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[REVIEW]: cppdlr: Imaginary time calculations using the discrete Lehmann representation #6297

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editorialbot opened this issue Jan 29, 2024 · 76 comments
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accepted C++ CMake published Papers published in JOSS recommend-accept Papers recommended for acceptance in JOSS. review TeX Track: 3 (PE) Physics and Engineering

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editorialbot commented Jan 29, 2024

Submitting author: @jasonkaye (Jason Kaye)
Repository: https://github.com/flatironinstitute/cppdlr/
Branch with paper.md (empty if default branch): joss
Version: 1.2.0
Editor: @kyleniemeyer
Reviewers: @jarvist, @stevenrbrandt
Archive: 10.5281/zenodo.13177024

Status

status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/8fd2af732c1adedb99b271dfc91d7e1e"><img src="https://joss.theoj.org/papers/8fd2af732c1adedb99b271dfc91d7e1e/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/8fd2af732c1adedb99b271dfc91d7e1e/status.svg)](https://joss.theoj.org/papers/8fd2af732c1adedb99b271dfc91d7e1e)

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

@jarvist and @stevenrbrandt, 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 @kyleniemeyer 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 @jarvist

📝 Checklist for @stevenrbrandt

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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=0.06 s (1060.2 files/s, 143707.7 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
C++                             17            728            872           1735
C/C++ Header                     7            346           1069            822
CMake                           15            116            205            600
reStructuredText                 8            192            122            463
CSS                              2             80             20            354
TeX                              1             27              0            286
XML                              1              6              8            226
Markdown                         5             53              0            161
YAML                             4             12              6            130
MATLAB                           1             14             11             66
HTML                             2              6              0             60
JavaScript                       2              0             13              2
-------------------------------------------------------------------------------
SUM:                            65           1580           2326           4905
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

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Wordcount for paper.md is 895

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

OK DOIs

- 10.1103/PhysRevB.98.035104 is OK
- 10.1103/PhysRevB.105.235115 is OK
- 10.1007/s10444-023-10067-7 is OK
- 10.1103/PhysRevB.107.245123 is OK
- 10.1103/PhysRevB.96.035147 is OK
- 10.1103/PhysRevB.84.075145 is OK
- 10.1063/5.0003145 is OK
- 10.1103/PhysRevB.98.075127 is OK
- 10.1103/PhysRev.139.A796 is OK
- 10.3389/fchem.2019.00377 is OK
- 10.1103/PhysRevB.106.L220502 is OK

MISSING DOIs

- 10.1103/physrevresearch.6.013099 may be a valid DOI for title: Precursory Cooper Flow in Ultralow-Temperature Superconductors
- 10.1103/physrevb.108.184501 may be a valid DOI for title: A comparative study of the superconductivity in the Holstein and optical Su-Schrieffer-Heeger models

INVALID DOIs

- https://doi.org/10.1016/j.cpc.2022.108458 is INVALID because of 'https://doi.org/' prefix
- http://dx.doi.org/10.1016/j.cpc.2015.04.023 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1016/j.softx.2022.101266 is INVALID because of 'https://doi.org/' prefix

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

@jasonkaye
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@editorialbot generate preprint

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

@jasonkaye
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@editorialbot generate pdf

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

@jasonkaye
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@editorialbot generate preprint

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

@jarvist
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jarvist commented Apr 26, 2024

I'm sorry that this review is taking so long.
@Neutrino155 has had to withdraw for personal reasons.

I've found it extremely difficult to find an expert reviewer - most people seem quite reticent to express an opinion given the standing of the authors in the field.

I will now take the unusual step of reviewing it myself, while continuing to search for an expert to weigh in with an external view of the physics.

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jarvist commented Apr 26, 2024

@editorialbot remove @Neutrino155 from reviewers

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@Neutrino155 is not in the reviewers list

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jarvist commented Apr 26, 2024

@editorialbot add @jarvist to reviewers

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@jarvist added to the reviewers list!

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jarvist commented Apr 26, 2024

Review checklist for @jarvist

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/flatironinstitute/cppdlr/?
  • License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
  • Contribution and authorship: Has the submitting author (@jasonkaye) 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?

@kyleniemeyer
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@editorialbot assign me as editor

@editorialbot editorialbot assigned kyleniemeyer and unassigned jarvist Jun 11, 2024
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Assigned! @kyleniemeyer is now the editor

@kyleniemeyer
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@editorialbot add @stevenrbrandt as reviewer

Steve Brandt has agreed to provide another review within the next few weeks or so. Thanks!

