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[REVIEW]: The Generalized Green's function Cluster Expansion: A Python package for simulating polarons #5115

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editorialbot opened this issue Jan 29, 2023 · 63 comments
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accepted published Papers published in JOSS Python recommend-accept Papers recommended for acceptance in JOSS. review Shell TeX Track: 3 (PE) Physics and Engineering

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editorialbot commented Jan 29, 2023

Submitting author: @matthewcarbone (Matthew Carbone)
Repository: https://github.com/matthewcarbone/GGCE
Branch with paper.md (empty if default branch): joss-manuscript
Version: v0.1.4
Editor: @jarvist
Reviewers: @Neutrino155, @st3r4g
Archive: 10.5281/zenodo.8352947

Status

status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/688705844ea344353b86815d8345f8d5"><img src="https://joss.theoj.org/papers/688705844ea344353b86815d8345f8d5/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/688705844ea344353b86815d8345f8d5/status.svg)](https://joss.theoj.org/papers/688705844ea344353b86815d8345f8d5)

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

@Neutrino155 & @st3r4g, 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 @jarvist 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 @st3r4g

📝 Checklist for @Neutrino155

@editorialbot
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Hello humans, I'm @editorialbot, a robot that can help you with some common editorial tasks.

For a list of things I can do to help you, just type:

@editorialbot commands

For example, to regenerate the paper pdf after making changes in the paper's md or bib files, type:

@editorialbot generate pdf

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Software report:

github.com/AlDanial/cloc v 1.88  T=0.16 s (382.5 files/s, 77521.9 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          44           2024           3401           5805
TeX                              1             30              0            311
Markdown                         5             91              0            242
Jupyter Notebook                 1              0            430             64
YAML                             2              2              4             34
DOS Batch                        1              8              1             26
TOML                             1              1              1             21
reStructuredText                 5             13             14             19
make                             1              4              7              9
Bourne Shell                     1              0              1              2
-------------------------------------------------------------------------------
SUM:                            62           2173           3859           6533
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

@editorialbot
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Wordcount for paper.md is 1932

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👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

@jarvist
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jarvist commented Jan 29, 2023

Thank you Stefano @st3r4g Brad @Neutrino155 for agreeing to review! The key instructions and links to guidance are in the first piece of boilerplate written by @editorialbot above ^^^^.
I also find the list of commands for @editorialbot very helpful. https://joss.readthedocs.io/en/latest/editorial_bot.html

@jarvist
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jarvist commented Jan 29, 2023

Conflict of interest declaration: I am a PhD supervisor to Brad @Neutrino155 .

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

OK DOIs

- 10.1103/PhysRevLett.97.036402 is OK
- 10.1103/PhysRevLett.107.076403 is OK
- 10.21468/SciPostPhys.11.3.062 is OK

MISSING DOIs

- 10.1103/physrevb.104.035106 may be a valid DOI for title: Numerically exact generalized Green’s function cluster expansions for electron-phonon problems
- 10.1103/physrevb.104.l140307 may be a valid DOI for title: Bond-Peierls polaron: Moderate mass enhancement and current-carrying ground state
- 10.1038/s41563-020-0647-2 may be a valid DOI for title: Charge transport in high-mobility conjugated polymers and molecular semiconductors
- 10.1103/physrevlett.97.036402 may be a valid DOI for title: Green’s function of a dressed particle
- 10.1103/physrevb.74.245104 may be a valid DOI for title: Green’s function of the Holstein polaron
- 10.1038/s41598-017-01228-y may be a valid DOI for title: Phonon-mediated repulsion, sharp transitions and (quasi) self-trapping in the extended Peierls-Hubbard model
- 10.1103/physrevlett.121.247001 may be a valid DOI for title: Light bipolarons stabilized by Peierls electron-phonon coupling
- 10.1103/physrevlett.105.266605 may be a valid DOI for title: Sharp transition for single polarons in the one-dimensional Su-Schrieffer-Heeger model
- 10.1103/physrevlett.122.246403 may be a valid DOI for title: Polarons from first principles, without supercells
- 10.1016/j.cpc.2016.07.028 may be a valid DOI for title: EPW: Electron–phonon coupling, transport and superconducting properties using maximally localized Wannier functions
- 10.1016/j.cpc.2021.107970 may be a valid DOI for title: Perturbo: A software package for ab initio electron–phonon interactions, charge transport and ultrafast dynamics
- 10.1103/physrevb.97.115203 may be a valid DOI for title: Charge transport in organic molecular semiconductors from first principles: The bandlike hole mobility in a naphthalene crystal
- 10.1143/jpsj.54.4483 may be a valid DOI for title: Thermo field dynamics in equilibrium and non-equilibrium interacting quantum systems
- 10.1007/978-1-4612-1986-6_8 may be a valid DOI for title: Efficient Management of Parallelism in Object Oriented Numerical Software Libraries
- 10.1109/tpds.2021.3084070 may be a valid DOI for title: The PetscSF Scalable Communication Layer

