editorialbot commented 5 months ago

Submitting author: !--author-handle-->@bartandrews@RMeli<!--end-editor-- Reviewers: @AlexBuccheri, @katherineding Archive: 10.5281/zenodo.10809833

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/3cd996ede201132d57ab9c9a7cc56955"><img src="https://joss.theoj.org/papers/3cd996ede201132d57ab9c9a7cc56955/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/3cd996ede201132d57ab9c9a7cc56955/status.svg)](https://joss.theoj.org/papers/3cd996ede201132d57ab9c9a7cc56955)

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

@AlexBuccheri & @katherineding, 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 @RMeli 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 @AlexBuccheri

📝 Checklist for @katherineding

bartandrews commented 4 months ago

@editorialbot commands

editorialbot commented 4 months ago

Hello @bartandrews, here are the things you can ask me to do:


# List all available commands
@editorialbot commands

# Get a list of all editors's GitHub handles
@editorialbot list editors

# Adds a checklist for the reviewer using this command
@editorialbot generate my checklist

# Set a value for branch
@editorialbot set joss-paper as branch

# Run checks and provide information on the repository and the paper file
@editorialbot check repository

# Check the references of the paper for missing DOIs
@editorialbot check references

# Generates the pdf paper
@editorialbot generate pdf

# Generates a LaTeX preprint file
@editorialbot generate preprint

# Get a link to the complete list of reviewers
@editorialbot list reviewers

bartandrews 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

- 10.1088/0370-1298/68/10/304 is OK
- 10.1103/PhysRevB.14.2239 is OK
- 10.1016/j.cpc.2017.09.033 is OK
- 10.1038/s41699-023-00378-0 is OK
- 10.1088/0034-4885/77/12/126401 is OK
- 10.1103/RevModPhys.89.011004 is OK
- 10.1103/PhysRevLett.128.166402 is OK
- 10.1088/1367-2630/ac4126 is OK
- 10.1063/1.1611351 is OK
- 10.1142/9781848160224_0014 is OK
- 10.4007/annals.2009.170.303 is OK
- 10.1103/RevModPhys.91.015005 is OK
- 10.1038/nature12186 is OK
- 10.1103/PhysRevLett.111.185301 is OK
- 10.1103/PhysRevB.101.235312 is OK
- 10.1038/ncomms9629 is OK
- 10.1103/PhysRevB.103.075132 is OK
- 10.1103/PhysRevB.104.184501 is OK
- 10.1038/s42005-019-0151-7 is OK
- 10.1007/BF01342591 is OK
- 10.1038/nature25011 is OK
- 10.1126/science.aao1401 is OK
- 10.1103/PhysRevB.108.205144 is OK
- 10.1103/PhysRevB.96.165150 is OK
- 10.1038/s41586-022-05576-2 is OK
- 10.1007/s10955-014-0992-0 is OK
- 10.1088/0256-307X/26/12/123701 is OK
- 10.1088/1751-8113/47/18/185202 is OK
- 10.1103/PhysRevLett.127.246403 is OK

MISSING DOIs

- No DOI given, and none found for title: Energy Spectrum of a Conduction Electron in a Magn...
- No DOI given, and none found for title: pyqula
- No DOI given, and none found for title: DiagHam
- No DOI given, and none found for title: Stability of fractional Chern insulators with a no...
- No DOI given, and none found for title: Superconductivity in a Topological Lattice Model w...

INVALID DOIs

- None

bartandrews 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

- 10.1088/0370-1298/68/10/304 is OK
- 10.1103/PhysRevB.14.2239 is OK
- 10.1016/j.cpc.2017.09.033 is OK
- 10.1038/s41699-023-00378-0 is OK
- 10.1088/0034-4885/77/12/126401 is OK
- 10.1103/RevModPhys.89.011004 is OK
- 10.1103/PhysRevLett.128.166402 is OK
- 10.1088/1367-2630/ac4126 is OK
- 10.1063/1.1611351 is OK
- 10.1142/9781848160224_0014 is OK
- 10.4007/annals.2009.170.303 is OK
- 10.1103/RevModPhys.91.015005 is OK
- 10.1038/nature12186 is OK
- 10.1103/PhysRevLett.111.185301 is OK
- 10.48550/arXiv.2310.05758 is OK
- 10.1103/PhysRevB.101.235312 is OK
- 10.48550/arXiv.2308.10935 is OK
- 10.1038/ncomms9629 is OK
- 10.1103/PhysRevB.103.075132 is OK
- 10.1103/PhysRevB.104.184501 is OK
- 10.1038/s42005-019-0151-7 is OK
- 10.1007/BF01342591 is OK
- 10.1038/nature25011 is OK
- 10.1126/science.aao1401 is OK
- 10.1103/PhysRevB.108.205144 is OK
- 10.1103/PhysRevB.96.165150 is OK
- 10.1038/s41586-022-05576-2 is OK
- 10.1007/s10955-014-0992-0 is OK
- 10.1088/0256-307X/26/12/123701 is OK
- 10.1088/1751-8113/47/18/185202 is OK
- 10.1103/PhysRevLett.127.246403 is OK