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@stevenrbrandt added to the reviewers list!

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Done! version is now 1.2.0

@kyleniemeyer
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@editorialbot set 10.5281/zenodo.13177024 as archive

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Done! archive is now 10.5281/zenodo.13177024

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@editorialbot check references

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

OK DOIs

- 10.1103/PhysRevB.98.035104 is OK
- 10.1103/PhysRevB.105.235115 is OK
- 10.1016/j.cpc.2022.108458 is OK
- 10.1007/s10444-023-10067-7 is OK
- 10.1103/PhysRevB.107.245123 is OK
- 10.1016/j.cpc.2015.04.023 is OK
- 10.1103/PhysRevB.96.035147 is OK
- 10.1103/PhysRevB.84.075145 is OK
- 10.1063/5.0003145 is OK
- 10.1103/PhysRevB.98.075127 is OK
- 10.1103/PhysRev.139.A796 is OK
- 10.3389/fchem.2019.00377 is OK
- 10.1103/PhysRevB.106.L220502 is OK
- 10.1103/PhysRevResearch.6.013099 is OK
- 10.1103/PhysRevB.108.184501 is OK
- 10.1016/j.softx.2022.101266 is OK

MISSING DOIs

- No DOI given, and none found for title: Decomposing imaginary time Feynman diagrams using ...
- No DOI given, and none found for title: Discrete Lehmann representation of three-point fun...
- No DOI given, and none found for title: Electron Correlations in Narrow Energy Bands
- No DOI given, and none found for title: Two-Particle Response Function Tool-box (TPRF) for...
- No DOI given, and none found for title: pydlr: Imaginary time calculations using the Discr...
- No DOI given, and none found for title: libdr: Imaginary time calculations using the Discr...
- No DOI given, and none found for title: Julia implementation of the discrete Lehmann repre...
- No DOI given, and none found for title: cppdlr: Imaginary time calculations using the disc...
- No DOI given, and none found for title: cppdlr: Imaginary time calculations using the disc...
- No DOI given, and none found for title: nda: C++ library for multi-dimensional arrays
- No DOI given, and none found for title: Stabilizing the calculation of the self-energy in ...
- No DOI given, and none found for title: Chirped amplitude mode in photo-excited supercondu...

INVALID DOIs

- None

@kyleniemeyer
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@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.98.035104 is OK
- 10.1103/PhysRevB.105.235115 is OK
- 10.1016/j.cpc.2022.108458 is OK
- 10.1007/s10444-023-10067-7 is OK
- 10.1103/PhysRevB.107.245123 is OK
- 10.1016/j.cpc.2015.04.023 is OK
- 10.1103/PhysRevB.96.035147 is OK
- 10.1103/PhysRevB.84.075145 is OK
- 10.1063/5.0003145 is OK
- 10.1103/PhysRevB.98.075127 is OK
- 10.1103/PhysRev.139.A796 is OK
- 10.3389/fchem.2019.00377 is OK
- 10.1103/PhysRevB.106.L220502 is OK
- 10.1103/PhysRevResearch.6.013099 is OK
- 10.1103/PhysRevB.108.184501 is OK
- 10.1016/j.softx.2022.101266 is OK

MISSING DOIs

- No DOI given, and none found for title: Decomposing imaginary time Feynman diagrams using ...
- No DOI given, and none found for title: Discrete Lehmann representation of three-point fun...
- No DOI given, and none found for title: Electron Correlations in Narrow Energy Bands
- No DOI given, and none found for title: Two-Particle Response Function Tool-box (TPRF) for...
- No DOI given, and none found for title: pydlr: Imaginary time calculations using the Discr...
- No DOI given, and none found for title: libdr: Imaginary time calculations using the Discr...
- No DOI given, and none found for title: Julia implementation of the discrete Lehmann repre...
- No DOI given, and none found for title: cppdlr: Imaginary time calculations using the disc...
- No DOI given, and none found for title: cppdlr: Imaginary time calculations using the disc...
- No DOI given, and none found for title: nda: C++ library for multi-dimensional arrays
- No DOI given, and none found for title: Stabilizing the calculation of the self-energy in ...
- No DOI given, and none found for title: Chirped amplitude mode in photo-excited supercondu...

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#5726, 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 Aug 5, 2024
@kyleniemeyer
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Thanks @jasonkaye - please review the paper proof, and then I will accept.

@jasonkaye
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@editorialbot generate pdf

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

@jasonkaye
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@kyleniemeyer My apologies, but we needed to make a couple of small edits to affiliations and references, which we have pushed to our repo---see also the generated pdf above. If you could regenerate the final proof with these changes, I can take a final read over and confirm. Thanks.

