and Flows in BECs and Active M...

INVALID DOIs

- None

lucydot commented 4 months ago

Note that the missing DOIs are for PhD theses (where DOIs have not been assigned). In this case, links to institutional repository has been provided instead.

lucydot commented 4 months ago

@vidarsko I've recommended acceptance - great to work with you, and thank you for your submission to JOSS!

editorialbot commented 4 months ago

:wave: @openjournals/pe-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/5478, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

vidarsko commented 4 months ago

@lucydot Fantastic, great to work with you too.

And many thanks to the reviewers @sharanroongta, @flokno and @sbacchio for taking the time and all the helpful suggestions.

kyleniemeyer commented 4 months ago

Hi @vidarsko, I made a few small edits to the paper: https://github.com/vidarsko/ComFiT/pull/20. Could you review and merge those?

vidarsko commented 4 months ago

@kyleniemeyer Done!

kyleniemeyer commented 4 months ago

@editorialbot generate pdf

editorialbot commented 4 months ago

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

kyleniemeyer commented 4 months ago

@editorialbot accept

editorialbot commented 4 months ago

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

editorialbot commented 4 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: Skogvoll given-names: Vidar orcid: "https://orcid.org/0000-0003-4941-6886" - family-names: Rønning given-names: Jonas orcid: "https://orcid.org/0000-0001-5289-7276" doi: 10.5281/zenodo.11395524 message: If you use this software, please cite our article in the Journal of Open Source Software. preferred-citation: authors: - family-names: Skogvoll given-names: Vidar orcid: "https://orcid.org/0000-0003-4941-6886" - family-names: Rønning given-names: Jonas orcid: "https://orcid.org/0000-0001-5289-7276" date-published: 2024-06-11 doi: 10.21105/joss.06599 issn: 2475-9066 issue: 98 journal: Journal of Open Source Software publisher: name: Open Journals start: 6599 title: "ComFiT: a Python library for computational field theory with topological defects" type: article url: "https://joss.theoj.org/papers/10.21105/joss.06599" volume: 9 title: "ComFiT: a Python library for computational field theory with topological defects" ```

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 4 months ago

🐘🐘🐘 👉 Toot for this paper 👈 🐘🐘🐘

editorialbot commented 4 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/5484
Wait five minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.06599
If everything looks good, then close this review issue.
Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

kyleniemeyer commented 4 months ago

Congratulations @vidarsko on your article's publication in JOSS! Please consider signing up as a reviewer if you haven't already.

Many thanks to @flokno, @sharanroongta, and @sbacchio for reviewing this submission, and @lucydot for editing.

editorialbot commented 4 months ago

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

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</a>

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   :target: https://doi.org/10.21105/joss.06599

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