INVALID DOIs

- None

@st3r4g
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st3r4g commented Jan 30, 2023

Review checklist for @st3r4g

Conflict of interest

  • I confirm that I have read the JOSS conflict of interest (COI) policy and that: I have no COIs with reviewing this work or that any perceived COIs have been waived by JOSS for the purpose of this review.

Code of Conduct

General checks

  • Repository: Is the source code for this software available at the https://github.com/matthewcarbone/GGCE?
  • License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
  • Contribution and authorship: Has the submitting author (@matthewcarbone) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
  • Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines
  • Data sharing: If the paper contains original data, data are accessible to the reviewers. If the paper contains no original data, please check this item.
  • Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
  • Human and animal research: If the paper contains original data research on humans subjects or animals, does it comply with JOSS's human participants research policy and/or animal research policy? If the paper contains no such data, please check this item.

Functionality

  • Installation: Does installation proceed as outlined in the documentation?
  • Functionality: Have the functional claims of the software been confirmed?
  • Performance: If there are any performance claims of the software, have they been confirmed? (If there are no claims, please check off this item.)

Documentation

  • A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
  • Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
  • Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
  • Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
  • Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
  • Community guidelines: Are there clear guidelines for third parties wishing to 1) Contribute to the software 2) Report issues or problems with the software 3) Seek support

Software paper

  • Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
  • A statement of need: Does the paper have a section titled 'Statement of need' that clearly states what problems the software is designed to solve, who the target audience is, and its relation to other work?
  • State of the field: Do the authors describe how this software compares to other commonly-used packages?
  • Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
  • References: Is the list of references complete, and is everything cited appropriately that should be cited (e.g., papers, datasets, software)? Do references in the text use the proper citation syntax?

@Neutrino155
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Neutrino155 commented Feb 7, 2023

Review checklist for @Neutrino155

Conflict of interest

  • I confirm that I have read the JOSS conflict of interest (COI) policy and that: I have no COIs with reviewing this work or that any perceived COIs have been waived by JOSS for the purpose of this review.

Code of Conduct

General checks

  • Repository: Is the source code for this software available at the https://github.com/matthewcarbone/GGCE?
  • License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
  • Contribution and authorship: Has the submitting author (@matthewcarbone) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
  • Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines
  • Data sharing: If the paper contains original data, data are accessible to the reviewers. If the paper contains no original data, please check this item.
  • Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
  • Human and animal research: If the paper contains original data research on humans subjects or animals, does it comply with JOSS's human participants research policy and/or animal research policy? If the paper contains no such data, please check this item.

Functionality

  • Installation: Does installation proceed as outlined in the documentation?
  • Functionality: Have the functional claims of the software been confirmed?
  • Performance: If there are any performance claims of the software, have they been confirmed? (If there are no claims, please check off this item.)

Documentation

  • A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
  • Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
  • Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
  • Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
  • Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
  • Community guidelines: Are there clear guidelines for third parties wishing to 1) Contribute to the software 2) Report issues or problems with the software 3) Seek support

Software paper

  • Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
  • A statement of need: Does the paper have a section titled 'Statement of need' that clearly states what problems the software is designed to solve, who the target audience is, and its relation to other work?
  • State of the field: Do the authors describe how this software compares to other commonly-used packages?
  • Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
  • References: Is the list of references complete, and is everything cited appropriately that should be cited (e.g., papers, datasets, software)? Do references in the text use the proper citation syntax?

@jarvist
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jarvist commented Mar 16, 2023

Dear @Neutrino155 and @st3r4g , how are you getting on with your reviews?

@st3r4g
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st3r4g commented Mar 17, 2023

sorry for the delay, I was busy in the last weeks

@Kevin-Mattheus-Moerman
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@st3r4g @Neutrino155 have you been able to pick up this review? Thanks again for your help!