MISSING DOIs

- No DOI given, and none found for title: Energy Spectrum of a Conduction Electron in a Magn...
- No DOI given, and none found for title: pyqula
- No DOI given, and none found for title: DiagHam

INVALID DOIs

- None

bartandrews commented 4 months ago

@editorialbot generate preprint

editorialbot commented 4 months ago

:page_facing_up: Preprint file created: Find it here in the Artifacts list :page_facing_up:

bartandrews commented 4 months ago

@RMeli I have now finished implementing the reviewer suggestions :+1: (NB: I would like to bump the version number one more time before publication. Please let me know when is the right time to do this.)

RMeli commented 4 months ago

Thanks @bartandrews. I'll have a look at everything and I'll let you know when you should go ahead and bump the version number.

RMeli commented 4 months ago

Post-Review Checklist for Editor and Authors

Additional Author Tasks After Review is Complete

Double check authors and affiliations (including ORCIDs)
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.
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.
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 pull request)
[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

RMeli commented 4 months ago

@editorialbot generate pdf

RMeli 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

- 10.1088/0370-1298/68/10/304 is OK
- 10.1103/PhysRevB.14.2239 is OK
- 10.1016/j.cpc.2017.09.033 is OK
- 10.1038/s41699-023-00378-0 is OK
- 10.1088/0034-4885/77/12/126401 is OK
- 10.1103/RevModPhys.89.011004 is OK
- 10.1103/PhysRevLett.128.166402 is OK
- 10.1088/1367-2630/ac4126 is OK
- 10.1063/1.1611351 is OK
- 10.1142/9781848160224_0014 is OK
- 10.4007/annals.2009.170.303 is OK
- 10.1103/RevModPhys.91.015005 is OK
- 10.1038/nature12186 is OK
- 10.1103/PhysRevLett.111.185301 is OK
- 10.48550/arXiv.2310.05758 is OK
- 10.1103/PhysRevB.101.235312 is OK
- 10.48550/arXiv.2308.10935 is OK
- 10.1038/ncomms9629 is OK
- 10.1103/PhysRevB.103.075132 is OK
- 10.1103/PhysRevB.104.184501 is OK
- 10.1038/s42005-019-0151-7 is OK
- 10.1007/BF01342591 is OK
- 10.1038/nature25011 is OK
- 10.1126/science.aao1401 is OK
- 10.1103/PhysRevB.108.205144 is OK
- 10.1103/PhysRevB.96.165150 is OK
- 10.1038/s41586-022-05576-2 is OK
- 10.1007/s10955-014-0992-0 is OK
- 10.1088/0256-307X/26/12/123701 is OK
- 10.1088/1751-8113/47/18/185202 is OK
- 10.1103/PhysRevLett.127.246403 is OK

MISSING DOIs

- No DOI given, and none found for title: Energy Spectrum of a Conduction Electron in a Magn...
- No DOI given, and none found for title: pyqula
- No DOI given, and none found for title: DiagHam

INVALID DOIs

- None

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:

RMeli commented 4 months ago

Paper looks good. The missing DOIs are for two unpublished repositories, and for a very old paper:

Azbel, M. Y. (1964). Energy spectrum of a conduction electron in a magnetic field. Journal of Experimental and Theoretical Physics, 19(3), 634–645.

RMeli commented 4 months ago

@bartandrews please go ahead and make a new release. Please also archive it on Zenodo/figshare/etc and post the DOI here.

bartandrews commented 4 months ago

@RMeli Thank you for checking the paper! I have also checked it again, and I am happy with it. (As far as I know, there are no DOIs available for the references marked as "missing DOIs".)

The new version number is v1.0.3 and the DOI is here: https://doi.org/10.5281/zenodo.10809833

RMeli commented 4 months ago

Thanks @bartandrews. Can you please ensure that the title on Zenodo matches the one of the paper (you can simply amend it on Zenodo)? After that, we should be good to go!

bartandrews commented 4 months ago

@RMeli all done :+1:

RMeli commented 4 months ago

@editorialbot set 1.0.3 as version

editorialbot commented 4 months ago

Done! version is now 1.0.3

RMeli commented 4 months ago

@editorialbot set 10.5281/zenodo.10809833 as archive

editorialbot commented 4 months ago

Done! archive is now 10.5281/zenodo.10809833

RMeli 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:

RMeli commented 4 months ago

@editorialbot recommend-accept

Thank you @bartandrews for submitting to JOSS. Based on the extensive comments from the reviewers (and my own assessment), I'm happy to recommend this paper for acceptance! The EiC will now perform the final checks. Thank you for engaging so well with the review process.