@kyleniemeyer
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@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.98.035104 is OK
- 10.1103/PhysRevB.105.235115 is OK
- 10.1016/j.cpc.2022.108458 is OK
- 10.1007/s10444-023-10067-7 is OK
- 10.1103/PhysRevB.107.245123 is OK
- 10.1016/j.cpc.2015.04.023 is OK
- 10.1103/PhysRevB.96.035147 is OK
- 10.1103/PhysRevB.84.075145 is OK
- 10.1063/5.0003145 is OK
- 10.1103/PhysRevB.98.075127 is OK
- 10.1103/PhysRev.139.A796 is OK
- 10.3389/fchem.2019.00377 is OK
- 10.1103/PhysRevB.106.L220502 is OK
- 10.1103/PhysRevResearch.6.013099 is OK
- 10.1103/PhysRevB.108.184501 is OK
- 10.1016/j.softx.2022.101266 is OK

MISSING DOIs

- No DOI given, and none found for title: Decomposing imaginary time Feynman diagrams using ...
- No DOI given, and none found for title: Discrete Lehmann representation of three-point fun...
- No DOI given, and none found for title: Electron Correlations in Narrow Energy Bands
- No DOI given, and none found for title: Two-Particle Response Function Tool-box (TPRF) for...
- No DOI given, and none found for title: pydlr: Imaginary time calculations using the Discr...
- No DOI given, and none found for title: libdr: Imaginary time calculations using the Discr...
- No DOI given, and none found for title: Julia implementation of the discrete Lehmann repre...
- No DOI given, and none found for title: cppdlr: Imaginary time calculations using the disc...
- No DOI given, and none found for title: cppdlr: Imaginary time calculations using the disc...
- No DOI given, and none found for title: nda: C++ library for multi-dimensional arrays
- No DOI given, and none found for title: Stabilizing the calculation of the self-energy in ...
- No DOI given, and none found for title: Chirped amplitude mode in photo-excited supercondu...

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#5730, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

@jasonkaye
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@kyleniemeyer I have reviewed the final proof and everything looks good. Thanks.

@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:
- family-names: Kaye
  given-names: Jason
  orcid: "https://orcid.org/0000-0001-8045-6179"
- family-names: Strand
  given-names: Hugo U. R.
  orcid: "https://orcid.org/0000-0002-7263-4403"
- family-names: Wentzell
  given-names: Nils
  orcid: "https://orcid.org/0000-0003-3613-007X"
contact:
- family-names: Kaye
  given-names: Jason
  orcid: "https://orcid.org/0000-0001-8045-6179"
doi: 10.5281/zenodo.13177024
message: If you use this software, please cite our article in the
  Journal of Open Source Software.
preferred-citation:
  authors:
  - family-names: Kaye
    given-names: Jason
    orcid: "https://orcid.org/0000-0001-8045-6179"
  - family-names: Strand
    given-names: Hugo U. R.
    orcid: "https://orcid.org/0000-0002-7263-4403"
  - family-names: Wentzell
    given-names: Nils
    orcid: "https://orcid.org/0000-0003-3613-007X"
  date-published: 2024-08-06
  doi: 10.21105/joss.06297
  issn: 2475-9066
  issue: 100
  journal: Journal of Open Source Software
  publisher:
    name: Open Journals
  start: 6297
  title: "cppdlr: Imaginary time calculations using the discrete Lehmann
    representation"
  type: article
  url: "https://joss.theoj.org/papers/10.21105/joss.06297"
  volume: 9
title: "cppdlr: Imaginary time calculations using the discrete Lehmann
  representation"

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.06297 joss-papers#5731
  2. Wait five minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.06297
  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 Aug 6, 2024
@kyleniemeyer
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Congratulations @jasonkaye on your article's publication in JOSS! Thanks for your patience throughout this process.

Many thanks to @jarvist and @stevenrbrandt for reviewing this submission.

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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.06297/status.svg)](https://doi.org/10.21105/joss.06297)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.06297">
  <img src="https://joss.theoj.org/papers/10.21105/joss.06297/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.06297/status.svg
   :target: https://doi.org/10.21105/joss.06297

This is how it will look in your documentation:

DOI

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:

@jasonkaye
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Congratulations @jasonkaye on your article's publication in JOSS! Thanks for your patience throughout this process.

Many thanks to @jarvist and @stevenrbrandt for reviewing this submission.

Great, thanks @kyleniemeyer for your help.

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