@Neutrino155
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Hello! @Kevin-Mattheus-Moerman, yes, very sorry for the delay. Should be able to complete it soon.

@jarvist
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jarvist commented May 19, 2023

Great! Thank you very much @Neutrino155 and @st3r4g !

I'm not sure if GitHub would have generated emails about the checkboxes being clicked.

@matthewcarbone - there appear to be a few outstanding items, which might be not be in place currently, i.e. automated tests and documentation. (Issues generated above.)
Other than that, it looks like we're mostly there.

@jarvist
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jarvist commented May 19, 2023

i.e. just clicking around, I found this blank documentation page: https://matthewcarbone.github.io/GGCE/tutorials/finite_t.html

@jarvist
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jarvist commented May 19, 2023

@st3r4g - have you had time to read the software paper yet?

@st3r4g
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st3r4g commented May 26, 2023

I will conclude in the following couple of days

@matthewcarbone
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@jarvist

Ok all done!

Let me know if you need anything else on my end!

@matthewcarbone
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@jarvist just pinging you again since you basically said to. No rush, and not that I haven't dragged my feet on this a bit... 😁

Thanks!

@matthewcarbone
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@jarvist not sure if there's any other way to poke you but I'm trying again! Any updates?

@jarvist
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jarvist commented Sep 29, 2023

The poke was noticed this time ^_^

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jarvist commented Sep 29, 2023

@editorialbot set 10.5281/zenodo.8352947 as archive

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Done! archive is now 10.5281/zenodo.8352947

@jarvist
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jarvist commented Sep 29, 2023

@editorialbot set v0.1.4 as version

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Done! version is now v0.1.4

@jarvist
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jarvist commented Sep 29, 2023

@editorialbot check repository

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Software report:

github.com/AlDanial/cloc v 1.88  T=0.09 s (721.5 files/s, 146383.2 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          44           2024           3401           5805
TeX                              1             29              0            326
Markdown                         5             91              0            242
Jupyter Notebook                 1              0            430             64
YAML                             2              2              4             34
DOS Batch                        1              8              1             26
TOML                             1              1              1             21
reStructuredText                 5             13             14             19
make                             1              4              7              9
Bourne Shell                     1              0              1              2
-------------------------------------------------------------------------------
SUM:                            62           2172           3859           6548
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

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Wordcount for paper.md is 1931

@jarvist
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jarvist commented Sep 29, 2023

@editorialbot generate pdf

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👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

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jarvist commented Sep 29, 2023

@editorialbot recommend-accept

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Attempting dry run of processing paper acceptance...

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

OK DOIs

- 10.1103/PhysRevB.104.035106 is OK
- 10.1103/PhysRevB.104.L140307 is OK
- 10.1007/978-3-642-01896-1 is OK
- 10.1080/00107514.2012.661781 is OK
- 10.1021/acsenergylett.1c00506 is OK
- 10.1038/s41563-020-0647-2 is OK
- 10.1515/9781400837021 is OK
- 10.1103/PhysRevLett.97.036402 is OK
- 10.1103/PhysRevB.74.245104 is OK
- 10.1038/s41598-017-01228-y is OK
- 10.1103/PhysRevLett.121.247001 is OK
- 10.1103/PhysRevLett.105.266605 is OK
- 10.1103/RevModPhys.89.015003 is OK
- 10.1103/PhysRevLett.122.246403 is OK
- 10.1103/PhysRevB.99.235139 is OK
- 10.1103/PhysRevLett.129.076402 is OK
- 10.1103/PhysRevB.106.075119 is OK
- 10.1016/j.cpc.2016.07.028 is OK
- 10.1103/PhysRevB.94.201201 is OK
- 10.1103/PhysRevLett.121.226603 is OK
- 10.1016/j.cpc.2021.107970 is OK
- 10.1103/PhysRevB.97.115203 is OK
- 10.1142/S0217979296000817 is OK
- 10.1143/JPSJ.54.4483 is OK
- 10.1103/PhysRevLett.107.076403 is OK
- 10.21468/SciPostPhys.11.3.062 is OK
- 10.1007/978-1-4612-1986-6_8 is OK
- 10.1109/TPDS.2021.3084070 is OK

MISSING DOIs

- None

INVALID DOIs

- None

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👋 @openjournals/pe-eics, this paper is ready to be accepted and published.