Thank you very much again @AlexBuccheri and @katherineding for the in depth and constructive review!

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

- 10.1088/0370-1298/68/10/304 is OK
- 10.1103/PhysRevB.14.2239 is OK
- 10.1016/j.cpc.2017.09.033 is OK
- 10.1038/s41699-023-00378-0 is OK
- 10.1088/0034-4885/77/12/126401 is OK
- 10.1103/RevModPhys.89.011004 is OK
- 10.1103/PhysRevLett.128.166402 is OK
- 10.1088/1367-2630/ac4126 is OK
- 10.1063/1.1611351 is OK
- 10.1142/9781848160224_0014 is OK
- 10.4007/annals.2009.170.303 is OK
- 10.1103/RevModPhys.91.015005 is OK
- 10.1038/nature12186 is OK
- 10.1103/PhysRevLett.111.185301 is OK
- 10.48550/arXiv.2310.05758 is OK
- 10.1103/PhysRevB.101.235312 is OK
- 10.48550/arXiv.2308.10935 is OK
- 10.1038/ncomms9629 is OK
- 10.1103/PhysRevB.103.075132 is OK
- 10.1103/PhysRevB.104.184501 is OK
- 10.1038/s42005-019-0151-7 is OK
- 10.1007/BF01342591 is OK
- 10.1038/nature25011 is OK
- 10.1126/science.aao1401 is OK
- 10.1103/PhysRevB.108.205144 is OK
- 10.1103/PhysRevB.96.165150 is OK
- 10.1038/s41586-022-05576-2 is OK
- 10.1007/s10955-014-0992-0 is OK
- 10.1088/0256-307X/26/12/123701 is OK
- 10.1088/1751-8113/47/18/185202 is OK
- 10.1103/PhysRevLett.127.246403 is OK

MISSING DOIs

- No DOI given, and none found for title: Energy Spectrum of a Conduction Electron in a Magn...
- No DOI given, and none found for title: pyqula
- No DOI given, and none found for title: DiagHam

INVALID DOIs

- None

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/5123, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

bartandrews commented 4 months ago

Likewise, a big thank you to @RMeli, @AlexBuccheri, and @katherineding for your constructive comments and feedback, which have enabled me to significantly improve the package :pray:

kyleniemeyer commented 3 months ago

@editorialbot accept

editorialbot commented 3 months ago

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

editorialbot commented 3 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: Andrews given-names: Bartholomew orcid: "https://orcid.org/0000-0002-9079-7433" doi: 10.5281/zenodo.10809833 message: If you use this software, please cite our article in the Journal of Open Source Software. preferred-citation: authors: - family-names: Andrews given-names: Bartholomew orcid: "https://orcid.org/0000-0002-9079-7433" date-published: 2024-03-26 doi: 10.21105/joss.06356 issn: 2475-9066 issue: 95 journal: Journal of Open Source Software publisher: name: Open Journals start: 6356 title: "HofstadterTools: A Python package for analyzing the Hofstadter model" type: article url: "https://joss.theoj.org/papers/10.21105/joss.06356" volume: 9 title: "HofstadterTools: A Python package for analyzing the Hofstadter model" ```

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 3 months ago

🐘🐘🐘 👉 Toot for this paper 👈 🐘🐘🐘

editorialbot commented 3 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/5177
Wait five minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.06356
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 3 months ago

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

Many thanks to @AlexBuccheri and @katherineding for reviewing this, and @RMeli for editing.

editorialbot commented 3 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.06356/status.svg)](https://doi.org/10.21105/joss.06356)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.06356">
  <img src="https://joss.theoj.org/papers/10.21105/joss.06356/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.06356/status.svg
   :target: https://doi.org/10.21105/joss.06356

This is how it will look in your documentation:

We need your help!

The Journal of Open Source Software is a community-run journal and relies upon volunteer effort. If you'd like to support us please consider doing either one (or both) of the the following:

Volunteering to review for us sometime in the future. You can add your name to the reviewer list here: https://reviewers.joss.theoj.org/join
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openjournals / joss-reviews

[REVIEW]: HofstadterTools: A Python package for analyzing the Hofstadter model #6356

Status

Reviewer instructions & questions

Checklists

Post-Review Checklist for Editor and Authors

Additional Author Tasks After Review is Complete

Editor Tasks Prior to Acceptance