Check final proof 👉📄 Download article

If the paper PDF and the deposit XML files look good in openjournals/joss-papers#4631, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

@editorialbot editorialbot added the recommend-accept Papers recommended for acceptance in JOSS. label Sep 29, 2023
@jarvist
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jarvist commented Sep 29, 2023

OK, that's me @matthewcarbone ! Congratulations on getting this far. The 'Editor in Chief' team should be along shortly for the final checks and balances.

EiC; the paper has a disclaimer from the US Govt in the acknowledgments. It all looks fairly benign & boiler-plate, but I've never seen one of these in a JOSS I've edited, so I would like to flag it up for your attention.

@kyleniemeyer
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Thanks @jarvist - I think that disclaimer is fine.

Everything else with the paper also looks good to me.

@kyleniemeyer
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@editorialbot accept

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

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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:
- email: [email protected]
  family-names: Carbone
  given-names: Matthew R.
  orcid: "https://orcid.org/0000-0002-5181-9513"
- family-names: Fomichev
  given-names: Stepan
  orcid: "https://orcid.org/0000-0002-1622-9382"
- family-names: Millis
  given-names: Andrew J.
  orcid: "https://orcid.org/0000-0001-9413-6344"
- family-names: Berciu
  given-names: Mona
  orcid: "https://orcid.org/0000-0002-6736-1893"
- family-names: Reichman
  given-names: David R.
  orcid: "https://orcid.org/0000-0002-5265-5637"
- family-names: Sous
  given-names: John
  orcid: "https://orcid.org/0000-0002-9994-5789"
contact:
- email: [email protected]
  family-names: Carbone
  given-names: Matthew R.
  orcid: "https://orcid.org/0000-0002-5181-9513"
- family-names: Sous
  given-names: John
  orcid: "https://orcid.org/0000-0002-9994-5789"
doi: 10.5281/zenodo.8352947
message: If you use this software, please cite our article in the
  Journal of Open Source Software.
preferred-citation:
  authors:
  - email: [email protected]
    family-names: Carbone
    given-names: Matthew R.
    orcid: "https://orcid.org/0000-0002-5181-9513"
  - family-names: Fomichev
    given-names: Stepan
    orcid: "https://orcid.org/0000-0002-1622-9382"
  - family-names: Millis
    given-names: Andrew J.
    orcid: "https://orcid.org/0000-0001-9413-6344"
  - family-names: Berciu
    given-names: Mona
    orcid: "https://orcid.org/0000-0002-6736-1893"
  - family-names: Reichman
    given-names: David R.
    orcid: "https://orcid.org/0000-0002-5265-5637"
  - family-names: Sous
    given-names: John
    orcid: "https://orcid.org/0000-0002-9994-5789"
  date-published: 2023-10-01
  doi: 10.21105/joss.05115
  issn: 2475-9066
  issue: 90
  journal: Journal of Open Source Software
  publisher:
    name: Open Journals
  start: 5115
  title: "The Generalized Green's function Cluster Expansion: A Python
    package for simulating polarons"
  type: article
  url: "https://joss.theoj.org/papers/10.21105/joss.05115"
  volume: 8
title: "The Generalized Green's function Cluster Expansion: A Python
  package for simulating polarons"

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.

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🐘🐘🐘 👉 Toot for this paper 👈 🐘🐘🐘

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🚨🚨🚨 THIS IS NOT A DRILL, YOU HAVE JUST ACCEPTED A PAPER INTO JOSS! 🚨🚨🚨

Here's what you must now do:

  1. Check final PDF and Crossref metadata that was deposited 👉 Creating pull request for 10.21105.joss.05115 joss-papers#4638
  2. Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.05115
  3. If everything looks good, then close this review issue.
  4. Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

@editorialbot editorialbot added accepted published Papers published in JOSS labels Oct 1, 2023
@kyleniemeyer
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Congratulations @matthewcarbone on your article's publication in JOSS! Please consider signing up as a reviewer if you haven't already.

Many thanks to @Neutrino155 and @st3r4g for reviewing this, and @jarvist for editing.

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🎉🎉🎉 Congratulations on your paper acceptance! 🎉🎉🎉

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.05115/status.svg)](https://doi.org/10.21105/joss.05115)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.05115">
  <img src="https://joss.theoj.org/papers/10.21105/joss.05115/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.05115/status.svg
   :target: https://doi.org/10.21105/joss.05115

This is how it will look in your documentation:

DOI

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